高序生物巨分子的動態及功能解析：以穿膜蛋白，核醣體及蛋白-DNA複合體為例

簡易檢索 / 詳目顯示

回結果列表

研究生：	陳偉順 Chan, Wai Soon
論文名稱：	高序生物巨分子的動態及功能解析：以穿膜蛋白，核醣體及蛋白-DNA複合體為例 Spatio-Temporal Characterization and Functional Elucidation of Higher-Order Biomacromolecules Exemplified with Transmembrane Proteins, Ribosome and DNA-Protein Complexes
指導教授：	楊立威 Yang, Lee-Wei
口試委員:	蔡惠旭 Tsai, Hui-Hsu 楊進木 Yang, Jinn-Moon 鄭惠春 Cheng, Hui-Chun 潘榮隆 Pan, Rong-Long
學位類別：	博士 Doctor
系所名稱：	生命科學暨醫學院 - 生物資訊與結構生物研究所 Institute of Bioinformatics and Structural Biology
論文出版年：	2019
畢業學年度：	107
語文別：	英文
論文頁數：	210
中文關鍵詞：	環狀對稱、蛋白-蛋白對接、距離約束、單分子螢光共振能量轉移、傾斜角度、同源多聚體穿膜蛋白、分子動力模擬、阿拉伯芥磷酸轉運蛋白、磷酸轉運蛋白、質子化態、pH值、量子力學/分子動力學法、焦磷酸水解酶、配位數、親核性水分子、蛋白-DNA對接、彈力網路模型、高斯網路模型、固有動態域、動態域平面、時間尺度、動態大小、非勻向彈力網路模型、主成分分析、維納－辛欽定理、強度加權週期、核醣體、冪定律
外文關鍵詞：	cyclic symmetry (Cn symmetry), protein-protein docking, distance restraints, single molecule Förster resonance energy transfer (smFRET), tilt angle, homo-oligomeric transmembrane protein (HoTP), Cyclic Symmetry-Imposed Packing (SIP), molecular dynamics (MD) simulations, Arabidopsis PHT1;1 (AtPHT1;1), protonation state, pH, QM/MM, hydronium ion (H3O+), Vigna radiata H+-translocating pyrophosphatase (VrH+-PPase), protein-DNA docking, coordination number, nucleophilic water, elastic network model (ENM), gaussian network model (GNM), intrinsic dynamics domains (IDD), d-plane, motion timescale, motion size, anisotropic network model (ANM), principal component analysis (PCA), Wiener–Khintchine theorem (WKT), Intensity-Weighted Period (IWP), power law
相關次數：	點閱：2 下載：0
分享至:	分享至facebook 分享至twitter

查詢本校圖書館目錄查詢臺灣博碩士論文知識加值系統勘誤回報

高效精確的生物代謝過程必須依賴多種生物分子包含蛋白質、DNA和RNA等的相互協作。而這些生物分子通常需要形成高序複合體(higher-order complexes)或稱生物巨分子(biomacromolecules)才能完整的執行其功能。要了解生物巨分子作用機制的第一步就是揭示它們的高序結構，但現今結構分析技術（如X-ray 晶體繞射、NMR、cryo-EM）解析這些巨大的多聚體分子結構仍然是一大挑戰，尤其是那些在膜中的多聚體(oligomer)。為了解決這個技術難題，許多以統計方法或物理生物化學為基礎的巨分子組裝算法被開發並應用於整合各種實驗結果來建構複雜的生物巨分子結構。
穿膜蛋白是其中一類相當重要的生物巨分子，它們參與了細胞訊息傳遞(cell signaling, transport)、運送膜內外的各種物質、維持膜內電位(electrochemical gradient)。從RCSB PDB中穿膜蛋白的統計資料發現有約66%的α-螺旋穿膜蛋白(α-helical transmembrane)是屬於同源多聚體的穿膜蛋白(homo-oligomeric transmembrane proteins, HoTPs)且這些HoTPs有約92%是環狀對稱(cyclic symmetric或Cn symmetric)。我們利用HoTPs環狀對稱與立體結構限制這兩個特性，分別開發兩個結構篩選器SIP (Symmetry-Imposed Packing)及DR (distance-restraints)，用於移除在分子對接結果中不符合前述條件的對接模型(docking poses)。SIP主要是比較同源二聚體(dimer)對接模型與由此對接模型推測的理想Cn對稱多聚體的差異作為篩選依據。這個理想Cn對稱多聚體推測過程不需要事先知道形成多聚體所需的單體個數(n)。僅使用SIP的狀況下，在7個HoTPs單體結構的對接結果中，有71%的可以在前10個對接模型中找到近似自然結構的模型(near-native poses)；以31個HoTP的同源建模結構(homology modeled structure)為基礎的對接結果，則有29%符合上述結果。而相同的對接結果但未經SIP處理前，分別只有14%及3%。當SIP再加上多聚體單體個數(n)給定時，近似自然結構出現在對接結果的前10個模型中在測試集佔有高達76%；比起SIP，其他算法如M-ZDOCK及Sam在相同條件下，分別僅有55%與47%。我們將3個已知部分殘基之間距離HoTPs的對接結果以DR及SIP處理後，發現3個HoTPs的近似自然結構在54,000個對接模型中皆被排名在第一名；而僅使用SIP處理，近似自然結構的排名分別是第一、一和十。我們將DR單獨用於一個有殘基距離資訊的水溶性蛋白(soluble protein)，其近似自然結構也出現在第一名。
我們分別研究了AtPht1;1 (transmembrane phosphate transporter)與H+-VrPPase (Vigna radiata pyrophosphatase) 兩個穿膜蛋白的分子運作機制。 AtPht1;1為利用質子(proton)濃度梯度將磷酸(phosphate)及氫離子從細胞膜外運送至膜內的共同轉運蛋白(symporter)。我們主要以磷酸結合inward-occluded態的AtPht1;1同源結構建模，研究可質子化殘基的質子化態(protonation state)如何誘導已結合於催化位磷酸的釋放。為了重現質子濃度梯度，AtPht1;1的可質子化殘基被區分為曝露於胞外及胞內，並分別以pH 4及pH 7質子化。在本研究中，我們依據PROPKA預測的pKa來指定殘基的質子化態。藉由觀察AtPht1;1的分子動力模擬(molecular dynamics simulations)中可質子化殘基pKa的變化，發現當ASP38 and ASP308的去質子化會導致催化位磷酸釋出。
H+-VrPPase以焦磷酸水解(hydrolysis)所釋出的能量為動力，可以抵抗濃度梯度運送質子穿過細胞膜。先前研究指出在高解析度的H+-VrPPase X-ray結構中，有一個直接與配體接觸的水分子參與焦磷酸水解過程，他們稱該分子為「親核性水分子」(nucleophilic water)。我們建立將H+-VrPPase鑲嵌於雙層POPC膜(POPC lipid bilayer)的全原子模型，並把X-ray解出的水分子放入相對應位置後進行模擬。然而我們發現原本「親核性水分子」很快地被附近的鉀離子取代，由此現象推測該位置適合帶正電的離子而非極性分子(如：水分子)。在這個位置附近有兩個帶負電的Asp殘基可以幫助穩定該位置上的鉀離子，而原本「親核性水分子」很可能是帶正電的H3O+ (hydronium ion)。我們進一步將原分子模擬系統的該水分子置換成H3O+後，在整個模擬過程中，該H3O+穩定存在此位置。
蛋白-DNA/RNA複合體(protein-DNA complex)負責起始及調控生物中心教條(轉錄transcription與轉譯translation)，對於生物的重要程度不亞於膜蛋白。我們發現蛋白-DNA結合的方位與蛋白質自身固有動態(intrinsic dynamics)有高度相關。因此我們基於蛋白質最慢的運動模式(slowest dynamics)建構了一個「動態域平面」(dynamics domain interfaces)，可將蛋白質分離成兩群運動方向相反的殘基群。從104個蛋白-DNA複合體的統計結果顯示有97%的DNA被其蛋白質的動態域平面切過。將該動態域平面運用於篩選DNA與DNA結合蛋白的剛體對接(rigid-body docking)的結果，比起使用隨機平面或立體互補性做篩選，近似自然結構的豐富度分別提升2.5倍及1.6倍之多。這個結果闡述了蛋白質的動態限制了蛋白質與DNA的結合方位(orientation)進而提高結合位(binding site)的搜尋精確度。
生物巨分子執行其功能時的構型動態(conformational dynamics)可以從結構被解析出來。分子動力模擬(molecular dynamics simulation, MD)是一個相當有力的理論工具來評估蛋白質的運動大小時間。但由於分子動力模擬非常消耗運算資源及時間，故本研究將計算成本低廉的彈力網路模型(elastic network model, ENM)轉換為估量分子運動時間及運動大小的工具並將其應用於核糖體(ribosome)上。
我們從分子模擬的軌跡分析了沿著主成分(principal components, PCs)的非諧波運動，接著以準諧波分析(Quasi-harmonic analysis)與WKT (Wiener–Khintchine theorem)評估每個PC運動模式的強度加權週期(Intensity-Weighted Period, IWP)，該週期即為本研究所定義的「週期t」。此「週期」的時間尺度與核磁共振(NMR)的order parameters相符。我們把每個PC運動模式的IWP與振動大小(fluctuation size)利用振動曲線映射法(fluctuation-profile mapping, FPM)對應到ENM的每個運動模式。我們發現ENM運動模式的特徵值(eigenvalues, λENM)可以透過利用冪定律(power law)轉換成振動週期及大小。最後我們分別得到用於評估蛋白質運動時間尺度及運動大小的兩個方程式t(ns) = 56.1λENM-1.6和σ2(Å2) = 32.7λENM-3.0。該方程式能推廣應用於評估NMR構型(NMR-resolved conformers)、X-Ray晶體繞射的ADP profile(anisotropic displacement parameters)與核糖體功能性運動的時間及大小。

Efficient and accurate biological processes require proper coordination of participating molecular components including but not limited to proteins, DNA and RNA. These molecules tend to form higher-order complexes (biomacromolecules) to perform their functions. To understand how these biomacromolecules work, we first need to elucidate their higher-order structures. The size and oligomeric state of these bio-macromolecules, especially for those in the membrane, pose a serious challenge to structural determination methods such as X-ray crystallography, NMR and cryo-EM. To fill in the gap, computational approaches that implement statistically or physicochemically derived rules governing molecular assemblage have become sophisticated enough in utilizing and integrating experimental data towards solving complicated biomacromolecules.
One very important group of biomacromolecules are transmembrane proteins which perform various functions such as cell signaling, transport of materials across membranes, maintenance of electrochemical gradient and others. Our statistical survey of transmembrane proteins in RCSB PDB show that ~66% of α-helical transmembrane proteins are homo-oligomeric transmembrane proteins (HoTPs). The survey also found that ~92% of these HoTPs are cyclic (Cn) symmetric. Given the prevalence of Cn symmetric HoTPs and the benefits of incorporating geometry restraints in aiding quaternary structure determination, we introduce two new filters, the distance-restraints (DR) and the Symmetry-Imposed Packing (SIP) filters. SIP relies on a new method that can rebuild the closest ideal Cn symmetric complex from docking poses containing a homo-dimer without prior knowledge of the number (n) of monomers. Using only the geometrical filter, SIP, near-native poses of 7 HoTPs in their monomeric states can be correctly identified in the top-10 for 71% of all cases, or 29% among 31 HoTP structures obtained through homology modeling, while ZDOCK alone returns 14% and 3%, respectively. When the n is given, the optional n-mer filter is applied with SIP and returns the near-native poses for 76% of the test set within the top-10, outperforming M-ZDOCK’s 55% and Sam’s 47%. While applying only SIP to three HoTPs that comes with distance restraints, we found the near-native poses were ranked 1st, 1st and 10th among 54,000 possible decoys. The results are further improved to 1st, 1st and 3rd when both DR and SIP filters are used. By applying only DR, a soluble system with distance restraints is recovered at the 1st-ranked pose.
We have studied two of these transmembrane proteins in mechanistic details. One is the transmembrane phosphate transporter, AtPht1;1 and the other is the transmembrane proton pump, Vigna radiata pyrophosphatase (H+-VrPPase). As for the phosphate transporter, AtPht1;1, it transports phosphates across the membrane using the proton gradient. Thus, it transports both protons and phosphates from the extra-cellular side to the intra-cellular side, acting as a symporter. There is only the homology modeled structure of AtPht1;1 in the inward-occluded state with a phosphate bound to the binding site. We wanted to study how the protonation states of protonizable residue sidechains could induce the release of the bound phosphate to the cytoplasmic side. To replicate the proton gradient across the membrane, the protonizable residues in the protein were split into those that are exposed to the extra-cellular side (with pH 4) and the others to the intra-cellular side (with pH 7). Their protonation states were assigned based on their predicted pKa by PROPKA. Monitoring the pKa changes of protonizable residues during MD simulations, we were able to identify two residues, ASP38 and ASP308, when deprotonated results in the release of phosphate to the cytoplasmic side.
H+-VrPPase catalyzes the hydrolysis of pyrophosphate into two phosphates, using the energy generated to pump protons against the proton gradient across the membrane. The high-resolution X-ray structure of H+-VrPPase has been solved showing waters near the binding site of the ligand. The authors proposed that one of the waters directly interacting with the ligand is involved in the catalysis of pyrophosphate into phosphate and thus called it the "nucleophilic water". To study this in more detail we performed all-atom MD simulations of H+-VrPPase embedded in a POPC lipid bilayer and solvated with water. However, the MD simulation results show that the position of the "nucleophilic water" does not favor waters, instead a nearby K+ ion moves and replaces the waters at this position. This implies that there is a preference for an extra positive charge at this position rather than a polar molecule like water. It is unsurprising considering that nearby this position are two aspartic acids which are negatively charged. It is possible that the "nucleophilic water" is a hydronium ion which is positive charged. We have performed MD simulations of "nucleophilic water" as a hydronium ion and showed that it is does not leave the site and the K+ ion does not move in and replace it.
Functional protein-DNA/RNA complexes that initiate and regulate the central dogma (transcription and translation) are of no less importance than membrane proteins. We find that protein–DNA docking orientation is a function of protein intrinsic dynamics, but the motions of the binding site itself does not necessarily display any unique patterns. We introduce a new technique that locates “dynamics interfaces” in proteins across which protein parts are anticorrelated in their slowest dynamics. The statistics show that such interfaces intersect the DNA in 97% of the 104 examined cases. These dynamic interfaces are then used to screen decoys generated by rigid-body docking of DNA molecules onto DNA-binding proteins. This enriches the near-native poses by 2.5- and 1.6-fold, as compared to a random guess and methods based on surface complementarity, respectively. Hence, dynamically permissible protein–DNA docking orientations can be used to filter and re-rank docking poses to enhance the prediction of DNA-binding sites although these sites do not have any distinct dynamics features.
Provided with the structures of the biomacromolecules, their conformational dynamics underlying the observed molecular functions can therefore be analyzed. Computationally expensive molecular dynamics (MD) simulation has been the only theoretical tool to gauge the time and sizes of these motions, though barely the slowest ones. Here, we convert a computationally cheap elastic network model (ENM) into a molecular timer and sizer to gauge the slowest functional motions of proteins and applied this to the ribosome. Quasi-harmonic analysis and the Wiener–Khintchine theorem (WKT) were used to define the Intensity-Weighted Period (IWP) which we define as the “time-period”, t, for the anharmonic motions along a principal components (PCs). We validated these timescales by NMR order parameters. The PCs with their respective IWPs and variances are then mapped to ENM modes using the newly introduced fluctuation-profile matching (FPM) method. We find that ENM mode eigenvalues (λENM) have a power law relationship with the assigned timescales and variances. Thus, the power laws t(ns) = 56.1λENM-1.6 and σ2(Å2) = 32.7λENM-3.0 are established allowing the characterization of the time scales of NMR-resolved conformers, crystallographic anisotropic displacement parameters, and important ribosomal motions, as well as motional sizes of the latter.

English Abstract    I
Chinese Abstract    IV
Acknowledgements    VII
Table of Contents    VIII
List of Figures    XIII
List of Tables    XVI
Chapter 1    DR-SIP: Protocols for Higher Order Structure Modeling with Distance Restraints- and Cyclic Symmetry-Imposed Packing    1
1    Introduction    1
2    Methods    4
2.1    Docking Protocols    5
2.2    Extracting Cn Symmetry Parameters from an Ideal Cn Symmetric Pose    7
2.3    Constructing the Ideal Cn Symmetric Pose that is Closest to a Non-Ideal Docking Pose or X-Ray Crystallographically Solved Structure    8
2.4    Cyclic Symmetry-Imposed Packing (SIP)    9
2.5    Distance-Restraints (DR) Filter    10
2.6    Shift Along Axis of Symmetry    10
2.7    Deviation from Ideal Rotation Angle    10
2.8    Clustering of Poses    10
2.9    Selecting the Representative for Each Cluster and Ranking of the Clusters    11
2.10    Evaluating the Quality of Docking Poses: Modified CAPRI Criteria for HoTPs    11
2.11    Data Sets    12
2.12    Optimizing the Cutoff Parameters for SIP    25
2.13    Sum of the Normalized M-ZDOCK Scores for the Top-100 Poses    25
2.14    Implementation of DR-SIP    26
3    Results    26
3.1    Statistical Analysis of 118 Structurally Solved α-Helical HoTPs    26
3.2    SIP Filter Performance without Distance Restraints    34
3.3    Performance of DR-SIP with Distance Restraints: Near-Native Poses Within the Top-3 Ranking Poses    44
4    Discussions    49
Chapter 2    Mechanochemical Coupling Found in PHT1;1 Facilitates Inorganic Phosphate Transport    54
1    Introduction    54
2    Results    57
2.1    Proton gradient across lipid membranes promotes phosphate fluctuations inside the channel.    57
2.2    Phosphate exits through a sequential deprotonation of Asp38 and Asp308 accompanied by proton release in two water channels.    63
2.3    QM/MM analysis reveals that it is more favorable to deprotonate Asp308 when Pi is further away from it    65
2.4    Pi releasing pathway gated by three transmembrane helices - TM1, TM4, and TM6    67
3    Discussion    68
3.1    Proposed model for Pi transport mechanism of PHT1;1    68
3.2    Use anisotropic network model (ANM) to describe conformational states of PHT1;1    69
3.3    Comparison of Pho84, PiPT and PHT1;1    71
3.4    Mutation data supports    71
4    Methods    73
4.1    Building the inward-occluded state of PHT1;1    73
4.2    Forcefield for H2PO4-    73
4.3    Building the initial protein-membrane system for performing MD simulations    74
4.4    Building protein-membrane systems with a proton gradient across the membrane    76
4.5    Starting structures for the simulations    77
4.6    Targeted MD (TMD) simulation for building the outward-facing state of PHT1;1    77
4.7    Root Mean Square Deviation (RMSD) calculations for simulation snapshots    80
4.8    Conformational transition of PHT1;1 during Pi releasing manifested in a 2D plane or 3D space spanned by dominant normal modes, derived from anisotropic network model (ANM) of outward-facing PHT1;1    80
4.9    QM/MM calculations    82
Chapter 3    Protonation State of Watnu in H+-VrPPase    84
1    Introduction    84
2    Results    85
2.1    Equilibration of the membrane-protein system.    85
2.2    Watnu is displaced by the K+ ion in the first 1.5 ns of simulations.    86
2.3    Coordination number analysis of Watnu in the crystal structure    87
2.4    Swapping K+ with water/H3O+.    88
2.5    Coordination number analysis of K+/H3O+ for the simulations with the swapped K+ and water/H3O+    89
2.6    Watnu interacts with ASP287 and ASP731.    90
3    Discussion    91
4    Methods    91
4.1    Equilibration Protocol for MD Simulation    91
4.2    Equilibration Analysis    92
4.3    Patching waters to hydronium ions (H3O+)    92
4.4    Computing the radius of the first hydration shell and coordination numbers (CNs)    95
4.5    Prediction of pKa’s    95
Chapter 4    Protein Dynamics and Contact Topology Reveal Protein-DNA Binding Orientation    97
1    Introduction    97
2    Materials and Methods    99
2.1    Dataset of DNA-bound and DNA-free proteins.    99
2.2    Definition of DNA-binding residues    106
2.3    Gaussian network model (GNM).    106
2.4    Anisotropic Network Model (ANM) and conformational changes upon DNA binding. The potential energy function of ANM penalizes changes of the Euclidean distance between two residues i and j from the equilibrium state:    107
2.5    Intrinsic dynamics domains, IDDs.    108
2.6    Determining D-planes    108
2.7    Determining GNM-based IDDs and D-plane.    110
2.8    Squared Displacement of CG nodes    113
2.9    Determining peaks and troughs in squared displacement profiles    113
2.10    Squared displacement of the distance between nodes i and j    113
2.11    Performance measures    114
2.12    Enrichment ratio for binding residues and enrichment factor for hits (EFH)    114
2.13    Generation of decoy sets.    115
2.14    Scoring decoys to determine native poses.    115
2.15    Enrichment factor of hits, EFH.    118
2.16    Random axis generation    118
2.17    Mean and variance of angle between two randomly oriented vectors    119
3    Results    120
3.1    Slow GNM modes predict conformational change upon DNA binding.    120
3.2    Folding core or flexible residues in a protein are not co-localized in DNA-binding sites.    120
3.3    D-planes of the free proteins intersect DNA from DNA-bound proteins.    123
3.4    Are DNA-binding residues close to D-planes?    134
3.5    IDD-based restraints enrich near-native poses.    135
4    Discussion    138
4.1    Predicting conformational change upon DNA binding by ENM models    138
4.2    Enthalpic considerations disfavor folding core residues from binding DNA.    139
4.3    DNA stays close to protein regions with minimal angular momentum and low vibrational entropy.    139
4.4    A plausible role for dynamics in determining binding orientations.    140
5    Conclusion    140
Chapter 5    An Efficient Timer and Sizer of Biomacromolecular Motions.    142
1    Introduction    142
2    Results    145
2.1    Overview    145
2.2    Determining the time scales of the anharmonic modes    147
2.3    Determining the time scales of experimentally observed dynamical variables    149
2.4    Determination of time scales of the ENM modes and inference of time scales from the ENM eigenvalues    157
2.5    ANM Mode Time Scale Assignment Through ANM-PCA Mode Mapping    157
2.6    Verification of the General ANM Power Law via the Dynamics Analysis of Ubiquitin, FGF2 and HPNAP    161
2.7    Derive ANM power law for the sizes of functional motions    161
2.8    Analysis of ribosomal motions    161
3    Discussion    166
3.1    Robustness Analysis    166
4    Methods    167
4.1    MD Simulations    167
4.2    Principal component analysis (PCA) of the covariance matrix computed from MD trajectories    168
4.3    Wiener–Khintchine theorem (WKT)    168
4.4    Intensity-Weighted Period (IWP), Relaxation Time and Characteristic Time    170
4.5    Theoretical Covariance Matrix Comprising a set of PC modes Derived from MD simulations    170
4.6    Computing the RMSF and ADP Profiles for ubiquitin derived from X-ray/NMR-determined Structures and MD    171
4.7    Order Parameter Profiles derived from NMR-determined structural ensemble and MD snapshots    171
4.8    Derivation of General Elastic Network Model (ENM) – the relation between covariance and Hessian    172
4.9    The Anisotropic Network Model (ANM)    176
4.10    Theoretical Covariance Matrix, RMSF and ADP from ANM With Removed Modes    176
4.11    Fitting the Time Power Laws    177
4.12    Fitting the Variance Power Law    177
4.13    Identifying the Functional Modes Corresponding to Ribosomal Body Rotation (Ratcheting) and Head Swiveling Motions    177
4.14    Predicting the Conformation of the Ribosome After the Ratcheting and Head Swiveling Motions    179
4.15    Identifying the Functional Modes and Conformations Corresponding to the L1 Stalk Closing Motion    179
4.16    Perturbation of the ANM for ubiquitin    179
Chapter 6    References    181
                                

Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
Agirrezabala, X., Liao, H. Y., Schreiner, E., Fu, J., Ortiz-Meoz, R. F., Schulten, K., … Frank, J. (2012). Structural characterization of mRNA-tRNA translocation intermediates. Proceedings of the National Academy of Sciences of the United States of America, 109(16), 6094–6099. https://doi.org/10.1073/pnas.1201288109
Ahmad, S., Gromiha, M. M., & Sarai, A. (2004). Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics (Oxford, England), 20(4), 477–486. https://doi.org/10.1093/bioinformatics/btg432
Alber, F., Förster, F., Korkin, D., Topf, M., & Sali, A. (2008). Integrating diverse data for structure determination of macromolecular assemblies. Annual Review of Biochemistry, 77, 443–477. https://doi.org/10.1146/annurev.biochem.77.060407.135530
Alford, R. F., Koehler Leman, J., Weitzner, B. D., Duran, A. M., Tilley, D. C., Elazar, A., & Gray, J. J. (2015). An integrated framework advancing membrane protein modeling and design. PLoS Computational Biology, 11(9), e1004398. https://doi.org/10.1371/journal.pcbi.1004398
Aloy, P., Moont, G., Gabb, H. A., Querol, E., Aviles, F. X., & Sternberg, M. J. (1998). Modelling repressor proteins docking to DNA. Proteins, 33(4), 535–549.
Amzel, L. M. (1997). Loss of translational entropy in binding, folding, and catalysis. Proteins, 28(2), 144–149. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/9188731
Andersson, M., Bondar, A. N., Freites, J. A., Tobias, D. J., Kaback, H. R., & White, S. H. (2012). Proton-coupled dynamics in lactose permease. Structure, 20(11), 1893–1904. https://doi.org/10.1016/j.str.2012.08.021
André, I., Strauss, C. E. M., Kaplan, D. B., Bradley, P., & Baker, D. (2008). Emergence of symmetry in homooligomeric biological assemblies. Proceedings of the National Academy of Sciences of the United States of America, 105(42), 16148–16152. https://doi.org/10.1073/pnas.0807576105
Atilgan, A. R., Durell, S. R., Jernigan, R. L., Demirel, M. C., Keskin, O., & Bahar, I. (2001). Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model. Biophysical Journal, 80(1), 505–515. https://doi.org/10.1016/S0006-3495(01)76033-X
Badis, G., Berger, M. F., Philippakis, A. A., Talukder, S., Gehrke, A. R., Jaeger, S. A., … Bulyk, M. L. (2009). Diversity and complexity in DNA recognition by transcription factors. Science (New York, N.Y.), 324(5935), 1720–1723. https://doi.org/10.1126/science.1162327
Baek, M., Park, T., Heo, L., Park, C., & Seok, C. (2017). GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure. Nucleic Acids Research, 45(W1), W320–W324. https://doi.org/10.1093/nar/gkx246
Bahar, I, Atilgan, a R., & Erman, B. (1997a). Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Folding & Design, 2(3), 173–181. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/9218955
Bahar, I, Atilgan, a R. R., & Erman, B. (1997b). Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Folding & Design, 2(3), 173–181. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/9218955
Bahar, I, Wallqvist, A., Covell, D. G., & Jernigan, R. L. (1998). Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry, 37(4), 1067–1075. https://doi.org/10.1021/bi9720641
Bahar, Ivet, Atilgan, A. R., Demirel, M. C., & Erman, B. (1998). Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability. Physical Review Letters, 80(12), 2733–2736. https://doi.org/10.1103/PhysRevLett.80.2733
Bahar, Ivet, Lezon, T. R., Yang, L.-W., & Eyal, E. (2010). Global dynamics of proteins: bridging between structure and function. Annual Review of Biophysics, 39(39), 23–42. https://doi.org/10.1146/annurev.biophys.093008.131258
Bairoch, A. (2000). The ENZYME database in 2000. Nucleic Acids Research, 28, 304–305. https://doi.org/10.1093/nar/28.1.304
Bakan, A., & Bahar, I. (2009). The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proceedings of the National Academy of Sciences, 106(34), 14349–14354. https://doi.org/10.1073/pnas.0904214106
Banitt, I., & Wolfson, H. J. (2011). ParaDock: a flexible non-specific DNA--rigid protein docking algorithm. Nucleic Acids Research, 39(20), e135. https://doi.org/10.1093/nar/gkr620
Berman, A. J., Kamtekar, S., Goodman, J. L., Lázaro, J. M., de Vega, M., Blanco, L., … Steitz, T. a. (2007). Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. The EMBO Journal, 26(14), 3494–3505. https://doi.org/10.1038/sj.emboj.7601780
Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Philip, E., Burkhardt, K., … Westbrook, J. D. (2002). The Protein Data Bank research papers The Protein Data Bank. 899–907.
Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. F., Brice, M. D., Rodgers, J. R., … Tasumi, M. (1977). The Protein Data Bank. A computer-based archival file for macromolecular structures. European Journal of Biochemistry / FEBS, 80, 319–324. https://doi.org/10.1016/S0022-2836(77)80200-3
Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., & Schwede, T. (2017). Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports, 7(1), 1–15. https://doi.org/10.1038/s41598-017-09654-8
Best, R. B., & Vendruscolo, M. (2004). Determination of Protein Structures Consistent with NMR Order Parameters. Journal of the American Chemical Society, 126(26), 8090–8091. https://doi.org/10.1021/ja0396955
Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., … Schwede, T. (2014). SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42(Web Server issue), W252-8. https://doi.org/10.1093/nar/gku340
Boas, M. L. (2006). Mathematical Methods in the Physical Sciences. In The Journal of Symbolic Logic (Vol. 57, pp. 340–389).
Bochkarev, A., Bochkareva, E., Frappier, L., & Edwards, A. M. (1998). The 2.2 A structure of a permanganate-sensitive DNA site bound by the Epstein-Barr virus origin binding protein, EBNA1. Journal of Molecular Biology, 284(5), 1273–1278. https://doi.org/10.1006/jmbi.1998.2247
Bock, L. V, Blau, C., Schröder, G. F., Davydov, I. I., Fischer, N., Stark, H., … Grubmüller, H. (2013). Energy barriers and driving forces in tRNA translocation through the ribosome. Nature Structural & Molecular Biology, 20(12), 1390–1396. https://doi.org/10.1038/nsmb.2690
Boehr, D. D., Nussinov, R., & Wright, P. E. (2009). The role of dynamic conformational ensembles in biomolecular recognition. Nature Chemical Biology, 5(11), 789–796. https://doi.org/10.1038/nchembio.232
Boskovic, J., Rivera-Calzada, A., Maman, J. D., Chacón, P., Willison, K. R., Pearl, L. H., & Llorca, O. (2003). Visualization of DNA-induced conformational changes in the DNA repair kinase DNA-PKcs. The EMBO Journal, 22(21), 5875–5882.
Bowman, B. R., Lee, S., Wang, S., & Verdine, G. L. (2008). Structure of the E. coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion-containing DNA. Structure (London, England : 1993), 16(8), 1166–1174. https://doi.org/10.1016/j.str.2008.04.012
Bromberg, S., & Dill, K. A. (1994). Side-chain entropy and packing in proteins. Protein Science : A Publication of the Protein Society, 3(7), 997–1009. https://doi.org/10.1002/pro.5560030702
Brooijmans, N., & Kuntz, I. D. (2003). Molecular recognition and docking algorithms. Annual Review of Biophysics and Biomolecular Structure, 32, 335–373. https://doi.org/10.1146/annurev.biophys.32.110601.142532
Bun-Ya, M., Nishimura, M., Harashima, S., & Oshima, Y. (1991). The PHO84 gene of Saccharomyces cerevisiae encodes an inorganic phosphate transporter. Molecular and Cellular Biology, 11(6), 3229–3238. https://doi.org/10.1128/mcb.11.6.3229
Caliskan, N., Katunin, V. I., Belardinelli, R., Peske, F., & Rodnina, M. V. (2014). Programmed -1 frameshifting by kinetic partitioning during impeded translocation. Cell, 157(7), 1619–1631. https://doi.org/10.1016/j.cell.2014.04.041
Case, D. a, Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., … Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. https://doi.org/10.1002/jcc.20290
Chandrasekaran, A., Chan, J., Lim, C., & Yang, L.-W. (2016). Protein dynamics and contact topology reveal protein-DNA binding orientation. Journal of Chemical Theory and Computation, 12(11), acs.jctc.6b00688. https://doi.org/10.1021/acs.jctc.6b00688
Chang, C.-C., Khan, I., Tsai, K.-L., Li, H., Yang, L.-W., Chou, R.-H., & Yu, C. (2016). Blocking the interaction between S100A9 and RAGE V domain using CHAPS molecule: A novel route to drug development against cell proliferation. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1864(11), 1558–1569. https://doi.org/10.1016/j.bbapap.2016.08.008
Chang, C. A., Chen, W., & Gilson, M. K. (2007). Ligand configurational entropy and protein binding. Proceedings of the National Academy of Sciences of the United States of America, 104(5), 1534–1539. https://doi.org/10.1073/pnas.0610494104
Chang, K.-C., Wen, J.-D., & Yang, L.-W. (2015). Functional Importance of Mobile Ribosomal Proteins. BioMed Research International, 2015, 1–11. https://doi.org/10.1155/2015/539238
Chasman, D. I., Flaherty, K. M., Sharp, P. A., & Kornberg, R. D. (1993). Crystal structure of yeast TATA-binding protein and model for interaction with DNA. Proceedings of the …, 90(17), 8174–8178.
Chaudhury, S., & Gray, J. J. (2008). Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. Journal of Molecular Biology, 381(4), 1068–1087. https://doi.org/10.1016/j.jmb.2008.05.042
ChemAxon. (2016). MarvinSketch. Retrieved from https://chemaxon.com/products/marvin
Chen, C., Zhang, H., Broitman, S. L., Reiche, M., Farrell, I., Cooperman, B. S., & Goldman, Y. E. (2013). Dynamics of translation by single ribosomes through mRNA secondary structures. Nature Structural & Molecular Biology, 20(5), 582–588. https://doi.org/10.1038/nsmb.2544
Chen, Y. C., & Lim, C. (2008). Common physical basis of macromolecule-binding sites in proteins. Nucleic Acids Research, 36(22), 7078–7087. https://doi.org/10.1093/nar/gkn868
Chen, Y. C., Wright, J. D., & Lim, C. (2012). DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Research, 40(Web Server issue), W249-56. https://doi.org/10.1093/nar/gks481
Chen, Y. C., Wu, C. Y., & Lim, C. (2007). Predicting DNA-binding amino acid residues from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation. Proteins, 67(3), 671–680. https://doi.org/10.1002/prot.21366
Chennubhotla, C., Rader, A. J., Yang, L.-W., & Bahar, I. (2005). Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies. Physical Biology, 2(4), S173-80. https://doi.org/10.1088/1478-3975/2/4/S12
Chng, C.-P., & Yang, L.-W. (2008). Coarse-grained models reveal functional dynamics--II. Molecular dynamics simulation at the coarse-grained level--theories and biological applications. Bioinformatics and Biology Insights, 2, 171–185. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2735960&tool=pmcentrez&rendertype=abstract
Cho, H. S., Ha, N. C., Kang, L. W., Chung, K. M., Back, S. H., Jang, S. K., & Oh, B. H. (1998). Crystal structure of RNA helicase from genotype 1b hepatitis C virus. A feasible mechanism of unwinding duplex RNA. The Journal of Biological Chemistry, 273(24), 15045–15052. https://doi.org/10.1074/jbc.273.24.15045
Choi, U. B., Strop, P., Vrljic, M., Chu, S., Brunger, A. T., & Weninger, K. R. (2010). Single-molecule FRET-derived model of the synaptotagmin 1-SNARE fusion complex. Nature Structural & Molecular Biology, 17(3), 318–324. https://doi.org/10.1038/nsmb.1763
Chung, S. J., & Verdine, G. L. (2004). Structures of end products resulting from lesion processing by a DNA glycosylase/lyase. Chemistry & Biology, 11(12), 1643–1649. https://doi.org/10.1016/j.chembiol.2004.09.014
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., … de Hoon, M. J. L. (2009). Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics (Oxford, England), 25(11), 1422–1423. https://doi.org/10.1093/bioinformatics/btp163
Cornish, P. V., Ermolenko, D. N., Noller, H. F., & Ha, T. (2008). Spontaneous Intersubunit Rotation in Single Ribosomes. Molecular Cell, 30(5), 578–588. https://doi.org/10.1016/j.molcel.2008.05.004
Csermely, P., Palotai, R., & Nussinov, R. (2010). Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends in Biochemical Sciences, 35(10), 539–546. https://doi.org/10.1016/j.tibs.2010.04.009
Cunningham, R. P., Garcin, E. D., Hosfield, D. J., Desai, S. A., Haas, B. J., Bjo, M., & Tainer, J. A. (2008). DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. 15(0027), 515–522. https://doi.org/10.1038/nsmb.1414
Dang, L. X., Schenter, G. K., Glezakou, V.-A., & Fulton, J. L. (2006). Molecular simulation analysis and X-ray absorption measurement of Ca2+, K+ and Cl- ions in solution. The Journal of Physical Chemistry. B, 110(47), 23644–23654. https://doi.org/10.1021/jp064661f
Dang, S., Sun, L., Huang, Y., Lu, F., Liu, Y., Gong, H., … Yan, N. (2010). Structure of a fucose transporter in an outward-open conformation. Nature, 467(7316), 734–738. https://doi.org/10.1038/nature09406
de Jesus, A. J., & Allen, T. W. (2013). The determinants of hydrophobic mismatch response for transmembrane helices. Biochimica et Biophysica Acta, 1828(2), 851–863. https://doi.org/10.1016/j.bbamem.2012.09.012
Delarue, M., & Sanejouand, Y.-H. (2002). Simplified Normal Mode Analysis of Conformational Transitions in DNA-dependent Polymerases: the Elastic Network Model. Journal of Molecular Biology, 320(5), 1011–1024. https://doi.org/10.1016/S0022-2836(02)00562-4
Demirel, M., Atilgan, A., & Bahar, I. (1998). Identification of kinetically hot residues in proteins. Protein Science, 7, 2522–2532.
Deplancke, B., Mukhopadhyay, A., Ao, W., Elewa, A. M., Grove, C. A., Martinez, N. J., … Walhout, A. J. M. (2006). A gene-centered C. elegans protein-DNA interaction network. Cell, 125(6), 1193–1205. https://doi.org/10.1016/j.cell.2006.04.038
Dimura, M., Peulen, T. O., Hanke, C. A., Prakash, A., Gohlke, H., & Seidel, C. A. (2016). Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Current Opinion in Structural Biology, 40, 163–185. https://doi.org/10.1016/j.sbi.2016.11.012
Drozdowicz, Y. M., Kissinger, J. C., & Rea, P. A. (2000). AVP2, a sequence-divergent, K(+)-insensitive H(+)-translocating inorganic pyrophosphatase from Arabidopsis. Plant Physiology, 123(1), 353–362. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=59009&tool=pmcentrez&rendertype=abstract
Drozdowicz, Y. M., & Rea, P. A. (2001). Vacuolar H(+) pyrophosphatases: from the evolutionary backwaters into the mainstream. Trends in Plant Science, 6(5), 206–211. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/11335173
Du, D., van Veen, H. W., Murakami, S., Pos, K. M., & Luisi, B. F. (2015). Structure, mechanism and cooperation of bacterial multidrug transporters. Current Opinion in Structural Biology, 33, 76–91. https://doi.org/10.1016/j.sbi.2015.07.015
Dutta, A., & Bahar, I. (2010). Metal-binding sites are designed to achieve optimal mechanical and signaling properties. Structure (London, England : 1993), 18(9), 1140–1148. https://doi.org/10.1016/j.str.2010.06.013
Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., … Pande, V. S. (2017). OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Computational Biology, 13(7), e1005659. https://doi.org/10.1371/journal.pcbi.1005659
Edgar, R. C. (2004). MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113. https://doi.org/10.1186/1471-2105-5-113
Eyal, E., Chennubhotla, C., Yang, L.-W., & Bahar, I. (2007). Anisotropic Fluctuations of Amino Acids in Protein Structures: Insights from X-Ray Crystallography and Elastic Network Models. Bioinformatics, 23(13), i175–i184. https://doi.org/10.1093/bioinformatics/btm186
Fagerberg, L., Jonasson, K., von Heijne, G., Uhlen, M., & Berglund, L. (2010). Prediction of the human membrane proteome. Proteomics, 10(6), 1141–1149. https://doi.org/10.1002/pmic.200900258
Fei, J., Kosuri, P., MacDougall, D. D., & Gonzalez, R. L. (2008). Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Molecular Cell, 30(3), 348–359. https://doi.org/10.1016/j.molcel.2008.03.012
Ferreiro, D. U., & de Prat-Gay, G. (2003). A protein-DNA binding mechanism proceeds through multi-state or two-state parallel pathways. Journal of Molecular Biology, 331(1), 89–99. https://doi.org/10.1016/s0022-2836(03)00720-4
Fisher, R. (1936). The use of multiple measurements in taxonomic problems. Annals of Eugenics, 7, 179–188.
Flory, P. J., Gordon, M., & McCrum, N. G. (1976). Statistical Thermodynamics of Random Networks [and Discussion]. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 351(1666), 351–380. https://doi.org/10.1098/rspa.1976.0146
Frank, J., & Agrawal, R. K. (2000). A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature, 406(6793), 318–322. https://doi.org/10.1038/35018597
Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., … Fox, D. J. (2016). Gaussian16.
Furihata, T., Suzuki, M., & Sakurai, H. (1992). Kinetic Characterization of Two Phosphate Uptake Systems with Different Affinities in Suspension-Cultured Catharanthus roseus Protoplasts. Plant and Cell Physiology, 33(8), 1151–1157. https://doi.org/10.1093/oxfordjournals.pcp.a078367
Gabb, H. a, Jackson, R. M., & Sternberg, M. J. (1997). Modelling protein docking using shape complementarity, electrostatics and biochemical information. Journal of Molecular Biology, 272(1), 106–120. https://doi.org/10.1006/jmbi.1997.1203
Gao, M., & Skolnick, J. (2009). From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. PLoS Computational Biology, 5(3), e1000341. https://doi.org/10.1371/journal.pcbi.1000341
Garcin, E. D., Hosfield, D. J., Desai, S. a, Haas, B. J., Björas, M., Cunningham, R. P., & Tainer, J. a. (2008). DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nature Structural & Molecular Biology, 15(5), 515–522. https://doi.org/10.1038/nsmb.1414
Ghelis, C., & Yon, J. (1982). Structural characteristics of folded proteins. In B. Horecker, N. O. Kaplan, J. Marmur, & H. A. Scheraga (Eds.), Protein Folding (1st ed., pp. 37–135). https://doi.org/10.1016/B978-0-12-281520-1.50009-3
Golan, G., Zharkov, D. O., Grollman, A. P., Dodson, M. L., McCullough, A. K., Lloyd, R. S., & Shoham, G. (2006). Structure of T4 pyrimidine dimer glycosylase in a reduced imine covalent complex with abasic site-containing DNA. Journal of Molecular Biology, 362(2), 241–258. https://doi.org/10.1016/j.jmb.2006.06.059
Gorman, J., & Greene, E. C. (2008). Visualizing one-dimensional diffusion of proteins along DNA. Nature Structural & Molecular Biology, 15(8), 768–774. https://doi.org/10.1038/nsmb.1441
Götz, A. W., Williamson, M. J., Xu, D., Poole, D., Le Grand, S., & Walker, R. C. (2012). Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. Journal of Chemical Theory and Computation, 8(5), 1542–1555. https://doi.org/10.1021/ct200909j
Gowers, D. (2005). Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA. Proceedings of the National Academy of Sciences, 2005(25), 15883–15888.
Gowers, R., Linke, M., Barnoud, J., Reddy, T., Melo, M., Seyler, S., … Beckstein, O. (2016). MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall & S. Rostrup (Eds.), Proceedings of the 15th Python in Science Conference (pp. 98–105). https://doi.org/10.25080/Majora-629e541a-00e
Gu, M. . R. C. M. (2010). Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism. Proc.Natl.Acad.Sci.USA, 107, 521–528. https://doi.org/20080715
Guo, S., Yin, H., Zhang, X., Zhao, F., Li, P., Chen, S., … Zhang, H. (2006). Molecular cloning and characterization of a vacuolar H+ -pyrophosphatase gene, SsVP, from the halophyte Suaeda salsa and its overexpression increases salt and drought tolerance of Arabidopsis. Plant Molecular Biology, 60(1), 41–50. https://doi.org/10.1007/s11103-005-2417-6
Guo, Z., & Noller, H. F. (2012). Rotation of the Head of the 30S Ribosomal Subunit During mRNA Translocation. Proceedings of the National Academy of Sciences, 109(50), 20391–20394. https://doi.org/10.1073/pnas.1218999109
Gupta, A. A., Chou, R. H., Li, H., Yang, L. W., & Yu, C. (2013). Structural insights into the interaction of human S100B and basic fibroblast growth factor (FGF2): Effects on FGFR1 receptor signaling. Biochimica et Biophysica Acta - Proteins and Proteomics, 1834(12), 2606–2619. https://doi.org/10.1016/j.bbapap.2013.09.012
Haliloglu, T., Bahar, I., & Erman, B. (1997). Gaussian Dynamics of Folded Proteins. Physical Review Letters, 79(16), 3090–3093. https://doi.org/10.1103/PhysRevLett.79.3090
Haliloglu, T., & Erman, B. (2009). Analysis of Correlations between Energy and Residue Fluctuations in Native Proteins and Determination of Specific Sites for Binding. Physical Review Letters, 102(8), 088103. https://doi.org/10.1103/PhysRevLett.102.088103
Harding, M. M. (2002). Metal-ligand geometry relevant to proteins and in proteins: Sodium and potassium. Acta Crystallographica Section D: Biological Crystallography, 58(5), 872–874. https://doi.org/10.1107/S0907444902003712
He, C., Hus, J.-C., Sun, L. J., Zhou, P., Norman, D. P. G., Dötsch, V., … Verdine, G. L. (2005). A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli ada. Molecular Cell, 20(1), 117–129. https://doi.org/10.1016/j.molcel.2005.08.013
Henrick, K., & Thornton, J. M. (1998). PQS: a protein quaternary structure file server. Trends in Biochemical Sciences, 23(9), 358–361. https://doi.org/10.1016/S0968-0004(98)01253-5
Henry, E. R., & Szabo, A. (1985). Influence of Vibrational Motion on Solid State Line Shapes and NMR Relaxation. The Journal of Chemical Physics, 82(11), 4753. https://doi.org/10.1063/1.448692
Hinsen, K. (1998). Analysis of domain motions by approximate normal mode calculations. Proteins, 33(3), 417–429.
Ho, K. L., McNae, I. W., Schmiedeberg, L., Klose, R. J., Bird, A. P., & Walkinshaw, M. D. (2008). MeCP2 binding to DNA depends upon hydration at methyl-CpG. Molecular Cell, 29(4), 525–531. https://doi.org/10.1016/j.molcel.2007.12.028
Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters. Proteins: Structure, Function, and Bioinformatics, 65(3), 712–725. https://doi.org/10.1002/prot.21123
Horton, J. R., Liebert, K., Hattman, S., Jeltsch, A., & Cheng, X. (2005). Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase. Cell, 121(3), 349–361. https://doi.org/10.1016/j.cell.2005.02.021
Huang, J., & Mackerell, A. D. (2013). CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. Journal of Computational Chemistry, 34(25), 2135–2145. https://doi.org/10.1002/jcc.23354
Huang, S. Y. (2014). Search strategies and evaluation in protein-protein docking: Principles, advances and challenges. Drug Discovery Today, 19(8), 1081–1096. https://doi.org/10.1016/j.drudis.2014.02.005
Huang, Y.-T., Liu, T.-H., Lin, S.-M., Chen, Y.-W., Pan, Y.-J., Lee, C.-H., … Pan, R.-L. (2013). Squeezing at entrance of proton transport pathway in proton-translocating pyrophosphatase upon substrate binding. The Journal of Biological Chemistry, 288(27), 19312–19320. https://doi.org/10.1074/jbc.M113.469353
Hurwitz, N., Schneidman-Duhovny, Di., & Wolfson, H. J. (2016). Memdock: An α-helical membrane protein docking algorithm. Bioinformatics (Oxford, England), 32(16), 2444–2450. https://doi.org/10.1093/bioinformatics/btw184
Hyeon, C., & Thirumalai, D. (2011). Capturing the essence of folding and functions of biomolecules using coarse-grained models. Nature Communications, 2, 487. https://doi.org/10.1038/ncomms1481
Jasti, J., Furukawa, H., Gonzales, E. B., & Gouaux, E. (2007). Structure of acid-sensing ion channel 1 at 1.9 Å resolution and low pH. Nature, 449(7160), 316–323. https://doi.org/10.1038/nature06163
Jen-jacobson, L., Engler, L. E., Ames, J. T., Kurpiewski, M. R., & Grigorescu, A. (2000). Thermodynamic Parameters of Specific and Nonspecific Protein-DNA Binding. Supramolecular Chemistry, 12(2), 143–160. https://doi.org/10.1080/10610270008027446
Jenner, L. B., Demeshkina, N., Yusupova, G., & Yusupov, M. (2010). Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nature Structural & Molecular Biology, 17(5), 555–560. https://doi.org/10.1038/nsmb.1790
Jia, H., Korolev, S., Niedziela-Majka, A., Maluf, N. K., Gauss, G. H., Myong, S., … Lohman, T. M. (2011). Rotations of the 2B sub-domain of E. coli UvrD helicase/translocase coupled to nucleotide and DNA binding. Journal of Molecular Biology, 411(3), 633–648. https://doi.org/10.1016/j.jmb.2011.06.019
Jia, Y.-B. (2017). Rotation in the space. Retrieved from Com S 477/577 Notes website: http://web.cs.iastate.edu/~cs577/handouts/rotation.pdf
Jo, S., Lim, J. B., Klauda, J. B., & Im, W. (2009). CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophysical Journal, 97(1), 50–58. https://doi.org/10.1016/j.bpj.2009.04.013
Joh, N. H., Wang, T., Bhate, M. P., Acharya, R., Wu, Y., Grabe, M., … DeGrado, W. F. (2014). De novo design of a transmembrane Zn2+-transporting four-helix bundle. Science, 346(6216), 1520–1524. https://doi.org/10.1126/science.1261172
Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., & Madden, T. L. (2008). NCBI BLAST: a better web interface. Nucleic Acids Research, 36(Web Server issue), W5-9. https://doi.org/10.1093/nar/gkn201
Jouhet, J., Maréchal, E., & Block, M. A. (2007). Glycerolipid transfer for the building of membranes in plant cells. Progress in Lipid Research, 46(1), 37–55. https://doi.org/10.1016/j.plipres.2006.06.002
Kabsch, W. (1976). A solution for the best rotation to relate two sets of vectors. Acta Crystallographica Section A, 32(5), 922–923. https://doi.org/10.1107/S0567739476001873
Kalinin, S., Peulen, T., Sindbert, S., Rothwell, P. J., Berger, S., Restle, T., … Seidel, C. a M. (2012). A toolkit and benchmark study for FRET-restrained high-precision structural modeling. Nature Methods, 9(12), 1218–1227. https://doi.org/10.1038/NMETH.2222
Kalodimos, C. G., Biris, N., Bonvin, A. M. J. J., Levandoski, M. M., Guennuegues, M., Boelens, R., & Kaptein, R. (2004). Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science (New York, N.Y.), 305(5682), 386–389. https://doi.org/10.1126/science.1097064
Kamtekar, S., Berman, A. J., Wang, J., Lázaro, J. M., De Vega, M., Blanco, L., … Steitz, T. a. (2004). Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage φ29. Molecular Cell, 16(4), 609–618. https://doi.org/10.1016/j.molcel.2004.10.019
Kamtekar, S., Berman, A. J., Wang, J., Lázaro, J. M., de Vega, M., Blanco, L., … Steitz, T. a. (2006). The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition. The EMBO Journal, 25(6), 1335–1343. https://doi.org/10.1038/sj.emboj.7601027
Khalili-Araghi, F., Gumbart, J., Wen, P. C., Sotomayor, M., Tajkhorshid, E., & Schulten, K. (2009). Molecular dynamics simulations of membrane channels and transporters. Current Opinion in Structural Biology, 19, 128–137. https://doi.org/10.1016/j.sbi.2009.02.011
Khan, M. I., Su, Y.-K., Zou, J., Yang, L.-W., Chou, R.-H., & Yu, C. (2018). S100B as an antagonist to block the interaction between S100A1 and the RAGE V domain. PloS One, 13(2), e0190545. https://doi.org/10.1371/journal.pone.0190545
Kim, T., & Im, W. (2010). Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation. Biophysical Journal, 99(1), 175–183. https://doi.org/10.1016/j.bpj.2010.04.015
Kim, Y. . G. J. H. . H. S. . S. P. B. (1993). Crystal structure of a yeast TBP/TATA-box complex. Nature, 365, 512–520. https://doi.org/8413604
Kim, Y., Eom, S. H., Wang, J., Lee, D. S., Suh, S. W., & Steitz, T. a. (1995). Crystal structure of Thermus aquaticus DNA polymerase. Nature, Vol. 376, pp. 612–616. https://doi.org/10.1038/376612a0
Kitao, A., & Go, N. (1999). Investigating Protein Dynamics in Collective Coordinate Space. Current Opinion in Structural Biology, 9(2), 164–169. https://doi.org/10.1016/S0959-440X(99)80023-2
Kitao, A., Hirata, F., & Gō, N. (1991). The Effects of Solvent on the Conformation and the Collective Motions of Protein: Normal Mode Analysis and Molecular Dynamics Simulations of Melittin in Water and in Vacuum. Chemical Physics, 158(2–3), 447–472. https://doi.org/10.1016/0301-0104(91)87082-7
Kort, R., Komori, H., Adachi, S., Miki, K., & Eker, A. (2004). DNA apophotolyase from Anacystis nidulans: 1.8 A structure, 8-HDF reconstitution and X-ray-induced FAD reduction. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 7), 1205–1213. https://doi.org/10.1107/S0907444904009321
Kozakov, D., Hall, D. R., Xia, B., Porter, K. A., Padhorny, D., Yueh, C., … Vajda, S. (2017). The ClusPro web server for protein–protein docking. Nature Protocols, 12(2), 255–278. https://doi.org/10.1038/nprot.2016.169
Krissinel, E., & Henrick, K. (2007). Inference of macromolecular assemblies from crystalline state. Journal of Molecular Biology, 372(3), 774–797. https://doi.org/10.1016/j.jmb.2007.05.022
Kurkcuoglu, O., Doruker, P., Sen, T. Z., Kloczkowski, A., & Jernigan, R. L. (2008). The ribosome structure controls and directs mRNA entry, translocation and exit dynamics. Physical Biology, 5(4), 046005. https://doi.org/10.1088/1478-3975/5/4/046005
Labahn, J., Schärer, O. D., Long, a, Ezaz-Nikpay, K., Verdine, G. L., & Ellenberger, T. E. (1996). Structural basis for the excision repair of alkylation-damaged DNA. Cell, 86(2), 321–329.
Lam, S. K., Pitrou, A., & Seibert, S. (2015). Numba. Proceedings of the Second Workshop on the LLVM Compiler Infrastructure in HPC - LLVM ’15, 1–6. https://doi.org/10.1145/2833157.2833162
Lamoureux, J. S., Stuart, D., Tsang, R., Wu, C., & Glover, J. N. M. (2002). Structure of the sporulation-specific transcription factor Ndt80 bound to DNA. The EMBO Journal, 21(21), 5721–5732.
Lee, A. L., Flynn, P. F., & Wand, A. J. (1999). Comparison of 2 H and 13 C NMR Relaxation Techniques for the Study of Protein Methyl Group Dynamics in Solution. Journal of the American Chemical Society, 121(12), 2891–2902. https://doi.org/10.1021/ja983758f
Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., … Im, W. (2015). CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation, acs.jctc.5b00935. https://doi.org/10.1021/acs.jctc.5b00935
Lee, J. Y., & Yang, W. (2006). UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke. Cell, 127(7), 1349–1360. https://doi.org/10.1016/j.cell.2006.10.049
Lensink, M. F., Méndez, R., & Wodak, S. J. (2007). Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins, 69(4), 704–718. https://doi.org/10.1002/prot.21804
Levy, E. D., Erba, E. B., Robinson, C. V., & Teichmann, S. A. (2008). Assembly reflects evolution of protein complexes. Nature, 453(7199), 1262–1265. https://doi.org/10.1038/nature06942
Levy, Y., Onuchic, J. N., & Wolynes, P. G. (2007). Fly-Casting in Protein−DNA Binding: Frustration between Protein Folding and Electrostatics Facilitates Target Recognition. Journal of the American Chemical Society, 129(4), 738–739. https://doi.org/10.1021/ja065531n
Li, H., Chang, Y.-Y., Yang, L.-W., & Bahar, I. (2015). iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Research, 44(November 2015), 415–422. https://doi.org/10.1093/nar/gkv1236
Li, Hongchun, Chang, Y.-Y., Lee, J. Y., Bahar, I., & Yang, L.-W. (2017). DynOmics: dynamics of structural proteome and beyond. Nucleic Acids Research, 45(W1), W374–W380. https://doi.org/10.1093/nar/gkx385
Li, Hongchun, Chang, Y.-Y. Y., Yang, L.-W. W., & Bahar, I. (2016). iGNM 2.0: The Gaussian Network Model Database for Biomolecular Structural Dynamics. Nucleic Acids Research, 44(D1), D415-22. https://doi.org/10.1093/nar/gkv1236
Li, Hongchun, Sakuraba, S., Chandrasekaran, A., & Yang, L.-W. (2014). Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs). Journal of Chemical Information and Modeling, 54(8), 2275–2285. https://doi.org/10.1021/ci500261z
Li, Jing, Shaikh, S. A., Enkavi, G., Wen, P.-C., Huang, Z., & Tajkhorshid, E. (2013). Transient formation of water-conducting states in membrane transporters. Proceedings of the National Academy of Sciences of the United States of America, 110(19), 7696–7701. https://doi.org/10.1073/pnas.1218986110
Li, Jisheng, Yang, H., Peer, W. A., Richter, G., Blakeslee, J., Bandyopadhyay, A., … Gaxiola, R. (2005). Arabidopsis H+-PPase AVP1 regulates auxin-mediated organ development. Science (New York, N.Y.), 310(5745), 121–125. https://doi.org/10.1126/science.1115711
Li, W., Wolynes, P., & Takada, S. (2011). Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins. Proceedings of the National …. https://doi.org/10.1073/pnas.1018983108/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1018983108
Liang, B., & Tamm, L. K. (2016). NMR as a tool to investigate the structure, dynamics and function of membrane proteins. Nature Structural & Molecular Biology, 23(6), 468–474. https://doi.org/10.1038/nsmb.3226
Lin, S.-M., Tsai, J., Hsiao, C.-D., Huang, Y.-T., Chiu, C.-L., Liu, M.-H., … Sun, Y.-J. (2012). Crystal structure of a membrane-embedded H+-translocating pyrophosphatase. Nature, 484(7394), 399–403. https://doi.org/10.1038/nature10963
Ling, H., Boudsocq, F., Woodgate, R., & Yang, W. (2001). Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell, 107(1), 91–102.
Liu, Y., Ke, M., & Gong, H. (2015). Protonation of Glu(135) Facilitates the Outward-to-Inward Structural Transition of Fucose Transporter. Biophysical Journal, 109(3), 542–551. https://doi.org/10.1016/j.bpj.2015.06.037
Lomize, A. L., Pogozheva, I. D., & Mosberg, H. I. (2011). Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes. Journal of Chemical Information and Modeling, 51(4), 930–946. https://doi.org/10.1021/ci200020k
Mancinelli, R., Botti, A., Bruni, F., Ricci, M. a, & Soper, A. K. (2007). Hydration of sodium, potassium, and chloride ions in solution and the concept of structure maker/breaker. Journal of Physical Chemistry B, 111(48), 13570–13577. https://doi.org/10.1021/jp075913v
Manning, C. D., Raghavan, P., & Schütze, H. (2008). Introduction to information retrieval. In L. Cowles (Ed.), Cambridge University Press (1st ed.). New York, NY, USA: Cambridge University Press.
Marcovitz, A., & Levy, Y. (2011). Frustration in protein-DNA binding influences conformational switching and target search kinetics. Proceedings of the National Academy of Sciences of the United States of America, 108(44), 17957–17962. https://doi.org/10.1073/pnas.1109594108
Marcovitz, A., & Levy, Y. (2013). Obstacles may facilitate and direct DNA search by proteins. Biophysical Journal, 104(9), 2042–2050. https://doi.org/10.1016/j.bpj.2013.03.030
Marsaglia, G. (1972). Choosing a point from the surface of a sphere. The Annals of Mathematical Statistics, 43(2), 645–646.
Maté, M. J., & Kleanthous, C. (2004). Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases. The Journal of Biological Chemistry, 279(33), 34763–34769. https://doi.org/10.1074/jbc.M403719200
McKinney, W. (2010). Data structures for statistical computing in Python. Proceedings of the 9th Python in Science Conference, 51–56.
McQuarrie, D. A. (2000a). Statistical Mechanics. University Science Books.
McQuarrie, D. A. (2000b). The time-correlation function formalism II. In Statistical Mechanics (pp. 543–592). University Science Books.
McWilliam, H., Li, W., Uludag, M., Squizzato, S., Park, Y. M., Buso, N., … Lopez, R. (2013). Analysis tool web services from the EMBL-EBI. Nucleic Acids Research, 41(W1), W597–W600. https://doi.org/10.1093/nar/gkt376
Mees, A., Klar, T., Gnau, P., Hennecke, U., Eker, A. P. M., Carell, T., & Essen, L.-O. (2004). Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair. Science (New York, N.Y.), 306(5702), 1789–1793. https://doi.org/10.1126/science.1101598
Méndez, R., Leplae, R., De Maria, L., & Wodak, S. J. (2003). Assessment of blind predictions of protein-protein interactions: Current status of docking methods. Proteins: Structure, Function and Genetics, 52(1), 51–67. https://doi.org/10.1002/prot.10393
Milburn, D., Laskowski, R. A., & Thornton, J. M. (1998). Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis. Protein Engineering, 11, 855–859. https://doi.org/061/13
Millman, K. J., & Aivazis, M. (2011). Python for scientists and engineers. Computing in Science & Engineering, 13(2), 9–12. https://doi.org/10.1109/MCSE.2011.36
Mimura, H., Nakanishi, Y., Hirono, M., & Maeshima, M. (2004). Membrane topology of the H+-pyrophosphatase of Streptomyces coelicolor determined by cysteine-scanning mutagenesis. The Journal of Biological Chemistry, 279(33), 35106–35112. https://doi.org/10.1074/jbc.M406264200
Minor, D. N. A., Ligand, G., Zacharias, M., Sklenar, H., & Delbruck, M. (1998). Harmonic Modes as Variables to Approximately Account for Receptor Flexibility in Ligand ᎐ Receptor Docking Simulations : Application to DNA Minor Groove Ligand Complex. Journal of Computational Chemistry, 20(3), 287–300.
Misson, J., Raghothama, K. G., Jain, A., Jouhet, J., Block, M. A., Bligny, R., … Thibaud, M.-C. (2005). A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. Proceedings of the National Academy of Sciences of the United States of America, 102(33), 11934–11939. https://doi.org/10.1073/pnas.0505266102
Mitra, K., & Frank, J. (2006). Ribosome dynamics: Insights from atomic structure modeling into cryo-electron microscopy maps. Annual Review of Biophysics and Biomolecular Structure, 35(1), 299–317. https://doi.org/10.1146/annurev.biophys.35.040405.101950
Młodzińska, E., & Zboińska, M. (2016). Phosphate Uptake and Allocation - A Closer Look at Arabidopsis thaliana L. and Oryza sativa L. Frontiers in Plant Science, 7, 1198. https://doi.org/10.3389/fpls.2016.01198
Moe, E., Leiros, I., Riise, E. K., Olufsen, M., Lanes, O., Smalås, A., & Willassen, N. P. (2004). Optimisation of the surface electrostatics as a strategy for cold adaptation of uracil-DNA N-glycosylase (UNG) from Atlantic cod (Gadus morhua). Journal of Molecular Biology, 343(5), 1221–1230. https://doi.org/10.1016/j.jmb.2004.09.004
Mohan, S., Donohue, J. P., & Noller, H. F. (2014). Molecular mechanics of 30S subunit head rotation. Proceedings of the National Academy of Sciences, 111(37), 13325–13330. https://doi.org/10.1073/pnas.1413731111
Moncelli, M. R., Becucci, L., Buoninsegni, F. T., & Guidelli, R. (1998). Surface dipole potential at the interface between water and self-assembled monolayers of phosphatidylserine and phosphatidic acid. Biophysical Journal, 74(5), 2388–2397. https://doi.org/10.1016/S0006-3495(98)77947-0
Monod, J., Wyman, J., & Changeux, J. P. (1965). On the nature of allosteric transitions: A plausible model. Journal of Molecular Biology, 12(1), 88–118. https://doi.org/10.1016/S0022-2836(65)80285-6
Montano, S. P., Cote, M. L., Fingerman, I., Pierce, M., Vershon, A. K., & Georgiadis, M. M. (2002). Crystal structure of the DNA-binding domain from Ndt80, a transcriptional activator required for meiosis in yeast. Proceedings of the National Academy of Sciences of the United States of America, 99(22), 14041–14046. https://doi.org/10.1073/pnas.222312199
Moraes, I., Evans, G., Sanchez-Weatherby, J., Newstead, S., & Stewart, P. D. S. (2014). Membrane protein structure determination — The next generation. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1838(1), 78–87. https://doi.org/10.1016/j.bbamem.2013.07.010
Morikawa, K., Ariyoshi, M., Vassylyev, D. G., Matsumoto, O., Katayanagi, K., & Ohtsuka, E. (1995). Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three active site mutants. Journal of Molecular Biology, 249(2), 360–375. https://doi.org/10.1006/jmbi.1995.0302
Morozov, A. V, Havranek, J. J., Baker, D., & Siggia, E. D. (2005). Protein-DNA binding specificity predictions with structural models. Nucleic Acids Research, 33(18), 5781–5798. https://doi.org/10.1093/nar/gki875
Mott, M. L., & Berger, J. M. (2007). DNA replication initiation: mechanisms and regulation in bacteria. Nature Reviews. Microbiology, 5(5), 343–354. https://doi.org/10.1038/nrmicro1640
Muschielok, A., Andrecka, J., Jawhari, A., Brückner, F., Cramer, P., & Michaelis, J. (2008). A nano-positioning system for macromolecular structural analysis. Nature Methods, 5(11), 965–971. https://doi.org/10.1038/nmeth.1259
Myers, L. C., Verdine, G. L., & Wagner, G. (1993). Solution Structure of the DNA Methyl Phosphotriester Repair Domain of Escherichia coli Ada. Biochemistry, 32(51), 14089–14094. https://doi.org/10.1021/bi00214a003
Narten, A. H., & Levy, H. A. (1971). Liquid Water: Molecular Correlation Functions from X‐Ray Diffraction. The Journal of Chemical Physics, 55(5), 2263–2269. https://doi.org/10.1063/1.1676403
Nederveen, A. J., & Bonvin, A. M. J. J. (2005). NMR Relaxation and Internal Dynamics of Ubiquitin from a 0.2 μs MD Simulation. Journal of Chemical Theory and Computation, 1(3), 363–374. https://doi.org/10.1021/ct0498829
Needleman, S. B., & Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48, 443–453. https://doi.org/10.1016/0022-2836(70)90057-4
Neely, R. K., Daujotyte, D., Grazulis, S., Magennis, S. W., Dryden, D. T. F., Klimasauskas, S., & Jones, A. C. (2005). Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes. Nucleic Acids Research, 33(22), 6953–6960. https://doi.org/10.1093/nar/gki995
Nicolay, S., & Sanejouand, Y.-H. (2006). Functional Modes of Proteins Are among the Most Robust. Physical Review Letters, 96(7), 078104. https://doi.org/10.1103/PhysRevLett.96.078104
Nussaume, L., Kanno, S., Javot, H., Marin, E., Pochon, N., Ayadi, A., … Thibaud, M.-C. (2011). Phosphate Import in Plants: Focus on the PHT1 Transporters. Frontiers in Plant Science, 2, 83. https://doi.org/10.3389/fpls.2011.00083
O’Gara, M., Zhang, X., Roberts, R. J., & Cheng, X. (1999). Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short non-specific DNA oligonucleotide. Journal of Molecular Biology, 287(2), 201–209.
Okan, O. B., Atilgan, A. R., & Atilgan, C. (2009). Nanosecond motions in proteins impose bounds on the timescale distributions of local dynamics. Biophysical Journal, 97(7), 2080–2088. https://doi.org/10.1016/j.bpj.2009.07.036
Okazaki, K.-I., & Takada, S. (2008). Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms. Proceedings of the National Academy of Sciences of the United States of America, 105(32), 11182–11187. https://doi.org/10.1073/pnas.0802524105
Olsson, M. H. M., Søndergaard, C. R., Rostkowski, M., & Jensen, J. H. (2011). PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical p K a Predictions. Journal of Chemical Theory and Computation, 7(2), 525–537. https://doi.org/10.1021/ct100578z
Ozbek, P., Soner, S., Erman, B., & Haliloglu, T. (2010). DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues. Nucleic Acids Research, 38(Web Server issue), W417-23. https://doi.org/10.1093/nar/gkq396
Pao, S. S., Paulsen, I. T., & Saier, M. H. (1998). Major facilitator superfamily. Microbiology and Molecular Biology Reviews : MMBR, 62(1), 1–34. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/9529885
Parikh, S. S., Walcher, G., Jones, G. D., Slupphaug, G., Krokan, H. E., Blackburn, G. M., & Tainer, J. a. (2000). Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. Proceedings of the National Academy of Sciences of the United States of America, 97(10), 5083–5088.
Parisien, M., Freed, K. F., & Sosnick, T. R. (2012). On docking, scoring and assessing protein-DNA complexes in a rigid-body framework. PloS One, 7(2), e32647. https://doi.org/10.1371/journal.pone.0032647
Park, S. H., & Opella, S. J. (2005). Tilt angle of a trans-membrane helix is determined by hydrophobic mismatch. Journal of Molecular Biology, 350(2), 310–318. https://doi.org/10.1016/j.jmb.2005.05.004
Park, S., Li, J., Pittman, J. K., Berkowitz, G. a, Yang, H., Undurraga, S., … Gaxiola, R. a. (2005). Up-regulation of a H+-pyrophosphatase (H+-PPase) as a strategy to engineer drought-resistant crop plants. Proceedings of the National Academy of Sciences of the United States of America, 102(52), 18830–18835. https://doi.org/10.1073/pnas.0509512102
Parker, J. S., Parizotto, E. a, Wang, M., Roe, S. M., & Barford, D. (2009). Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein. Molecular Cell, 33(2), 204–214. https://doi.org/10.1016/j.molcel.2008.12.012
Parker, J. S., Roe, S. M., & Barford, D. (2004). Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. The EMBO Journal, 23(24), 4727–4737. https://doi.org/10.1038/sj.emboj.7600488
Pearson, K. (1895). Note on Regression and Inheritance in the Case of Two Parents. Proceedings of the Royal Society of London (1854-1905), 58(1), 240–242. https://doi.org/10.1098/rspl.1895.0041
Pedersen, B. P., Kumar, H., Waight, A. B., Risenmay, A. J., Roe-Zurz, Z., Chau, B. H., … Stroud, R. M. (2013). Crystal structure of a eukaryotic phosphate transporter. Nature, 496(7446), 533–536. https://doi.org/10.1038/nature12042
Petty, T. J., Emamzadah, S., Costantino, L., Petkova, I., Stavridi, E. S., Saven, J. G., … Halazonetis, T. D. (2011). An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity. The EMBO Journal, 30(11), 2167–2176. https://doi.org/10.1038/emboj.2011.127
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., … Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802. https://doi.org/10.1002/jcc.20289
Pierce, B. G., Hourai, Y., & Weng, Z. (2011). Accelerating protein docking in ZDOCK using an advanced 3D convolution library. PloS One, 6(9), e24657. https://doi.org/10.1371/journal.pone.0024657
Pierce, B., Tong, W., & Weng, Z. (2005). M-ZDOCK: A grid-based approach for Cn symmetric multimer docking. Bioinformatics, 21(8), 1472–1478. https://doi.org/10.1093/bioinformatics/bti229
Poirier, Y., & Bucher, M. (2002). Phosphate transport and homeostasis in Arabidopsis. The Arabidopsis Book, 1, e0024. https://doi.org/10.1199/tab.0024
Poornam, G. P., Matsumoto, A., Ishida, H., & Hayward, S. (2009). A method for the analysis of domain movements in large biomolecular complexes. Proteins, 76(1), 201–212. https://doi.org/10.1002/prot.22339
Popovych, N., Sun, S., Ebright, R. H., & Kalodimos, C. G. (2006). Dynamically Driven Protein Allostery. Nature Structural & Molecular Biology, 13(9), 831–838. https://doi.org/10.1038/nsmb1132
Potestio, R., Pontiggia, F., & Micheletti, C. (2009). Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits. Biophysical Journal, 96(12), 4993–5002. https://doi.org/10.1016/j.bpj.2009.03.051
Privalov, P. L., Dragan, A. I., Crane-Robinson, C., Breslauer, K. J., Remeta, D. P., & Minetti, C. A. S. A. (2007). What drives proteins into the major or minor grooves of DNA? Journal of Molecular Biology, 365(1), 1–9. https://doi.org/10.1016/j.jmb.2006.09.059
Quistgaard, E. M., Löw, C., Guettou, F., & Nordlund, P. (2016). Understanding transport by the major facilitator superfamily (MFS): structures pave the way. Nature Publishing Group, 17(2), 1–10. https://doi.org/10.1038/nrm.2015.25
Rader, A. J., Vlad, D. H., & Bahar, I. (2005). Maturation dynamics of bacteriophage HK97 capsid. Structure (London, England : 1993), 13(3), 413–421. https://doi.org/10.1016/j.str.2004.12.015
Rask-Andersen, M., Masuram, S., & Schiöth, H. B. (2014). The druggable genome: Evaluation of drug targets in clinical trials suggests major shifts in molecular class and indication. Annual Review of Pharmacology and Toxicology, 54(August 2013), 9–26. https://doi.org/10.1146/annurev-pharmtox-011613-135943
Ratje, A. H., Loerke, J., Mikolajka, A., Brünner, M., Hildebrand, P. W., Starosta, A. L., … Spahn, C. M. T. T. (2010). Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature, 468(7324), 713–716. https://doi.org/10.1038/nature09547
Reddy, V. S., Shlykov, M. A., Castillo, R., Sun, E. I., & Saier, M. H. (2012). The major facilitator superfamily (MFS) revisited. The FEBS Journal, 279(11), 2022–2035. https://doi.org/10.1111/j.1742-4658.2012.08588.x
Remy, E., Cabrito, T. R., Batista, R. A., Teixeira, M. C., Sá-Correia, I., & Duque, P. (2012). The Pht1;9 and Pht1;8 transporters mediate inorganic phosphate acquisition by the Arabidopsis thaliana root during phosphorus starvation. The New Phytologist, 195(2), 356–371. https://doi.org/10.1111/j.1469-8137.2012.04167.x
Ritchie, D. W., & Grudinin, S. (2016). Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry. Journal of Applied Crystallography, 49(1), 158–167. https://doi.org/10.1107/S1600576715022931
Roberts, E., Eargle, J., Wright, D., & Luthey-Schulten, Z. (2006). MultiSeq: unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics, 7, 382. https://doi.org/10.1186/1471-2105-7-382
Rose, P. W., Beran, B., Bi, C., Bluhm, W. F., Dimitropoulos, D., Goodsell, D. S., … Bourne, P. E. (2011). The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Research, 39(Database issue), D392-401. https://doi.org/10.1093/nar/gkq1021
Rose, P. W., Prlić, A., Altunkaya, A., Bi, C., Bradley, A. R., Christie, C. H., … Burley, S. K. (2017). The RCSB protein data bank: Integrative view of protein, gene and 3D structural information. Nucleic Acids Research, 45(D1), D271–D281. https://doi.org/10.1093/nar/gkw1000
Rost, B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, 12(2), 85–94. https://doi.org/10.1093/protein/12.2.85
Roux, B., & Schulten, K. (2004). Computational studies of membrane channels. Structure (London, England : 1993), 12(8), 1343–1351. https://doi.org/10.1016/j.str.2004.06.013
Sagnella, D. E., & Voth, G. a. (1996). Structure and dynamics of hydronium in the ion channel gramicidin A. Biophysical Journal, 70(5), 2043–2051. https://doi.org/10.1016/S0006-3495(96)79773-4
Sakano, K. (1990). Proton/Phosphate Stoichiometry in Uptake of Inorganic Phosphate by Cultured Cells of Catharanthus roseus (L.) G. Don. Plant Physiology, 93(2), 479–483. https://doi.org/10.1104/pp.93.2.479
Sakata-Sogawa, K., & Shimamoto, N. (2004). RNA polymerase can track a DNA groove during promoter search. Proceedings of the National Academy of Sciences of the United States of America, 101(41), 14731–14735. https://doi.org/10.1073/pnas.0406441101
Samyn, D. R., Ruiz-Pávon, L., Andersson, M. R., Popova, Y., Thevelein, J. M., & Persson, B. L. (2012). Mutational analysis of putative phosphate- and proton-binding sites in the Saccharomyces cerevisiae Pho84 phosphate:H(+) transceptor and its effect on signalling to the PKA and PHO pathways. The Biochemical Journal, 445(3), 413–422. https://doi.org/10.1042/BJ20112086
Samyn, D. R., Van der Veken, J., Van Zeebroeck, G., Persson, B. L., & Karlsson, B. C. G. (2016). Key Residues and Phosphate Release Routes in the Saccharomyces cerevisiae Pho84 Transceptor: THE ROLE OF TYR179 IN FUNCTIONAL REGULATION. The Journal of Biological Chemistry, 291(51), 26388–26398. https://doi.org/10.1074/jbc.M116.738112
Sanbonmatsu, K. Y., Joseph, S., & Tung, C.-S. (2005). Simulating Movement of tRNA Into the Ribosome During Decoding. Proceedings of the National Academy of Sciences, 102(44), 15854–15859. https://doi.org/10.1073/pnas.0503456102
Sasmal, D. K., Pulido, L. E., Kasal, S., & Huang, J. (2016). Single-molecule fluorescence resonance energy transfer in molecular biology. Nanoscale, 8(48), 19928–19944. https://doi.org/10.1039/c6nr06794h
Schachtman, Reid, & Ayling. (1998). Phosphorus Uptake by Plants: From Soil to Cell. Plant Physiology, 116(2), 447–453. https://doi.org/10.1104/pp.116.2.447
Schlitter, J, Engels, M., & Krüger, P. (1994). Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. Journal of Molecular Graphics, 12(2), 84–89. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/7918256
Schlitter, Jürgen. (1993). Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chemical Physics Letters, 215(6), 617–621. https://doi.org/10.1016/0009-2614(93)89366-P
Schmidt, H. R., Zheng, S., Gurpinar, E., Koehl, A., Manglik, A., & Kruse, A. C. (2016). Crystal structure of the human σ1 receptor. Nature, 532(7600), 527–530. https://doi.org/10.1038/nature17391
Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005). PatchDock and SymmDock: Servers for rigid and symmetric docking. Nucleic Acids Research, 33(Web Server), W363–W367. https://doi.org/10.1093/nar/gki481
Seeger, M. A., Schiefner, A., Eicher, T., Verrey, F., Diederichs, K., & Pos, K. M. (2006). Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism. Science (New York, N.Y.), 313(5791), 1295–1298. https://doi.org/10.1126/science.1131542
Sekinger, E. A., Moqtaderi, Z., & Struhl, K. (2005). Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Molecular Cell, 18(6), 735–748. https://doi.org/10.1016/j.molcel.2005.05.003
Shaw, D. E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R. O., Eastwood, M. P., … Wriggers, W. (2010). Atomic-Level Characterization of the Structural Dynamics of Proteins. Science, 330(6002), 341–346. https://doi.org/10.1126/science.1187409
Shin, H., Shin, H. S., Dewbre, G. R., & Harrison, M. J. (2004). Phosphate transport in Arabidopsis: Pht1;1 and Pht1;4 play a major role in phosphate acquisition from both low- and high-phosphate environments. Plant Journal, 39(4), 629–642. https://doi.org/10.1111/j.1365-313X.2004.02161.x
Sillitoe, I., Cuff, A. L., Dessailly, B. H., Dawson, N. L., Furnham, N., Lee, D., … Orengo, C. a. (2013). New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Research, 41, D490-8. https://doi.org/10.1093/nar/gks1211
Slattery, M., Riley, T., Liu, P., Abe, N., Gomez-Alcala, P., Dror, I., … Mann, R. S. (2011). Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell, 147(6), 1270–1282. https://doi.org/10.1016/j.cell.2011.10.053
Søndergaard, C. R., Olsson, M. H. M., Rostkowski, M., & Jensen, J. H. (2011). Improved treatment of ligands and coupling effects in empirical calculation and rationalization of pKa values. Journal of Chemical Theory and Computation, 7(7), 2284–2295. https://doi.org/10.1021/ct200133y
Song, C., Weichbrodt, C., Salnikov, E. S., Dynowski, M., Forsberg, B. O., Bechinger, B., … Zeth, K. (2013). Crystal structure and functional mechanism of a human antimicrobial membrane channel. Proceedings of the National Academy of Sciences of the United States of America, 110(12), 4586–4591. https://doi.org/10.1073/pnas.1214739110
Soper, a K., Bruni, F., & Ricci, M. a. (1997). Site–site pair correlation functions of water from 25 to 400° C: Revised analysis of new and old diffraction data. J. Chem. Phys., 106(1), 247. https://doi.org/10.1063/1.473030
Soper, A.K., & Phillips, M. G. (1986). A new determination of the structure of water at 25°C. Chemical Physics, 107(1), 47–60. https://doi.org/10.1016/0301-0104(86)85058-3
Soper, Alan K., & Weckström, K. (2006). Ion solvation and water structure in potassium halide aqueous solutions. Biophysical Chemistry, 124(3), 180–191. https://doi.org/10.1016/j.bpc.2006.04.009
Sorenson, J. M., Hura, G., Glaeser, R. M., & Head-Gordon, T. (2000). What can X-ray scattering tell us about the radial distribution functions of water? Journal of Chemical Physics, 113(20), 9149–9161. https://doi.org/10.1063/1.1319615
Stansfeld, P. J., Goose, J. E., Caffrey, M., Carpenter, E. P., Parker, J. L., Newstead, S., & Sansom, M. S. P. (2015). MemProtMD: Automated insertion of membrane protein structures into explicit lipid membranes. Structure (London, England : 1993), 23(7), 1350–1361. https://doi.org/10.1016/j.str.2015.05.006
Stormo, G. D. (2000). DNA binding sites: representation and discovery. Bioinformatics (Oxford, England), 16(1), 16–23. https://doi.org/10.1093/bioinformatics/16.1.16
Sun, J., Viadiu, H., Aggarwal, A. K., & Weinstein, H. (2003). Energetic and structural considerations for the mechanism of protein sliding along DNA in the nonspecific BamHI-DNA complex. Biophysical Journal, 84(5), 3317–3325. https://doi.org/10.1016/S0006-3495(03)70056-3
Szilagyi, A., & Zhang, Y. (2014). Template-based structure modeling of protein-protein interactions. Current Opinion in Structural Biology, 24, 10–23. https://doi.org/10.1016/j.sbi.2013.11.005
Takahashi, H., Kambe, H., & Morita, A. (2018). A simple and effective solution to the constrained QM/MM simulations. The Journal of Chemical Physics, 148(13), 134119. https://doi.org/10.1063/1.5019874
Takemura, K., & Kitao, A. (2012). Water Model Tuning for Improved Reproduction of Rotational Diffusion and NMR Spectral Density. The Journal of Physical Chemistry. B, 116(22), 6279–6287. https://doi.org/10.1021/jp301100g
Tama, F., & Sanejouand, Y. H. (2001). Conformational change of proteins arising from normal mode calculations. Protein Engineering, 14(1), 1–6. https://doi.org/10.1093/protein/14.1.1
Tama, Florence, Valle, M., Frank, J., & Brooks, C. L. (2003). Dynamic Reorganization of the Functionally Active Ribosome Explored by Normal Mode Analysis and Cryo-Electron Microscopy. Proceedings of the National Academy of Sciences, 100(16), 9319–9323. https://doi.org/10.1073/pnas.1632476100
Thorpe, M. F. (2007). Comment on elastic network models and proteins. Physical Biology, 4(1), 60–63; discussion 64-5. https://doi.org/10.1088/1478-3975/4/1/N01
Tirion, Monique M. (1996). Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. Physical Review Letters, 77(9), 1905–1908. https://doi.org/10.1103/PhysRevLett.77.1905
Tirion, Monique Mm. (1996). Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. Physical Review Letters, 77(9), 1905–1908. https://doi.org/10.1103/PhysRevLett.77.1905
Tjandra, N., Feller, S. E., Pastor, R. W., & Bax, A. (1995). Rotational Diffusion Anisotropy of Human Ubiquitin from 15N NMR Relaxation. Journal of the American Chemical Society, 117(50), 12562–12566. https://doi.org/10.1021/ja00155a020
Tobi, D., & Bahar, I. (2005). Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proceedings of the National Academy of Sciences, 102(52), 18908–18913. https://doi.org/10.1073/pnas.0507603102
Tourigny, D. S., Fernandez, I. S., Kelley, A. C., & Ramakrishnan, V. (2013). Elongation Factor G Bound to the Ribosome in an Intermediate State of Translocation. Science, 340(6140), 1235490–1235490. https://doi.org/10.1126/science.1235490
Tovchigrechko, A., & Vakser, I. A. (2006). GRAMM-X public web server for protein-protein docking. Nucleic Acids Research, 34(Web Server), W310–W314. https://doi.org/10.1093/nar/gkl206
Trabuco, L. G., Schreiner, E., Eargle, J., Cornish, P., Ha, T., Luthey-Schulten, Z., & Schulten, K. (2010). The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. Journal of Molecular Biology, 402(4), 741–760. https://doi.org/10.1016/j.jmb.2010.07.056
Tsutakawa, S. E., Jingami, H., & Morikawa, K. (1999). Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex. Cell, 99(6), 615–623.
Tsutakawa, S. E., Muto, T., Kawate, T., Jingami, H., Kunishima, N., Ariyoshi, M., … Morikawa, K. (1999). Crystallographic and functional studies of very short patch repair endonuclease. Molecular Cell, 3(5), 621–628.
Tzeng, S.-R., & Kalodimos, C. G. (2012). Protein activity regulation by conformational entropy. Nature, 488(7410), 236–240. https://doi.org/10.1038/nature11271
Ullrich-Eberius, C. I., Novacky, A., Fischer, E., & Lüttge, U. (1981). Relationship between Energy-dependent Phosphate Uptake and the Electrical Membrane Potential in Lemna gibba G1. Plant Physiology, 67(4), 797–801. https://doi.org/10.1104/pp.67.4.797
Ullrich-Eberius, C. I., Novacky, A., & van Bel, A. J. E. (1984). Phosphate uptake in Lemna gibba G1: energetics and kinetics. Planta, 161(1), 46–52. Retrieved from http://www.jstor.org/stable/23377086
Ullrich, C. I., & Novacky, A. J. (1990). Extra- and Intracellular pH and Membrane Potential Changes Induced by K, Cl, H(2)PO(4), and NO(3) Uptake and Fusicoccin in Root Hairs of Limnobium stoloniferum. Plant Physiology, 94(4), 1561–1567. https://doi.org/10.1104/pp.94.4.1561
UniProt Consortium. (2019). UniProt: a worldwide hub of protein knowledge. Nucleic Acids Research, 47(D1), D506–D515. https://doi.org/10.1093/nar/gky1049
Valle, M., Zavialov, A., Sengupta, J., Rawat, U., Ehrenberg, M., & Frank, J. (2003). Locking and unlocking of ribosomal motions. Cell, 114(1), 123–134. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/12859903
van der Walt, S., Colbert, S. C., & Varoquaux, G. (2011). The NumPy array: A structure for efficient numerical computation. Computing in Science & Engineering, 13(2), 22–30. https://doi.org/10.1109/MCSE.2011.37
van Dijk, M., van Dijk, A. D. J., Hsu, V., Boelens, R., & Bonvin, A. M. J. J. (2006). Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Research, 34(11), 3317–3325. https://doi.org/10.1093/nar/gkl412
van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., … Bonvin, A. M. J. J. (2016). The HADDOCK2.2 web server: User-friendly integrative modeling of biomolecular complexes. Journal of Molecular Biology, 428(4), 720–725. https://doi.org/10.1016/j.jmb.2015.09.014
Vance, C. P., Uhde-Stone, C., & Allan, D. L. (2003). Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource. New Phytologist, 157(3), 423–447. https://doi.org/10.1046/j.1469-8137.2003.00695.x
Vanommeslaeghe, K., & MacKerell, a D. (2012). Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. Journal of Chemical Information and Modeling, 52(12), 3144–3154. https://doi.org/10.1021/ci300363c
Vijay-kumar, S., Bugg, C. E., & Cook, W. J. (1987). Structure of Ubiquitin Refined at 1.8 Å Resolution. Journal of Molecular Biology, 194(3), 531–544. https://doi.org/10.1016/0022-2836(87)90679-6
Viswanath, S., Dominguez, L., Foster, L. S., Straub, J. E., & Elber, R. (2015). Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization. Proteins, 83(12), 2170–2185. https://doi.org/10.1002/prot.24934
Wakefield, R. I., Smith, B. O., Nan, X., Free, a, Soteriou, a, Uhrin, D., … Barlow, P. N. (1999). The solution structure of the domain from MeCP2 that binds to methylated DNA. Journal of Molecular Biology, 291(5), 1055–1065. https://doi.org/10.1006/jmbi.1999.3023
Wang, J. . K. S. . B. A. J. . S. T. A. (2005). Correction of X-ray intensities from single crystals containing lattice-translocation defects. Acta Crystallogr.,Sect.D, 61, 67–74. https://doi.org/15608377
Wang, L., & Brown, S. J. (2006). BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Research, 34(Web Server issue), W243-8. https://doi.org/10.1093/nar/gkl298
Wang, Yong, Liu, Y., DeBerg, H. A., Nomura, T., Hoffman, M. T., Rohde, P. R., … Selvin, P. R. (2014). Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel. ELife, 2014(3), 1–21. https://doi.org/10.7554/eLife.01834.001
Wang, Yongmei, Rader, A. J., Bahar, I., & Jernigan, R. L. (2004). Global Ribosome Motions Revealed with Elastic Network Model. Journal of Structural Biology, 147(3), 302–314. https://doi.org/10.1016/j.jsb.2004.01.005
Weast, R. C., Astle, M. J., & BEYER eds., W. H. (1983). CRC Handbook of chemistry and physics. Boca Raton: CRC Press.
Whitford, P. C., Blanchard, S. C., Cate, J. H. D., & Sanbonmatsu, K. Y. (2013). Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome. PLoS Computational Biology, 9(3), e1003003. https://doi.org/10.1371/journal.pcbi.1003003
Whitford, P. C., Onuchic, J. N., & Sanbonmatsu, K. Y. (2010). Connecting Energy Landscapes with Experimental Rates for Aminoacyl-tRNA Accommodation in the Ribosome. Journal of the American Chemical Society, 132(38), 13170–13171. https://doi.org/10.1021/ja1061399
Wikipedia. (2019). Phosphate. Retrieved July 22, 2019, from https://en.wikipedia.org/wiki/Phosphate
Winkler, F., Banner, D., & Oefner, C. (1993). The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. The EMBO Journal, 12(5), 1781–1795.
Wong, J. H., Fiala, K. a., Suo, Z., & Ling, H. (2008). Snapshots of a Y-Family DNA Polymerase in Replication: Substrate-induced Conformational Transitions and Implications for Fidelity of Dpo4. Journal of Molecular Biology, 379(2), 317–330. https://doi.org/10.1016/j.jmb.2008.03.038
Yamagata, A., & Tainer, J. A. (2007). Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism. The EMBO Journal, 26(3), 878–890. https://doi.org/10.1038/sj.emboj.7601544
Yan, N. (2013). Structural advances for the major facilitator superfamily (MFS) transporters. Trends in Biochemical Sciences, Vol. 38, pp. 151–159. https://doi.org/10.1016/j.tibs.2013.01.003
Yang, C.-G., Yi, C., Duguid, E. M., Sullivan, C. T., Jian, X., Rice, P. a, & He, C. (2008). Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature, 452(7190), 961–965. https://doi.org/10.1038/nature06889
Yang, L.-W., Rader, A. J., Liu, X., Jursa, C. J., Chen, S. C., Karimi, H. A., & Bahar, I. (2006). oGNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Research, 34(Web Server), W24–W31. https://doi.org/10.1093/nar/gkl084
Yang, L., Liao, R. Z., Yu, J. G., & Liu, R. Z. (2009). DFT study on the mechanism of Escherichia coli inorganic pyrophosphatase. Journal of Physical Chemistry B, 113(18), 6505–6510. https://doi.org/10.1021/jp810003w
Yang, Lee-Wei. (2011). Models with Energy Penalty on Interresidue Rotation Address Insufficiencies of Conventional Elastic Network Models. Biophysical Journal, 100(7), 1784–1793. https://doi.org/10.1016/j.bpj.2011.02.033
Yang, Lee-Wei, & Bahar, I. (2005). Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure (London, England : 1993), 13(6), 893–904. https://doi.org/10.1016/j.str.2005.03.015
Yang, Lee-Wei, & Chng, C.-P. (2008). Coarse-Grained Models Reveal Functional Dynamics--I. Elastic Network Models--Theories, Comparisons and Perspectives. Bioinformatics and Biology Insights, 2, 25–45.
Yang, Lee-Wei, Eyal, E., Bahar, I., & Kitao, A. (2009). Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): Insights into functional dynamics. Bioinformatics (Oxford, England), 25(5), 606–614. https://doi.org/10.1093/bioinformatics/btp023
Yang, Lee-Wei, Eyal, E., Chennubhotla, C., Jee, J., Gronenborn, A. M., & Bahar, I. (2007). Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-Ray Data with Computational Predictions. Structure, 15(6), 741–749. https://doi.org/10.1016/j.str.2007.04.014
Yang, Lee-Wei, Kitao, A., Huang, B.-C., & Gō, N. (2014). Ligand-Induced Protein Responses and Mechanical Signal Propagation Described by Linear Response Theories. Biophysical Journal, 107(6), 1415–1425. https://doi.org/10.1016/j.bpj.2014.07.049
Yang, Z., Horton, J. R., Zhou, L., Zhang, X. J., Dong, A., Zhang, X., … Cheng, X. (2003). Structure of the bacteriophage T4 DNA adenine methyltransferase. Nat Struct Biol, 10(10), 849–855. https://doi.org/10.1038/nsb973
Yin, Y., Jensen, M. Ø., Tajkhorshid, E., & Schulten, K. (2006). Sugar binding and protein conformational changes in lactose permease. Biophysical Journal, 91(11), 3972–3985. https://doi.org/10.1529/biophysj.106.085993
Yu, B., Edstrom, W. C., Benach, J., Hamuro, Y., Weber, P. C., Gibney, B. R., & Hunt, J. F. (2006). Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB. Nature, 439(7078), 879–884. https://doi.org/10.1038/nature04561
Zheng, W., & Thirumalai, D. (2009). Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II. Biophysical Journal, 96(6), 2128–2137. https://doi.org/10.1016/j.bpj.2008.12.3897
Zhou, Q., Lai, Y., Bacaj, T., Zhao, M., Lyubimov, A. Y., Uervirojnangkoorn, M., … Brunger, A. T. (2015). Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis. Nature, 525(7567), 62–67. https://doi.org/10.1038/nature14975
Zhu, C., Byrd, R. H., Lu, P., & Nocedal, J. (1997). Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization. ACM Transactions on Mathematical Software, 23(4), 550–560. https://doi.org/10.1145/279232.279236
Zimmermann, M. T., & Jernigan, R. L. (2014). Elastic network models capture the motions apparent within ensembles of RNA structures. RNA (New York, N.Y.), 20(6), 792–804. https://doi.org/10.1261/rna.041269.113

簡易檢索 / 詳目顯示

相關論文