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研究生: 尚齊亞
Bhattacharya, Sankhya
論文名稱: 用於高通量蛋白質結晶的水凝膠微滴數字化微流體系統
Hydrogel Droplet Digitized Microfluidic System for High Throughput Protein Crystallisation
指導教授: 曾繁根
Tseng, Fan-gang
口試委員: 王雯靜
Wang, Wen-Ching
蘇育全
Su, Yu-Chuan
學位類別: 碩士
Master
系所名稱: 原子科學院 - 工程與系統科學系
Department of Engineering and System Science
論文出版年: 2018
畢業學年度: 106
語文別: 英文
論文頁數: 72
中文關鍵詞: 微機電系統水凝膠數字化微流控
外文關鍵詞: MEMS, Hydrogel, Digitization, microfuidics
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  • 蛋白質是連接基因和生物功能的所有生物的重要組成部分,其結晶已引起人們的興趣,因為通過X射線晶體學對三維結構的研究將為新藥設計和疾病治療提供重要信息。為了減少搜索努力,減少蛋白質溶液的量,並提高最終的準確性,在這裡我們展示蛋白質結晶優化使用內部製造水凝膠數字化微流體系統(hd-MFS)。該技術結合了反饋系統控制和改進的兩階段反饋系統控制(2s-FSC)算法,用於快速簡便地篩選獲得高質量和大蛋白質晶體所需的化學條件,可用於精確蛋白質的結構分析。我們通過結晶三種不同類型的蛋白質,包括溶菌酶,蛋白酶-K和KDM-4A,展現了我們技術的有效性。大量的蛋白質晶體可以通過從數千個可能的試驗池中並行進行少得多的結晶試驗(幾十個實驗)來獲得,因此我們的方法可以徹底篩選crystallisation條件,而不需要精密和昂貴的機器人解決方案。此外,反饋系統控制(2s-FSC)的擴展的兩階段方法不僅可以快速識別大量參數空間中的可能位置,而且還可以將最終搜索結果細化到更加封閉和準確的區域,其中所需的生物化學條件可以快速而準確地被識別以獲得大而優質的蛋白質晶體。我們強烈地相信,結合HD-MFS的FSC算法可以對在新藥設計中起關鍵作用的新蛋白質的結晶作出強有力的貢獻,該新蛋白質可以解決癌症,艾滋病和抗生物抗性等疾病的威脅


    Proteins are the essential components of all living creatures that links genes and bio-functionalities, and their crystallisations have attracted much interest as the study of the 3D structures through X-ray crystallography would provide critical informaion for novel drug design and diease treatment. To reduce searching efforts, minize amount of protein solutions, and increase final accuracy, here we demonstrate protein crystallisation optimization using in-house fabricated hydrogel-digitized MicroFluidic System (hd-MFS). This techinque is incorporated with Feeback-System-Control and a modified two-stage Feedback-System-Control (2s-FSC) algorithm for fast and easy screening chemical conditions required for obtaing high quality and large protein crystals, that can be used for accurate structural analysis of the protein. We have domnstrated the eficacy of our technique by crystallising three different types of proteins, including Lysozyme, Proteinase-K, and KDM-4A. Large protein crystals could be obtained by conducting much fewer crystallisation trials (tens experiments) in parallel, from a pool of thousands of possible trials, thus our methodology allows for thorough screening of crytallisation condtions without the need for ellaborate and expensive robotic solutions. In addition, the expanded two-stage approach for Feedback-System-Control (2s-FSC) can not only rapidly identifies the possible locations in a vast parameter space but also refine the final searching results in a more confined and accurate region, where the desired bio-chemical conditions can be identifed quickly and accurately for obtaining large and top quality protein crystals. We stongly belive that FSC algorithm incorporated with HD-MFS can be a strong contribuitions towards the crystallisation of novel protein which play a key role in novel drug design, that can tackle the menace of diseases such as cancer, aids and anti-biotic resistance.

    1 Introduction……………………………………………………………...........................(6) 1.1 General Introduction to protein crystallization………………………….......................(6) 1.2 The current state of art for Lab-on-chip systems for protein crystallization screening....................................(10) 1.3 Objectives and organization of the present research work .......(19) 1.4 Protein crystallization trial assessment……………………………… .(20) 1.5 Protein Crystallisation screening through Feedback Search Algorithm(FSC)…………………………………… ..........….....(22) 1.6 Hydrogel droplet digitized screening system………………………….................…......(31) 2 Fabrication of Hydrogel Digitised Microfluidic System (HDMS)..............................(34) 2.1 Materials and preparations............................... ................................(34) 2.2 Objectives of In-House Fabricated HDMS. …………… ..................(37) 2.3 In house fabrication methodology…………………… ..........…............(38) 2.4 Dose level selection of relevant parameters………… ...........…...(40) 3 Results………………………………………………………………......................…....(43) 3.1 Lysozyme Crstallisation Screening………………….................….........(43) 3.2 Proteinase-k Crystallisation Screening…………………....................….(48) 3.3 KDM4A Crystallisation Screening................................................(51) 3.4 KDM4A finer screenng..............................................................(53) 4 Summary and scope of future work……………........................……..(54) 4.1 Summary of the current work…………………………...................,,..(56) 4.2 Scope of future work……………………………………..….......................(58) 5 References................................................................................................(65)

    [1] I. R. Krauss, A. Merlino, A. Vergara, and F. Sica, “An overview of biological macromolecule crystallization,” International Journal of Molecular Sciences, vol. 14, no. 6. pp. 11643–11691, 2013.
    [2] C. Sauter et al., “Additives for the crystallization of proteins and nucleic acids,” J. Cryst. Growth, vol. 196, pp. 365–376, 1999.
    [3] Y. R. Liang et al., “3D-Printed High-Density Droplet Array Chip for Miniaturized Protein Crystallization Screening under Vapor Diffusion Mode,” ACS Appl. Mater. Interfaces, vol. 9, no. 13, pp. 11837–11845, 2017.
    [4] H. Hou et al., “A comparative study on the quality of protein crystals obtained using the cross-diffusion microbatch and sitting-drop vapor diffusion methods,” CrystEngComm, vol. 17, no. 29, pp. 5365–5371, 2015.
    [5] A. McPherson and J. A. Gavira, “Introduction to protein crystallization,” Acta Crystallographica Section F:Structural Biology Communications, vol. 70, no. 1. pp. 2–20, 2014.
    [6] R. Cudney, S. Patel, K. Weisgraber, Y. Newhouse, and A. McPherson, “Screening and optimization strategies for macromolecular crystal growth,” Acta Crystallogr. Sect. D Biol. Crystallogr., vol. 50, no. 4, pp. 414–423, 1994.
    [7] N. E. Chayen and E. Saridakis, “Protein crystallization for genomics: Towards high-throughput optimization techniques,” Acta Crystallogr. Sect. D Biol. Crystallogr., vol. 58, no. 6 II, pp. 921–927, 2002.
    [8] M. Yamanaka et al., “Optimization of salt concentration in PEG-based crystallization solutions,” in Journal of Synchrotron Radiation, 2011, vol. 18, no. 1, pp. 84–87.
    [9] C. W. Carter and C. W. Carter, “Protein Crystallization Using Incomplete Factorial-Experiments,” J. Biol. Chem., vol. 254, no. 23, pp. 2219–2223, 1979.
    [10] J. Jancarik and S. H. Kim, “Sparse matrix sampling. A screening method for crystallization of proteins,” J. Appl. Crystallogr., vol. 24, no. pt 4, pp. 409–411, 1991.
    [11] M. A. Dessau and Y. Modis, “Protein crystallization for X-ray crystallography.,” J. Vis. Exp., vol. 9, no. 47, pp. 1–6, 2011.
    [12] T. T. Tran, I. Sorel, and A. Lewit-Bentley, “Statistical experimental design of protein crystallization screening revisited,” Acta Crystallogr. Sect. D Biol. Crystallogr., vol. 60, no. 9, pp. 1562–1568, 2004.
    [13] P. Nowak-sliwinska et al., “Optimization of drug combinations using Feedback System Control,” Nat. Protoc., vol. 11, no. 2, pp. 302–315, 2016.
    [14] Y.-T. Chen et al., “A UV-sensitive hydrogel based combinatory drug delivery chip (UV gel-Drug Chip) for cancer cocktail drug screening,” RSC Adv., vol. 6, no. 50, pp. 44425–44434, 2016.
    [15] Y. Honda, X. Ding, F. Mussano, A. Wiberg, C. Ho, and I. Nishimura, “Guiding the osteogenic fate of mouse and human mesenchymal stem cells through feedback system control,” Sci. Rep., vol. 3, no. 1, p. 3420, 2013.
    [16] P. K. Wong, F. Yu, A. Shahangian, G. Cheng, R. Sun, and C.-M. Ho, “Closed-loop control of cellular functions using combinatory drugs guided by a stochastic search algorithm.,” Proc. Natl. Acad. Sci. U. S. A., vol. 105, no. 13, pp. 5105–10, 2008.
    [17] H. Yu et al., “Optimizing combinations of flavonoids deriving from Astragali Radix in activating the regulatory element of erythropoietin by a feedback system control scheme,” Evidence-based Complement. Altern. Med., vol. 2013, 2013.
    [18] F. Wei, B. Bai, and C. M. Ho, “Rapidly optimizing an aptamer based BoNT sensor by feedback system control (FSC) scheme,” Biosens. Bioelectron., vol. 30, no. 1, pp. 174–179, 2011.
    [19] H. Wang et al., “Mechanism-independent optimization of combinatorial nanodiamond and unmodified drug delivery using a phenotypically driven platform technology,” ACS Nano, vol. 9, no. 3, pp. 3332–3344, 2015.
    [20] O. D. Krishna and K. L. Kiick, “Protein- and peptide-modified synthetic polymeric biomaterials.,” Biopolymers, vol. 94, no. 1. pp. 32–48, 2010.
    [21] A. Sionkowska and A. Planecka, “The in fluence of UV radiation on silk fibroin,” Polym. Degrad. Stab., vol. 96, no. 4, pp. 523–528, 2011.
    [22] E. M. Ahmed, “Hydrogel: Preparation, characterization, and applications,” J. Adv. Res., vol. 6, no. 2, pp. 105–121, 2013.
    [23] C. J. Young, L. A. Poole-Warren, and P. J. Martens, “Combining submerged electrospray and UV photopolymerization for production of synthetic hydrogel microspheres for cell encapsulation,” Biotechnol. Bioeng., vol. 109, no. 6, pp. 1561–1570, 2012.
    [24] S. Matsumoto, S. Yamaguchi, A. Wada, T. Matsui, M. Ikeda, and I. Hamachi, “Photo-responsive gel droplet as a nano- or pico-litre container comprising a supramolecular hydrogel,” Chem. Commun., no. 13, p. 1545, 2008.
    [25] J. R. Luft and G. T. DeTitta, “Hangman: a macromolecular hanging-drop vapor-diffusion technique,” J. Appl. Crystallogr., vol. 25, no. pt 2, pp. 324–325, 1992.
    [26] N. A. Peppas, K. B. Keys, M. Torres-Lugo, and A. M. Lowman, “Poly(ethylene glycol)-containing hydrogels in drug delivery,” J. Control. Release, vol. 62, no. 1–2, pp. 81–87, 1999.
    [27] Dupont, “Teflon PTFE,” Prop. Handb., pp. 1–38, 1996.
    [28] Y. Han, D. Mayer, A. Offenhäusser, and S. Ingebrandt, “Surface activation of thin silicon oxides by wet cleaning and silanization,” Thin Solid Films, vol. 510, no. 1–2, pp. 175–180, 2006.
    [29] J. K. Dattagupta et al., “Crystallization of the fungal enzyme proteinase K and amino acid composition,” Journal of Molecular Biology, vol. 97, no. 2. pp. 267–271, 1975.

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