蛋白质力谱测试中生物分子链耦联技术
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摘要
蛋白质力谱测试是研究生物学的重要组成部分.蛋白质力谱测试的成功取决于两大技术:一是分子尺度的力谱测量能力,即皮牛量级的力学分辨力和纳米级别的空间分辨力;二是蛋白质样品制备能力,通过将微观生物分子链与介观微球/探针/基底耦联,实现对分子尺度蛋白质的有效测量.然而,蛋白质样品的耦联情况很难在视觉上直接观测,耦联效果的好坏决定测试的成败.因此,蛋白质样品相关制备方法、耦联工艺一直是单分子力谱测试中的研究重点.针对3种主要单分子力谱测试技术即光镊、磁镊及原子力显微术对测试蛋白质的需求特点,特别是对多分子链耦合样品的测试需求特点,介绍了多种基于基底修饰、蛋白质修饰和DNA链修饰的提高连接待测蛋白质与DNA链/微球/探针/玻片/云母片的方法,分析了各自的优缺点,并总结了典型的应用,为相关领域中样品的制备提供参考方案.
Protein force spectroscopy testing is one of the important components of the study of biology. The success of protein force spectroscopy testing depends on the following factors:the capability of force spectroscopy measurement at the molecular scale,namely piconewton-scale force resolution and nanometer-scale spatial resolution,and the protein sample preparation technique,which achieves effective measurement of protein samples at the molecular scale through the coupling of microscopic biomolecular chains with mesoscopic microspheres/probes/substrates. However,the coupling of protein samples is invisible and its coupling effect seriously affects the test efficiency.Therefore,the preparation method and coupling technology of protein samples are the key points in the measurement of single-molecule force spectroscopy. According to the various demands of three single-molecule force spectroscopy testing techniques on the samples,particularly the test requirement of multi-molecular chain-coupled samples,the authors introduce different methods to improve the connection efficiency between protein and DNA handles/microspheres/probes/glass slides/mica in optical tweezers,magnetic tweezers,and atomic force microscopy based on substrate,protein,and DNA modification,and discuss their advantages and disadvantages. The typical applications are summarized to provide a reference for the preparation of biological samples in related fields.
Protein force spectroscopy testing is one of the important components of the study of biology. The success of protein force spectroscopy testing depends on the following factors:the capability of force spectroscopy measurement at the molecular scale,namely piconewton-scale force resolution and nanometer-scale spatial resolution,and the protein sample preparation technique,which achieves effective measurement of protein samples at the molecular scale through the coupling of microscopic biomolecular chains with mesoscopic microspheres/probes/substrates. However,the coupling of protein samples is invisible and its coupling effect seriously affects the test efficiency.Therefore,the preparation method and coupling technology of protein samples are the key points in the measurement of single-molecule force spectroscopy. According to the various demands of three single-molecule force spectroscopy testing techniques on the samples,particularly the test requirement of multi-molecular chain-coupled samples,the authors introduce different methods to improve the connection efficiency between protein and DNA handles/microspheres/probes/glass slides/mica in optical tweezers,magnetic tweezers,and atomic force microscopy based on substrate,protein,and DNA modification,and discuss their advantages and disadvantages. The typical applications are summarized to provide a reference for the preparation of biological samples in related fields.
引文
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[23]Bauer Daniela,Merz Dale R,Pelz Benjamin,et al.Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK[J].Proceedings of the National Academy of Sciences,2015,112(33):10389-10394.
[24]Jahn Markus,Buchner Johannes,Hugel Thorsten,et al.Folding and assembly of the large molecular machine Hsp90 studied in single-molecule experiments[J].Proceedings of the National Academy of Sciences,2016,113(5):1232-1237.
[25]Gao Ying,Zorman Sylvain,Gundersen Gregory,et al.Single reconstituted neuronal SNARE complexes zipper in three distinct stages[J].Science,2012,337(6100),1340-1343.
[26]Jiao Junyi,Rebane Aleksander A,Ma Lu,et al.Kinetically coupled folding of a single HIV-1glycoprotein 41 complex in viral membrane fusion and inhibition[J].Proceedings of the National Academy of Sciences,2015,112(22):E2855-E2864.
[27]Zhang Yongli,Xi Zhiqun,Gao Ying,et al.Direct observation of helix staggering,sliding,and coiled coil misfolding[J].Biophysical Journal,2012,102(3):175a.
[28]Stigler Johannes,Ziegler Fabian,Gieseke Anja,et al.The complex folding network of single calmodulin molecules[J].Science,2011,334(6055):512-516.
[29]Woodside Michael T,Anthony Peter C,Behnke-Parks William M,et al.Direct measurement of the full,sequence-dependent folding landscape of a nucleic acid[J].Science,2006,314(5801):1001-1004.
[30]?oldák Gabriel,Stigler Johannes,Pelz Benjamin,et al.Ultrafast folding kinetics and cooperativity of villin headpiece in single-molecule force spectroscopy[J].Proceedings of the National Academy of Sciences,2013,110(45):18156-18161.
[31]Gao Ying,Sirinakis George,Zhang Yongli.Highly anisotropic stability and folding kinetics of a single coiled coil protein under mechanical tension[J].Journal of the American Chemical Society,2011,133(32):12749-12757.
[2]Lei Hai,He Chengzhi,Hu Chunguang,et al.Singlemolecule force spectroscopy trajectories of a single protein and its polyproteins are equivalent:A direct experimental validation based on a small protein Nu G2[J].Angewandte Chemie International Edition,2017,56(22):6117-6121.
[3]Ma Lu,Cai Yiying,Li Yanghui,et al.Single-molecule force spectroscopy of protein-membrane interactions[J].ELife,2017,6:e30493.
[4]Chen Hu,Fu Hongxia,Zhu Xiaoying,et al.Improved high-force magnetic tweezers for stretching and refolding of proteins and short DNA[J].Biophysical Journal,2011,100(2):517-523.
[5]Long Xi,Parks Joseph W,Bagshaw Clive R,et al.Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers spectroscopy[J].Nucleic Acids Research,2013,41(4):2746-2755.
[6]Lee Whasil,Zeng Xiancheng,Zhou Huanxiang,et al.Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations[J].Journal of Biological Chemistry,2010,285(49):38167-38172.
[7]Li Hongbin,Oberhauser Andres F,Fowler Susan B,et al.Atomic force microscopy reveals the mechanical design of a modular protein[J].Proceedings of the National Academy of Sciences,2000,97(12):6527-6531.
[8]Marszalek Piotr E,Dufrêne Yves F.Stretching single polysaccharides and proteins using atomic force microscopy[J].Chemical Society Reviews,2012,41(9):3523-3534.
[9]Los Georgyi V,Encell Lance P,McDougall Mark G,et al.HaloTag:A novel protein labeling technology for cell imaging and protein analysis[J].ACS Chemical Biology,2008,3(6):373-382.
[10]Taniguchi Yukinori,Kawakami Masaru.Application of HaloTag protein to covalent immobilization of recombinant proteins for single molecule force spectroscopy[J].Langmuir,2010,26(13):10433-10436.
[11]Yin Jun,Straight Paul D,McLoughlin Shaun M,et al.Genetically encoded short peptide tag for versatile protein labeling by Sfp phosphopantetheinyl transferase[J].Proceedings of the National Academy of Sciences of the United States of America,2005,102(44):15815-15820.
[12]Zakeri Bijan,Fierer Jacob O,Celik Emrah,et al.Peptide tag forming a rapid covalent bond to a protein,through engineering a bacterial adhesin[J].Proceedings of the National Academy of Sciences,2012,109(12):4347-4348.
[13]Pippig Diana A,Baumann Fabian,Strackharn Mathias,et al.Protein-DNA chimeras for nano assembly[J].ACS Nano,2014,8(7):6551-6555.
[14]Bauer Magnus S,Milles Lukas F,Sedlak Steffen M,et al.Monomeric streptavidin:A versatile regenerative handle for force spectroscopy[EB/OL].https://www.biorxiv.org/content/early/2018/03/08/276444.fill.pd,2018.
[15]Chen Hu,Chandrasekar Saranya,Sheetz Michael P,et al.Mechanical perturbation of filamin A immunoglobulin repeats 20-21 reveals potential nonequilibrium mechanochemical partner binding function[J].Scientific Reports,2013,3:1642.
[16]Chen Hu,Yuan Guohua,Winardhi Ricksen S,et al.Dynamics of equilibrium folding and unfolding transitions of titin immunoglobulin domain under constant forces[J].Journal of the American Chemical Society,2015,137(10):3540-3546.
[17]Chen Hu,Zhu Xiaoying,Cong Peiwen,et al.Differential mechanical stability of filamin A rod segments[J].Biophysical Journal,2011,101(5):1231-1237.
[18]Min Duyoung,Jefferson Robert E,Bowie James U,et al.Mapping the energy landscape for second-stage folding of a single membrane protein[J].Nature Chemical Biology,2015,11(12):981.
[19]Min Duyoung,Kim Kipom,Hyeon Changbong,et al.Mechanical unzipping and rezipping of a single SNAREcomplex reveals hysteresis as a force-generating mechanism[J].Nature Communications,2013,4:1705.
[20]Min Duyoung,Arbing Mark A,Jefferson Robert E,et al.A simple DNA handle attachment method for single molecule mechanical manipulation experiments[J].Protein Science,2016,25(8):1535-1544.
[21]Cecconi Ciro,Shank Elizabeth A,Dahlquist Frederick W,et al.Protein-DNA chimeras for single molecule mechanical folding studies with the optical tweezers[J].European Biophysics Journal,2008,37(6):729-738.
[22]Gebhardt J C M,Bornschl?gl T,Rief M,et al.Full distance-resolved folding energy landscape of one single protein molecule[J].Proceedings of the National Academy of Sciences,2010,107(5):2013-2018.
[23]Bauer Daniela,Merz Dale R,Pelz Benjamin,et al.Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK[J].Proceedings of the National Academy of Sciences,2015,112(33):10389-10394.
[24]Jahn Markus,Buchner Johannes,Hugel Thorsten,et al.Folding and assembly of the large molecular machine Hsp90 studied in single-molecule experiments[J].Proceedings of the National Academy of Sciences,2016,113(5):1232-1237.
[25]Gao Ying,Zorman Sylvain,Gundersen Gregory,et al.Single reconstituted neuronal SNARE complexes zipper in three distinct stages[J].Science,2012,337(6100),1340-1343.
[26]Jiao Junyi,Rebane Aleksander A,Ma Lu,et al.Kinetically coupled folding of a single HIV-1glycoprotein 41 complex in viral membrane fusion and inhibition[J].Proceedings of the National Academy of Sciences,2015,112(22):E2855-E2864.
[27]Zhang Yongli,Xi Zhiqun,Gao Ying,et al.Direct observation of helix staggering,sliding,and coiled coil misfolding[J].Biophysical Journal,2012,102(3):175a.
[28]Stigler Johannes,Ziegler Fabian,Gieseke Anja,et al.The complex folding network of single calmodulin molecules[J].Science,2011,334(6055):512-516.
[29]Woodside Michael T,Anthony Peter C,Behnke-Parks William M,et al.Direct measurement of the full,sequence-dependent folding landscape of a nucleic acid[J].Science,2006,314(5801):1001-1004.
[30]?oldák Gabriel,Stigler Johannes,Pelz Benjamin,et al.Ultrafast folding kinetics and cooperativity of villin headpiece in single-molecule force spectroscopy[J].Proceedings of the National Academy of Sciences,2013,110(45):18156-18161.
[31]Gao Ying,Sirinakis George,Zhang Yongli.Highly anisotropic stability and folding kinetics of a single coiled coil protein under mechanical tension[J].Journal of the American Chemical Society,2011,133(32):12749-12757.