The Important Roles of Water in Protein Folding: an Approach by Single Molecule Force Spectroscopy
- Corresponding author: Shu-Xun Cui, cuishuxun@swjtu.edu.cn
Citation:
Bo Cheng, Shu-Xun Cui. The Important Roles of Water in Protein Folding: an Approach by Single Molecule Force Spectroscopy[J]. Chinese Journal of Polymer Science,
;2018, 36(3): 379-384.
doi:
10.1007/s10118-018-2082-2
Ball P.. Water as an active constituent in cell biology[J]. Chem. Rev., 2008,108(1):74-108. doi: 10.1021/cr068037a
Cui S.. The possible roles of water in the prebiotic chemical evolution of DNA[J]. Phys. Chem. Chem. Phys., 2010,12(35):10147-10153.
Levy Y., Onuchic J. N.. Water mediation in protein folding and molecular recognition[J]. Annu. Rev. Biophys. Biomol. Struct., 2006,35:389-415. doi: 10.1146/annurev.biophys.35.040405.102134
Papoian G. A., Ulander J., Eastwood M. P., Luthey-Schulten Z., Wolynes P. G.. Water in protein structure prediction[J]. Proc. Natl. Acad. Sci. U. S. A., 2004,101(10):3352-3357. doi: 10.1073/pnas.0307851100
Scatena L. F., Brown M. G., Richmond G. L.. Water at hydrophobic surfaces:weak hydrogen bonding and strong orientation effects[J]. Science, 2001,292(5518):908-912. doi: 10.1126/science.1059514
Cui S., Yu J., Kuehner F., Schulten K., Gaub H. E.. Double-stranded DNA dissociates into single strands when dragged into a poor solvent[J]. J. Am. Chem. Soc., 2007,129(47):14710-14716. doi: 10.1021/ja074776c
Knubovets T., Osterhout J. J., Klibanov A. M.. Structure of lysozyme dissolved in neat organic solvents as assessed by NMR and CD spectroscopies[J]. Biotechnol. Bioeng., 1999,63(2):242-248. doi: 10.1002/(ISSN)1097-0290
Houen G., Svaerke C., Barkholt V.. The solubilities of denatured proteins in different organic solvents[J]. Acta Chem. Scand., 1999,53(12):1122-1126.
Hugel T., Seitz M.. The study of molecular interactions by AFM force spectroscopy[J]. Macromol. Rapid Commun., 2001,22(13):989-1016. doi: 10.1002/(ISSN)1521-3927
Janshoff A., Neitzert M., Oberdorfer Y., Fuchs H.. Force spectroscopy of molecular systems-single molecule spectroscopy of polymers and biomolecules[J]. Angew. Chem. Int. Ed., 2000,39(18):3212-3237. doi: 10.1002/(ISSN)1521-3773
Pang X., Cheng B., Cui S.. The solvent quality of water for poly(N-isopropylacrylamide) in the collapsed state:implications from single-molecule studies[J]. Chinese J. Polym. Sci., 2016,34(5):578-584. doi: 10.1007/s10118-016-1773-9
Cheng B., Wu S., Liu S., Rodriguez-Aliaga P., Yu J., Cui S.. Protein denaturation at a single-molecule level:the effect of nonpolar environments and its implications on the unfolding mechanism by proteases[J]. Nanoscale, 2015,7(7):2970-2977. doi: 10.1039/C4NR07140A
Improta S., Politou A. S., Pastore A.. Immunoglobulin-like modules from titin I-band:extensible components of muscle elasticity[J]. Structure, 1996,4(3):323-337. doi: 10.1016/S0969-2126(96)00036-6
Lu H., Schulten K.. The key event in force-induced unfolding of titin's immunoglobulin domains[J]. Biophys. J., 2000,79(1):51-65. doi: 10.1016/S0006-3495(00)76273-4
Li H., Oberhauser A. F., Fowler S. B., Clarke J., Fernandez J. M.. Atomic force microscopy reveals the mechanical design of a modular protein[J]. Proc. Natl. Acad. Sci. U. S. A., 2000,97(12):6527-6531. doi: 10.1073/pnas.120048697
Carrion-Vazquez M., Oberhauser A. F., Fowler S. B., Marszalek P. E., Broedel S. E., Clarke J., Fernandez J. M.. Mechanical and chemical unfolding of a single protein:a comparison[J]. Proc. Natl. Acad. Sci. U. S. A., 1999,96(7):3694-3699. doi: 10.1073/pnas.96.7.3694
Marszalek P. E., Lu H., Li H. B., Carrion-Vazquez M., Oberhauser A. F., Schulten K., Fernandez J. M.. Mechanical unfolding intermediates in titin modules[J]. Nature, 1999,402(6757):100-103. doi: 10.1038/47083
Rief M., Gautel M., Oesterhelt F., Fernandez J. M., Gaub H. E.. Reversible unfolding of individual titin immunoglobulin domains by AFM[J]. Science, 1997,276(5315):1109-1112. doi: 10.1126/science.276.5315.1109
Florin E. L., Rief M., Lehmann H., Ludwig M., Dornmair C., Moy V. T., Gaub H. E.. Sensing specific molecular-interactions with the atomic-force microscope[J]. Biosens. Bioelectron., 1995,10(9-10):895-901. doi: 10.1016/0956-5663(95)99227-C
Zhang W., Zhang X.. Single molecule mechanochemistry of macromolecules[J]. Prog. Polym. Sci., 2003,28(8):1271-1295. doi: 10.1016/S0079-6700(03)00046-7
Wan Z., Li L., Cui S.. Capturing the portrait of isolated individual natural cellulose molecules[J]. Biopolymers, 2008,89:1170-1173. doi: 10.1002/bip.21070
Cui S., Pang X., Zhang S., Yu Y., Ma H., Zhang X.. Unexpected temperature-dependent single chain mechanics of poly(N-isopropyl-acrylamide) in water[J]. Langmuir, 2012,28(11):5151-5157. doi: 10.1021/la300135w
Cui S. X., Albrecht C., Kuhner F., Gaub H. E.. Weakly bound water molecules shorten single-stranded DNA[J]. J. Am. Chem. Soc., 2006,128(20):6636-6639. doi: 10.1021/ja0582298
Cheung M. S., Garcia A. E., Onuchic J. N.. Protein folding mediated by solvation:water expulsion and formation of the hydrophobic core occur after the structural collapse[J]. Proc. Natl. Acad. Sci. U. S. A., 2002,99(2):685-690. doi: 10.1073/pnas.022387699
Head-Gordon T., Brown S.. Minimalist models for protein folding and design[J]. Curr. Opin. Struc. Biol., 2003,13(2):160-167. doi: 10.1016/S0959-440X(03)00030-7
Kellermayer M. S. Z., Smith S. B., Granzier H. L., Bustamante C.. Folding-unfolding transitions in single titin molecules characterized with laser tweezers[J]. Science, 1997,276(5315):1112-1116. doi: 10.1126/science.276.5315.1112
Luo Z., Zhang A., Chen Y., Shen Z., Cui S.. How big is big enough? Effect of length and shape of side chains on the single-chain enthalpic elasticity of a macromolecule[J]. Macromolecules, 2016,49(9):3559-3565. doi: 10.1021/acs.macromol.6b00247
Lum K., Chandler D., Weeks J. D.. Hydrophobicity at small and large length scales[J]. J. Phys. Chem. B, 1999,103(22):4570-4577. doi: 10.1021/jp984327m
Tanford C.. Protein denaturation[J]. Part C. Theoretical models for the mechanism of denaturation. Adv. Prot. Chem., 1970,24:1-95.
Kharakoz D. P.. Partial volumes and compressibilities of extended polypeptide chains in aqueous solution:additivity scheme and implication of protein unfolding at normal and high pressure[J]. Biochemistry, 1997,36(33):10276-10285. doi: 10.1021/bi961781c
Kumar A., Venkatesu P.. Overview of the stability of α-chymotrypsin in different solvent media[J]. Chem. Rev., 2012,112(7):4283-4307. doi: 10.1021/cr2003773
Larsericsdotter H., Oscarsson S., Buijs J.. Thermodynamic analysis of lysozyme adsorbed to silica[J]. J. Colloid Interface Sci., 2004,276(2):261-268. doi: 10.1016/j.jcis.2004.03.056
Dietz H., Rief M.. Exploring the energy landscape of GFP by single-molecule mechanical experiments[J]. Proc. Natl. Acad. Sci. U. S. A., 2004,101(46):16192-16197. doi: 10.1073/pnas.0404549101
Alexander P., Fahnestock S., Lee T., Orban J., Bryan P.. Thermodynamic analysis of the folding of the streptococcal protein G IgG-binding domains B1 and B2:why small proteins tend to have high denaturation temperatures[J]. Biochemistry, 1992,31(14):3597-3603. doi: 10.1021/bi00129a007
Liu C., Cui S., Wang Z., Zhang X.. Single-chain mechanical property of poly(N-vinyl-2-pyrrolidone) and interaction with small molecules[J]. J. Phys. Chem. B, 2005,109(31):14807-14812. doi: 10.1021/jp050227m
Oesterhelt F., Rief M., Gaub H. E.. Single molecule force spectroscopy by AFM indicates helical structure of poly(ethylene-glycol) in water[J]. New J. Phys., 1999,1:6.1-6.11.
Cui S.. Single-molecule force spectroscopy of biomacromolecules:comparative studies in aqueous solution and nonpolar solvents[J]. Acta Polymerica Sinica (in Chinese), 2016(9):1160-1165.
Xinyi Hong , Tailing Xue , Zhou Xu , Enrong Xie , Mingkai Wu , Qingqing Wang , Lina Wu . Non-Site-Specific Fluorescent Labeling of Proteins as a Chemical Biology Experiment. University Chemistry, 2024, 39(4): 351-360. doi: 10.3866/PKU.DXHX202310010
Shule Liu . Application of SPC/E Water Model in Molecular Dynamics Teaching Experiments. University Chemistry, 2024, 39(4): 338-342. doi: 10.3866/PKU.DXHX202310029
Yanhui Zhong , Ran Wang , Zian Lin . Analysis of Halogenated Quinone Compounds in Environmental Water by Dispersive Solid-Phase Extraction with Liquid Chromatography-Triple Quadrupole Mass Spectrometry. University Chemistry, 2024, 39(11): 296-303. doi: 10.12461/PKU.DXHX202402017
Wenbi Wu , Yinchu Dong , Haofan Liu , Xuebing Jiang , Li Li , Yi Zhang , Maling Gou . Modification of plasma protein for bioprinting via photopolymerization. Chinese Chemical Letters, 2024, 35(8): 109260-. doi: 10.1016/j.cclet.2023.109260
Hong-Jin Liao , Zhu Zhuo , Qing Li , Yoshihito Shiota , Jonathan P. Hill , Katsuhiko Ariga , Zi-Xiu Lu , Lu-Yao Liu , Zi-Ang Nan , Wei Wang , You-Gui Huang . A new class of crystalline X-ray induced photochromic materials assembled from anion-directed folding of a flexible cation. Chinese Chemical Letters, 2024, 35(8): 109052-. doi: 10.1016/j.cclet.2023.109052
Yixin Zhang , Ting Wang , Jixiang Zhang , Pengyu Lu , Neng Shi , Liqiang Zhang , Weiran Zhu , Nongyue He . Formation mechanism for stable system of nanoparticle/protein corona and phospholipid membrane. Chinese Chemical Letters, 2024, 35(4): 108619-. doi: 10.1016/j.cclet.2023.108619
Mingqi Wang , Shixin Fa , Jiate Yu , Guoxian Zhang , Yi Yan , Qing Liu , Qiuyu Zhang . Light-controlled protein imprinted nanospheres with variable recognition specificity. Chinese Chemical Letters, 2025, 36(2): 110124-. doi: 10.1016/j.cclet.2024.110124
Fang-Yuan Chen , Wen-Chao Geng , Kang Cai , Dong-Sheng Guo . Molecular recognition of cyclophanes in water. Chinese Chemical Letters, 2024, 35(5): 109161-. doi: 10.1016/j.cclet.2023.109161
Ying Li , Long-Jie Wang , Yong-Kang Zhou , Jun Liang , Bin Xiao , Ji-Shen Zheng . An improved installation of 2-hydroxy-4-methoxybenzyl (iHmb) method for chemical protein synthesis. Chinese Chemical Letters, 2024, 35(5): 109033-. doi: 10.1016/j.cclet.2023.109033
Si Ha , Jiacheng Zhu , Hua Xiang , Guoshun Luo . Hydrophobic tag tethering degrader as a promising paradigm of protein degradation: Past, present and future perspectives. Chinese Chemical Letters, 2024, 35(8): 109192-. doi: 10.1016/j.cclet.2023.109192
Wenhao Wang , Siyuan Peng , Zhengwei Huang , Xin Pan . Tuning amino/hydroxyl ratios of nanovesicles to manipulate protein corona-mediated in vivo fate. Chinese Chemical Letters, 2024, 35(11): 110134-. doi: 10.1016/j.cclet.2024.110134
Bo Liu , Shuaiqiang Shao , Junjie Cai , Zijian Zhang , Feng Tian , Kun Yang , Fan Li . Signal cascade amplification of streptavidin-biotin-modified immunofluorescence nanocapsules for ultrasensitive detection of glial fibrillary acidic protein. Chinese Chemical Letters, 2025, 36(3): 109814-. doi: 10.1016/j.cclet.2024.109814
Han-Min Wang , Yan-Chen Li , Lu-Lu Sun , Ming-Ye Tang , Jia Liu , Jiahao Cai , Lei Dong , Jia Li , Yi Zang , Hai-Hao Han , Xiao-Peng He . Protein-encapsulated long-wavelength fluorescent probe hybrid for imaging lipid droplets in living cells and mice with non-alcoholic fatty liver. Chinese Chemical Letters, 2024, 35(11): 109603-. doi: 10.1016/j.cclet.2024.109603
Kun Tang , Yu-Wu Zhong . Water reduction by an organic single-chromophore photocatalyst. Chinese Journal of Structural Chemistry, 2024, 43(8): 100376-100376. doi: 10.1016/j.cjsc.2024.100376
Gengchen Guo , Tianyu Zhao , Ruichang Sun , Mingzhe Song , Hongyu Liu , Sen Wang , Jingwen Li , Jingbin Zeng . Au-Fe3O4 dumbbell-like nanoparticles based lateral flow immunoassay for colorimetric and photothermal dual-mode detection of SARS-CoV-2 spike protein. Chinese Chemical Letters, 2024, 35(6): 109198-. doi: 10.1016/j.cclet.2023.109198
Yi Zhang , Biao Wang , Chao Hu , Muhammad Humayun , Yaping Huang , Yulin Cao , Mosaad Negem , Yigang Ding , Chundong Wang . Fe–Ni–F electrocatalyst for enhancing reaction kinetics of water oxidation. Chinese Journal of Structural Chemistry, 2024, 43(2): 100243-100243. doi: 10.1016/j.cjsc.2024.100243
Yang Yang , Jing-Li Luo , Xian-Zhu Fu . Water-oxidation intermediates enabling electrochemical propylene epoxidation. Chinese Journal of Structural Chemistry, 2024, 43(5): 100269-100269. doi: 10.1016/j.cjsc.2024.100269
Jinjie Lu , Qikai Liu , Yuting Zhang , Yi Zhou , Yanbo Zhou . Antibacterial performance of cationic quaternary phosphonium-modified chitosan polymer in water. Chinese Chemical Letters, 2024, 35(9): 109406-. doi: 10.1016/j.cclet.2023.109406
Wenhao Chen , Jian Du , Hanbin Zhang , Hancheng Wang , Kaicheng Xu , Zhujun Gao , Jiaming Tong , Jin Wang , Junjun Xue , Ting Zhi , Longlu Wang . Surface treatment of GaN nanowires for enhanced photoelectrochemical water-splitting. Chinese Chemical Letters, 2024, 35(9): 109168-. doi: 10.1016/j.cclet.2023.109168
Shuyuan Pan , Zehui Yang , Fang Luo . Ni-based electrocatalysts for urea assisted water splitting. Chinese Journal of Structural Chemistry, 2024, 43(8): 100373-100373. doi: 10.1016/j.cjsc.2024.100373