Please wait a minute...
Chin. Phys. B, 2021, Vol. 30(7): 078201    DOI: 10.1088/1674-1056/abfb56
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY Prev   Next  

Equilibrium folding and unfolding dynamics to reveal detailed free energy landscape of src SH3 protein by magnetic tweezers

Huanhuan Su(苏环环)1,†, Hao Sun(孙皓)1,†, Haiyan Hong(洪海燕)1, Zilong Guo(郭子龙)2,3, Ping Yu(余平)1, and Hu Chen(陈虎)1,2,3,‡
1 Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China;
2 Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China;
3 Oujiang Laboratory, Wenzhou 325000, China
Abstract  Src SH3 protein domain is a typical two-state protein which has been confirmed by research of denaturant-induced unfolding dynamics. Force spectroscopy experiments by optical tweezers and atomic force microscopy have measured the force-dependent unfolding rates with different kinds of pulling geometry. However, the equilibrium folding and unfolding dynamics at constant forces has not been reported. Here, using stable magnetic tweezers, we performed equilibrium folding and unfolding dynamic measurement and force-jump measurement of src SH3 domain with tethering points at its N- and C-termini. From the obtained force-dependent transition rates, a detailed two-state free energy landscape of src SH3 protein is constructed with quantitative information of folding free energy, transition state barrier height and position, which exemplifies the capability of magnetic tweezers to study protein folding and unfolding dynamics.
Keywords:  protein folding and unfolding      magnetic tweezers      free energy landscape      transition state  
Received:  17 March 2021      Revised:  15 April 2021      Accepted manuscript online:  26 April 2021
PACS:  82.37.Rs (Single molecule manipulation of proteins and other biological molecules)  
  82.20.Db (Transition state theory and statistical theories of rate constants)  
  87.15.R- (Reactions and kinetics)  
  87.14.E- (Proteins)  
Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11874309 and 11474237) and the 111 Project (Grant No. B16029).
Corresponding Authors:  Hu Chen     E-mail:  chenhu@xmu.edu.cn

Cite this article: 

Huanhuan Su(苏环环), Hao Sun(孙皓), Haiyan Hong(洪海燕), Zilong Guo(郭子龙), Ping Yu(余平), and Hu Chen(陈虎) Equilibrium folding and unfolding dynamics to reveal detailed free energy landscape of src SH3 protein by magnetic tweezers 2021 Chin. Phys. B 30 078201

[1] Dill K A and MacCallum J L 2012 Science 338 1042
[2] Aubin-Tam M E, Olivares A O, Sauer R T, Baker T A and Lang M J 2011 Cell 145 257
[3] Swanton E and Bulleid N J 2003 Mol. Membr. Biol. 20 99
[4] Ashraf G M, Greig N H, Khan T A, Hassan I, Tabrez S, Shakil S, Sheikh I A, Zaidi S K, Akram M, Jabir N R, Firoz C K, Naeem A, Alhazza I M, Damanhouri G A and Kamal M A 2014 CNS Neurol. Disord.-Drug Targets 13 1280
[5] Hanna J, Guerra-Moreno A, Ang J and Micoogullari Y 2019 Am. J. Pathol. 189 94
[6] Plaxco K W, Simons K T and Baker D 1998 J. Mol. Biol. 277 985
[7] Grantcharova V P, Riddle D S, Santiago J V and Baker D 1998 Nat. Struct. Biol. 5 714
[8] Guinn E J, Jagannathan B and Marqusee S 2015 Nat. Commun. 6 6861
[9] van Mierlo C P M and Steensma E 2000 J. Biotechnol. 79 281
[10] Yuan G H, Le S M, Yao M X, Qian H, Zhou X, Yan J and Chen H 2017 Angew. Chem. 56 5490
[11] Best R B, Fowler S B, Toca-Herrera J L and Clarke J 2002 Proc. Natl. Acad. Sci. USA 99 12143
[12] Cecconi C, Shank E A, Bustamante C and Marqusee S 2005 Science 309 2057
[13] Stigler J, Ziegler F, Gieseke A, Gebhardt J C M and Rief M 2011 Science 334 512
[14] Zhang X F, Guo Z L, Yu P, Li Q S, Zhou X and Chen H 2020 Chin. Phys. B 29 078701
[15] Williams P M, Fowler S B, Best R B, Toca-Herrera J L, Scott K A, Steward A and Clarke J 2003 Nature 422 446
[16] Ritchie D B and Woodside M T 2015 Curr. Opin. Struct. Biol. 34 43
[17] Chen H, Yuan G H, Winardhi R S, Yao M X, Popa I, Fernandez J M and Yan J 2015 J. Am. Chem. Soc. 137 3540
[18] Dahal N, Nowitzke J, Eis A and Popa I 2020 J. Phys. Chem. B 124 3283
[19] Wang Y Z, Hou X M, Ju H P, Xiao X, Xi X G, Dou S X, Wang P Y and Li W 2018 Chin. Phys B 27 068701
[20] Li W, Wong W J, Lim C J, Ju H P, Ming L, Yan J and Wang P Y 2015 Chin. Phys B 24 128704
[21] Guo Z, Hong H, Yuan G, Qian H, Li B, Cao Y, Wang W, Wu C X and Chen H 2020 Phys. Rev. Lett. 125 198101
[22] Grantcharova V P and Baker D 1997 Biochemistry 36 15685
[23] Yu H T, Rosen M K, Shin T B, Seideldugan C, Brugge J S and Schreiber S L 1992 Science 258 1665
[24] Efimov A V 1994 Structure 2 999
[25] Camara-Artigas A, Martin-Garcia J M, Morel B, Ruiz-Sanz J and Luque I 2009 FEBS Lett. 583 749
[26] Jagannathan B, Elms P J, Bustamante C and Marqusee S 2012 Proc. Natl. Acad. Sci. USA 109 17820
[27] Wu J H, Li P F, Dong C L, Jiang H T, Xue B, Gao X, Qin M, Wang W, Chen B and Cao Y 2018 Nat. Commun. 9 620
[28] Liu J W, Campos L A, Cerminara M, Wang X, Ramanathan R, English D S and Munoz V 2012 Proc. Natl. Acad. Sci. USA 109 179
[29] Valle-Orero J, Rivas-Pardo J A, Tapia-Rojo R, Popa I, Echelman D J, Haldar S and Fernandez J M 2017 Angew. Chem. Int. Ed. 56 9741
[30] Bell G I 1978 Science 200 618
[31] Zhuravlev P I, Hinczewski M, Chakrabarti S, Marqusee S and Thirumalai D 2016 Proc. Natl. Acad. Sci. USA 113 E715
[32] Fersht A R, Itzhaki L S, Elmasry N, Matthews J M and Otzen D E 1994 Proc. Natl. Acad. Sci. USA 91 10426
[1] Transition state and formation process of Stone—Wales defects in graphene
Jian-Hui Bai(白建会), Yin Yao(姚茵), and Ying-Zhao Jiang(姜英昭). Chin. Phys. B, 2022, 31(3): 036102.
[2] Surface for methane combustion: O(3P)+CH4→OH+CH3
Ya Peng(彭亚), Zhong-An Jiang(蒋仲安), Ju-Shi Chen(陈举师). Chin. Phys. B, 2020, 29(7): 073401.
[3] Theoretical investigation on the excited state intramolecular proton transfer in Me2N substituted flavonoid by the time-dependent density functional theory method
Hang Yin(尹航), Ying Shi(石英). Chin. Phys. B, 2018, 27(5): 058201.
[4] Solvent effects and potential of mean force study of the SN2 reaction of CH3F+CN- in water
Chen Li(李琛), Peng Liu(刘鹏), Yongfang Li(李永方), Dunyou Wang(王敦友). Chin. Phys. B, 2018, 27(3): 033401.
[5] Combined multi-level quantum mechanics theories and molecular mechanics study of water-induced transition state of OH-+CO2 reaction in aqueous solution
Chen Li(李琛), Meixing Niu(牛美兴), Peng Liu(刘鹏), Yongfang Li(李永方), Dunyou Wang(王敦友). Chin. Phys. B, 2017, 26(10): 103401.
[6] Accurate double many-body expansion potential energy surface of HS2(A2A') by scaling the external correlation
Lu-Lu Zhang(张路路), Yu-Zhi Song(宋玉志), Shou-Bao Gao(高守宝), Yuan Zhang(张媛), Qing-Tian Meng(孟庆田). Chin. Phys. B, 2016, 25(5): 053101.
[7] A multi-field approach to DNA condensation
Ran Shi-Yong (冉诗勇), Jia Jun-Li (贾俊丽). Chin. Phys. B, 2015, 24(12): 128702.
[8] Catch-bond behavior of DNA condensate under tension
Li Wei (李伟), Wong Wei-Juan, Lim Ci-Ji, Ju Hai-Peng (车海鹏), Li Ming (李明), Yan Jie (严洁), Wang Peng-Ye (王鹏业). Chin. Phys. B, 2015, 24(12): 128704.
[9] A statistical model for predicting thermal chemical reaction rate
Lin Zheng-Zhe (林正喆), Li Wang-Yao (李王尧), Ning Xi-Jing (宁西京). Chin. Phys. B, 2014, 23(5): 050501.
[10] Simple statistical model for predicting thermal atom diffusion on crystal surfaces
Yu Wei-Feng (于卫锋), Lin Zheng-Zhe (林正喆), Ning Xi-Jing (宁西京). Chin. Phys. B, 2013, 22(11): 116802.
[11] Transition state to mode locking in a passively mode-locked erbium-doped fibre ring laser
Liu Jia-Rui(刘佳锐), Xu Wen-Cheng(徐文成), Luo Zhi-Chao(罗智超), Luo Ai-Ping(罗爱平), and Yin Hai-Sen(殷海森). Chin. Phys. B, 2011, 20(5): 054203.
No Suggested Reading articles found!