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.
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 Science338 1042 [2] Aubin-Tam M E, Olivares A O, Sauer R T, Baker T A and Lang M J 2011 Cell145 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 Targets13 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. USA99 12143 [12] Cecconi C, Shank E A, Bustamante C and Marqusee S 2005 Science309 2057 [13] Stigler J, Ziegler F, Gieseke A, Gebhardt J C M and Rief M 2011 Science334 512 [14] Zhang X F, Guo Z L, Yu P, Li Q S, Zhou X and Chen H 2020 Chin. Phys. B29 078701 [15] Williams P M, Fowler S B, Best R B, Toca-Herrera J L, Scott K A, Steward A and Clarke J 2003 Nature422 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. B124 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 B27 068701 [20] Li W, Wong W J, Lim C J, Ju H P, Ming L, Yan J and Wang P Y 2015 Chin. Phys B24 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 Biochemistry36 15685 [23] Yu H T, Rosen M K, Shin T B, Seideldugan C, Brugge J S and Schreiber S L 1992 Science258 1665 [24] Efimov A V 1994 Structure2 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. USA109 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. USA109 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 Science200 618 [31] Zhuravlev P I, Hinczewski M, Chakrabarti S, Marqusee S and Thirumalai D 2016 Proc. Natl. Acad. Sci. USA113 E715 [32] Fersht A R, Itzhaki L S, Elmasry N, Matthews J M and Otzen D E 1994 Proc. Natl. Acad. Sci. USA91 10426
Altmetric calculates a score based on the online attention an article receives. Each coloured thread in the circle represents a different type of online attention. The number in the centre is the Altmetric score. Social media and mainstream news media are the main sources that calculate the score. Reference managers such as Mendeley are also tracked but do not contribute to the score. Older articles often score higher because they have had more time to get noticed. To account for this, Altmetric has included the context data for other articles of a similar age.
