Application of topological soliton in modeling protein folding: Recent progress and perspective

doi:10.1088/1674-1056/abaed9

中国物理B ›› 2020, Vol. 29 ›› Issue (10): 108705-.doi: 10.1088/1674-1056/abaed9

所属专题： SPECIAL TOPIC — Modeling and simulations for the structures and functions of proteins and nucleic acids

Xu-Biao Peng(彭绪彪)¹^,†(), Jiao-Jiao Liu(刘娇娇)¹, Jin Dai(戴劲)¹^,², Antti J Niemi¹^,²^,‡(), Jian-Feng He(何建锋)¹^,§()

收稿日期:2020-06-30 修回日期:2020-08-08 接受日期:2020-08-13 出版日期:2020-10-05 发布日期:2020-10-05
通讯作者: Xu-Biao Peng(彭绪彪), Antti J Niemi(何建锋), Jian-Feng He

Application of topological soliton in modeling protein folding: Recent progress and perspective

Xu-Biao Peng(彭绪彪)^1,†, Jiao-Jiao Liu(刘娇娇)¹, Jin Dai(戴劲)^1,2, Antti J Niemi^1,2,‡, and Jian-Feng He(何建锋)^1,§

¹ School of Physics, Beijing Institute of Technology, Beijing 100081, China
² Nordita, Stockholm University, Roslagstullsbacken 23, SE-106 91 Stockholm, Sweden

Received:2020-06-30 Revised:2020-08-08 Accepted:2020-08-13 Online:2020-10-05 Published:2020-10-05
Contact: ^†E-mail: xubiaopeng@bit.edu.cn ^‡E-mail: Antti.Niemi@physics.uu.se ^§Corresponding author. E-mail: hjf@bit.edu.cn

摘要/Abstract

Abstract:

Proteins are important biological molecules whose structures are closely related to their specific functions. Understanding how the protein folds under physical principles, known as the protein folding problem, is one of the main tasks in modern biophysics. Coarse-grained methods play an increasingly important role in the simulation of protein folding, especially for large proteins. In recent years, we proposed a novel coarse-grained method derived from the topological soliton model, in terms of the backbone C_α chain. In this review, we will first systematically address the theoretical method of topological soliton. Then some successful applications will be displayed, including the thermodynamics simulation of protein folding, the property analysis of dynamic conformations, and the multi-scale simulation scheme. Finally, we will give a perspective on the development and application of topological soliton.

Key words: protein folding, coarse-grained method, Landau free energy function, topological soliton

中图分类号: (Folding: thermodynamics, statistical mechanics, models, and pathways)

87.15.Cc

87.14.E- (Proteins) 87.15.A- (Theory, modeling, and computer simulation) 87.15.hm (Folding dynamics)

Xu-Biao Peng(彭绪彪), Jiao-Jiao Liu(刘娇娇), Jin Dai(戴劲), Antti J Niemi, Jian-Feng He(何建锋). [J]. 中国物理B, 2020, 29(10): 108705-.

Xu-Biao Peng(彭绪彪)†, Jiao-Jiao Liu(刘娇娇), Jin Dai(戴劲), Antti J Niemi‡, and Jian-Feng He(何建锋)§. Application of topological soliton in modeling protein folding: Recent progress and perspective[J]. Chin. Phys. B, 2020, 29(10): 108705-.

图/表 13

参考文献 47

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Proteins	PDB ID	Length of sequence	RMSD/Å
Villin headpiece 35	1YRF	29 aa	0.38
Myoglobin	1ABS	154 aa	0.78
HIV-1 reverse transcriptase protein	3DLK	18 aa	1.13
λ-repressor	1LMB	84 aa	0.51
Human islet amyloid polypeptide	2L86	37 aa	1.17
Myc proto-oncogene protein	1NKP	88 aa	0.98
Amyloid intra-cellular domain	3DXC	28 aa	0.46
Engrailed homeodomain	2JWT	61 aa	0.67
Parvalbumin-β	2PVB	57 aa	1.28

Application of topological soliton in modeling protein folding: Recent progress and perspective

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