干旱区生态环境知识资源中心(Arid): Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models

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DOI	10.1016/j.sbi.2020.10.005
	Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models
	Wang, Xiaowei; Unarta, Ilona Christy; Cheung, Peter Pak-Hang; Huang, Xuhui
通讯作者	Huang, XH (corresponding author), Hong Kong Univ Sci & Technol, Shenzhen Res Inst, Hitech Pk, Shenzhen 518057, Peoples R China. ; Huang, XH (corresponding author), Hong Kong Univ Sci & Technol, Ctr Syst Biol & Human Hlth, Dept Chem, State Key Lab Mol Neurosci,Kowloon, Hong Kong, Peoples R China. ; Huang, XH (corresponding author), Hong Kong Univ Sci & Technol, Bioengn Grad Program, Kowloon, Hong Kong, Peoples R China.
来源期刊	CURRENT OPINION IN STRUCTURAL BIOLOGY
ISSN	0959-440X
EISSN	1879-033X
出版年	2021
卷号	67 页码:69-77
英文摘要	Functional conformational changes of proteins can facilitate numerous biological events in cells. The Markov state model (MSM) built from molecular dynamics simulations provide a powerful approach to study them. We here introduce a protocol that is tailor-made for constructing MSMs to study the functional conformational changes of proteins. In this protocol, one of the important steps is to select proper molecular features that can collectively describe the slowest timescales of conformational changes of interest. We recommend spectral oASIS, the modified version of oASIS, as a promising approach for automatic feature selection. Recently developed deep learning methods could also serve efficient approaches for selecting features and finding collective variables. Using DNA repair enzymes and RNA polymerases as examples, we review recent applications of MSMs to elucidate molecular mechanisms of functional conformational changes. Finally, we discuss remaining challenges and future perspectives for constructing MSMs to study functional conformational changes of proteins.
类型	Article
语种	英语
收录类别	SCI-E
WOS记录号	WOS:000647700500009
WOS关键词	DYNAMICS ; PATHWAYS ; KINETICS ; SIMULATIONS
WOS类目	Biochemistry & Molecular Biology ; Cell Biology
WOS研究方向	Biochemistry & Molecular Biology ; Cell Biology
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/349917
作者单位	[Wang, Xiaowei; Cheung, Peter Pak-Hang; Huang, Xuhui] Hong Kong Univ Sci & Technol, Shenzhen Res Inst, Hitech Pk, Shenzhen 518057, Peoples R China; [Wang, Xiaowei; Cheung, Peter Pak-Hang; Huang, Xuhui] Hong Kong Univ Sci & Technol, Ctr Syst Biol & Human Hlth, Dept Chem, State Key Lab Mol Neurosci,Kowloon, Hong Kong, Peoples R China; [Unarta, Ilona Christy; Huang, Xuhui] Hong Kong Univ Sci & Technol, Bioengn Grad Program, Kowloon, Hong Kong, Peoples R China; Hong Kong Ctr Neurodegenerat Dis, Hong Kong, Peoples R China
推荐引用方式 GB/T 7714	Wang, Xiaowei,Unarta, Ilona Christy,Cheung, Peter Pak-Hang,et al. Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models[J],2021,67:69-77.
APA	Wang, Xiaowei,Unarta, Ilona Christy,Cheung, Peter Pak-Hang,&Huang, Xuhui.(2021).Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models.CURRENT OPINION IN STRUCTURAL BIOLOGY,67,69-77.
MLA	Wang, Xiaowei,et al."Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models".CURRENT OPINION IN STRUCTURAL BIOLOGY 67(2021):69-77.