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Multiscale simulations of protein folding: application to formation of secondary structures
Xu, Ji1,2; Ren, Ying1; Li, Jinghai1
2013-07-01
Source PublicationJOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
ISSN0739-1102
Volume31Issue:7Pages:779-787
AbstractA multiscale simulation method of protein folding is proposed, using atomic representation of protein and solvent, combing genetic algorithms to determine the key protein structures from a global view, with molecular dynamic simulations to reveal the local folding pathways, thus providing an integrated landscape of protein folding. The method is found to be superior to previously investigated global search algorithms or dynamic simulations alone. For secondary structure formation of a selected peptide, RN24, the structures and dynamics produced by this method agree well with corresponding experimental results. Three most populated conformations are observed, including hairpin, -sheet and -helix. The energetic barriers separating these three structures are comparable to the kinetic energy of the atoms of the peptide, implying that the transition between these states can be easily triggered by kinetic perturbations, mainly through electrostatic interactions between charged atoms. Transitions between -helix and -sheet should jump over at least two energy barriers and may stay in the energetic trap of hairpin. It is proposed that the structure of proteins should be jointly governed by thermodynamic and dynamic factors; free energy is not the exclusive dominant for stability of proteins.
KeywordProtein Folding Stability Multiscale Compromise Mesoscale Genetic Algorithm Molecular Dynamics Simulation
SubtypeArticle
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
DOI10.1080/07391102.2012.709461
Indexed BySCI
Language英语
WOS KeywordMOLECULAR-DYNAMICS SIMULATIONS ; LINEAR CONSTRAINT SOLVER ; ARTIFICIAL PERIODICITY ; GENETIC ALGORITHM ; COMPLEX-SYSTEMS ; PEPTIDES ; TIME ; RIBONUCLEASE ; LINCS ; FLOW
WOS Research AreaBiochemistry & Molecular Biology ; Biophysics
WOS SubjectBiochemistry & Molecular Biology ; Biophysics
WOS IDWOS:000320981700009
Citation statistics
Cited Times:14[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ipe.ac.cn/handle/122111/13324
Collection研究所(批量导入)
Affiliation1.Chinese Acad Sci, Inst Proc Engn, State Key Lab Multiphase Complex Syst, Beijing 100190, Peoples R China
2.Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China
Recommended Citation
GB/T 7714
Xu, Ji,Ren, Ying,Li, Jinghai. Multiscale simulations of protein folding: application to formation of secondary structures[J]. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS,2013,31(7):779-787.
APA Xu, Ji,Ren, Ying,&Li, Jinghai.(2013).Multiscale simulations of protein folding: application to formation of secondary structures.JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS,31(7),779-787.
MLA Xu, Ji,et al."Multiscale simulations of protein folding: application to formation of secondary structures".JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 31.7(2013):779-787.
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