Molecular Dynamics Simulation for the β-Sheet Aggregation of Peptides

Chem. J. Chinese Universities ›› 2010, Vol. 31 ›› Issue (8): 1626.

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Molecular Dynamics Simulation for the β-Sheet Aggregation of Peptides

LÜ Ming², ZHAO Xi³, SHEN Xing-Gui¹, GAO Xue-Feng^1*

1. Edmond H. Fischer Signal Transduction Laboratory, College of Life Sciences, Jilin University, Changchun 130012, China;
2. Key Lab for Molecular Enzymology and Engineering of Ministry of Education,
3. State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, China

Received:2009-12-28 Online:2010-08-10 Published:2010-08-10
Contact: GAO Xue-Feng. E-mail: gaoxf@jlu.edu.cn
Supported by:
中国博士后科学基金(批准号: 20070411004)资助.

Abstract

Abstract: The aggregations and thermodynamics stability of a nine peptide forming amyloidal fibril were studied using molecular dynamics simulation methods under acidic and alkaline condition, respectively. The results show that the peptide can form parallel β-sheet under alkaline condition, whereas forms anti-parallel β-sheet under acidic condition, and thermodynamics stability of the anti-parallel β-sheet is more stable than that of parallel β-sheet. The above observations are consistent with the experimental results. In addition, in the two β-sheet forms, the peptide chain both extends along direction of the corresponding sheet and forms left-helix, but the angle between adjacent peptide chains are different: the angel in parallel β-sheet form is less than that in anti-parallel β-sheet form. Therefore, it is concluded that parallel β-sheet is form easily aggregation, comparing with the anti-parallel β-sheet. The conclusion can explain why the diameter of amyloidal fibril under alkaline condition is larger than that under acidic condition in experiment.

Key words: Amyloidal fibril, Molecular dynamics simulation, Reaction-field, Left-helix

TrendMD:

Lü Ming, ZHAO Xi, SHEN Xing-Gui, GAO Xue-Feng*. Molecular Dynamics Simulation for the β-Sheet Aggregation of Peptides[J]. Chem. J. Chinese Universities, 2010, 31(8): 1626.

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Molecular Dynamics Simulation for the β-Sheet Aggregation of Peptides

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