期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 36, 期 22, 页码 1709-1718出版社
WILEY
DOI: 10.1002/jcc.23989
关键词
allostery; molecular dynamics simulations; PDZ domain; inter-residue energy conductivity; ligand binding
资金
- Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan [22104009]
- Grants-in-Aid for Scientific Research [22104009] Funding Source: KAKEN
Protein function is regulated not only by the structure but also by physical dynamics and thermal fluctuations. We have developed the computer program, CURrent calculation for proteins (CURP), for the flow analysis of physical quantities within thermally fluctuating protein media. The CURP program was used to calculate the energy flow within the third PDZ domain of the neuronal protein PSD-95, and the results were used to illustrate the energy exchange network of inter-residue interactions based on atomistic molecular dynamics simulations. The removal of the 3 helix is known to decrease ligand affinity by 21-fold without changing the overall protein structure; nevertheless, we demonstrated that the helix constitutes an essential part of the network graph. (c) 2015 Wiley Periodicals, Inc.
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