2000 Fiscal Year Final Research Report Summary
Dynamics of a Globular Protein and Water Molecules surrounding the Protein with the Independent Molecule Model
Project/Area Number |
10640397
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Research Category |
Grant-in-Aid for Scientific Research (C)
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Allocation Type | Single-year Grants |
Section | 一般 |
Research Field |
物理学一般
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Research Institution | YATSUSHIRO NATIONAL COLLEGE OF TECHNOLOGY |
Principal Investigator |
YOSHIOKI Shuzo Department of Information and Electronic Engineering, YATSUSHIRO NATIONAL COLLEGE OF TECHNOLOGY Professor, 情報電子工学科, 教授 (30132674)
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Project Period (FY) |
1998 – 2000
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Keywords | dynamics of protein / dynamics of water molecule / Eulerian angle / dihedral angle of protein / normal mode analysis / BPTI / thermal vibrating ellipsoid / ORTEP |
Research Abstract |
The main purpose of this study is to theoretically investigate dynamics of a globular protein (bovine pancreatic trypsin inhibitor (BPTI) consisting of 58 amino acid residues) and water molecules surrounding the protein, using the independent molecule model proposed in this study. The independent molecule model is categorized into three models depending on how the water molecules are treated. In a first model (frozen water model), water molecules surrounding the protein are assumed to be frozen and the protein is allowed to move in a cavity surrounded by these waters. In a second model (rigid water model), each water molecule surrounding the protein is treated as a rigid body, but is allowed to move with respect to the vibrating protein. In the last model (flexible water model), each water molecule surrounding the protein IS internally vibrating and undergoing rigid-body motions. The comparison between three water models was done to investigate dynamics of the protein. In addition, interactions between protein and water molecule is investigated only for the flexible water model. In this analysis, the internal and external vibrating frequencies are calculated for the BPTI and 358 water molecules surrounding the protein, and the thermal vibrating ellipsoid of all atoms are estimated. Water molecules hydrogen-bonding to the protein are picked. We have derived information about the relationship between the magnitude of an ellipsoid of an H-bonding atom and the anisotropy of its ellipsoid, and the relationship between the magnitude of the ellipsoid and the H-bond strength. Moreover, we see a relationship between vibrational frequencies assuming rigid-body motion of the water molecules and the H-bond strength of the water taking a part in its H-bonding.
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