Dynamic structure of subtilisin-eglin c complex studied by normal mode analysis.
Normal mode analysis of subtilisin-eglin c complex was performed to investigate the dynamics at the interface between the enzyme and the inhibitor. The internal motions of the complex calculated from the normal modes were divided into three parts: the internal motions changing the shape of each molecule, the external rigid-body motions changing their mutual dispositions, and the coupling between the internal and external motions. From the results of the analysis, the following characteristic features were found in the dynamics at the interface regions: 1) negative correlation between the internal and external motions within each molecule, and 2) positive correlation between the external motions of the two molecules. The former decreases the apparent amplitudes of motions at the interface. The latter minimizes the interference between individual motions of the two molecules. These dynamic characteristics allow the enzyme and the inhibitor to move as freely as possible. This finding suggests that the experimental evidence of the large entropy gain on binding should be attributed not only to strong hydrophobic interactions, but also to the dynamic structure of the complex, which is found to minimize an unavoidable loss of the conformational entropy on binding.
Department of Chemistry, Graduate School of Science, Kyoto University, Japan.
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H
Ishida
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Jochi
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A
Kidera
D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins; D015843:Serpins / Q000737:chemistry* / Q000378:metabolism; D013381:Subtilisins / Q000737:chemistry* / Q000378:metabolism
D011506:Proteins; D015843:Serpins; C028656:eglin proteinase inhibitors; D013381:Subtilisins