蛋白�?-リガンドの接近過程に伴う溶媒双極子場

Chem-Bio Informatics Journal

三友 大輔¹  浜崎 伸展¹  園部 裕樹¹  肥後 順一¹  伊東 純一¹  宮川 博夫²  池部 仁善¹  梅沢 公二¹  八木�? 良介¹  山岸 明彦¹  高野 憲和¹ 

[1]東京薬科大学生命科学部

[2]大正製薬株式会社

关键词: Hydration;    水和;    Molecular binding;    分子結合;    Molecular recognition;    分子認識;    Molecular interaction;    分子間相互作用;    Molecular dynamics simulation;    分子動力学シミュレーション;   

DOI  :  10.1273/cbij.8.14

学科分类：生物化学/生物物理

来源: Chem-Bio Informatics Society

【 摘 要 】

References(25)Cited-By(3)We did a molecular dynamics simulation of a system consisting of a peptide and a protein in explicit solvent to study biomolecular approach process.In the initial structure of simulation, the minimum inter-biomolecular distance was 30 Å.During the simulation, the biomolecules approached and contacted to each other.In spite of diffusive motions of water molecules, the orientations of water molecules tended to order in the inter-biomolecular zone showing coherent spatial patterns (solvent site-dipole field) of the ordering.The degree of ordering was synchronized well with the inter-biomolecular distance.This result strongly suggests that the biomolecules distant to each other can interact via the solvent site-dipole field.The effective range for the coherent ordering (i.e., the interaction range via the solvent site-dipole field) was larger than 20 Å.A bridge-like structure of the solvent orientational ordering connected the two biomolecules.Biological and physicochemical significance of the ordering is discussed.

【 授权许可】

Unknown