A multicanonical molecular dynamics study for a model protein-g

M. Isobe; H. Shimizu; Y. Hiwatari

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A multicanonical molecular dynamics study for a model protein-g

机译：模型蛋白-g的多规范分子动力学研究

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We have performed the multicanonical molecular dynamics simulation on a simple model protein-g (PDB id: 2gb1). We have treated the protein-g in terms of a model composing only of charged, hydrophobic, and neutral spherical bead-monomers. Since the hydrophobic interaction is considered to have a large effect on protein folding, we particularly focus on the competition between effects of Coulomb interaction and the hydrophobic interaction. We found that the transition from a random coil to compact state is greatly influenced by both parameters and forms of the hydrophobic potential function.

机译：我们已经对简单模型的蛋白质-g（PDB id：2gb1）进行了多规范分子动力学模拟。我们已经按照仅由带电，疏水和中性球形珠粒单体组成的模型处理了蛋白质-g。由于疏水相互作用被认为对蛋白质折叠有很大影响，因此我们特别关注库仑相互作用与疏水相互作用之间的竞争。我们发现，从随机线圈到致密状态的转变在很大程度上受疏水势函数的参数和形式的影响。

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《Computer physics communications》 |2001年第3期|共4页
作者
M. Isobe; H. Shimizu; Y. Hiwatari;
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正文语种 eng
中图分类计算机的应用;
关键词
multicanonical molecular dynamics simulation; protein folding; solvent effect; Coulomb interaction; hydrophobic interaction;

机译：多规范分子动力学模拟;蛋白质折叠;溶剂作用;库仑相互作用;疏水相互作用;

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1. A multicanonical molecular dynamics study for a model protein-g [J] . M. Isobe, H. Shimizu, Y. Hiwatari Computer physics communications . 2001,第1a3期

机译：模型蛋白-g的多规范分子动力学研究
2. Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations [J] . Ishitani R, Terada T, Shimizu K Molecular simulation . 2008,第3期

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6. Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor. [O] . J. Guenot, P. A. Kollman 1992

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7. A Multicanonical Molecular Dynamics Study on a Simple Bead-Spring Model for Protein Folding [O] . Isobe, Masaharu, Shimizu, Hisashi, Hiwatari, Yasuaki 2001

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A multicanonical molecular dynamics study for a model protein-g

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