Computer simulation study on protein structure using molecular dynamics and Monte Carlo method = 분자동력학 및 몬테카를로 방법에 의한 단백질 구조에 관한 전산 모의실험 연구

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Chapter 1. Computer Simulation is useful tool investigating the physical properties of various molecular systems, including biomolecules, polymers, organic molecules, and materials, which are very difficult to approach by experiment. We will summarize the fundamentals on Molecular Dynamics and Monte Carlo Procedure, main part of the molecular simulation. Chapter 2. We have performed NPT molecular dynamics simulations (Langevin Piston Method) on two type of solvated proteins - "denaturation-unfavorable" protein (insulin) and "denaturation-favorable protein" (ribonuclease A) at high pressure (from 1 bar up to 20 kbar). The method is based on the extended system formalism introduced by Andersen, where the deterministic equations of motion for the piston degree of freedom are replaced by Langevin equation. We report the structural changes of proteins (ribonuclease A and insulin) and water molecules through radius of gyration, solvent accessible surface area, hydrogen bond pattern, and the topology of water clusters connected by the hydrogen bonded circular network. The solvent accessibility of ribonuclease A are mainly decreased by hydrophilic residues rather than hydrophobic residues under high pressure. From the results of hydrogen bond analysis, we have found that α-helix is more stable than β-sheet under high pressure. In addition, from the analysis of the water cluster, we have observed that for ribonuclease A, 5-membered ring structure is more favorable than 6-membered ring as higher pressure. However, for insulin, the ratio of 5 to 6-ring is constant over the pressure ranges, for which we have performed MD simulation. This indicates that the water structure around insulin does not change under high pressure Chapter 3. A new Monte Carlo sampling scheme, namely the Modified Valley Restrained Monte Carlo procedure, is used to obtain the global energy minimum conformations for polypeptides, such as Met-enkephalin and Melittin. For each peptide, we found close ag...
Jung, Kyung-Hoon정경훈
한국과학기술원 : 화학과,
Issue Date
157935/325007 / 000955382

학위논문(박사) - 한국과학기술원 : 화학과, 2000.2, [ vii, 96 p. ]


Valley function; Optimization; Protein; Monte Carlo; Water ring; Denaturation; High pressure; Molecular dynamics; Simulation; Sampling; 추출; 골함수; 최적화; 단백질; 몬테 카를로; 변성화; 모의실험; 분자동력학; 고압; 물 구조

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