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제116회 대한화학회 학술발표회, 총회 및 기기전시회 안내 The Study of Context-Dependent Protein Hydrophobicity Based on Site-Directed Thermodynamic Analysis

2015년 8월 27일 16시 49분 59초
PHYS.P-266 이곳을 클릭하시면 발표코드에 대한 설명을 보실 수 있습니다.
10월 16일 (금요일) 13:00~14:30
저자 및
정종영, 함시현1,*
숙명여자대학교 화학과 나노바이오전산화학연구실, Korea
1숙명여자대학교 화학과, Korea
Hydrophobicity of a protein is one of the major factors controlling protein folding and protein-protein interaction. Conventionally, the protein hydrophobicity is estimated based on the summation of constituting amino acid hydrophobicity scales determined as an individual free amino acid, assuming that those scales are maintained in a protein-context. Here, we challenge this assumption by applying fluctuating thermodynamic framework for elucidating protein context-dependent hydrophobicity. We considered the following three globular protein systems with the distinct secondary structures, i.e. villin headpiece subdomain (HP35), WW domain, and B domain of protein A (BdpA). For those protein systems, the extensive atomistic MD simulations and the solvation free energy analysis were performed followed by the site-directed thermodynamic analysis to investigate the context-dependent hydrophobicity of constituting amino acids. We compared the hydrophobicity of a free amino acid, quantified by the free energy change upon hydration, with the residual hydrophobicity, quantified by the hydration free energy of a residue embedded in the protein context. We find that the residual hydrophobicity is significantly altered from the hydrophobicity of a free amino acid due to the protein structural effects such as secondary structure formation, salt-bridge formation and hydrophobic-core formation. Our results thus provide a new comprehension on the context-dependence of amino acid hydrophobicity, which will contribute to understanding how the hydrophobicity drives protein folding and protein-protein binding.