Proceeding of EDISON Challenge (EDISON SW 활용 경진대회 논문집)
- 2016.03a
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- Pages.163-166
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- 2016
Protein Context-Dependent Hydrophobicity of Amino Acids in Protein
- Cho, Hanul (Department of Chemistry, Sookmyung Woman's University) ;
- Ham, Sihyun (Department of Chemistry, Sookmyung Woman's University)
- Published : 2016.03.22
Abstract
Hydrophobicity is the key concept to understand the water plays in protein folding, protein aggregation, and protein-protein interaction. Traditionally, the hydrophobicity of protein is defined based on the scales of the hydrophobicity of residue, assuming that the hydrophobicity of free amino acids is maintained. Here, we explore how the hydrophobicity of constituting amino acids in protein rely on the protein context, in particular, on the total charge and secondary structures of a protein. To this end, we calculate and investigate the hydration free energy of three short proteins based on the integral-equation theory of liquids. We find that the hydration free energy of charged amino acids is significantly affected by the protein total charge and exhibits contrasting behavior depending on the protein total charge being positive or negative. We also observe that amino acids in the
Keywords
- Hydration Free Energy;
- B Domain of Protein A;
- Villin Headpiece Subdomain;
- Pin WW Domain;
- Hydrophobicity