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Can the Structure of the Hydrophobic Core Determine the Complexation Site?

Chapter
Part of the Focus on Structural Biology book series (FOSB, volume 8)

Abstract

Stabilization of the tertiary protein structure is most often attributed to hydrophobic interactions, although this type of interaction is not specifically reflected in protein force fields. Initial attempts to extend the analysis of traditional nonbinding interactions with factors representing hydrophobic interactions (Levitt 1976) were not particularly successful, even though the influence of the aqueous environment on molecular dynamics cannot be underestimated in respect to experimental observations.

Keywords

Hydrophobic core Oil drop Tertiary structure stabilization Fuzzy oil drop Effective atom Gauss function Pair-wise interaction Theoretical hydrophobicity distribution Observed hydrophobicity distribution Idealized hydrophobicity distribution Empirical hydrophobicity distribution Hydrophobicity deficiency Hydrophobicity excess Kullback–Leibler entropy Divergence entropy Random distribution Structural discordance Downhill proteins Antifreeze proteins Fast-folding proteins 

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Department of Bioinformatics and TelemedicineJagiellonian University – Medical CollegeCracowPoland
  2. 2.Faculty of Physics, Astronomy and Applied Computer ScienceJagiellonian UniversityCracowPoland

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