Can the Structure of the Hydrophobic Core Determine the Complexation Site? - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 39

Chapter 3
Can the Structure of the Hydrophobic
Core Determine the Complexation Site?

Mateusz Banach , Leszek Konieczny, and Irena Roterman-Konieczna

Keywords Hydrophobic core ￿ Oil drop ￿ Tertiary structure stabilization ￿ Fuzzy oil
drop ￿ Effective atom ￿ Gauss function ￿ Pair-wise interaction ￿ Theoretical hydro-
phobicity distribution ￿ Observed hydrophobicity distribution ￿ Idealized hydropho-
bicity distribution ￿ Empirical hydrophobicity distribution ￿ Hydrophobicity de fi ciency
￿ Hydrophobicity excess ￿ Kullback-Leibler entropy ￿ Divergence entropy ￿ Random
distribution ￿ Structural discordance ￿ Downhill proteins ￿ Antifreeze proteins
￿ Fast-folding proteins

3.1 Introduction

Stabilization of the tertiary protein structure is most often attributed to hydropho-
bic 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.

M. Banach ￿ L. Konieczny ￿ I. Roterman-Konieczna ( * )
Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College,
Lazarza 16 , 31-530 Cracow , Poland
e-mail: [e-mail]
Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University,
Reymonta 4 , 30-059 Cracow , Poland