Can the Structure of the Hydrophobic Core Determine the Complexation Site?
- 993 Downloads
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.
KeywordsHydrophobic 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
- Nalewajski RF (2006) Information theory of molecular systems. Elsevier, Amsterdam. ISBN 978-0-444-51966-5Google Scholar
- Prymula K, Piwowar M, Kochanczyk M, Flis L, Malawski M, Szepieniec T, Evangelista G, Minervini G, Polticelli F, Wiśniowski Z, Sałapa K, Matczyńska E, Roterman I (2009) In silico structural study of random amino acid sequence proteins not present in nature. Chem Biodivers 6(12):2311–2336PubMedCrossRefGoogle Scholar
- Sakamoto K, Bu G, Chen S, Takei Y, Hibi K, Kodera Y, McCormick LM, NakaoA NM, Muramatsu T, Kadomatsu K (2011) Premature ligand-receptor interaction during biosynthesis limits the production of growth factor midkine and its receptor LDL receptor-related protein 1. J Biol Chem 286(10):8405–8413PubMedCrossRefGoogle Scholar