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Eur Biophys J. 2016 May;45(4):341-6. doi: 10.1007/s00249-015-1100-3. Epub 2015 Dec 11.

Vector description of electric and hydrophobic interactions in protein homodimers.

Author information

1
Departament de Medicina Experimental and Institut de Recerca Biomèdica de Lleida, Universitat de Lleida, Lleida, Spain. angel.mozo@mex.udl.cat.
2
Laboratorio de Inmunología, Universidad de la Repuública Regional Norte-Salto, Salto, Uruguay.
3
Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.

Abstract

This article describes the formation of homodimers from their constituting monomers, based on the rules set by a simple model of electric and hydrophobic interactions. These interactions are described in terms of the electric dipole moment (D) and hydrophobic moment vectors (H) of proteins. The distribution of angles formed by the two dipole moments of monomers constituting dimers were analysed, as well as the distribution of angles formed by the two hydrophobic moments. When these distributions were fitted to Gaussian curves, it was found that for biological dimers, the D vectors tend mostly to adopt a perpendicular arrangement with respect to each other, in which the constituting dipoles have the least interaction. A minor population tends towards an antiparallel arrangement implying maximum electric attraction. Also in biological dimers, the H vectors of most monomers tend to interact in such a way that the total hydrophobic moment of the dimer increases with respect to those of the monomers. This shows that hydrophobic moments have a tendency to align. In dimers originating in the crystallisation process, the distribution of angles formed by both hydrophobic and electric dipole moments appeared rather featureless, probably because of unspecific interactions in the crystallisation processes. The model does not describe direct interactions between H and D vectors although the distribution of angles formed by both vectors in dimers was analysed. It was found that in most cases these angles tended to be either small (both moments aligned parallel to each other) or large (antiparallel disposition).

KEYWORDS:

Angle distribution; Electric dipole moment; Hydrophobic moment; Protein assembly; Protein dimer; Protein monomer

PMID:
26658743
DOI:
10.1007/s00249-015-1100-3
[Indexed for MEDLINE]

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