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Protein under pressure: Molecular dynamics simulation of the arc repressor
Author(s) -
Trzesniak Daniel,
Lins Roberto D.,
van Gunsteren Wilfred F.
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21034
Subject(s) - dimer , intramolecular force , intermolecular force , molecular dynamics , monomer , hydrogen bond , chemistry , crystallography , repressor , dissociation (chemistry) , molten globule , chemical physics , biophysics , computational chemistry , stereochemistry , molecule , biochemistry , polymer , organic chemistry , circular dichroism , gene , biology , transcription factor
Experimental nuclear magnetic resonance results for the Arc Repressor have shown that this dimeric protein dissociates into a molten globule at high pressure. This structural change is accompanied by a modification of the hydrogen‐bonding pattern of the intermolecular β‐sheet: it changes its character from intermolecular to intramolecular with respect to the two monomers. Molecular dynamics simulations of the Arc Repressor, as a monomer and a dimer, at elevated pressure have been performed with the aim to study this hypothesis and to identify the major structural and dynamical changes of the protein under such conditions. The monomer appears less stable than the dimer. However, the complete dissociation has not been seen because of the long timescale needed to observe this phenomenon. In fact, the protein structure altered very little when increasing the pressure. It became slightly compressed and the dynamics of the side‐chains and the unfolding process slowed down. Increasing both, temperature and pressure, a tendency of conversion of intermolecular into intramolecular hydrogen bonds in the β‐sheet region has been detected, supporting the mentioned hypothesis. Also, the onset of denaturation of the separated chains was observed. Proteins 2006. © 2006 Wiley‐Liss, Inc.