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Protein thermal stabilization by charged compatible solutes: Computational studies in rubredoxin from Desulfovibrio gigas
Author(s) -
Micaelo Nuno M.,
Victor Bruno L.,
Soares Cláudio M.
Publication year - 2008
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.21948
Subject(s) - rubredoxin , chemistry , aqueous solution , desulfovibrio , desulfovibrio vulgaris , molecular dynamics , molecule , salt (chemistry) , hydrogen bond , thermodynamics , crystallography , computational chemistry , physics , biology , organic chemistry , bacteria , sulfate , genetics
Molecular dynamics simulation studies of rubredoxin from Desulfovibrio gigas (RDG) were used to characterize the molecular mechanism of thermal stabilization by the compatible solute (CS) diglycerol‐phospate (DGP). DGP is a negatively charged CS that accumulates under salt stress in Archaeoglobus fulgidus . Experimental results show that a 100 m M DGP solution exerts a strong protection effect in the half‐life of RDG at 363 K (Lamosa et al ., Appl Environ Microbiol 2000;66:1974–1979). RDG was simulated in four aqueous solutions at 300 and 363 K: pure aqueous media, 100 m M DGP, 100 m M NaCl, and 500 m M DGP. Our work shows that the 100 m M DGP solution is able to maintain the average protein structure when the temperature is increased, preventing the occurrence of large‐scale deviation of a mobile loop involved in the first steps of RDG unfolding. The molecular mechanism of thermal denaturation protection by DGP seems to involve the direct interaction between the protein and the CS by hydrogen bond interactions near the mobile loop. Several clusters of DGP molecules are formed and preferentially localized at neutral electrostatic regions of the surface. The increase of DGP concentration to 500 m M did not yield better stabilization of the protein suggesting that the thermal protective role of this charged CS is achieved at low concentrations, as shown experimentally. Proteins 2008. © 2008 Wiley‐Liss, Inc.