Exploring the role of the solvent in the denaturation of a protein: a molecular dynamics study of the DNA binding domain of the 434 repressor

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Department of Biochemistry and Molecular Pharmacology

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Amino Acid Sequence; Binding Sites; Chemistry, Physical; Computer Simulation; DNA; Hydrogen Bonding; Magnetic Resonance Spectroscopy; Models, Molecular; Molecular Sequence Data; Physicochemical Phenomena; *Protein Denaturation; Protein Folding; Repressor Proteins; *Solvents; Viral Proteins


Biochemistry, Biophysics, and Structural Biology | Pharmacology, Toxicology and Environmental Health


Molecular dynamics simulations of the DNA binding domain of 434 repressor are presented which aim at unraveling the role of solvent in protein denaturation. Four altered solvent models, each mimicking various possible aspects of the addition of a denaturant to the aqueous solvent, were used in the simulations to analyze their effects on the stability of the protein. The solvent was altered by selectively changing the Coulombic interaction between water and protein atoms and between different water molecules. The use of a modified solvent model has the advantage of mimicking the presence of denaturant without having denaturant molecules present in the simulation, which would require much longer simulations. In these simulations, only an increase in the solvent-protein Coulombic interaction causes initiation of protein unfolding in a manner consistent with NMR data. The altered solvent thus provides a model of a denaturing environment for studying protein unfolding.


Biochemistry. 1995 Nov 21;34(46):15057-67.

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