Molecular dynamics simulation of a Zif268-DNA complex in water. Spatial patterns and fluctuations sensed from a nanosecond trajectory

Article Abstract:

A nanosecond-long molecular dynamics simulation of a fully charged protein-DNA system (Zif268-DNA) in water revealed that the complex can be simulated with a general force field when the solvation and counterion effects are correctly represented. The full complex, the protein and the 12-base consensus sequence were found to have a root-mean-square deviations (rmsd) of 2, 1.95 and 1.35 angstroms, respectively, while the counterions exhibited an rmsd of 1.2 angstroms. The fluctuation of the rmds correlated with temperature factors for the protein and DNA.

DNA, Molecular dynamics, Solvation, Complex compounds, Coordination compounds

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Amino acid residues at protein-protein interfaces: why is propensity so different from relative abundance?

Article Abstract:

Polar residues have the highest propensity to be at the protein-protein interfaces. The thermodynamic factor, which compensates for the hydration hindrance of the polar residues that takes place upon protein-protein association, is studied.

Science & research, Thermal properties, Chemistry, Physical and theoretical, Physical chemistry, Amino acids, Structure, Chemical properties

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