Using a charging coordinate in studies of ionization induced partial unfolding

Article Abstract:

Charge induced structural changes are studied by a new approach by observing the [pK.sub.a] of the Val66Glu mutant of staphylococcal nuclease. It is shown that standard free energy perturbation (FEP) approaches give extremely disappointing results while the new approach gives realistic results and the reduced [pK.sub.a] reflects the protein structural change and water penetration process and the barrier for partial unfolding cannot be surmounted by the regular FEP approach.

Staphylococcus

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Conformational averaging in pK calculations: Improvement and limitations in prediction of ionization properties of proteins

Article Abstract:

The combination of molecular dynamics simulation and a continuum electrostatic model is used to calculate the pK values of individual titratable groups in one structure of Bacillus circulans xylanase and two structures of Bacillus agaradhaerens xylanese. The influence of the structure and the simulation length are investigated.

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Magnetic effects of disulfide bridges: A density functional and semiempirical study

Article Abstract:

A study is conducted to investigate the magnetic effects of disulfide bridges on surrounding protons. It is shown that for distances commonly sampled in protein structures, the effect of disulfide on neighboring protons is sizable.

Usage, Sulfides, Density functionals, Density functional theory, Chemical properties

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