Rotation of structural water inside a protein: calculation of the rate and vibrational entropy of activation

Article Abstract:

The rotation of a water molecule buried inside a protein bovine pancreatic trypsin inhibitor (BPTI) was examined. Reaction path calculations using conjugate peak refinement were employed to compute the transition state and activation energy for the rotation in both BPTI and ice. The behavior of the structural water, which results to the interchange of two water hydrogens, was found to be similar in both ice and BPTI. The complex process involves two successive rotations around the orthogonal axes.

Water, Proteins, Vibrational spectra

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Temperature effects on protein motions: a molecular dynamics study of RNase-Sa

Article Abstract:

The dynamics of the enzyme ribonuclease-Sa as a function of temperature is explored through a series of molecular dynamics simulations. The enzyme is preorganized dynamically, regions with low plasticity confer specificity while the more flexible regions have the fluidity to facilitate energetically inexpensive conformational rearrangements such as those required to achieve the transition state.

Thermal properties, Ribonuclease

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Evolution of rate-promoting oscillations in a model enzyme

Article Abstract:

The evolutionary scheme coupled to approximate normal-mode analysis to explore the means by which catalytic fitness is increased is presented. Results reveal that the number and distribution of loose, intermediate, and stiff domains in the body of an enzyme molecule can govern fluctuation patterns leading to increased catalytic fitness.

Oscillation, Oscillations, Chemical properties

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