ABSTRACT
The determination of the conformational preferences in unfolded states of proteins constitutes an important challenge in structural biology. We use inter-residue distances estimated from site-directed spin-labeling NMR experimental measurements as ensemble-averaged restraints in all-atom molecular dynamics simulations to characterise the residual structure of the Delta131Delta fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that Delta131Delta under these conditions shows a tendency to form transiently hydrophobic clusters similar to those present in the native state of wild-type staphylococcal nuclease. Only rarely, however, all these interactions are simultaneously realized to generate conformations with an overall native topology.
Subject(s)
Micrococcal Nuclease/chemistry , Peptide Fragments/chemistry , Protein Folding , Computer Simulation , Hydrophobic and Hydrophilic Interactions , Monte Carlo Method , Nuclear Magnetic Resonance, Biomolecular , Protein Denaturation , Protein Structure, SecondaryABSTRACT
The kinetics of the racemization of 2-benzoylcyclohexanone 1 in hexanes, ethanol, and mixtures thereof have been investigated by time dependence of enantiomeric purity using enantioselective HPLC. In pure hexanes and ethanol, the racemization half-lives were determined as 552 and 23.8 min, respectively, at 66 degrees C. Surprisingly, racemization of 1 in mixtures of hexanes and ethanol was found to involve an induction period followed by a sigmoidal decrease of the enantiomeric excess with half-lives varying between 11.5 and 24.0 min. This unexpected solvent influence on the rate of racemization of 1 was attributed to complex isomerization mechanisms involving three possibly interconverting enol tautomers of 1.
