The role of the denatured state in protein stability is studied by theoretical methods based on molecular dynamics simulations. The results show that the free energy differences depend significantly on the denatured-state structures in the case of thermal denaturation. By modeling the denatured-state structures in various denaturation conditions, more quantitative analyses of protein stability and folding will be possible.
We have developed a new methodology for predicting tertiary structure of protein in solvent from the first principles, which combines the RISM theory for incorporating the solvent effects and a powerful method for sampling the structure space of protein. Roles of water in stabilizing protein structure and alcohol effects have been analyzed, and subjects to be treated in further studies have been discussed.
Hydrogen bonding plays an essential role in maintaining the structures and thus the functions of biological macromolecules, such as nucleic acids and proteins. Recently, scalar nuclear spin couplings (J couplings) across hydrogen bonds have been observed for various hydrogen bond pairs, such as N-H…N in nucleic acids and N-H…O=C in proteins. The coupling values range from 0.8 to 10Hz, depending on the systems and the interacting nuclei. As scalar couplings are known to be dominated by the Fermi contact term, these values can, in principle, be correlated to the nature of the hydrogen bonds.
A differential response generated from a retinal protein, bacteriorhodopsin, at the electrode/electrolyte interface in an electrochemical cell was found to be a capacitive current caused by a potential change on the electrode that responds to a pH change arising from proton release and uptake during illumination of bacteriorhodopsin. The molecular mechanism for the proton-pumping of bacteriorhodopsin was rationalized by comparing capacitive currents of several mutant proteins that had been displaced the key amino acids for proton transfer. An extended study based on this method revealed that the other retinal proteins, halorhodopsin and phoborhodopsin, are also able to release and uptake protons under certain conditions.