One of the major aims of this research is the understanding of the folding and stabilizing thermodynamics of native proteins, which is now studied predominantly by site-directed mutagenesis. Methods of determining protein stability (free energy) depend on melting and extrapolation procedures which are still not adequately understood. We have worked on this problem for some time, and this proposal suggests methods for further advances. One of the techniques used in stability studies is circular dichroism (CD). CD measurements are more in use now than ever before, because of the intense interest in the protein folding problem, yet most of the theoretical advances in protein CD were accomplished in the 1960's. In our view the past 20 years of improved computational methods and experience in calculating the electronic structure of molecules has provided a basis for the reinvestigation of some of the unsolved problems of that previous era. In particular the results for the n-pi* transition provide new input into the interpretation of the CD of proteins, especially random regions of the polypeptide chain, which resisted earlier explanation. The project also has a DNA component. We will do Monte Carlo calculations generating DNA molecules and averaging their persistence, moments of the end to end distance, and optical tensors. The results should provide a basis for the interpretation of the flexibility and optical properties of restriction length DNA segments. The results should be useful in studies of DNA curvature, flexibility and in the interpretation of certain aspects of pulsed gel electrophoresis. Finally there is no adequate theory of the circular dichroism of DNA in its liquid crystalline form. In fact there is no theory of the optical properties of liquid crystals in absorbing regions of the spectrum. We will apply known procedures to solve this problem.
Showing the most recent 10 out of 22 publications
