The overall objective of this project is to improve the methods of analysis and broaden the applications of optical spectroscopy, especially circular dichroism (CD), to the study of proteins and nucleic acids. There has been a major resurgence of interest in CD in recent years because of its value in monitoring protein folding, in secondary structural analysis of proteins, in characterizing mutant proteins, in following conformational transitions in DNA and RNA, and in measuring protein-protein and protein-nucleic acid equilibria and kinetics. During the next five years, the project will concentrate on four major areas: (1) intrinsic CD of proteins, i.e. backbone and side-chain contributions; (2) extrinsic CD of proteins due to protein-ligand interactions; (3) electronic structure of the nucleic acid bases and the CD of oligonucleotides; (4) experimental studies of proteins involved in transcription and its regulation. In the first area, the basic theoretical model used in calculating the CD of polypeptides will be extended to include high-energy transitions, static-field effects, and interpeptide charge transfer. The extended version of the DeVoe or classical polarizability model will be applied more extensively to provide more satisfactory band shapes. Calculations of the contributions of specific aromatic side chains will be performed and the results compared to those from site-directed mutagenesis. Combined CD-molecular dynamics (MD) calculations will be performed on model polypeptides and small proteins. With respect to the second area, the CD of heme transitions will be calculated for high-resolution X-ray-derived structures of many proteins, and for MD trajectories for carbonmonoxymyoglobin heme isomers. Our work on interpreting static-field effects on the electronic structure of the nucleic acid bases will be extended to nucleotides and base pairs. In addition, the CD of oligonucleotides for which NMR structures have been determined will be calculated and compared with experiment. The conformation of the C-terminal domain of the large subunit of eukaryotic RNA polymerase II, which consists of a long sequence of a repeating heptapeptides, will be investigated. The Tax protein of human type I leukemia virus and its interactions with basic-leucine zipper proteins, as well as basic helix-loop-helix proteins, will be studied by CD and fluorescence.
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