High resolution NMR has become an important tool for the determination of solution structutes of proteins and nucleic acids. The principal goals of this project are the development of algorithms and computer codes that allow one to make the best use of NMR data in determining solution structures of biomolecules, and to assess in a systematic fashion the accuracy and precision of the resulting structures. This will involve the following components: Better modelling of macromolecular spin relaxation; studies on protein and nucleic acid dynamics. A major effort will involve the development and testing of improved models for calculating NOESY intensities, based on phenomenological models for molecular motion and disorder, including a new quasi-harmonic approach. These models will be tested by comparisons with experimental data and with aqueous molecular dynamics simulations on myoglobin, plastocyanin, and a B-form DNA duplex. Improved methods for obtaining initial structures. We have developed methods for improving distance bounds through systematic searches of the conformational space of peptide fragments. We plan to extend and automate these methods into a robust method for checking input data and generating initial structures. Predictions of conformation-dependent chemical shifts. Chemical shift dispersion in folded macromolecules can potentially offer useful structural information. We plan to develop a semi-empirical treatment for the non-exchangeable protons in nucleic acids, and to carry out ab initio quantum chemistry calculations to calibrate ring-current intensity factors and magnetic susceptibility anisotropies for peptide groups and sugars. These results will be used to develop a refined structures for soybean leghemoglobin. Applications to important biological macromolecules. These will include: (a) studies of conformational heterogeneity and disorder in plastocyanin and thioredoxin (b) a chemical shift-based refinement of the solution structure of soybean leghemoglobin; (c) studies of the B-form DNA duplex d(GCGTTAACGC)2 and of complexes of calicheamicin, duocarmycin and SN6999 with DNA; (d) solution structures of TFIIA and LEF-1 DNA binding domains and their complexes with DNA.
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