PROTEIN STRUCTURE VIA QUANTUM CHEMISTRY AND NMR

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The broad, long term objective of this research is to develop new ways of predicting, refining and validating protein structures, both in solution, in membranes, and in the crystalline solid state. The health relatedness is that detailed knowledge of protein structure should lead to new ways of investigating function, such as peptide - calmodulin interactions, interleukin-receptor interactions, and protein-inhibitor interactions. In this work, we will develop use of the nuclear magnetic resonance (NMR) chemical shift of primarily 13C and 15N nuclei in proteins as novel probes of structure. In particular, we will compute the Ramachandran shielding surfaces for many heavy atoms in the naturally occurring amino-acids, then use these shielding surfaces to predict and refine structure using a Z- surface approach, and back calculation. The use of chemical shifts as structural restraints has recently been made possible by using quantum chemical methods on high performance workstations. The shielding surfaces we develop will be made available to other groups, and will enable incorporation of many hundreds - perhaps up to approx. 1000 heavy atom chemical shift restraints into protein structure determinations. The effects of molecular motion on observed chemical shifts will be investigated by using molecular dynamics shielding trajectories, combined with shielding surfaces and bond length and bond angle shielding derivatives. Information on which force fields in energy minimization/molecular dynamics best describe protein structure will be obtained from the work proposed. Initial proteins to be investigated include the cytokines interleukin-1beta and interleukin-8, ubiquitin, as well as calmodulin and calmodulin-peptide complexes. Suitable data files for refinement will be obtained from A. Gronenborn, G.M. Clore and J. Wand. This work will provide a unique approach to the refinement and determination of protein structure, will be applicable to both solution, membrane and crystalline solid-state structure analysis, and should thus be of great interest to many groups working on protein structure refinement/determination using x-ray diffraction, nuclear magnetic resonance spectroscopy, as well as computational chemistry.