The general fold of a polypeptide chain appears to be largely controlled by the interior residues, those that do not contact the solvent. packing of the side chains in the sense of a three dimensional jigsaw puzzle is thought to play a major role in fine adjustmentS of the chain conformation. packing effects are exquisitely sensitive to packing density, and thus to cavity distribution within the protein. The focus of this aspect of the work during this grant period will be to obtain a useful measure of residue shape and establish the importance of """"""""fit"""""""" in the folding process. Strangely enough the answer is not obvious. The second focus of the work will be on the surface of the protein, the region immediately involved in biological function. It is our intent to try to develop a general chemical labeling procedure for identifying the solvent accessible surface of a protein at the level of individual residues. The changes in the surface during protein folding, during oligomerization reactions, or during ligand binding reflect most of the biological functions under study in molecular biology. Since at least 50% of this surface is normally saturated hydrocarbons the most reactive chemical species are required to label it at all. We will try methylene. The analytical technique for identifying labeled areas will be mass spectroscopy. The most appropriate technique for sequencing the labeled samples will be established. The procedures will be validated on proteins of known structures starting with ribonuclease-S and thiroedoxin. The method will then be applied to the association and structure of the transmembrane helices in several systems, and to the higher order structures of delta-gamma resolvase in collaboration with the laboratories of D.M. Engelman, T.A. Steitz, and N. Grindley. These latter problems are beyond the reach of X-ray or NMR procedures at this time.
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