ANALYSIS AND DESIGN OF PROTEIN STRUCTURES

Duke University, Durham NC

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Abstract

The broad, long-range objective of this work is to contribute to the fundamental understanding and eventual control of 3-dimensional protein structure and folding. We approach this problem by study of the known 3-D protein structures; by the design, production, characterization, and redesign of new model proteins; and by the development of new methods. On the experimental side, we are presently working on core redesigns of thioredoxin and of ROP protein. As a result of conclusions from our previous protein design work, our major theoretical emphasis now is on understanding the determinants of uniqueness in 3-D structures, including the likely role of sidechain packing. Recently we have had a breakthrough in methodology that allows us both to visualize and to quantitate very fine details of molecular interaction; this change resulted from a synergy between a recognition of the importance of hydrogens, the developed flexibility of our own computer programs, and especially the recent increase in availability of extremely high-resolution protein structures. We have constructed a carefully validated database of 100 structures at 1.7 Angstrom units or better, with all explicit H atoms added and optimized, which is available on our Web site at http://kinemage.biochem-duke.edu. Those accurate structures are analyzed with "small-probe contact dots", which leave a patch of dot surface wherever two atoms are within 0.5 Angstrom units of touching one another. The contact dots are amazingly sensitive to fine details or to any problems, but they demonstrate directly the great accuracy of recent high-resolution structures. We have used them so far to analyze conformational features, such as preferred sidechain conformations, and to guide our protein design work. It is also highly promising that this technique will be able to help significantly in the crystallographic refinement process.