NEW METHODS OF BIOMOLECULAR STRUCTURE DETERMINATION

Hauptman-Woodward Medical Research Inst, Buffalo NY

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Abstract

X-ray diffraction or crystallography, with its unique ability to reveal the atomic or near-atomic structures of a wide range of biomedically important molecules, is the cornerstone of modern structural biology. As a resent of recent genome studies, there is now a need for efficient X-ray crystallographic analysis of hundreds of new proteins. This project addresses one of the critical steps in crystallography, the solution of the so-called 'phase problem.' Previous work within this project has resulted in the development of a powerful-direct methods algorithm, known as Shake-and-Bake, and a computer program, SnB, that can resolve the phase problem for structures with as many as 1300 unique non-hydrogen atoms. The selenium substructures of much larger proteins containing as many as 80 methionine residues can also be solved provided that these residues have been replaced by selenomethionine. The substructure can then be used as a bootstrap to locate the remainder of the protein molecule. The overall goal now is to extend the power and scope of the Shake-and- Bake algorithm. The ability of SnB to solve very large selenomethionine substructures (>100 Se sites) will be enhanced by the addition of a masking function to permit use of prior information concerning the molecular envelope or restrictions provided by non-crystallographic symmetry. Strategies will be devised for utilizing information from reference-beam diffraction to facilitate successful lower-resolution applications. Practical direct-methods algorithms will be developed for getting the most from diffraction data from one derivative (SIR) or for one wavelength with anomalous scattering (SAS). Concepts and routines from the PHASES program package will be used to integrate direct methods with other information and techniques commonly used in protein crystallography and to create pathway for the automated production of interpretable protein electron-density maps. Finally, the SnB website, http://www.hwi.buffalo.edu/SnB/, will be maintained for program dissemination and user education.