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Structure Determination of a New Protein From Backbone-Centered NMR Data and NMR-Assisted Structure Prediction

By K. L. Mayer, Y. Qu, S. Bansal, P. D. Leblond, F. E. Jenney, P. S. Brereton, M. W. W. Adams, Y. Xu and J. H. Prestegard

Abstract

ABSTRACT Targeting of proteins for structure determination in structural genomic programs often includes the use of threading and fold recognition methods to exclude proteins belonging to well-populated fold families, but such methods can still fail to recognize preexisting folds. The authors illustrate here a method in which limited amounts of structural data are used to improve an initial homology search and the data are subsequently used to produce a structure by data-constrained refinement of an identified structural template. The data used are primarily NMR-based residual dipolar couplings, but they also include additional chemical shift and backbone-nuclear Overhauser effect data. Using this methodology, a backbone structure was efficiently produced for a 10 kDa protein (PF1455) from Pyrococcus furiosus. Its relationship to existing structures and its probable function are discussed. Proteins 2006;65:480–489. VC 2006 Wiley-Liss, Inc. Key words: protein structure prediction; structural genomics; residual dipolar couplings; Pyrococcus furiosus; simulated annealin

Year: 2008
OAI identifier: oai:CiteSeerX.psu:10.1.1.132.8920
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