Paper Citing NAMD - Abstract
Makowski, Lee; Gore, David; Mandava, Suneeta; Minh, David; Park, Sanghyun; Rodi, Diane J.; Fischetti, Robert F.
X-ray Solution Scattering Studies of the Structural Diversity Intrinsic to Protein Ensembles
BIOPOLYMERS, 95:531-542, AUG 2011
It is becoming increasingly clear that characterization of the protein ensemble-the collection of all conformations of which the protein is capable-will be a critical step in developing a full understanding of the linkage between structure, dynamics, and function. X-ray solution scattering in the small angle (SAXS) and wide-angle (WAXS) regimes represents an important new window to exploring the behavior of ensembles. The characteristics of the ensemble express themselves in X-ray solution scattering data in predictable ways. Here we present an overview of the effect that structural diversity intrinsic to protein ensembles has on scattering data. We then demonstrate the observation of these effects in scattering from four molecular systems; myoglobin; ubiquitin; alcohol dehydrogenase; and HIV protease; and demonstrate the modulation of these ensembles by ligand binding, mutation, and environmental factors. The observations are analyzed quantitatively in terms of the average spatial extent of structural fluctuations occurring within these proteins under different experimental conditions. The insights which these analyses support are discussed in terms of the function of the various proteins. (C) 2011 Wiley Periodicals, Inc. Biopolymers 95: 531-542, 2011.
