NDLI: CLOUDS, a protocol for deriving a molecular proton density via NMR.

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CLOUDS, a protocol for deriving a molecular proton density via NMR.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Grishaev, Alexander Llinás, Miguel
Description	Author Affiliation: Grishaev A ( Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA.);
Abstract	We demonstrate the feasibility of computing realistic spatial proton distributions for proteins in solution from experimental NMR nuclear Overhauser effect data only and with minimal assignments. The method, CLOUDS, relies on precise and abundant interproton distance restraints calculated via a relaxation matrix analysis of sets of experimental nuclear Overhauser effect spectroscopy crosspeaks. The MIDGE protocol was adapted for this purpose. A gas of unassigned, unconnected H atoms is condensed into a structured proton distribution (cloud) via a molecular dynamics simulated-annealing scheme in which the internuclear distances and van der Waals repulsive terms are the only active restraints. Proton densities are generated by combining a large number of such clouds, each computed from a different trajectory. After filtering by reference to the cloud closest to the mean, a minimal dispersion proton density (foc) is identified. The latter affords a quasi-continuous hydrogen-only probability distribution that conveys immediate information on the protein surface topology (grooves, protrusions, potential binding site cavities, etc.), directly related to the molecular structure. Feasibility of the method was tested on NMR data measured on two globular protein domains of low regular secondary structure content, the col 2 domain of human matrix metalloproteinase-2 and the kringle 2 domain of human plasminogen, of 60 and 83 amino acid residues, respectively.
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	10
Volume Number	99
Language	English
Publisher	National Academy of Sciences
Publisher Date	2002-05-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Matrix Metalloproteinase 2 Chemistry Plasminogen Kringles Models, Molecular Nuclear Magnetic Resonance, Biomolecular Protein Structure, Tertiary Protons Research Support, U.S. Gov't, P.H.S. Multidisciplinary
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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