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PMID: 8994627 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Construction of hydrodynamic bead models from high-resolution X-ray crystallographic or nuclear magnetic resonance data.

Biophysical journal ·Vol. 72 ·No. 1 ·1997-01-00 ·Pages 408-15

Byron O

Abstract

Computer software such as HYDRO, based upon a comprehensive body of theoretical work, permits the hydrodynamic modeling of macromolecules in solution, which are represented to the computer interface as an assembly of spheres. The uniqueness of any satisfactory resultant model is optimized by incorporating into the modeling procedure the maximal possible number of criteria to which the bead model must conform. An algorithm (AtoB, for atoms to beads) that permits the direct construction of bead models from high resolution x-ray crystallographic or nuclear magnetic resonance data has now been formulated and tested. Models so generated then act as informed starting estimates for the subsequent iterative modeling procedure, thereby hastening the convergence to reasonable representations of solution conformation. Successful application of this algorithm to several proteins shows that predictions of hydrodynamic parameters, including those concerning solvation, can be confirmed.

MeSH Terms

Algorithms Animals Apoferritins/chemistry Computer Simulation Crystallography, X-Ray/methods Drosophila/enzymology Fructose-Bisphosphate Aldolase/chemistry Macromolecular Substances Magnetic Resonance Spectroscopy/methods Models, Structural Protein Conformation Protein Structure, Secondary Proteins/chemistry Reproducibility of Results Software

Chemicals

Macromolecular Substances Proteins Apoferritins Fructose-Bisphosphate Aldolase

Authors & Affiliations

1 authors, click to expand affiliations / ORCID

Byron O

Department of Biochemistry, University of Leicester, United Kingdom. obl@le.ac.uk

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24 references, click to expand

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Article Info

Journal

Biophysical journal

Abbr.

Biophys J

ISSN

0006-3495

DOI

10.1016/S0006-3495(97)78681-8

obl@le.ac.uk

Published

1997-01-00

Pages

408-15

Language

English

Region

United States

NLM ID

0370626

PMCID

PMC1184331

Subset

External Links

PubMed source DOI: 10.1016/S0006-3495(97)78681-8 PMC Full Text View journal details

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Construction of hydrodynamic bead models from high-resolution X-ray crystallographic or nuclear magnetic resonance data.

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