A comparison of the restrained molecular dynamics and distance geometry methods for determining three‐dimensional structures of proteins on the basis of interproton distances
- 23 March 1987
- journal article
- research article
- Published by Wiley in FEBS Letters
- Vol. 213 (2) , 269-277
- https://doi.org/10.1016/0014-5793(87)81504-1
Abstract
A direct comparison of the metric matrix distance geometry and restrained molecular dynamics methods for determining three-dimensional structures of proteins on the basis of interproton distances is presented using crambin as a model system. It is shown that both methods reproduce the overall features of the secondary and tertiary structure (shape and polypeptide fold). The region of conformational space sampled by the converged structures generated by the two methods is similar in size, and in both cases the converged structures are distributed about mean structures which are closer to the X-ray structure than any of the individual structures. The restrained molecular dynamics structures are superior to those obtained from distance geometry as regards local backbone conformation, side chain positions and non-bonding energies.Keywords
This publication has 13 references indexed in Scilit:
- Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determinationJournal of Molecular Biology, 1986
- Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin.Proceedings of the National Academy of Sciences, 1986
- Structure refinement of oligonucleotides by molecular dynamics with nuclear overhauser effect interproton distance restraints: Application to 5′ d(C-G-T-A-C-G)2Journal of Molecular Biology, 1986
- Calculation of protein conformations by proton-proton distance constraintsJournal of Molecular Biology, 1985
- Solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coliJournal of Molecular Biology, 1985
- A protein structure from nuclear magnetic resonance data: lac Repressor headpieceJournal of Molecular Biology, 1985
- An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solutionJournal of Molecular Biology, 1985
- Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonanceJournal of Molecular Biology, 1983
- CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsJournal of Computational Chemistry, 1983
- DYNAMICS OF PROTEINS: ELEMENTS AND FUNCTIONAnnual Review of Biochemistry, 1983