Literature DB >> 12463636

Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50.

Steven Hayward1, Richard A Lee.   

Abstract

DynDom is a program that analyses conformational change in proteins for dynamic domains, hinge axes, and hinge-bending regions. Here, a number of improvements and additions are reported which have been implemented in the new version 1.50. The most significant improvement is in the determination of the hinge-bending residues. A new routine also compares quantities relating to the main-chain dihedrals of bending residues with the hinge-bending motion. This version of the program can now be run from the DynDom website at: http://www.sys.uea.ac.uk/dyndom.

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Year:  2002        PMID： 12463636     DOI： 10.1016/s1093-3263(02)00140-7

Source DB:  PubMed          Journal:  J Mol Graph Model        ISSN： 1093-3263            Impact factor:   2.518


  124 in total

1.  Trapping a 96 degrees domain rotation in two distinct conformations by engineered disulfide bridges.

Authors:  Robert Schultz-Heienbrok; Timm Maier; Norbert Sträter
Journal:  Protein Sci       Date:  2004-07       Impact factor: 6.725

2.  Structure and mechanism of the UvrA-UvrB DNA damage sensor.

Authors:  Danaya Pakotiprapha; Martin Samuels; Koning Shen; Johnny H Hu; David Jeruzalmi
Journal:  Nat Struct Mol Biol       Date:  2012-02-05       Impact factor: 15.369

3.  Structure of complement C6 suggests a mechanism for initiation and unidirectional, sequential assembly of membrane attack complex (MAC).

Authors:  Alexander E Aleshin; Ingrid U Schraufstatter; Boguslaw Stec; Laurie A Bankston; Robert C Liddington; Richard G DiScipio
Journal:  J Biol Chem       Date:  2012-01-20       Impact factor: 5.157

4.  Differences in intradomain and interdomain motion confer distinct activation properties to structurally similar Gα proteins.

Authors:  Janice C Jones; Alan M Jones; Brenda R S Temple; Henrik G Dohlman
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-23       Impact factor: 11.205

5.  The effect of end constraints on protein loop kinematics.

Authors:  Steven Hayward; Akio Kitao
Journal:  Biophys J       Date:  2010-05-19       Impact factor: 4.033

6.  Crystal structure of hexokinase KlHxk1 of Kluyveromyces lactis: a molecular basis for understanding the control of yeast hexokinase functions via covalent modification and oligomerization.

Authors:  E Bartholomeus Kuettner; Karina Kettner; Antje Keim; Dmitri I Svergun; Daniela Volke; David Singer; Ralf Hoffmann; Eva-Christina Müller; Albrecht Otto; Thomas M Kriegel; Norbert Sträter
Journal:  J Biol Chem       Date:  2010-10-12       Impact factor: 5.157

7.  Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway.

Authors:  Rob A Schmitz; Andreas Dietl; Melanie Müller; Tom Berben; Huub J M Op den Camp; Thomas R M Barends
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2020-04-28       Impact factor: 1.056

8.  The crystal structure of the ligand-binding module of human TAG-1 suggests a new mode of homophilic interaction.

Authors:  Mario Mörtl; Peter Sonderegger; Kay Diederichs; Wolfram Welte
Journal:  Protein Sci       Date:  2007-08-31       Impact factor: 6.725

9.  Diversification of function in the haloacid dehalogenase enzyme superfamily: The role of the cap domain in hydrolytic phosphoruscarbon bond cleavage.

Authors:  Sushmita D Lahiri; Guofeng Zhang; Debra Dunaway-Mariano; Karen N Allen
Journal:  Bioorg Chem       Date:  2006-10-27       Impact factor: 5.275

10.  Full domain closure of the ligand-binding core of the ionotropic glutamate receptor iGluR5 induced by the high affinity agonist dysiherbaine and the functional antagonist 8,9-dideoxyneodysiherbaine.

Authors:  Karla Frydenvang; L Leanne Lash; Peter Naur; Pekka A Postila; Darryl S Pickering; Caleb M Smith; Michael Gajhede; Makoto Sasaki; Ryuichi Sakai; Olli T Pentikaïnen; Geoffrey T Swanson; Jette S Kastrup
Journal:  J Biol Chem       Date:  2009-03-18       Impact factor: 5.157
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