Literature DB >> 3860838

Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme.

B Brooks, M Karplus.   

Abstract

A method is presented for finding particular normal modes for large molecules such as proteins and nucleic acids. The method is based on an iterative approach that extracts eigenvectors of interest from the full second-derivative matrix. Application of the method to the interdomain (hinge-bending) motion of lysozyme yields a frequency of 3.6 cm-1. This is similar to the value obtained from earlier adiabatic-energy-minimization studies. Analysis of the mode shows that the relaxation associated with the hinge bending is highly delocalized; that is, the dihedral angle and energy changes are distributed over many residues, including some (e.g., Trp-28) that are distant from the cleft and hinge region.

Entities:  

Mesh：

Substances：

Year:  1985        PMID： 3860838      PMCID： PMC390485          DOI： 10.1073/pnas.82.15.4995

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  16 in total

1.  Modified Ritz Method.

Authors:  D H Weinstein
Journal:  Proc Natl Acad Sci U S A       Date:  1934-09       Impact factor: 11.205

Review 2.  The conformation properties of proteins in solution.

Authors:  R J Williams
Journal:  Biol Rev Camb Philos Soc       Date:  1979-11

3.  Internal motions of antibody molecules.

Authors:  J A McCammon; M Karplus
Journal:  Nature       Date:  1977-08-25       Impact factor: 49.962

4.  The Protein Data Bank: a computer-based archival file for macromolecular structures.

Authors:  F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal:  J Mol Biol       Date:  1977-05-25       Impact factor: 5.469

5.  On the conformation of the hen egg-white lysozyme molecule.

Authors:  C C Blake; G A Mair; A C North; D C Phillips; V R Sarma
Journal:  Proc R Soc Lond B Biol Sci       Date:  1967-04-18

6.  Segmental flexibility in an antibody molecule.

Authors:  J Yguerabide; H F Epstein; L Stryer
Journal:  J Mol Biol       Date:  1970-08       Impact factor: 5.469

Review 7.  Structural domains in proteins and their role in the dynamics of protein function.

Authors:  J Janin; S J Wodak
Journal:  Prog Biophys Mol Biol       Date:  1983       Impact factor: 3.667

8.  Inelastic neutron scattering analysis of hexokinase dynamics and its modification on binding of glucose.

Authors:  B Jacrot; S Cusack; A J Dianoux; D M Engelman
Journal:  Nature       Date:  1982-11-04       Impact factor: 49.962

9.  Viscoelasticity of protein crystal as a probe of the mechanical properties of a protein molecule. Hen egg-white lysozyme.

Authors:  T Y Morozova; V N Morozov
Journal:  J Mol Biol       Date:  1982-05-05       Impact factor: 5.469

10.  Dynamics of DNA oligomers.

Authors:  B Tidor; K K Irikura; B R Brooks; M Karplus
Journal:  J Biomol Struct Dyn       Date:  1983-10
View more
  89 in total

1.  Intrinsic flexibility and gating mechanism of the potassium channel KcsA.

Authors:  Yufeng Shen; Yifei Kong; Jianpeng Ma
Journal:  Proc Natl Acad Sci U S A       Date:  2002-02-12       Impact factor: 11.205

2.  Efficient generation of feasible pathways for protein conformational transitions.

Authors:  Moon K Kim; Robert L Jernigan; Gregory S Chirikjian
Journal:  Biophys J       Date:  2002-09       Impact factor: 4.033

3.  MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids.

Authors:  Z W Cao; Y Xue; L Y Han; B Xie; H Zhou; C J Zheng; H H Lin; Y Z Chen
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

Review 4.  New advances in normal mode analysis of supermolecular complexes and applications to structural refinement.

Authors:  Jianpeng Ma
Journal:  Curr Protein Pept Sci       Date:  2004-04       Impact factor: 3.272

5.  Normal modes of symmetric protein assemblies. Application to the tobacco mosaic virus protein disk.

Authors:  T Simonson; D Perahia
Journal:  Biophys J       Date:  1992-02       Impact factor: 4.033

6.  Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state.

Authors:  Yoann Cote; Patrick Senet; Patrice Delarue; Gia G Maisuradze; Harold A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-11       Impact factor: 11.205

7.  Manipulation of conformational change in proteins by single-residue perturbations.

Authors:  C Atilgan; Z N Gerek; S B Ozkan; A R Atilgan
Journal:  Biophys J       Date:  2010-08-04       Impact factor: 4.033

8.  Protein backbone ensemble generation explores the local structural space of unseen natural homologs.

Authors:  Christian D Schenkelberg; Christopher Bystroff
Journal:  Bioinformatics       Date:  2016-01-18       Impact factor: 6.937

9.  Structural insight into the role of thrombospondin-1 binding to calreticulin in calreticulin-induced focal adhesion disassembly.

Authors:  Qi Yan; Joanne E Murphy-Ullrich; Yuhua Song
Journal:  Biochemistry       Date:  2010-05-04       Impact factor: 3.162

10.  Multiscale dynamics of macromolecules using normal mode Langevin.

Authors:  J A Izaguirre; C R Sweet; V S Pande
Journal:  Pac Symp Biocomput       Date:  2010
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.