Literature DB >> 15078222

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

Jianpeng Ma1.   

Abstract

Normal mode analysis is an effective computational method for studying large-amplitude low-frequency molecular deformations that are ubiquitously involved in the functions of biological macromolecules, especially supermolecular complexes. The recent years have witnessed a substantial advance in methodology development in the field. This review is intended to summarize some of the important advances that enable one to simulate deformations of supermolecular complexes at expended resolution- and length-scales, with particular emphasis on the implications in structural refinement against low- to intermediate-resolution structural data such as those from electron cryomicroscopy and fibre diffraction.

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Year:  2004        PMID: 15078222      PMCID: PMC2688808          DOI: 10.2174/1389203043486892

Source DB:  PubMed          Journal:  Curr Protein Pept Sci        ISSN: 1389-2037            Impact factor:   3.272


  42 in total

1.  Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis.

Authors: 
Journal:  Phys Rev Lett       Date:  1996-08-26       Impact factor: 9.161

2.  Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study.

Authors:  A Thomas; K Hinsen; M J Field; D Perahia
Journal:  Proteins       Date:  1999-01-01

3.  Substructure synthesis method for simulating large molecular complexes.

Authors:  Dengming Ming; Yifei Kong; Yinghao Wu; Jianpeng Ma
Journal:  Proc Natl Acad Sci U S A       Date:  2002-12-23       Impact factor: 11.205

4.  Mega-Dalton biomolecular motion captured from electron microscopy reconstructions.

Authors:  Pablo Chacón; Florence Tama; Willy Wriggers
Journal:  J Mol Biol       Date:  2003-02-14       Impact factor: 5.469

5.  Conformational flexibility of pyruvate dehydrogenase complexes: a computational analysis by quantized elastic deformational model.

Authors:  Yifei Kong; Dengming Ming; Yinghao Wu; James K Stoops; Z Hong Zhou; Jianpeng Ma
Journal:  J Mol Biol       Date:  2003-06-27       Impact factor: 5.469

6.  Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory.

Authors:  Florence Tama; Willy Wriggers; Charles L Brooks
Journal:  J Mol Biol       Date:  2002-08-09       Impact factor: 5.469

7.  Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics.

Authors:  P Gros; W F van Gunsteren; W G Hol
Journal:  Science       Date:  1990-09-07       Impact factor: 47.728

8.  The hinge-bending mode of a lysozyme-inhibitor complex.

Authors:  R E Bruccoleri; M Karplus; J A McCammon
Journal:  Biopolymers       Date:  1986-09       Impact factor: 2.505

9.  Essential dynamics of proteins.

Authors:  A Amadei; A B Linssen; H J Berendsen
Journal:  Proteins       Date:  1993-12

10.  Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis.

Authors:  Jacob Brink; Steven J Ludtke; Yifei Kong; Salih J Wakil; Jianpeng Ma; Wah Chiu
Journal:  Structure       Date:  2004-02       Impact factor: 5.006

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  31 in total

1.  Theoretical analysis of twist/bend ratio and mechanical moduli of bacterial flagellar hook and filament.

Authors:  Terence C Flynn; Jianpeng Ma
Journal:  Biophys J       Date:  2004-05       Impact factor: 4.033

2.  An analysis of core deformations in protein superfamilies.

Authors:  Alejandra Leo-Macias; Pedro Lopez-Romero; Dmitry Lupyan; Daniel Zerbino; Angel R Ortiz
Journal:  Biophys J       Date:  2004-11-12       Impact factor: 4.033

3.  Accurate prediction of the bound form of the Akt pleckstrin homology domain using normal mode analysis to explore structural flexibility.

Authors:  Hoang T Tran; Shuxing Zhang
Journal:  J Chem Inf Model       Date:  2011-08-25       Impact factor: 4.956

4.  Making ATP.

Authors:  Jianhua Xing; Jung-Chi Liao; George Oster
Journal:  Proc Natl Acad Sci U S A       Date:  2005-10-10       Impact factor: 11.205

5.  How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues.

Authors:  Turkan Haliloglu; Ozlem Keskin; Buyong Ma; Ruth Nussinov
Journal:  Biophys J       Date:  2004-12-13       Impact factor: 4.033

6.  iGNM: a database of protein functional motions based on Gaussian Network Model.

Authors:  Lee-Wei Yang; Xiong Liu; Christopher J Jursa; Mark Holliman; A J Rader; Hassan A Karimi; Ivet Bahar
Journal:  Bioinformatics       Date:  2005-04-28       Impact factor: 6.937

7.  The role of shape in determining molecular motions.

Authors:  Mingyang Lu; Jianpeng Ma
Journal:  Biophys J       Date:  2005-07-29       Impact factor: 4.033

8.  A natural coarse graining for simulating large biomolecular motion.

Authors:  Holger Gohlke; M F Thorpe
Journal:  Biophys J       Date:  2006-06-30       Impact factor: 4.033

9.  The conformational coupling and translocation mechanism of vitamin B12 ATP-binding cassette transporter BtuCD.

Authors:  Jingwei Weng; Jianpeng Ma; Kangnian Fan; Wenning Wang
Journal:  Biophys J       Date:  2007-10-19       Impact factor: 4.033

10.  Higher susceptibility to halothane modulation in open- than in closed-channel alpha4beta2 nAChR revealed by molecular dynamics simulations.

Authors:  Lu Tian Liu; Esmael J Haddadian; Dan Willenbring; Yan Xu; Pei Tang
Journal:  J Phys Chem B       Date:  2010-01-14       Impact factor: 2.991

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