Literature DB >> 21760758

A New Method for Coarse-Grained Elastic Normal-Mode Analysis.

Mingyang Lu1, Billy Poon, Jianpeng Ma.   

Abstract

In this paper, we report a new method for coarse-grained elastic normal-mode analysis. The purpose is to overcome a long-standing problem in the conventional analysis called the tip effect that makes the motional patterns (eigenvectors) of some low-frequency modes irrational. The new method retains the merits of a conventional method such as not requiring lengthy initial energy minimization, which always distorts structures, and also delivers substantially more accurate low-frequency modes with no tip effect for proteins of any size. This improvement of modes is crucial for certain types of applications such as structural refinement or normal-mode-based sampling.

Year:  2006        PMID： 21760758      PMCID： PMC3133770          DOI： 10.1021/ct050307u

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN： 1549-9618            Impact factor:   6.006


  33 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.  Domain movements in human fatty acid synthase by quantized elastic deformational model.

Authors:  Dengming Ming; Yifei Kong; Salih J Wakil; Jacob Brink; Jianpeng Ma
Journal:  Proc Natl Acad Sci U S A       Date:  2002-06-11       Impact factor: 11.205

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.  Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy.

Authors:  Florence Tama; Mikel Valle; Joachim Frank; Charles L Brooks
Journal:  Proc Natl Acad Sci U S A       Date:  2003-07-23       Impact factor: 11.205

6.  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

7.  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

8.  Folding of small helical proteins assisted by small-angle X-ray scattering profiles.

Authors:  Yinghao Wu; Xia Tian; Mingyang Lu; Mingzhi Chen; Qinghua Wang; Jianpeng Ma
Journal:  Structure       Date:  2005-11       Impact factor: 5.006

9.  The role of shape in determining molecular motions.

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

10.  Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<-->R2 transition.

Authors:  Chunyan Xu; Dror Tobi; I Bahar
Journal:  J Mol Biol       Date:  2003-10-10       Impact factor: 5.469
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  37 in total

1.  Structure of the N-terminal fragment of Escherichia coli Lon protease.

Authors:  Mi Li; Alla Gustchina; Fatima S Rasulova; Edward E Melnikov; Michael R Maurizi; Tatyana V Rotanova; Zbigniew Dauter; Alexander Wlodawer
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-07-09

2.  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

3.  Analyzing the flexibility of RNA structures by constraint counting.

Authors:  Simone Fulle; Holger Gohlke
Journal:  Biophys J       Date:  2008-02-15       Impact factor: 4.033

4.  Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution.

Authors:  Billy K Poon; Xiaorui Chen; Mingyang Lu; Nand K Vyas; Florante A Quiocho; Qinghua Wang; Jianpeng Ma
Journal:  Proc Natl Acad Sci U S A       Date:  2007-04-30       Impact factor: 11.205

5.  Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 A crystallographic resolution.

Authors:  Xiaorui Chen; Billy K Poon; Athanasios Dousis; Qinghua Wang; Jianpeng Ma
Journal:  Structure       Date:  2007-08       Impact factor: 5.006

6.  Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit.

Authors:  H Lee Woodcock; Wenjun Zheng; An Ghysels; Yihan Shao; Jing Kong; Bernard R Brooks
Journal:  J Chem Phys       Date:  2008-12-07       Impact factor: 3.488

7.  Deciphering the mismatch recognition cycle in MutS and MSH2-MSH6 using normal-mode analysis.

Authors:  Shayantani Mukherjee; Sean M Law; Michael Feig
Journal:  Biophys J       Date:  2009-03-04       Impact factor: 4.033

8.  All-atom contact model for understanding protein dynamics from crystallographic B-factors.

Authors:  Da-Wei Li; Rafael Brüschweiler
Journal:  Biophys J       Date:  2009-04-22       Impact factor: 4.033

9.  Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement.

Authors:  Xiaorui Chen; Mingyang Lu; Billy K Poon; Qinghua Wang; Jianpeng Ma
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-03-19

10.  Investigating the structural dynamics of the PIEZO1 channel activation and inactivation by coarse-grained modeling.

Authors:  Wenjun Zheng; Frederick Sachs
Journal:  Proteins       Date:  2017-09-23
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