NDLI: A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase.

Content Provider	PubMed Central
Author	Li, Guohui Cui, Qiang
Abstract	A block normal mode (BNM) algorithm, originally proposed by Tama et al., (Proteins Struct. Func. Genet. 41:1-7, 2000) was implemented into the simulation program CHARMM. The BNM approach projects the hessian matrix into local translation/rotation basis vectors and, therefore, dramatically reduces the size of the matrix involved in diagonalization. In the current work, by constructing the atomic hessian elements required in the projection operation on the fly, the memory requirement for the BNM approach has been significantly reduced from that of standard normal mode analysis and previous implementation of BNM. As a result, low frequency modes, which are of interest in large-scale conformational changes of large proteins or protein-nucleic acid complexes, can be readily obtained. Comparison of the BNM results with standard normal mode analysis for a number of small proteins and nucleic acids indicates that many properties dominated by low frequency motions are well reproduced by BNM; these include atomic fluctuations, the displacement covariance matrix, vibrational entropies, and involvement coefficients for conformational transitions. Preliminary application to a fairly large system, Ca(2+)-ATPase (994 residues), is described as an example. The structural flexibility of the cytoplasmic domains (especially domain N), correlated motions among residues on domain interfaces and displacement patterns for the transmembrane helices observed in the BNM results are discussed in relation to the function of Ca(2+)-ATPase. The current implementation of the BNM approach has paved the way for developing efficient sampling algorithms with molecular dynamics or Monte Carlo for studying long-time scale dynamics of macromolecules.
Related Links	http://dx.doi.org/10.1016/s0006-3495(02)75257-0
Ending Page	2474
Page Count	18
Starting Page	2457
File Format	PDF
ISSN	00063495
e-ISSN	15420086
Journal	Biophysical Journal
Issue Number	5
Volume Number	83
Language	English
Publisher Date	2002-11-01
Access Restriction	Open
Subject Keyword	Biophysics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Biophysics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Effects of Surface Water on Protein Dynamics Studied by a Novel Coarse-Grained Normal Mode Approach

Normal Mode-Based Fitting of Atomic Structure into Electron Density Maps: Application to Sarcoplasmic Reticulum Ca-ATPase

Transconformations of the SERCA1 Ca-ATPase: A Normal Mode Study

A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography

Analysis of Functional Motions in Brownian Molecular Machines with an Efficient Block Normal Mode Approach: Myosin-II and Ca2+-ATPase

REACH Coarse-Grained Normal Mode Analysis of Protein Dimer Interaction Dynamics

Normal mode based fitting of atomic structure into electron density maps: application to SR Ca-ATPase

A Coarse-Grained Molecular Model for Glycosaminoglycans: Application to Chondroitin, Chondroitin Sulfate, and Hyaluronic Acid

Coarse-Grained Peptide Modeling Using a Systematic Multiscale Approach

A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase.

Similar Documents

Effects of Surface Water on Protein Dynamics Studied by a Novel Coarse-Grained Normal Mode Approach

Normal Mode-Based Fitting of Atomic Structure into Electron Density Maps: Application to Sarcoplasmic Reticulum Ca-ATPase

Transconformations of the SERCA1 Ca-ATPase: A Normal Mode Study

A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography

Analysis of Functional Motions in Brownian Molecular Machines with an Efficient Block Normal Mode Approach: Myosin-II and Ca2+-ATPase

REACH Coarse-Grained Normal Mode Analysis of Protein Dimer Interaction Dynamics

Normal mode based fitting of atomic structure into electron density maps: application to SR Ca-ATPase

A Coarse-Grained Molecular Model for Glycosaminoglycans: Application to Chondroitin, Chondroitin Sulfate, and Hyaluronic Acid

Coarse-Grained Peptide Modeling Using a Systematic Multiscale Approach

A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase.