Normal mode analysis based on an elastic network model for biomolecules in the protein data Bank, which uses dihedral angles as independent variables

Hiroshi Wako, Shigeru Endo

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Abstract We have developed a computer program, named PDBETA, that performs normal mode analysis (NMA) based on an elastic network model that uses dihedral angles as independent variables. Taking advantage of the relatively small number of degrees of freedom required to describe a molecular structure in dihedral angle space and a simple potential-energy function independent of atom types, we aimed to develop a program applicable to a full-atom system of any molecule in the Protein Data Bank (PDB). The algorithm for NMA used in PDBETA is the same as the computer program FEDER/2, developed previously. Therefore, the main challenge in developing PDBETA was to find a method that can automatically convert PDB data into molecular structure information in dihedral angle space. Here, we illustrate the performance of PDBETA with a protein-DNA complex, a protein-tRNA complex, and some non-protein small molecules, and show that the atomic fluctuations calculated by PDBETA reproduce the temperature factor data of these molecules in the PDB. A comparison was also made with elastic-network-model based NMA in a Cartesian-coordinate system.

Original languageEnglish
Pages (from-to)22-30
Number of pages9
JournalComputational Biology and Chemistry
Volume44
DOIs
Publication statusPublished - 2013

Fingerprint

Dihedral angle
Biomolecules
Normal Modes
Network Model
Databases
Proteins
Protein
Molecules
Molecular Structure
Molecular structure
Computer program listings
Software
Potential energy functions
Cartesian coordinate system
Atoms
Information Structure
Potential Function
Transfer RNA
Energy Function
Convert

Keywords

  • Elastic network model Normal mode analysis Dihedral angle space Protein Data Bank Protein-DNA complex Protein-tRNA complex

ASJC Scopus subject areas

  • Biochemistry
  • Structural Biology
  • Organic Chemistry
  • Computational Mathematics

Cite this

@article{471beda2389a4d398af8cb43738a17ad,
title = "Normal mode analysis based on an elastic network model for biomolecules in the protein data Bank, which uses dihedral angles as independent variables",
abstract = "Abstract We have developed a computer program, named PDBETA, that performs normal mode analysis (NMA) based on an elastic network model that uses dihedral angles as independent variables. Taking advantage of the relatively small number of degrees of freedom required to describe a molecular structure in dihedral angle space and a simple potential-energy function independent of atom types, we aimed to develop a program applicable to a full-atom system of any molecule in the Protein Data Bank (PDB). The algorithm for NMA used in PDBETA is the same as the computer program FEDER/2, developed previously. Therefore, the main challenge in developing PDBETA was to find a method that can automatically convert PDB data into molecular structure information in dihedral angle space. Here, we illustrate the performance of PDBETA with a protein-DNA complex, a protein-tRNA complex, and some non-protein small molecules, and show that the atomic fluctuations calculated by PDBETA reproduce the temperature factor data of these molecules in the PDB. A comparison was also made with elastic-network-model based NMA in a Cartesian-coordinate system.",
keywords = "Elastic network model Normal mode analysis Dihedral angle space Protein Data Bank Protein-DNA complex Protein-tRNA complex",
author = "Hiroshi Wako and Shigeru Endo",
year = "2013",
doi = "10.1016/j.compbiolchem.2013.02.006",
language = "English",
volume = "44",
pages = "22--30",
journal = "Computational Biology and Chemistry",
issn = "1476-9271",
publisher = "Elsevier Limited",

}

TY - JOUR

T1 - Normal mode analysis based on an elastic network model for biomolecules in the protein data Bank, which uses dihedral angles as independent variables

AU - Wako, Hiroshi

AU - Endo, Shigeru

PY - 2013

Y1 - 2013

N2 - Abstract We have developed a computer program, named PDBETA, that performs normal mode analysis (NMA) based on an elastic network model that uses dihedral angles as independent variables. Taking advantage of the relatively small number of degrees of freedom required to describe a molecular structure in dihedral angle space and a simple potential-energy function independent of atom types, we aimed to develop a program applicable to a full-atom system of any molecule in the Protein Data Bank (PDB). The algorithm for NMA used in PDBETA is the same as the computer program FEDER/2, developed previously. Therefore, the main challenge in developing PDBETA was to find a method that can automatically convert PDB data into molecular structure information in dihedral angle space. Here, we illustrate the performance of PDBETA with a protein-DNA complex, a protein-tRNA complex, and some non-protein small molecules, and show that the atomic fluctuations calculated by PDBETA reproduce the temperature factor data of these molecules in the PDB. A comparison was also made with elastic-network-model based NMA in a Cartesian-coordinate system.

AB - Abstract We have developed a computer program, named PDBETA, that performs normal mode analysis (NMA) based on an elastic network model that uses dihedral angles as independent variables. Taking advantage of the relatively small number of degrees of freedom required to describe a molecular structure in dihedral angle space and a simple potential-energy function independent of atom types, we aimed to develop a program applicable to a full-atom system of any molecule in the Protein Data Bank (PDB). The algorithm for NMA used in PDBETA is the same as the computer program FEDER/2, developed previously. Therefore, the main challenge in developing PDBETA was to find a method that can automatically convert PDB data into molecular structure information in dihedral angle space. Here, we illustrate the performance of PDBETA with a protein-DNA complex, a protein-tRNA complex, and some non-protein small molecules, and show that the atomic fluctuations calculated by PDBETA reproduce the temperature factor data of these molecules in the PDB. A comparison was also made with elastic-network-model based NMA in a Cartesian-coordinate system.

KW - Elastic network model Normal mode analysis Dihedral angle space Protein Data Bank Protein-DNA complex Protein-tRNA complex

UR - http://www.scopus.com/inward/record.url?scp=84875720013&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84875720013&partnerID=8YFLogxK

U2 - 10.1016/j.compbiolchem.2013.02.006

DO - 10.1016/j.compbiolchem.2013.02.006

M3 - Article

C2 - 23537565

AN - SCOPUS:84875720013

VL - 44

SP - 22

EP - 30

JO - Computational Biology and Chemistry

JF - Computational Biology and Chemistry

SN - 1476-9271

ER -