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Title: Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces

Abstract

Here, protein-protein interactions are ubiquitous and essential for cellular processes. High-resolution X-ray crystallographic structures of protein complexes can elucidate the details of their function and provide a basis for many computational and experimental approaches. Here we demonstrate that existing annotations of protein complexes, including those provided by the Protein Data Bank (PDB) itself, contain a significant fraction of incorrect annotations. Results: We have developed a method for identifying protein complexes in the PDB X-ray structures by a four step procedure: (1) comprehensively collecting all protein-protein interfaces; (2) clustering similar protein-protein interfaces together; (3) estimating the probability that each cluster is relevant based on a diverse set of properties; and (4) finally combining these scores for each entry in order to predict the complex structure. Unlike previous annotation methods, consistent prediction of complexes with identical or almost identical protein content is insured. The resulting clusters of biologically relevant interfaces provide a reliable catalog of evolutionary conserved protein-protein interactions.

Authors:
 [1];  [2]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Mayo Clinic, Scottsdale, AZ (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1263826
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
BMC Bioinformatics
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 1471-2105
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Bordner, Andrew J., and Gorin, Andrey A. Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces. United States: N. p., 2008. Web. doi:10.1186/1471-2105-9-234.
Bordner, Andrew J., & Gorin, Andrey A. Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces. United States. doi:10.1186/1471-2105-9-234.
Bordner, Andrew J., and Gorin, Andrey A. Mon . "Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces". United States. doi:10.1186/1471-2105-9-234. https://www.osti.gov/servlets/purl/1263826.
@article{osti_1263826,
title = {Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces},
author = {Bordner, Andrew J. and Gorin, Andrey A.},
abstractNote = {Here, protein-protein interactions are ubiquitous and essential for cellular processes. High-resolution X-ray crystallographic structures of protein complexes can elucidate the details of their function and provide a basis for many computational and experimental approaches. Here we demonstrate that existing annotations of protein complexes, including those provided by the Protein Data Bank (PDB) itself, contain a significant fraction of incorrect annotations. Results: We have developed a method for identifying protein complexes in the PDB X-ray structures by a four step procedure: (1) comprehensively collecting all protein-protein interfaces; (2) clustering similar protein-protein interfaces together; (3) estimating the probability that each cluster is relevant based on a diverse set of properties; and (4) finally combining these scores for each entry in order to predict the complex structure. Unlike previous annotation methods, consistent prediction of complexes with identical or almost identical protein content is insured. The resulting clusters of biologically relevant interfaces provide a reliable catalog of evolutionary conserved protein-protein interactions.},
doi = {10.1186/1471-2105-9-234},
journal = {BMC Bioinformatics},
number = 1,
volume = 9,
place = {United States},
year = {2008},
month = {5}
}

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Cited by: 24 works
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Works referenced in this record:

Principles of protein-protein interactions.
journal, January 1996

  • Jones, S.; Thornton, J. M.
  • Proceedings of the National Academy of Sciences, Vol. 93, Issue 1
  • DOI: 10.1073/pnas.93.1.13

Electrostatic aspects of protein–protein interactions
journal, April 2000


Structural Characterisation and Functional Significance of Transient Protein–Protein Interactions
journal, January 2003


Statistical analysis and prediction of protein-protein interfaces
journal, May 2005

  • Bordner, Andrew J.; Abagyan, Ruben
  • Proteins: Structure, Function, and Bioinformatics, Vol. 60, Issue 3
  • DOI: 10.1002/prot.20433

Protein docking using surface matching and supervised machine learning
journal, April 2007

  • Bordner, Andrew J.; Gorin, Andrey A.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 68, Issue 2
  • DOI: 10.1002/prot.21406

Interrogating protein interaction networks through structural biology
journal, April 2002

  • Aloy, P.; Russell, R. B.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 9
  • DOI: 10.1073/pnas.092147999

MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading
journal, October 2002

  • Lu, Long; Lu, Hui; Skolnick, Jeffrey
  • Proteins: Structure, Function, and Genetics, Vol. 49, Issue 3
  • DOI: 10.1002/prot.10222

Discriminating between homodimeric and monomeric proteins in the crystalline state
journal, July 2000


Conservation helps to identify biologically relevant crystal contacts
journal, October 2001

  • Valdar, William S. J.; Thornton, Janet M.
  • Journal of Molecular Biology, Vol. 313, Issue 2
  • DOI: 10.1006/jmbi.2001.5034

A Dissection of Specific and Non-specific Protein–Protein Interfaces
journal, February 2004

  • Prasad Bahadur, Ranjit; Chakrabarti, Pinak; Rodier, Francis
  • Journal of Molecular Biology, Vol. 336, Issue 4
  • DOI: 10.1016/j.jmb.2003.12.073

Automatic inference of protein quaternary structure from crystals
journal, September 2003

  • Ponstingl, Hannes; Kabir, Thomas; Thornton, Janet M.
  • Journal of Applied Crystallography, Vol. 36, Issue 5
  • DOI: 10.1107/S0021889803012421

PQS: a protein quaternary structure file server
journal, September 1998


Inference of Macromolecular Assemblies from Crystalline State
journal, September 2007


PIBASE: a comprehensive database of structurally defined protein interfaces
journal, January 2005


PROTCOM: searchable database of protein complexes enhanced with domain-domain structures
journal, January 2007

  • Kundrotas, P. J.; Alexov, E.
  • Nucleic Acids Research, Vol. 35, Issue Database
  • DOI: 10.1093/nar/gkl768

3D Complex: A Structural Classification of Protein Complexes
journal, January 2006


PRISM: protein interactions by structural matching
journal, July 2005

  • Ogmen, U.; Keskin, O.; Aytuna, A. S.
  • Nucleic Acids Research, Vol. 33, Issue Web Server
  • DOI: 10.1093/nar/gki585

3did: interacting protein domains of known three-dimensional structure
journal, December 2004


SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions
journal, January 2007

  • Jefferson, E. R.; Walsh, T. P.; Roberts, T. J.
  • Nucleic Acids Research, Vol. 35, Issue Database
  • DOI: 10.1093/nar/gkl836

SCOPPI: a structural classification of protein-protein interfaces
journal, January 2006


Random Forests
journal, January 2001


Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
journal, December 1983


Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

  • Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
  • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
  • DOI: 10.1093/nar/25.17.3389

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications
journal, April 2004

  • Keskin, Ozlem; Tsai, Chung-Jung; Wolfson, Haim
  • Protein Science, Vol. 13, Issue 4, p. 1043-1055
  • DOI: 10.1110/ps.03484604

The Pfam protein families database
journal, January 2004

  • Bateman, Alex; Coin, Lachlan; Durbin, Richard
  • Nucleic Acids Research, Vol. 32, Issue S1, p. D138-D141
  • DOI: 10.1093/nar/gkh121

EMBOSS: The European Molecular Biology Open Software Suite
journal, June 2000


Specific versus non-specific contacts in protein crystals
journal, December 1997


Protein-protein interactions: A review of protein dimer structures
journal, January 1995


Hydrogen bonds and salt bridges across protein-protein interfaces
journal, September 1997

  • Xu, D.; Tsai, C. J.; Nussinov, R.
  • Protein Engineering Design and Selection, Vol. 10, Issue 9
  • DOI: 10.1093/protein/10.9.999

Basis of biological specificity
journal, April 1984


iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions
journal, September 2004


Inferring Domain-Domain Interactions From Protein-Protein Interactions
journal, October 2002


    Works referencing / citing this record:

    Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions
    journal, January 2014


    Protein interface classification by evolutionary analysis
    journal, January 2012

    • Duarte, Jose M.; Srebniak, Adam; Schärer, Martin A.
    • BMC Bioinformatics, Vol. 13, Issue 1
    • DOI: 10.1186/1471-2105-13-334