Modelling the structure of latexin-carboxypeptidase A complex based on chemical cross-linking and molecular docking

Dmitri Mouradov, Ari Craven, Jade K Forwood, Jack U Flanagan, Raquel García-Castellanos, F Xavier Gomis-Rüth, David A Hume, Jennifer L Martin, Bostjan Kobe, Thomas Huber

Research output: Contribution to journalArticlepeer-review

Abstract

We have determined the three-dimensional structure of the protein complex between latexin and carboxypeptidase A using a combination of chemical cross-linking, mass spectrometry and molecular docking. The locations of three intermolecular cross-links were identified using mass spectrometry and these constraints were used in combination with a speed-optimised docking algorithm allowing us to evaluate more than 3 x 10(11) possible conformations. While cross-links represent only limited structural constraints, the combination of only three experimental cross-links with very basic molecular docking was sufficient to determine the complex structure. The crystal structure of the complex between latexin and carboxypeptidase A4 determined recently allowed us to assess the success of this structure determination approach. Our structure was shown to be within 4 A r.m.s. deviation of Calpha atoms of the crystal structure. The study demonstrates that cross-linking in combination with mass spectrometry can lead to efficient and accurate structural modelling of protein complexes.
Original languageEnglish
Pages (from-to)9-16
Number of pages8
JournalProtein engineering, design & selection : PEDS
Volume19
Issue number1
DOIs
Publication statusPublished - Jan 2006

Keywords

  • Algorithms
  • Amino Acid Sequence
  • Antigens
  • Carboxypeptidases A
  • Computer Simulation
  • Cross-Linking Reagents
  • Mass Spectrometry
  • Molecular Sequence Data
  • Protein Binding
  • Protein Conformation

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