Modelling the structure of latexin-carboxypeptidase A complex based on chemical cross-linking and molecular docking
Date
2006
Authors
Mouradov, Dmitri
Craven, Ari
Forwood, Jade
Flanagan, Jack U
Garcia-Castellanos, Raquel
Gomis-Ruth, F. Xavier
Hume, D A
Martin, Jennifer Louise
Kobe, Bostjan
Huber, Thomas
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Oxford University Press
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 × 1011 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 Å r.m.s. deviation of Cα 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.
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Keywords
Keywords: Chemical cross-linking; Latexin-carboxypeptidaseA; Molecular docking; Protein complex structure; Algorithms; Complexation; Crosslinking; Mass spectrometry; Mathematical models; Molecular structure; Enzymes; carboxypeptidase; protein; algorithm; article; a Chemical cross-linking; Latexin-carboxypeptidaseA; Mass spectrometry; Molecular docking; Protein complex structure
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Source
Protein Engineering Design and Selection
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Journal article
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2037-12-31
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