title: A method for integrative structure determination of protein-protein complexes.
abstract: BACKGROUND
  Structural characterization of protein interactions is necessary for understanding and modulating biological processes. On one hand, X-ray crystallography or NMR spectroscopy provide atomic resolution structures but the data collection process is typically long and the success rate is low. On the other hand, computational methods for modeling assembly structures from individual components frequently suffer from high false-positive rate, rarely resulting in a unique solution.
  
  
  RESULTS
  Here, we present a combined approach that computationally integrates data from a variety of fast and accessible experimental techniques for rapid and accurate structure determination of protein-protein complexes. The integrative method uses atomistic models of two interacting proteins and one or more datasets from five accessible experimental techniques: a small-angle X-ray scattering (SAXS) profile, 2D class average images from negative-stain electron microscopy micrographs (EM), a 3D density map from single-particle negative-stain EM, residue type content of the protein-protein interface from NMR spectroscopy and chemical cross-linking detected by mass spectrometry. The method is tested on a docking benchmark consisting of 176 known complex structures and simulated experimental data. The near-native model is the top scoring one for up to 61% of benchmark cases depending on the included experimental datasets; in comparison to 10% for standard computational docking. We also collected SAXS, 2D class average images and 3D density map from negative-stain EM to model the PCSK9 antigen-J16 Fab antibody complex, followed by validation of the model by a subsequently available X-ray crystallographic structure.
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA. dina@salilab.org
authors.forename: Dina
authors.initials: D
authors.lastname: Schneidman-Duhovny
authors.forename: Andrea
authors.initials: A
authors.lastname: Rossi
authors.forename: Agustin
authors.initials: A
authors.lastname: Avila-Sakar
authors.forename: Seung Joong
authors.initials: SJ
authors.lastname: Kim
authors.forename: Javier
authors.initials: J
authors.lastname: Velázquez-Muriel
authors.forename: Pavel
authors.initials: P
authors.lastname: Strop
authors.forename: Hong
authors.initials: H
authors.lastname: Liang
authors.forename: Kristin A
authors.initials: KA
authors.lastname: Krukenberg
authors.forename: Maofu
authors.initials: M
authors.lastname: Liao
authors.forename: Ho Min
authors.initials: HM
authors.lastname: Kim
authors.forename: Solmaz
authors.initials: S
authors.lastname: Sobhanifar
authors.forename: Volker
authors.initials: V
authors.lastname: Dötsch
authors.forename: Arvind
authors.initials: A
authors.lastname: Rajpal
authors.forename: Jaume
authors.initials: J
authors.lastname: Pons
authors.forename: David A
authors.initials: DA
authors.lastname: Agard
authors.forename: Yifan
authors.initials: Y
authors.lastname: Cheng
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
mesh_terms: D000936:Antigen-Antibody Complex / Q000737:chemistry; D018360:Crystallography, X-Ray; D008854:Microscopy, Electron; D062105:Molecular Docking Simulation / Q000379:methods*; D046912:Multiprotein Complexes / Q000737:chemistry*; D053838:Scattering, Small Angle; D012984:Software; D014961:X-Ray Diffraction
chemical_list: D000936:Antigen-Antibody Complex; D046912:Multiprotein Complexes