Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35.
The 28th-35th rounds of the Critical Assessment of PRotein Interactions (CAPRI) served as a practical benchmark for our RosettaDock protein-protein docking protocols, highlighting strengths and weaknesses of the approach. We achieved acceptable or better quality models in three out of 11 targets. For the two α-repeat protein-green fluorescent protein (αrep-GFP) complexes, we used a novel ellipsoidal partial-global docking method (Ellipsoidal Dock) to generate models with 2.2 Å/1.5 Å interface RMSD, capturing 49%/42% of the native contacts, for the 7-/5-repeat αrep complexes. For the DNase-immunity protein complex, we used a new predictor of hydrogen-bonding networks, HBNet with Bridging Waters, to place individual water models at the complex interface; models were generated with 1.8 Å interface RMSD and 12% native water contacts recovered. The targets for which RosettaDock failed to create an acceptable model were typically difficult in general, as six had no acceptable models submitted by any CAPRI predictor. The UCH-L5-RPN13 and UCH-L5-INO80G de-ubiquitinating enzyme-inhibitor complexes comprised inhibitors undergoing significant structural changes upon binding, with the partners being highly interwoven in the docked complexes. Our failure to predict the nucleosome-enzyme complex in Target 95 was largely due to tight constraints we placed on our model based on sparse biochemical data suggesting two specific cross-interface interactions, preventing the correct structure from being sampled. While RosettaDock's three successes show that it is a state-of-the-art docking method, the difficulties with highly flexible and multi-domain complexes highlight the need for better flexible docking and domain-assembly methods. Proteins 2017; 85:479-486. © 2016 Wiley Periodicals, Inc.
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland.
Nicholas A
NA
Marze
T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.|Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland.
Jeliazko R
JR
Jeliazkov
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland.
Shourya S
SS
Roy Burman
Department of Biochemistry, University of Washington, Seattle, Washington.|Institute for Protein Design, University of Washington, Seattle, Washington.
Scott E
SE
Boyken
Department of Biochemistry, University of Washington, Seattle, Washington.|Institute for Protein Design, University of Washington, Seattle, Washington.
Frank
F
DiMaio
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland.|Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland.|Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.|Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland.
Jeffrey J
0000-0001-6380-2324
JJ
Gray
D000074183:ATPases Associated with Diverse Cellular Activities; D000465:Algorithms; D020816:Amino Acid Motifs; D019985:Benchmarking; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D004265:DNA Helicases / Q000737:chemistry; D004268:DNA-Binding Proteins; D003851:Deoxyribonucleases / Q000737:chemistry; D010450:Endopeptidases / Q000737:chemistry; D006860:Hydrogen Bonding; D062105:Molecular Docking Simulation / Q000379:methods*; D009707:Nucleosomes / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D012107:Research Design; D012984:Software; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D004268:DNA-Binding Proteins; D009707:Nucleosomes; D014867:Water; D003851:Deoxyribonucleases; D010450:Endopeptidases; C091939:ubiquitin isopeptidase; D000074183:ATPases Associated with Diverse Cellular Activities; D004265:DNA Helicases; C524421:INO80 protein, human
CAPRI; Rosetta; conformational change; protein-protein docking; water-mediated interfaces
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