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55. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

Author

Moretti, Rocco, Fleishman, Sarel J, Agius, Rudi, Torchala, Mieczyslaw, Bates, Paul A., Kastritis, Panagiotis L, Rodrigues, João P. G. L. M., Trellet, Mikael, Bonvin, Alexandre M. J. J., Cui, Meng, Rooman, Marianne, Gillis, Dimitri, Dehouck, Yves, Moal, Iain, Romero-Durana, Miguel, Pérez-Cano, Laura, Pallara, Chiara, Jimenez, Brian, Fernández-Recio, Juan, Flores, Samuel C, Pacella, Michael, Praneeth Kilambi, Krishna, Gray, Jeffrey J, Popov, Petr, Grudinin, Sergei, Esquivel-Rodríguez, Juan, Kihara, Daisuke, Zhao, Nan, Korkin, Dmitry, Zhu, Xiaolei, Demerdash, Omar N A, Mitchell, Julie, Kanamori, Eiji, Tsuchiya, Yuko, Nakamura, Haruki, Lee, Hasup, Park, Hahnbeom, Seok, Chaok, Sarmiento, Jamica, Liang, Shide, Teraguchi, Shusuke, Standley, Daron M, Shimoyama, Hiromitsu, Terashi, Genki, Takeda-Shitaka, Mayuko, Iwadate, Mitsuo, Umeyama, Hideaki, Beglov, Dmitri, Hall, David R, Kozakov, Dima, Vajda, Sandor, Pierce, Brian G, Hwang, Howook, Vreven, Thom, Weng, Zhiping, Huang, Yangyu, Li, Haotian, Yang, Xiufeng, Ji, Xiaofeng, Liu, Shiyong, Xiao, Yi, Zacharias, Martin, Qin, Sanbo, Zhou, Huan-Xiang, Huang, Sheng-You, Zou, Xiaoqin, Velankar, Sameer, Janin, Joel, Wodak, Shoshana J, Baker, David, Department of Biochemistry [Washington ], University of Washington [Seattle], Molecular Carcinogenesis [Sutton], Institute of cancer research, Weizmann Institute of Science [Rehovot, Israël], Biomolecular Modelling laboratory [London], Cancer Research UK London Research Institute, Bijvoet Center of Biomolecular Research [Utrecht], Utrecht University [Utrecht], Virginia Commonwealth University (VCU), Département d'Informatique [Bruxelles] (ULB), Faculté des Sciences [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), Université libre de Bruxelles (ULB), Unite de Bioinformatique genomique et structurale (3BIO-BIO-INFO), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Department of Cell and Molecular Biology [Uppsala], Uppsala University, Johns Hopkins University (JHU), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS), Department of Computer Science [Purdue], Purdue University [West Lafayette], University of Missouri [Columbia] (Mizzou), University of Missouri System, Department of Mathematics [Madison], University of Wisconsin-Madison, Japan Biological Informatics Consortium [Tokyo], Ochanomizu University, Osaka University [Osaka], Seoul National University [Seoul] (SNU), Kitasato University, Chuo University (Chuo University), Department of Biomedical Engineering [Boston], Boston University [Boston] (BU), University of Massachusetts Medical School [Worcester] (UMASS), University of Massachusetts System (UMASS), Huazhong University of Science and Technology [Wuhan] (HUST), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Florida State University [Tallahassee] (FSU), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Institut de biochimie et biophysique moléculaire et cellulaire (IBBMC), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), University of Toronto, and The Hospital for sick children [Toronto] (SickKids)

Subjects
binding, deep mutational scanning, Mutation, Protein Interaction Mapping, yeast display, hemagglutinin, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Databases, Protein, CAPRI, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Algorithms, Article, Protein Binding
Abstract

International audience; Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful methods explicitly considered the effects of mutation on monomer stability in addition to binding affinity, carried out explicit side-chain sampling and backbone relaxation, evaluated packing, electrostatic, and solvation effects, and correctly identified around a third of the beneficial mutations. Much room for improvement remains for even the best techniques, and large-scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of both existing and new prediction methodologies.

Published
2013
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56. Reassessing buried surface areas in protein-protein complexes

Author

Chakravarty, Devlina, Guharoy, Mainak, Robert, Charles H., Chakrabarti, Pinak, Janin, Joel, Institut de biologie physico-chimique (IBPC), Centre National de la Recherche Scientifique (CNRS), Laboratoire de biochimie théorique [Paris] (LBT (UPR_9080)), Université Paris Diderot - Paris 7 (UPD7)-Institut de biologie physico-chimique (IBPC), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de biochimie et biophysique moléculaire et cellulaire (IBBMC), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie physico-chimique (IBPC (FR_550)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut de biologie physico-chimique (IBPC (FR_550)), and Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
protein-protein interaction, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, solvent accessible surface, conformation changes, binding free energy
Abstract

International audience; The buried surface area (BSA), which measures the size of the interface in a protein-protein complex may differ from the accessible surface area (ASA) lost upon association (which we call DSA), if conformation changes take place. To evaluate the DSA, we measure the ASA of the interface atoms in the bound and unbound states of the components of 144 protein-protein complexes taken from the Protein-Protein Interaction Affinity Database of Kastritis et al. (2011). We observe differences exceeding 20%, and a systematic bias in the distribution. On average, the ASA calculated in the bound state of the components is 3.3% greater than in their unbound state, and the BSA, 7% greater than the DSA. The bias is observed even in complexes where the conformation changes are small. An examination of the bound and unbound structures points to a possible origin: local movements optimize contacts with the other component at the cost of internal contacts, and presumably also the binding free energy.

Published
2013
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57. Protein–protein interactions

Author

Janin, Joel, Bonvin, Alexandre M. J. J., Janin, Joel, and Bonvin, Alexandre M. J. J.

Abstract

We are proud to present the first edition of the Protein–protein interactions Section of Current Opinion in Structural Biology. The Section is new, but the topic has been present in the journal from the very start. Volume 1, Issue 1, dated February 1991, had a review by Janin entitled Protein–protein interactions and assembly, and others by Bode and Huber on Proteinase–inhibitor interaction, and by Chothia on Antigen recognition. The Editorial Overview, signed by TE Creighton and PS Kim, noted that ‘several new X-ray structures of protein complexes had been determined’, and stated that, for such complexes, the ‘overall goal was to understand the specificities of the binding reactions [and the] differential affinities’. At the time, most of the known structures displaying protein–protein interactions were oligomeric protein complexes, which are permanent assemblies. Protease–inhibi- tor and antigen–antibody complexes were the only examples of transient, although highly affine, interactions for which the questions of specificity and affinity could be raised, and therefore, the three reviews of Issue 1 pretty much covered the field. Soon afterwards, new X-ray structures illustrated the role of protein–protein interactions in several major cellular processes. A landmark was the structure of the transducin Ga–Gbg complex by Paul Sigler and collaborators (Lambright et al., 1996, Nature 379:311). Transducin is the G protein that is coupled with rhodopsin in the retina, a key step of the visual signal transduction. The Ga–Gbg complex has many features that had not been seen in earlier structures. It is short-lived, whereas protease–inhibitor and antigen–antibody complexes are stable for hours or days; it displays large conformation changes, all essential to function. The December 1997 issue of Current Opinion in Structural Biology reviewed that structure and those of other complexes involved in signal transduction. Many more were determined afterwards, and they have been re

Published
2013

58. Protein–protein interactions

Author

Sub NMR Spectroscopy, Janin, Joel, Bonvin, Alexandre M. J. J., Sub NMR Spectroscopy, Janin, Joel, and Bonvin, Alexandre M. J. J.

Published
2013

61. Molecular Biology: A Selection of Papers

Author

Janin, Joel

Subjects
Molecular Biology (Book) -- Book reviews, Books -- Book reviews, Environmental issues, Science and technology, Zoology and wildlife conservation
Published
1990

69. Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase

Author

Admiraal, Suzanne J., Schneider, Benoit, Meyer, Philippe, Janin, Joel, Veron, Michel, Deville-Bonne, and Herschlag, Daniel

Subjects
Protein kinases -- Research, Catalysis -- Research, Biological sciences, Chemistry
Abstract

Research was conducted to examine the nucleophilic activation in the NDP kinase reaction. The catalytic advantage provided by a covalent linkage and a binding pocket for the nucleophile was investigated using a mutant form of the enzyme lacking the nucleophilic histidine (H122G). Results demonstrate the catalytic role for activation of the nucleophile by positioning in phosphoryl transfer catalyzed by NDP kinase.

Published
1999

71. Structural features of protein-nucleic acid recognition sites

Author

Nadassy, Katalin, Wodak, Shoshana J., and Janin, Joel

Subjects
Protein binding -- Research, Genetic regulation -- Research, Nucleic acids -- Research, Proteins -- Conformation, Biological sciences, Chemistry
Abstract

The atomic models of 75 X-ray structures of protein-nucleic acid complexes were analyzed. Results showed that the interface area varied between 1120 and 5800 Angstroms. The nature of the atoms, amino acids, and nucleotide residues that constitute the interface was examined and the polar interactions they make reviewed. The manner in which the protein-nucleic acid interfaces are packed was also investigated, permitting a general description of the conformation changes that take place in the protein and nucleic acid components of the complexes to be presented.

Published
1999

77. Mechanism of phosphoryl transfer by nucleoside diphosphate kinase pH dependence and role of the active site Lys16 and Tyr56 residues.

Author

Schneider, Benoit, Babolat, Manuel, Ying Wu Xu, Janin, Joel, Veron, Michel, and Deville-Bonne, Dominique

Subjects
PHOSPHORYLASES, NUCLEOSIDES
Abstract

Examines the mechanism of phosphoryl transfer by nucleoside diphosphate (NDP) kinase. Use of nucleotide analogues in antiviral therapies; Efficiency of NDP kinase; Analysis of the kinetics parameters of mutant NDP kinase.

Published
2001
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82. Confirmations and limitations

Author

Janin, Joel

Subjects
Allosteric proteins -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Published
1989

90. Contributors to Volume 354

Author

Allison, R. Donald, Amici, Adolfo, Ballinger, Marcus D., Barford, David, Batlle, Alcira, Blanot, Didier, Boehlein, Susan K., Bouhss, Ahmed, Branchaud, Bruce P., Bruner, Michael, Cartwright, Jared L., Chang, Christopher H., Bugg, Timothy D.H., Chih, Hung-Wei, Collet, Jean-franÇois, Cook, Paul F., Dementin, SÉbastien, Deville-Bonne, Dominique, Dodson, M.L., Douglas, Donald J., Dunford, H. Brian, Edmondson, Dale E., Emanuelli, Monica, Fleming, Sarah M., Frey, Perry A., Geeganage, Sandaruwan, Lund, Astrid GrÄs, Gross, Jeffrey W., Han, Sanghwsa, Hiratake, Jun, Horenstein, Benjamin A., Huhta, Marja S., Huynh, Boi Hanh, Inoue, Makoto, Janin, JoËl, Karsten, William E., Konermann, Lars, Krebs, Carsten, Kurtz, Andrew J., Langley, G. John, Lindahl, Paul A., Lloyd, R. Stephen, Madhavapeddi, Prashanti, Magni, Giulio, Marquez-curtis, Leah A., Marsh, E. Neil G., Mclennan, Alexander G., Miziorko, Henry M., Mosi, Renee M., Parquet, Claudine, Purich, Daniel L., Raffaelli, Nadia, Reed, George H., Richards, Nigel G.J., Robertson, Thomas A., Rose, David R., Rousseau, Denis L., Roymoulik, IpsIta, Ruggieri, Silverio, Sakata, Kanzo, Schneider, Gunter, Schnizer, Holly G., Schuster, Sheldon M., Sprenger, Georg A., Stewart, Jon D., Stroobant, Vincent, Stuehr, Dennis J., Tipton, Peter A., Turner, B. Elizabeth, Van Heijenoort, Jean, Van Schaftingen, Emile, Vinarov, Dmitriy A., Wang, Zhi-qiang, Wei, Chin-chuan, Wicki, Jacqueline, and Withers, Stephen G.

Published
2002
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