Literature DB >> 24008843

Structure homology and interaction redundancy for discovering virus-host protein interactions.

Benoît de Chassey1, Laurène Meyniel-Schicklin, Anne Aublin-Gex, Vincent Navratil, Thibaut Chantier, Patrice André, Vincent Lotteau.   

Abstract

Virus-host interactomes are instrumental to understand global perturbations of cellular functions induced by infection and discover new therapies. The construction of such interactomes is, however, technically challenging and time consuming. Here we describe an original method for the prediction of high-confidence interactions between viral and human proteins through a combination of structure and high-quality interactome data. Validation was performed for the NS1 protein of the influenza virus, which led to the identification of new host factors that control viral replication.

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Year:  2013        PMID: 24008843      PMCID: PMC3807215          DOI: 10.1038/embor.2013.130

Source DB:  PubMed          Journal:  EMBO Rep        ISSN: 1469-221X            Impact factor:   8.807


  27 in total

1.  Influenza A virus NS1 protein activates the PI3K/Akt pathway to mediate antiapoptotic signaling responses.

Authors:  Christina Ehrhardt; Thorsten Wolff; Stephan Pleschka; Oliver Planz; Wiebke Beermann; Johannes G Bode; Mirco Schmolke; Stephan Ludwig
Journal:  J Virol       Date:  2007-01-17       Impact factor: 5.103

2.  Using Dali for structural comparison of proteins.

Authors:  Liisa Holm; Sakari Kääriäinen; Chris Wilton; Dariusz Plewczynski
Journal:  Curr Protoc Bioinformatics       Date:  2006-07

3.  Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM.

Authors:  Nurcan Tuncbag; Attila Gursoy; Ruth Nussinov; Ozlem Keskin
Journal:  Nat Protoc       Date:  2011-08-11       Impact factor: 13.491

4.  Global landscape of HIV-human protein complexes.

Authors:  Stefanie Jäger; Peter Cimermancic; Natali Gulbahce; Jeffrey R Johnson; Kathryn E McGovern; Starlynn C Clarke; Michael Shales; Gaelle Mercenne; Lars Pache; Kathy Li; Hilda Hernandez; Gwendolyn M Jang; Shoshannah L Roth; Eyal Akiva; John Marlett; Melanie Stephens; Iván D'Orso; Jason Fernandes; Marie Fahey; Cathal Mahon; Anthony J O'Donoghue; Aleksandar Todorovic; John H Morris; David A Maltby; Tom Alber; Gerard Cagney; Frederic D Bushman; John A Young; Sumit K Chanda; Wesley I Sundquist; Tanja Kortemme; Ryan D Hernandez; Charles S Craik; Alma Burlingame; Andrej Sali; Alan D Frankel; Nevan J Krogan
Journal:  Nature       Date:  2011-12-21       Impact factor: 49.962

5.  RIG-I-mediated antiviral responses to single-stranded RNA bearing 5'-phosphates.

Authors:  Andreas Pichlmair; Oliver Schulz; Choon Ping Tan; Tanja I Näslund; Peter Liljeström; Friedemann Weber; Caetano Reis e Sousa
Journal:  Science       Date:  2006-10-12       Impact factor: 47.728

6.  A novel biclustering approach to association rule mining for predicting HIV-1-human protein interactions.

Authors:  Anirban Mukhopadhyay; Ujjwal Maulik; Sanghamitra Bandyopadhyay
Journal:  PLoS One       Date:  2012-04-23       Impact factor: 3.240

7.  VirusMINT: a viral protein interaction database.

Authors:  Andrew Chatr-aryamontri; Arnaud Ceol; Daniele Peluso; Aurelio Nardozza; Simona Panni; Francesca Sacco; Michele Tinti; Alex Smolyar; Luisa Castagnoli; Marc Vidal; Michael E Cusick; Gianni Cesareni
Journal:  Nucleic Acids Res       Date:  2008-10-30       Impact factor: 16.971

8.  Literature-curated protein interaction datasets.

Authors:  Michael E Cusick; Haiyuan Yu; Alex Smolyar; Kavitha Venkatesan; Anne-Ruxandra Carvunis; Nicolas Simonis; Jean-François Rual; Heather Borick; Pascal Braun; Matija Dreze; Jean Vandenhaute; Mary Galli; Junshi Yazaki; David E Hill; Joseph R Ecker; Frederick P Roth; Marc Vidal
Journal:  Nat Methods       Date:  2009-01       Impact factor: 28.547

9.  VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks.

Authors:  Vincent Navratil; Benoît de Chassey; Laurène Meyniel; Stéphane Delmotte; Christian Gautier; Patrice André; Vincent Lotteau; Chantal Rabourdin-Combe
Journal:  Nucleic Acids Res       Date:  2008-11-04       Impact factor: 16.971

10.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.

Authors:  Da Wei Huang; Brad T Sherman; Richard A Lempicki
Journal:  Nucleic Acids Res       Date:  2008-11-25       Impact factor: 16.971

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  16 in total

1.  Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection.

Authors:  Heeju Noh; Jason E Shoemaker; Rudiyanto Gunawan
Journal:  Nucleic Acids Res       Date:  2018-04-06       Impact factor: 16.971

2.  HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry.

Authors:  Emine Guven-Maiorov; Asma Hakouz; Sukejna Valjevac; Ozlem Keskin; Chung-Jung Tsai; Attila Gursoy; Ruth Nussinov
Journal:  J Mol Biol       Date:  2020-02-13       Impact factor: 5.469

3.  Cellular DDX21 RNA helicase inhibits influenza A virus replication but is counteracted by the viral NS1 protein.

Authors:  Guifang Chen; Chien-Hung Liu; Ligang Zhou; Robert M Krug
Journal:  Cell Host Microbe       Date:  2014-04-09       Impact factor: 21.023

4.  Prediction of Host-Pathogen Interactions for Helicobacter pylori by Interface Mimicry and Implications to Gastric Cancer.

Authors:  Emine Guven-Maiorov; Chung-Jung Tsai; Buyong Ma; Ruth Nussinov
Journal:  J Mol Biol       Date:  2017-10-26       Impact factor: 5.469

5.  Interface-Based Structural Prediction of Novel Host-Pathogen Interactions.

Authors:  Emine Guven-Maiorov; Chung-Jung Tsai; Buyong Ma; Ruth Nussinov
Journal:  Methods Mol Biol       Date:  2019

6.  VirHostNet 2.0: surfing on the web of virus/host molecular interactions data.

Authors:  Thibaut Guirimand; Stéphane Delmotte; Vincent Navratil
Journal:  Nucleic Acids Res       Date:  2014-11-11       Impact factor: 16.971

Review 7.  Computational approaches for prediction of pathogen-host protein-protein interactions.

Authors:  Esmaeil Nourani; Farshad Khunjush; Saliha Durmuş
Journal:  Front Microbiol       Date:  2015-02-24       Impact factor: 5.640

8.  Non-interacting proteins may resemble interacting proteins: prevalence and implications.

Authors:  Guillaume Launay; Nicoletta Ceres; Juliette Martin
Journal:  Sci Rep       Date:  2017-01-13       Impact factor: 4.379

9.  A Structure-Informed Atlas of Human-Virus Interactions.

Authors:  Gorka Lasso; Sandra V Mayer; Evandro R Winkelmann; Tim Chu; Oliver Elliot; Juan Angel Patino-Galindo; Kernyu Park; Raul Rabadan; Barry Honig; Sagi D Shapira
Journal:  Cell       Date:  2019-08-29       Impact factor: 41.582

10.  Uncovering New Pathogen-Host Protein-Protein Interactions by Pairwise Structure Similarity.

Authors:  Tao Cui; Weihui Li; Lei Liu; Qiaoyun Huang; Zheng-Guo He
Journal:  PLoS One       Date:  2016-01-22       Impact factor: 3.240

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