TITLE

Predicting the Binding Patterns of Hub Proteins: A Study Using Yeast Protein Interaction Networks

AUTHOR(S)
Andorf, Carson M.; Honavar, Vasant; Sen, Taner Z.
PUB. DATE
February 2013
SOURCE
PLoS ONE;Feb2013, Vol. 8 Issue 2, p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Protein-protein interactions are critical to elucidating the role played by individual proteins in important biological pathways. Of particular interest are hub proteins that can interact with large numbers of partners and often play essential roles in cellular control. Depending on the number of binding sites, protein hubs can be classified at a structural level as singlish-interface hubs (SIH) with one or two binding sites, or multiple-interface hubs (MIH) with three or more binding sites. In terms of kinetics, hub proteins can be classified as date hubs (i.e., interact with different partners at different times or locations) or party hubs (i.e., simultaneously interact with multiple partners). Methodology: Our approach works in 3 phases: Phase I classifies if a protein is likely to bind with another protein. Phase II determines if a protein-binding (PB) protein is a hub. Phase III classifies PB proteins as singlish-interface versus multiple-interface hubs and date versus party hubs. At each stage, we use sequence-based predictors trained using several standard machine learning techniques. Conclusions: Our method is able to predict whether a protein is a protein-binding protein with an accuracy of 94% and a correlation coefficient of 0.87; identify hubs from non-hubs with 100% accuracy for 30% of the data; distinguish date hubs/party hubs with 69% accuracy and area under ROC curve of 0.68; and SIH/MIH with 89% accuracy and area under ROC curve of 0.84. Because our method is based on sequence information alone, it can be used even in settings where reliable protein-protein interaction data or structures of protein-protein complexes are unavailable to obtain useful insights into the functional and evolutionary characteristics of proteins and their interactions. Availability: We provide a web server for our three-phase approach: http://hybsvm.gdcb.iastate.edu.
ACCESSION #
87624970

 

Related Articles

  • Beta Atomic Contacts: Identifying Critical Specific Contacts in Protein Binding Interfaces. Liu, Qian; Kwoh, Chee Keong; Hoi, Steven C. H. // PLoS ONE;Apr2013, Vol. 8 Issue 4, p1 

    Specific binding between proteins plays a crucial role in molecular functions and biological processes. Protein binding interfaces and their atomic contacts are typically defined by simple criteria, such as distance-based definitions that only use some threshold of spatial distance in previous...

  • The PyRosetta Toolkit: A Graphical User Interface for the Rosetta Software Suite. Adolf-Bryfogle, Jared; Dunbrack Jr., Roland L. // PLoS ONE;Jul2013, Vol. 8 Issue 7, p1 

    The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience....

  • Signal transduction: Molecular monogamy. Endy, Drew; Yaffe, Michael B. // Nature;12/11/2003, Vol. 426 Issue 6967, p614 

    Discusses protein-manipulation experiments using baker's yeast. Protein-based signal-transduction systems assembled through protein-protein interactions; Mechanisms contributing to the binding specificity; Results of Zarrinpar and colleagues' study of the interaction between two proteins from...

  • Sec15 interacts with Rab11 via a novel domain and affects Rab11 localization in vivo. Wu, Shuya; Mehta, Sunil Q.; Pichaud, Franck; Bellen, Hugo J.; Quiocho, Florante A. // Nature Structural & Molecular Biology;Oct2005, Vol. 12 Issue 10, p879 

    Sec15, a component of the exocyst, recognizes vesicle-associated Rab GTPases, helps target transport vesicles to the budding sites in yeast and is thought to recruit other exocyst proteins. Here we report the characterization of a 35-kDa fragment that comprises most of the C-terminal half of...

  • Structural similarity of genetically interacting proteins. Dror, Oranit; Schneidman-Duhovny, Dina; Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J.; Sharan, Roded // BMC Systems Biology;2008, Vol. 2, Special section p1 

    Background: The study of gene mutants and their interactions is fundamental to understanding gene function and backup mechanisms within the cell. The recent availability of large scale genetic interaction networks in yeast and worm allows the investigation of the biological mechanisms underlying...

  • WSsas: a web service for the annotation of functional residues through structural homologues. David Talavera; Roman A. Laskowski; Janet M. Thornton // Bioinformatics;May2009, Vol. 25 Issue 9, p1192 

    Motivation: Annotation tools help scientists to traverse the gap between characterized and uncharacterized proteins. Tools for the prediction of protein function include those which predict the function of entire proteins or complexes, those annotating functional domains and those which predict...

  • Protein–protein binding affinity prediction on a diverse set of structures. Moal, Iain H.; Agius, Rudi; Bates, Paul A. // Bioinformatics;Nov2011, Vol. 27 Issue 21, p3002 

    Motivation: Accurate binding free energy functions for protein–protein interactions are imperative for a wide range of purposes. Their construction is predicated upon ascertaining the factors that influence binding and their relative importance. A recent benchmark of binding affinities...

  • Non-covalent interactions: Fold globally, bond locally. Zondlo, Neal J. // Nature Chemical Biology;Aug2010, Vol. 6 Issue 8, p567 

    The article presents a study conducted by G. J. Bartlett and colleagues on the role of n→π* interactions in the stabilization of protein structure. The study shows that n→π* interactions are ubiquitous in proteins, which are likely to occur in α-helices and in...

  • Trigger factor finds new jobs and contacts. Hoffmann, Anja; Bukau, Bernd // Nature Structural & Molecular Biology;Oct2009, Vol. 16 Issue 10, p1006 

    The article discusses the study which demonstrated the first crystal structure of ribosome-associated chaperone Trigger factor in complex with a protein substrate. It says that the study would widen the range of proteins and nascent chain sequences that can be accommodated by Trigger factor,...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics