Structural deformation upon protein-protein interaction: A structural alphabet approach

Martin, Juliette; Regad, Leslie; Lecornet, Hélène; Camproux, Anne-Claude
January 2008
BMC Structural Biology;2008, Vol. 8, Special section p1
Academic Journal
Background: In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. Results: In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backbone. Using a control set to distinguish induced fit from experimental error and natural protein flexibility, we show that the fraction of structural letters modified upon binding is significantly greater than in the control set (36% versus 28%). This proportion is even greater in the interface regions (41%). Interface regions preferentially involve coils. Our analysis further reveals that some structural letters in coil are not favored in the interface. We show that certain structural letters in coil are particularly subject to modifications at the interface, and that the severity of structural change also varies. These information are used to derive a structural letter substitution matrix that summarizes the local structural changes observed in our data set. We also illustrate the usefulness of our approach to identify common binding motifs in unrelated proteins. Conclusion: Our study provides qualitative information about induced fit. These results could be of help for flexible docking.


Related Articles

  • Sun, soccer and…where's the sand?  // Four Four Two;Sep2011, Issue 207, p127 

    The article reports that the Gillette Beach Soccer Championship in Malta has been postponed due to lack of beach space where the tournament was supposed to take place.

  • Homology Inference of Protein-Protein Interactions via Conserved Binding Sites. Tyagi, Manoj; Thangudu, Ratna R.; Dachuan Zhang; Bryant, Stephen H.; Madej, Thomas; Panchenko, Anna R. // PLoS ONE;Jan2012, Vol. 7 Issue 1, p1 

    The coverage and reliability of protein-protein interactions determined by high-throughput experiments still needs to be improved, especially for higher organisms, therefore the question persists, how interactions can be verified and predicted by computational approaches using available data on...

  • Types of interfaces for homodimer folding and binding. Karthikraja, Velmurugan; Suresh, Abishek; Lulu, Sajitha; Kangueane, Uma; Kangueane, Pandjassarame // Bioinformation;2009, Vol. 4 Issue 3, p101 

    Homodimers have a role in catalysis and regulation through the formation of stable interfaces. These interfaces are formed through different folding mechanisms such as 2-state without stable intermediate (2S), 3-state with monomer intermediate (3SMI) and 3-state with dimer intermediate (3SDI)....

  • Alignment of Non-Covalent Interactions at Protein-Protein Interfaces. Hongbo Zhu; Sommer, Ingolf; Lengauer, Thomas; Domingues, Francisco S. // PLoS ONE;2008, Vol. 3 Issue 4, p1 

    Background: The study and comparison of protein-protein interfaces is essential for the understanding of the mechanisms of interaction between proteins. While there are many methods for comparing protein structures and protein binding sites, so far no methods have been reported for comparing the...

  • How Proteins Get in Touch: Interface Prediction in the Study of Biomolecular Complexes. De Vries, Sjoerd J.; Bonvin, Alexandre M. J. J. // Current Protein & Peptide Science;Aug2008, Vol. 9 Issue 4, p394 

    Protein-protein interface prediction is a booming field, with a substantial growth in the number of new methods being published the last two years. The increasing number of available three-dimensional structures of protein-protein complexes has enabled large-scale statistical analyses of protein...

  • The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold. Ciccarelli, Francesca D.; Izaurralde, Elisa; Bork, Peer // BMC Bioinformatics;2003, Vol. 4, p64 

    Background: Multimeric protein complexes have a role in many cellular pathways and are highly interconnected with various other proteins. The characterization of their domain composition and organization provides useful information on the specific role of each region of their sequence. Results:...

  • Computational Structural Analysis: Multiple Proteins Bound to DNA. Tomovic, Andrija; Oakeley, Edward J. // PLoS ONE;2008, Vol. 3 Issue 9, p1 

    Background: With increasing numbers of crystal structures of protein:DNA and protein:protein:DNA complexes publically available, it is now possible to extract sufficient structural, physical-chemical and thermodynamic parameters to make general observations and predictions about their...

  • 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...


Read the Article


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

Try another library?
Sign out of this library

Other Topics