ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces

Saha, Rudra P.; Bahadur, Ranjit P.; Pal, Arumay; Mandal, Saptarshi; Chakrabarti, Pinak
January 2006
BMC Structural Biology;2006, Vol. 6, p11
Academic Journal
Background: Molecular recognition is all pervasive in biology. Protein molecules are involved in enzyme regulation, immune response, signal transduction, oligomer assembly, etc. Delineation of physical and chemical features of the interface formed by protein-protein association would allow us to better understand protein interaction networks on one hand, and to design molecules that can engage a given interface and thereby control protein function on the other hand. Results: ProFace is a suite of programs that uses a file, containing atomic coordinates of a multichain molecule, as input and analyzes the interface between any two or more subunits. The interface residues are shown segregated into spatial patches (if such a clustering is possible based on an input threshold distance) and/or core and rim regions. A number of physicochemical parameters defining the interface is tabulated. Among the different output files, one contains the list of interacting residues across the interface. Results can be used to infer if a particular interface belongs to a homodimeric molecule. Conclusion: A web-server, ProFace (available at http://www.boseinst.ernet.in/resources/bioinfo/ stag.html) has been developed for dissecting protein-protein interfaces and deriving various physicochemical parameters.


Related Articles

  • Transient protein–protein interactions. Acuner Ozbabacan, Saliha Ece; Engin, Hatice Billur; Gursoy, Attila; Keskin, Ozlem // PEDS: Protein Engineering, Design & Selection;Sep2011, Vol. 24 Issue 9, p635 

    Transient complexes are crucial for diverse biological processes such as biochemical pathways and signaling cascades in the cell. Here, we give an overview of the transient interactions; the importance of transient interactions as drug targets; and the structural characterization of transient...

  • Real-time monitoring of receptor and G-protein interactions in living cells. Galés, Céline; Rebois, R. Victor; Hogue, Mireille; Trieu, Phan; Breit, Andreas; Hébert, Terence E.; Bouvier, Michel // Nature Methods;Mar2005, Vol. 2 Issue 3, p177 

    G protein–coupled receptors (GPCRs) represent the largest family of proteins involved in signal transduction. Here we present a bioluminescence resonance energy transfer (BRET) assay that directly monitors in real time the early interactions between human GPCRs and their cognate G-protein...

  • Monitoring regulated protein-protein interactions using split TEV. Wehr, Michael C.; Laage, Rico; Bolz, Ulrike; Fischer, Tobias M.; Grünewald, Sylvia; Scheek, Sigrid; Bach, Alfred; Nave, Klaus-Armin; Rossner, Moritz J. // Nature Methods;Dec2006, Vol. 3 Issue 12, p985 

    Signaling cascades integrate extracellular stimuli primarily through regulated protein-protein interactions (PPIs). Intracellular signal transduction strictly depends on PPIs occurring at the membrane and in the cytosol. To monitor constitutive and regulated protein interactions within living...

  • SAM Domain-Based Protein Oligomerization Observed by Live-Cell Fluorescence Fluctuation Spectroscopy. Slaughter, Brian D.; Huff, Joseph M.; Wiegraebe, Winfried; Schwartz, Joel W.; Li, Rong // PLoS ONE;2008, Vol. 3 Issue 4, p1 

    Sterile-alpha-motif (SAM) domains are common protein interaction motifs observed in organisms as diverse as yeast and human. They play a role in protein homo- and hetero-interactions in processes ranging from signal transduction to RNA binding. In addition, mutations in SAM domain and...

  • IP-FCM Measures Physiologic Protein-Protein Interactions Modulated by Signal Transduction and Small-Molecule Drug Inhibition. Smith, Stephen E. P.; Bida, Anya T.; Davis, Tessa R.; Sicotte, Hugues; Patterson, Steven E.; Gil, Diana; Schrum, Adam G.; Kanellopoulos, Jean // PLoS ONE;Sep2012, Vol. 7 Issue 9, Special section p1 

    Protein-protein interactions (PPI) mediate the formation of intermolecular networks that control biological signaling. For this reason, PPIs are of outstanding interest in pharmacology, as they display high specificity and may represent a vast pool of potentially druggable targets. However, the...

  • Yeast Two-Hybrid, a Powerful Tool for Systems Biology. Brückner, Anna; Polge, Cécile; Lentze, Nicolas; Auerbach, Daniel; Schlattner, Uwe // International Journal of Molecular Sciences;Jun2009, Vol. 10 Issue 6, p2763 

    A key property of complex biological systems is the presence of interaction networks formed by its different components, primarily proteins. These are crucial for all levels of cellular function, including architecture, metabolism and signalling, as well as the availability of cellular energy....

  • SIGNAL TRANSDUCTION: Mastering hopscotch. Patterson, Mark // Nature Reviews Genetics;Mar2002, Vol. 3 Issue 3, p162 

    Discusses research being done on JAK/STAT signal transduction. Reference to a study by Chen et al; Basic mechanism of JAK/STAT signalling.

  • From an armadillo to electricity. Ladurner, Andreas G. // Nature Structural Biology;Jan2003, Vol. 10 Issue 1, p12 

    Provides information on cellular signal transduction process. Function of electrical gradients; Elements that moderate the signal transduction process; Hypothesis on the binding of triphosphate to the receptor.

  • Structures of RabGGTase—substrate/product complexes provide insights into the evolution of protein prenylation. Zhong Guo; Yao-Wen Wu; Das, Debapratim; Delon, Christine; Cramer, Janinna; Shen Yu; Thuns, Sandra; Lupilova, Nataliya; Waldmann, Herbert; Brunsveld, Luc; Goody, Roger S; Alexandrov, Kirill; Blankenfeldt, Wulf // EMBO Journal;9/24/2008, Vol. 27 Issue 18, p2444 

    Post-translational isoprenylation of proteins is carried out by three related enzymes: farnesyltransferase, geranylgeranyl transferase-I, and Rab geranylgeranyl transferase (RabGGTase). Despite the fact that the last one is responsible for the largest number of individual protein prenylation...


Read the Article


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

Try another library?
Sign out of this library

Other Topics