Protein-Peptide Complex Prediction through Fragment Interaction Patterns

The number of protein-peptide interactions in a cell is so large that experimental determination of all these complex structures would be a daunting task. Although homology modeling and refinement protocols have vastly improved the number and quality of predicted structural models, ab initio methods...

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Bibliographic Details
Published in:Structure (London) 2013-05, Vol.21 (5), p.789-797
Main Authors: Verschueren, Erik, Vanhee, Peter, Rousseau, Frederic, Schymkowitz, Joost, Serrano, Luis
Format: Article
Language:English
Subjects:
Accessibility
Algorithms
Backbone
Binding Sites
Docking
Fragmentation
Mathematical models
Models, Molecular
Peptides - chemistry
Peptides - metabolism
Protein Conformation
Proteins
Proteins - chemistry
Proteins - metabolism
Proteïnes
Pèptids
Química
Sampling
Tasks
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Summary:The number of protein-peptide interactions in a cell is so large that experimental determination of all these complex structures would be a daunting task. Although homology modeling and refinement protocols have vastly improved the number and quality of predicted structural models, ab initio methods are still challenged by both the large number of possible docking sites and the conformational space accessible to flexible peptides. We present a method that addresses these challenges by sampling the entire accessible surface of a protein with a reduced conformational space of interacting backbone fragment pairs from unrelated structures. We demonstrate its potential by predicting ab initio the bound structure for a variety of protein-peptide complexes. In addition, we show the potential of our method for the discovery of domain interaction sites and domain-domain docking. [Display omitted] ► Polypeptide fragment interaction patterns predict bound protein-peptide complexes ► Peptide structures can be refined or extended by polypeptide fragment alphabets ► Interacting polypeptide fragment pairs guide domain-domain interface identification ► Interacting polypeptide fragment scaffolds have potential to dock protein domains The ability to predict structures of various protein/protein complexes is critical for developing a systems view of cellular function. Verschueren et al. develop a method for de novo prediction of protein/peptide complexes and show that it also performs domain interaction site discovery and domain-domain docking.
ISSN:0969-2126
1878-4186
DOI:10.1016/j.str.2013.02.023