Dec 17, 2014

Computational Investigation Of Structural Interfaces Of Protein Complexes With Short Linear Motifs

BioRxiv : the Preprint Server for Biology
George Locke, Alexandre V Morozov

Abstract

Protein complexes with short linear motifs (SLiMs) are known to play important regulatory functions in eukaryotes. In this investigation, I have studied the structures deposited in PDB with SLiMs. The structures Were grouped into three broad categories of protein-protein, protein-peptide and the rest as others. Protein-peptide complexes Were found to be most highly represented. The interfaces Were evaluated for geometric features and conformational variables. It was observed that protein-protein and protein-peptide complexes show characteristic differences in residue pairings, which Were quantified by evaluating normalized contact residue pairing frequencies. Interface residues adopt characteristic canonical residue conformations in the Ramachandran space, with a pronounced preference for positive Φ conformations. It was observed that phosphorylated residues have an unusual propensity to adopt the unusual positive Φ conformations at the interface.

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Mentioned in this Paper

Protein Binding
Recombination, Genetic
Gene Expression
Biophysics
Ligand Binding Domain
High Throughput Analysis
Nucleotides
Protein Domain
DNA Binding
Base Sequence

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