Analysis of residue conformations in peptides in Cambridge structural database and protein‐peptide structural complexes

Abstract

A comprehensive statistical analysis of the geometric parameters of peptide chains in a reduced dataset of protein-peptide complexes in Protein Data Bank (PDB) is presented. The angular variables describing the backbone conformations of amino acid residues in peptide chains shed insights into the conformational preferences of peptide residues interacting with protein partners. Nonparametric statistical approaches are employed to evaluate the interrelationships and associations in structural variables. Grouping of residues based on their structure into chemical classes reveals characteristic trends in parameter relationships. A comparison of canonical amino acid residues in free peptide structures in Cambridge structural database (CSD) with identical residues in PDB complexes, suggests that the information can be integrated from both the structural repositories enabling efficient and accurate modeling of biologically active peptides.

A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts

“…(d) Comparison of Conformations in Different Environments. Raghavender compared the backbone conformations of amino acid residues in (a) small peptides bound to proteins in Protein Data Bank (PDB) structures and (b) unbound peptides in CSD structures . Aliphatic residues (Ala, Ile, Leu, and Val) occurred often enough in both to allow meaningful comparison and were found to show broadly similar geometric trends, but with the CSD residues being somewhat more conformationally variable.…”

Computational Investigation of Structural Interfaces of Protein Complexes with Short Linear Motifs

“…Polypeptide chains with less than or equal to 30 residues were treated as peptides in this analysis. The reason for using such a large value for peptide length definition is arbitrary and to an extent is based on our observation of synthetic peptides of length > 30 in both PDB and Cambridge Structural Database 43 . In addition, SLiMs are known to be short (3-10 amino acids) and >30 residues are treated as IDRs.…”

“…The reason for using such a large value for peptide length definition is arbitrary and to an extent is based on our observation of synthetic peptides of length >30 in both PDB and Cambridge Structural Database. 48 In The structures were divided into three classes as protein− protein, protein-peptide and others. The third category of 20 structures consists of mostly monomeric and small molecule bound proteins, with one example of a peptide−peptide complex (2JO9) and one multiprotein-peptide complex (3VI4).…”