Disallowed spots in protein structures

• Published in: Biochimica et biophysica acta. General subjects Vol. 1867; no. 12; p. 130493
• Main Authors: Kumar, Mayank, Rathore, R.S.
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.12.2023
• Subjects: data collection; Disallowed conformation; disulfides; Folding; ligands; Protein conformation; Protein structure; Ramachandran (φ,ψ) map; Steric map; Ramachandran (φ,ψ) map; Steric map; Protein structure; Protein conformation; Folding; Disallowed conformation
• DOI: 10.1016/j.bbagen.2023.130493
• ISSN: 0304-4165; 1872-8006

Ramachandran (ϕ, ψ) steric map was introduced in 1963 to describe available conformation space for protein structures. Subsequently, residues were observed in high-energy disallowed regions of the map. To unequivocally identify the locations of disallowed conformations of residues, we got 36 noise-free protein structures (resolution ≤1 Å, Rwork/Rfree ≤ 0.10). These stringent criteria were applied to rule out data or model errors or any crystallographic disorders. No disallowed conformation was found in the dataset. Further, we also examined disallowed conformations in a larger dataset (resolution ≤1.5 Å, devoid of any model errors, or disorders). The observed locations of disallowed residues are referred as disallowed spots. These spots include short loops of 3–5 residues, and locations where residues participate in disulfide bonding or intramolecular interactions or inter-molecular interactions with neighboring water, metals or ligands. Conformational sampling revealed that short loops in between secondary structures hardly have any opportunity to relieve from conformational strain. Residues involved in interactions, which provide energetic compensation for high-energy conformational states, were relieved from strain once the causative interaction was removed. The present study aims to identify disallowed spots in the native state of proteins, wherein residues are forced to be trapped in high-energy disallowed conformations. Moreover, it was also observed that pre-Pro, Ser, Asp, trans-Pro, Val, Asn & Gly have higher tendency to occur in disallowed conformation, which could be attributed to factors such as conformational restrictions, residue propensity of secondary structures and compensating sidechain and mainchain interactions, stabilizing turn-mimics. •Occurrence of 0.1% residues in disallowed regions of protein native structure.•The observed locations of disallowed residues are referred as disallowed spots.•Disallowed spots are in exposed short loops of length 3–5 residues.•Disallowed spots are in residues involved in different types of interactions.•pre-Pro, Ser, Asp, trans-Pro, Val, Asn and Gly, have higher frequency in the disallowed region.