Disallowed spots in protein structures

Ramachandran (phi, psi) 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 & Aring;, Rwork/Rfree <= 0.10). These stringent criteria were applied to rule out data or model errors or any crys-tallographic disorders. No disallowed conformation was found in the dataset. Further, we also examined dis-allowed conformations in a larger dataset (resolution <= 1.5 & Aring;, 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 dis-allowed 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 re-strictions, residue propensity of secondary structures and compensating sidechain and mainchain interactions, stabilizing turn-mimics.

Automated summary

The Ramachandran steric map is used to describe the conformation space of protein structures. This study focused on identifying disallowed spots in protein structures and found that certain residues tend to occur in disallowed conformations. Short loops and residues involved in interactions were particularly affected by conformational strain. Additionally, certain amino acids were found to have a higher tendency to occur in disallowed conformations.