An Automated Approach to Segregate and Identify Functional or Disordered Loop Regions in Protein Structures using their Ramachandran Maps

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The loops which connect or flank helices/sheets in protein structures are known to be functionally important. However, ironically they also belong to the part of protein whose structure is least accurately predicted. Here, a new method to isolate and analyze loop regions in protein structure is proposed using the spatial coordinates of the solved 3D structure. The extent of dispersion among points of successive amino acid residues in the Ramachandran map of protein region is utilized to calculate the Mean Separation between these points in the Ramachandran Plot (MSRP). Based on analysis of 2935 protein secondary structure regions obtained using DSSP software, spanning a range from 2 to 64 residues, taken from a set of 170 proteins, it is shown that helices (MSRP < 17) and strands (MSRP < 64) stand effectively demarcated from the loop regions (MSRP > 130). Analysis of 43 DNA binding and 98 ligand binding proteins revealed several loop regions with clear change in MSRP subsequent to binding. The population of such loops correlated with the magnitude of backbone displacement in the protein subsequent to binding. Can changes in MSRP quantify the temporal oscillations in dihedral angles among structured/unstructured regions in proteins? Molecular dynamics simulations (10 ns) revealed that deviations in MSRP among different snapshots in the trajectory were at least two-fold higher for unstructured proteins (PDB codes: 2SOB, 1LXL, 2HDL & 1VZS) in comparison with folded proteins (PDB codes: 1BGF & 1MUN). Additionally it was observed that deviations in MSRP were highest amongst loop regions, while it was lowest amongst alpha-helical regions. The above results validate use of MSRP parameter as a tool to identify & investigate functionally active loops and unstructured regions in protein structures.