ArticleJournal of biological physics2017
Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins.
Article in Journal of biological physics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- DeepBindGCN: Integrating Molecular Vector Representation with Graph Convolutional Neural Networks for Protein-Ligand Interaction Prediction.Molecules (Basel, Switzerland) · 2023Article
- Characterization, protein modeling, and molecular docking of factor C from Indonesian horseshoe crab (Tachypleus gigas).Journal, genetic engineering & biotechnology · 2023Article
- Aerosol capture and coronavirus spike protein deactivation by enzyme functionalized antiviral membranes.Communications materials · 2022Article
- Hydrogen bonds in anoplin peptides aid in identification of a structurally stable therapeutic drug scaffold.Journal of molecular modeling · 2020Article
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2 authors.
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Abstract
In theory, a polypeptide chain can adopt a vast number of conformations, each corresponding to a set of backbone rotation angles. Many of these conformations are excluded due to steric overlaps. Ramachandran and coworkers were the first to look into this problem by plotting backbone dihedral angles in a two-dimensional plot. The conformational space in the Ramachandran map is further refined by considering the energetic contributions of various non-bonded interactions. Alternatively, the conformation adopted by a polypeptide chain may also be examined by investigating interactions between the residues. Since the Ramachandran map essentially focuses on local interactions (residues closer in sequence), out of interest, we have analyzed the dihedral angle preferences of residues that make non-local interactions (residues far away in sequence and closer in space) in the folded structures of proteins. The non-local interactions have been grouped into different types such as hydrogen bond, van der Waals interactions between hydrophobic groups, ion pairs (salt bridges), and ππ-stacking interactions. The results show the propensity of amino acid residues in proteins forming local and non-local interactions. Our results point to the vital role of different types of non-local interactions and their effect on dihedral angles in forming secondary and tertiary structural elements to adopt their native fold.
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