Ramachandran maps for side chains in globular proteins

Research output: Contribution to journalArticlepeer-review

Abstract

The Ramachandran plot for backbone ϕ,ψ-angles in a blocked monopeptide has played a central role in understanding protein structure. Curiously, a similar analysis for side chain χ-angles has been comparatively neglected. Instead, efforts have focused on compiling various types of side chain libraries extracted from proteins of known structure. Departing from this trend, the following analysis presents backbone-based maps of side chains in blocked monopeptides. As in the original ϕ,ψ-plot, these maps are derived solely from hard-sphere steric repulsion. Remarkably, the side chain biases exhibit marked similarities to corresponding biases seen in high-resolution protein structures. Consequently, some of the entropic cost for side chain localization in proteins is prepaid prior to the onset of folding events because conformational bias is built into the chain at the covalent level. Furthermore, side chain conformations are seen to experience fewer steric restrictions for backbone conformations in either the α or β basins, those map regions where repetitive ϕ,ψ-angles result in α-helices or strands of β-sheet, respectively. Here, these α and β basins are entropically favored for steric reasons alone; a blocked monopeptide is too short to accommodate the peptide hydrogen bonds that stabilize repetitive secondary structure. Thus, despite differing energetics, α/β-basins are favored for both monopeptides and repetitive secondary structure, underpinning an energetically unfrustrated compatibility between these two levels of protein structure.

Original languageEnglish (US)
Pages (from-to)357-364
Number of pages8
JournalProteins: Structure, Function and Bioinformatics
Volume87
Issue number5
DOIs
StatePublished - May 2019
Externally publishedYes

Keywords

  • Ramachandran maps
  • protein folding
  • residue side chains
  • steric restrictions

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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