Perspective on "Stereochemistry of polypeptide chain conformations"

Lavery, Richard

doi:10.1007/s002149900022

Cited by 3 publications

(1 citation statement)

References 20 publications

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“…Recent papers describe how addition of hydrogen bond satisfaction causes the plot to contract, while extreme values of the τ‐angle (the C′‐Cα‐N scalar angle) cause the plot to expand . Even so, the basic plot has withstood the test of time and has become one of the few results in all of biological chemistry where a discrepancy between theory and experiment can raise doubt about the experiment …”

Section: Introductionmentioning

confidence: 99%

Ramachandran maps for side chains in globular proteins

Rose

2019

Proteins

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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.

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Section: Introductionmentioning

confidence: 99%

Ramachandran maps for side chains in globular proteins

Rose

2019

Proteins

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Perspective

Rose

2001

Protein Science

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Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints

Porter

Rose

2010

Proc. Natl. Acad. Sci. U.S.A.

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A protein backbone has two degrees of conformational freedom per residue, described by its φ,ψ-angles. Accordingly, the energy landscape of a blocked peptide unit can be mapped in two dimensions, as shown by Ramachandran, Sasisekharan, and Ramakrishnan almost half a century ago. With atoms approximated as hard spheres, the eponymous Ramachandran plot demonstrated that steric clashes alone eliminate ¾ of φ,ψ-space, a result that has guided all subsequent work. Here, we show that adding hydrogen-bonding constraints to these steric criteria eliminates another substantial region of φ,ψ-space for a blocked peptide; for conformers within this region, an amide hydrogen is solvent-inaccessible, depriving it of a hydrogen-bonding partner. Yet, this "forbidden" region is well populated in folded proteins, which can provide longer-range intramolecular hydrogen-bond partners for these otherwise unsatisfied polar groups. Consequently, conformational space expands under folding conditions, a paradigm-shifting realization that prompts an experimentally verifiable conjecture about likely folding pathways.protein folding | hydrogen bonding | β-turns | helix nucleation

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Perspective on "Stereochemistry of polypeptide chain conformations"

Cited by 3 publications

References 20 publications

Ramachandran maps for side chains in globular proteins

Ramachandran maps for side chains in globular proteins

Perspective

Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints

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