Perspective

Rose, George D.

doi:10.1002/pro.101691

Cited by 4 publications

(2 citation statements)

References 17 publications

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“…This iconic plot is a compact representation of a profound organizing idea, one that ranks among the fundamentals of structural biochemistry (3)(4)(5). In particular, each peptide unit has only two degrees of freedom, specified by its backbone torsion angles φ and ψ, so all sterically allowed conformations of the alanyl dipeptide can be described by a two-dimensional plot (Fig.…”

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confidence: 99%

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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confidence: 99%

Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints

Porter

Rose

2010

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

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“…It deals with the torsional angles-phi (Φ) and psi (Ψ)-of the residues (amino acids) contained in a peptide. Different aspects of his life have been dealt by various authors (Sarma, 1998;Anonymous, 2016;Mahanti, 2004;Balaram & Ramaseshan, 2001, pp.908-991;Vijayan, 2001, pp.81-97;2001, p.544;Ramakrishnan, 2001Ramakrishnan, , pp.1689Ramakrishnan, -1691Rose, 2001Rose, , pp.1691Rose, -1693Subramanian, 2001, pp. 489-491;Vijayan & Johnson, 2005).…”

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confidence: 99%