ArticleProceedings of the National Academy of Sciences of the United States of America2011
Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed.
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- Insight into the High-Efficiency Benzo(a)pyrene Degradation Ability ofInternational journal of molecular sciences · 2023Article
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- Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1.Scientific reports · 2021Article
- Identification of a G-Protein-Independent Activator of GIRK Channels.Cell reports · 2020Article
- The characterization of Thermotoga maritima Arginine Binding Protein variants demonstrates that minimal local strains have an important impact on protein stability.Scientific reports · 2019Article
- 3D-QSAR and Molecular Docking Studies on the TcPMCA1-Mediated Detoxification of Scopoletin and Coumarin Derivatives.International journal of molecular sciences · 2017Article
- Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins.Journal of biological physics · 2017Article
- A closer look into the α-helix basin.Scientific reports · 2016Article
- Tertiary alphabet for the observable protein structural universe.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Extension of the classical classification of β-turns.Scientific reports · 2016Article
- Beyond basins: φ,ψ preferences of a residue depend heavily on the φ,ψ values of its neighbors.Protein science : a publication of the Protein Society · 2016Article
- A novel secondary structure based on fused five-membered rings motif.Scientific reports · 2016Article
- The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design.Protein engineering, design & selection : PEDS · 2016Article
- Unconventional N-H…N Hydrogen Bonds Involving Proline Backbone Nitrogen in Protein Structures.Biophysical journal · 2016Article
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Abstract
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 3/4 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.
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