ArticleBiophysical journal2012
The power of hard-sphere models: explaining side-chain dihedral angle distributions of Thr and Val.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 31 citations in OpenAlex.
- Residue burial encodes a protein's fold.bioRxiv : the preprint server for biology · 2026Article
- Core packing of well-defined X-ray and NMR structures is the same.Protein science : a publication of the Protein Society · 2022Article
- A threonine zipper that mediates protein-protein interactions: Structure and prediction.Protein science : a publication of the Protein Society · 2018Article
- Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.Proteins · 2018Article
- Distribution of dipeptides in different protein structural classes: an effort to find new similarities.European biophysics journal : EBJ · 2018Article
- Collective repacking reveals that the structures of protein cores are uniquely specified by steric repulsive interactions.Protein engineering, design & selection : PEDS · 2017Article
- Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences.Journal of the American Chemical Society · 2017Article
- Protein design: Past, present, and future.Biopolymers · 2015Review
- Intrinsic α-helical and β-sheet conformational preferences: a computational case study of alanine.Protein science : a publication of the Protein Society · 2014Article
- New insights into the interdependence between amino acid stereochemistry and protein structure.Biophysical journal · 2013Article
- In silico insights of L-glutamate: structural features in vacuum and in complex with its receptor.Journal of amino acids · 2013Article
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3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The energy functions used to predict protein structures typically include both molecular-mechanics and knowledge-based terms. In contrast, our approach is to develop robust physics- and geometry-based methods. Here, we investigate to what extent simple hard-sphere models can be used to predict side-chain conformations. The distributions of the side-chain dihedral angle χ(1) of Val and Thr in proteins of known structure show distinctive features: Val side chains predominantly adopt χ(1) = 180°, whereas Thr side chains typically adopt χ(1) = 60° and 300° (i.e., χ(1) = ±60° or g- and g(+) configurations). Several hypotheses have been proposed to explain these differences, including interresidue steric clashes and hydrogen-bonding interactions. In contrast, we show that the observed side-chain dihedral angle distributions for both Val and Thr can be explained using only local steric interactions in a dipeptide mimetic. Our results emphasize the power of simple physical approaches and their importance for future advances in protein engineering and design.
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