ArticleProtein science : a publication of the Protein Society2008
Structures, basins, and energies: a deconstruction of the Protein Coil Library.
Article in Protein science : a publication of the Protein Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
- Classification of intramolecular side-chain hydrogen bonds in coil fragments of globular proteins.Protein science : a publication of the Protein Society · 2025Article
- Exploring LCST- and UCST-like Behavior of Branched Molecules Bearing Repeat Units of Elastin-like Peptides as Side Components.Biomacromolecules · 2024Article
- Fluid protein fold space and its implications.BioEssays : news and reviews in molecular, cellular and developmental biology · 2023Article
- Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins.Molecules (Basel, Switzerland) · 2021Review
- Impact of Heat on Coil Hydrodynamic Size Yields the Energetics of Denatured State Conformational Bias.The journal of physical chemistry. B · 2019Article
- Computational design of structured loops for new protein functions.Biological chemistry · 2019Review
- Experimentally Derived and Computationally Optimized Backbone Conformational Statistics for Blocked Amino Acids.Journal of chemical theory and computation · 2019Article
- AnACS catalysis · 2019Article
- A random forest learning assisted "divide and conquer" approach for peptide conformation search.Scientific reports · 2018Article
- Modeling the Early Stages of Phase Separation in Disordered Elastin-like Proteins.Biophysical journal · 2018Article
- Tuning the Flexibility of Glycine-Serine Linkers To Allow Rational Design of Multidomain Proteins.Biochemistry · 2017Article
- 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
- An amino acid code for irregular and mixed protein packing.Proteins · 2015Article
- Reducing the dimensionality of the protein-folding search problem.Protein science : a publication of the Protein Society · 2012Article
- A thermodynamic definition of protein domains.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- (φ,ψ)₂ motifs: a purely conformation-based fine-grained enumeration of protein parts at the two-residue level.Journal of molecular biology · 2012Article
- J-coupling constants for a trialanine peptide as a function of dihedral angles calculated by density functional theory over the full Ramachandran space.Physical chemistry chemical physics : PCCP · 2011Article
- Populations of the three major backbone conformations in 19 amino acid dipeptides.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Counting peptide-water hydrogen bonds in unfolded proteins.Protein science : a publication of the Protein Society · 2011Article
- Ramachandran redux.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
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3 authors.
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Abstract
Globular proteins adopt complex folds, composed of organized assemblies of alpha-helix and beta-sheet together with irregular regions that interconnect these scaffold elements. Here, we seek to parse the irregular regions into their structural constituents and to rationalize their formative energetics. Toward this end, we dissected the Protein Coil Library, a structural database of protein segments that are neither alpha-helix nor beta-strand, extracted from high-resolution protein structures. The backbone dihedral angles of residues from coil library segments are distributed indiscriminately across the phi,psi map, but when contoured, seven distinct basins emerge clearly. The structures and energetics associated with the two least-studied basins are the primary focus of this article. Specifically, the structural motifs associated with these basins were characterized in detail and then assessed in simple simulations designed to capture their energetic determinants. It is found that conformational constraints imposed by excluded volume and hydrogen bonding are sufficient to reproduce the observed ,psi distributions of these motifs; no additional energy terms are required. These three motifs in conjunction with alpha-helices, strands of beta-sheet, canonical beta-turns, and polyproline II conformers comprise approximately 90% of all protein structure.
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