ArticleProtein science : a publication of the Protein Society2005
A novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA).
Article in Protein science : a publication of the Protein Society, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed.
- Generation of unfolded outer membrane protein ensembles defined by hydrodynamic properties.European biophysics journal : EBJ · 2023Article
- Dipole Cooperativity and Polarization Frustration Determine the Secondary Structure Distribution of Short Alanine Peptides in Water.The journal of physical chemistry. B · 2023Article
- Exploring Nearest Neighbor Interactions and Their Influence on the Gibbs Energy Landscape of Unfolded Proteins and Peptides.International journal of molecular sciences · 2022Review
- Beta turn propensity and a model polymer scaling exponent identify intrinsically disordered phase-separating proteins.The Journal of biological chemistry · 2021Article
- Article
- Glycine in Water Favors the Polyproline II State.Biomolecules · 2020Article
- Polyglutamine Solution-State Structural Propensity Is Repeat Length Dependent.The journal of physical chemistry. B · 2019Article
- UV Resonance Raman Structural Characterization of an (In)soluble Polyglutamine Peptide.The journal of physical chemistry. B · 2019Article
- Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites.Protein science : a publication of the Protein Society · 2013Article
- Temperature and urea have opposing impacts on polyproline II conformational bias.Biochemistry · 2013Article
- Insight towards the conserved water mediated recognition of catalytic and structural Zn(+2) ions in human Matrix Metalloproteinase-8 enzyme: A study by MD-simulation methods.Bioinformation · 2013Article
- Characterization of ABL exon 7 deletion by molecular genetic and bioinformatic methods reveals no association with imatinib resistance in chronic myeloid leukemia.Medical oncology (Northwood, London, England) · 2012Article
- Conserved water-mediated H-bonding dynamics of catalytic His159 and Asp158: insight into a possible acid-base coupled mechanism in plant thiol protease.Journal of molecular modeling · 2012Article
- Scaling properties of glycine-rich sequences in guanidine hydrochloride solutions.Biophysical journal · 2012Article
- Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder.Nucleic acids research · 2011Article
- The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures.Protein engineering, design & selection : PEDS · 2010Article
- Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins.PLoS computational biology · 2009Article
- Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease.Journal of biosciences · 2009Article
- Electrostatic effects in unfolded staphylococcal nuclease.Protein science : a publication of the Protein Society · 2008Article
- Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling.BMC structural biology · 2007Article
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5 authors.
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Abstract
In aqueous solution, the ensemble of conformations sampled by peptides and unfolded proteins is largely determined by their interaction with water. It has been a long-standing goal to capture these solute-water energetics accurately and efficiently in calculations. Historically, accessible surface area (ASA) has been used to estimate these energies, but this method breaks down when applied to amphipathic peptides and proteins. Here we introduce a novel method in which hydrophobic ASA is determined after first positioning water oxygens in hydrogen-bonded orientations proximate to all accessible peptide/protein backbone N and O atoms. This conditional hydrophobic accessible surface area is termed CHASA. The CHASA method was validated by predicting the polyproline-II (P(II)) and beta-strand conformational preferences of non-proline residues in the coil library (i.e., non-alpha-helix, non-beta-strand, non-beta-turn library derived from X-ray elucidated structures). Further, the method successfully rationalizes the previously unexplained solvation energies in polyalanyl peptides and compares favorably with published experimentally determined P(II) residue propensities. We dedicate this paper to Frederic M. Richards.
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