ArticleProtein engineering, design & selection : PEDS2010
The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures.
Article in Protein engineering, design & selection : PEDS, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed, 24 citations in OpenAlex.
- WatCon: A Python Tool for Analysis of Conserved Water Networks Across Protein Families.JACS Au · 2025Article
- African walnut (Frontiers in nutrition · 2025Article
- Proline, a unique amino acid whose polymer, polyproline II helix, and its analogues are involved in many biological processes: a review.Amino acids · 2024Review
- Dipole Cooperativity and Polarization Frustration Determine the Secondary Structure Distribution of Short Alanine Peptides in Water.The journal of physical chemistry. B · 2023Article
- Investigation of theRSC advances · 2020Article
- Conformational analysis of short polar side-chain amino-acids through umbrella sampling and DFT calculations.Journal of molecular modeling · 2016Article
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2 authors at 1 institution in 1 country.
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Abstract
It has been suggested that denatured proteins are predisposed toward the left-handed polyproline II (P(II)) conformation. One possible source of P(II) stability in the denatured state is water bridges. Water bridges are networks of water molecules that link nearby hydrogen bond acceptors and/or donors on proteins. On the basis of the proposed behavior of P(II) and water bridges, the propensity of a residue to participate in water bridges should be correlated with its P(II) propensity. To test this hypothesis, we analyzed the following data sets: 2351 high-resolution crystal structures, and the native and denatured states of 188 different proteins from all-atom, explicit-solvent molecular dynamics (MD) simulations, which are part of our Dynameomics effort. We found that water bridges do not explain the high frequency of P(II) in denatured states; such bridges are less frequent around P(II) than around other conformations. Thus, this analysis casts doubt on water bridges as a dominant factor determining the residue-based P(II) propensities.
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