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• W2143694831 abstract "It has been suggested that denatured proteins are predisposed toward the left-handed polyproline II (PII) conformation. One possible source of PII 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 PII and water bridges, the propensity of a residue to participate in water bridges should be correlated with its PII 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 PII in denatured states; such bridges are less frequent around PII than around other conformations. Thus, this analysis casts doubt on water bridges as a dominant factor determining the residue-based PII propensities." @default.
• W2143694831 created "2016-06-24" @default.
• W2143694831 creator A5021239442 @default.
• W2143694831 creator A5025008465 @default.
• W2143694831 date "2009-11-16" @default.
• W2143694831 modified "2023-10-17" @default.
• W2143694831 title "The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures" @default.
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• W2143694831 doi "https://doi.org/10.1093/protein/gzp069" @default.
• W2143694831 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2791050" @default.
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• W2143694831 hasPublicationYear "2009" @default.
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