ArticlePLoS computational biology2010
Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Quantitative Integration of FRET and Molecular Dynamics for Modeling Flexible Peptides.The journal of physical chemistry. B · 2026Article
- Tunable CH/π Interactions within a Tryptophan Zipper Motif to Stabilize the Fold of Long β-Hairpin Peptides.ACS chemical biology · 2023Article
- Physical Chemistry of the Protein Backbone: Enabling the Mechanisms of Intrinsic Protein Disorder.The journal of physical chemistry. B · 2020Review
- Microsecond sub-domain motions and the folding and misfolding of the mouse prion protein.eLife · 2019Article
- Hydrophobic-hydrophilic forces in protein folding.Biopolymers · 2017Article
- Covalent dye attachment influences the dynamics and conformational properties of flexible peptides.PloS one · 2017Article
- Cooperation of local motions in the Hsp90 molecular chaperone ATPase mechanism.Nature chemical biology · 2016Article
- A DFT study on the role of long range correlation interaction and solvent effects in homochiral and heterochiral cyclic trimerization of imidazole based heterocyclic amino acids.Journal of molecular modeling · 2016Article
- Force field-dependent solution properties of glycine oligomers.Journal of computational chemistry · 2015Article
- Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation.Journal of the American Chemical Society · 2015Article
- Macrocycles: lessons from the distant past, recent developments, and future directions.Chemical science · 2015Article
- Residual structure in unfolded proteins.Current opinion in structural biology · 2012Review
- Contemporary strategies for peptide macrocyclization.Nature chemistry · 2011Review
- Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Universality in the timescales of internal loop formation in unfolded proteins and single-stranded oligonucleotides.Biophysical journal · 2010Article
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Authors and funding
5 authors.
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Abstract
Characterization of the length dependence of end-to-end loop-closure kinetics in unfolded polypeptide chains provides an understanding of early steps in protein folding. Here, loop-closure in poly-glycine-serine peptides is investigated by combining single-molecule fluorescence spectroscopy with molecular dynamics simulation. For chains containing more than 10 peptide bonds loop-closing rate constants on the 20-100 nanosecond time range exhibit a power-law length dependence. However, this scaling breaks down for shorter peptides, which exhibit slower kinetics arising from a perturbation induced by the dye reporter system used in the experimental setup. The loop-closure kinetics in the longer peptides is found to be determined by the formation of intra-peptide hydrogen bonds and transient beta-sheet structure, that accelerate the search for contacts among residues distant in sequence relative to the case of a polypeptide chain in which hydrogen bonds cannot form. Hydrogen-bond-driven polypeptide-chain collapse in unfolded peptides under physiological conditions found here is not only consistent with hierarchical models of protein folding, that highlights the importance of secondary structure formation early in the folding process, but is also shown to speed up the search for productive folding events.
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