ArticleProceedings of the National Academy of Sciences of the United States of America2012
Measurement of energy landscape roughness of folded and unfolded proteins.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
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- UV photochemistry of the L-cystine disulfide bridge in aqueous solution investigated by femtosecond X-ray absorption spectroscopy.Nature communications · 2024Article
- Interpreting forces as deep learning gradients improves quality of predicted protein structures.Biophysical journal · 2024Article
- Selective chiral dimerization and folding driven by arene-perfluoroarene force.Chemical science · 2024Article
- Nonequilibrium Self-Assembly Time Forecasting by the Stochastic Landscape Method.The journal of physical chemistry. B · 2023Article
- Monoclonal antibody stability can be usefully monitored using the excitation-energy-dependent fluorescence edge-shift.The Biochemical journal · 2020Article
- Quantifying residue-specific conformational dynamics of a highly reactive 29-mer peptide.Scientific reports · 2020Article
- Thermal activation of 'allosteric-like' large-scale motions in a eukaryotic Lactate Dehydrogenase.Scientific reports · 2017Article
- A Rough Energy Landscape to Describe Surface-Linked Antibody and Antigen Bond Formation.Scientific reports · 2016Article
- Meandering Down the Energy Landscape of Protein Folding: Are We There Yet?Biophysical journal · 2016Review
- Direct measurement of the tryptophan-mediated photocleavage kinetics of a protein disulfide bond.Physical chemistry chemical physics : PCCP · 2016Article
- Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Microsecond protein dynamics observed at the single-molecule level.Nature communications · 2015Article
- Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations.Biophysical journal · 2015Article
- N-terminal domain of prion protein directs its oligomeric association.The Journal of biological chemistry · 2014Article
- Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2014Article
- The design and synthesis of alanine-rich α-helical peptides constrained by an S,S-tetrazine photochemical trigger: a fragment union approach.The Journal of organic chemistry · 2014Article
- Kinetic response of a photoperturbed allosteric protein.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
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8 authors.
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Abstract
The dynamics of protein conformational changes, from protein folding to smaller changes, such as those involved in ligand binding, are governed by the properties of the conformational energy landscape. Different techniques have been used to follow the motion of a protein over this landscape and thus quantify its properties. However, these techniques often are limited to short timescales and low-energy conformations. Here, we describe a general approach that overcomes these limitations. Starting from a nonnative conformation held by an aromatic disulfide bond, we use time-resolved spectroscopy to observe nonequilibrium backbone dynamics over nine orders of magnitude in time, from picoseconds to milliseconds, after photolysis of the disulfide bond. We find that the reencounter probability of residues that initially are in close contact decreases with time following an unusual power law that persists over the full time range and is independent of the primary sequence. Model simulations show that this power law arises from subdiffusional motion, indicating a wide distribution of trapping times in local minima of the energy landscape, and enable us to quantify the roughness of the energy landscape (4-5 k(B)T). Surprisingly, even under denaturing conditions, the energy landscape remains highly rugged with deep traps (>20 k(B)T) that result from multiple nonnative interactions and are sufficient for trapping on the millisecond timescale. Finally, we suggest that the subdiffusional motion of the protein backbone found here may promote rapid folding of proteins with low contact order by enhancing contact formation between nearby residues.
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