ArticleProceedings of the National Academy of Sciences of the United States of America2014
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed.
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- Top-Down Machine Learning of Coarse-Grained Protein Force Fields.Journal of chemical theory and computation · 2023Article
- The "Beacon" Structural Model of Protein Folding: Application for Trp-Cage in Water.Molecules (Basel, Switzerland) · 2023Article
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- Evolution and folding of repeat proteins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
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- Some Clues about Enzymes from Psychrophilic Microorganisms.Microorganisms · 2022Review
- Arrow of Time, Entropy, and Protein Folding: Holistic View on Biochirality.International journal of molecular sciences · 2022Review
- Protein Dynamics to Define and Refine Disordered Protein Ensembles.The journal of physical chemistry. B · 2022Article
- How physical forces drive the process of helical membrane protein folding.EMBO reports · 2022Review
- A Rationalization of the Effect That TMAO, Glycine, and Betaine Exert on the Collapse of Elastin-like Polypeptides.Life (Basel, Switzerland) · 2022Article
- Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology.International journal of molecular sciences · 2021Review
- Dynamics in natural and designed elastins and their relation to elastic fiber structure and recoil.Biophysical journal · 2021Article
- Entropic singularities give rise to quantum transmission.Nature communications · 2021Article
- Differential Stabilities of Mefloquine-Bound Human andACS omega · 2021Article
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5 authors.
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Abstract
The loss of conformational entropy is a major contribution in the thermodynamics of protein folding. However, accurate determination of the quantity has proven challenging. We calculate this loss using molecular dynamic simulations of both the native protein and a realistic denatured state ensemble. For ubiquitin, the total change in entropy is TΔSTotal = 1.4 kcal⋅mol(-1) per residue at 300 K with only 20% from the loss of side-chain entropy. Our analysis exhibits mixed agreement with prior studies because of the use of more accurate ensembles and contributions from correlated motions. Buried side chains lose only a factor of 1.4 in the number of conformations available per rotamer upon folding (ΩU/ΩN). The entropy loss for helical and sheet residues differs due to the smaller motions of helical residues (TΔShelix-sheet = 0.5 kcal⋅mol(-1)), a property not fully reflected in the amide N-H and carbonyl C=O bond NMR order parameters. The results have implications for the thermodynamics of folding and binding, including estimates of solvent ordering and microscopic entropies obtained from NMR.
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