ArticleThe journal of physical chemistry. B2015
Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations.
Article in The journal of physical chemistry. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 90 citations in OpenAlex.
- Temperature-Dependent Dynamics of Aβ42 and α-Synuclein Monomers and Early Oligomerization of Aβ42: Shared Residues Mediate Intra- and Intermolecular β-Sheets.ACS chemical neuroscience · 2026Article
- Full-Length Context Disrupts Folding of IgG-Binding Domains of Protein A.bioRxiv : the preprint server for biology · 2025Article
- Deep generative modeling of temperature-dependent structural ensembles of proteins.Communications chemistry · 2025Article
- Biomolecular Condensates as Emerging Biomaterials: Functional Mechanisms and Advances in Computational and Experimental Approaches.Advanced materials (Deerfield Beach, Fla.) · 2025Review
- The molecular basis for cellular function of intrinsically disordered protein regions.Nature reviews. Molecular cell biology · 2024Review
- Modulating hierarchical self-assembly in thermoresponsive intrinsically disordered proteins through high-temperature incubation time.Scientific reports · 2023Article
- SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2023Article
- A synergy between site-specific and transient interactions drives the phase separation of a disordered, low-complexity domain.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- The Analytical Flory Random Coil Is a Simple-to-Use Reference Model for Unfolded and Disordered Proteins.The journal of physical chemistry. B · 2023Article
- A General Picture of Cucurbit[8]uril Host-Guest Binding: Recalibrating Bonded Interactions.Molecules (Basel, Switzerland) · 2023Article
- The analytical Flory random coil is a simple-to-use reference model for unfolded and disordered proteins.bioRxiv : the preprint server for biology · 2023Article
- Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure.Journal of computer-aided molecular design · 2022Article
- Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Rules of Physical Mathematics Govern Intrinsically Disordered Proteins.Annual review of biophysics · 2022Review
- Theoretical modelling of liquid-liquid phase separation: from particle-based to field-based simulation.Biophysics reports · 2022Article
- Molecular interactions contributing to FUS SYGQ LC-RGG phase separation and co-partitioning with RNA polymerase II heptads.Nature structural & molecular biology · 2021Article
- The Protein Folding Problem: The Role of Theory.Journal of molecular biology · 2021Review
- SAMPL7 TrimerTrip host-guest binding poses and binding affinities from spherical-coordinates-biased simulations.Journal of computer-aided molecular design · 2021Article
- Folded domain charge properties influence the conformational behavior of disordered tails.Current research in structural biology · 2021Article
- Refining All-Atom Protein Force Fields for Polar-Rich, Prion-like, Low-Complexity Intrinsically Disordered Proteins.The journal of physical chemistry. B · 2020Article
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3 authors at 2 institutions in 1 country.
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Abstract
We use all-atom molecular simulation with explicit solvent to study the properties of selected intrinsically disordered proteins and unfolded states of foldable proteins, which include chain dimensions and shape, secondary structure propensity, solvent accessible surface area, and contact formation. We find that the qualitative scaling behavior of the chains matches expectations from theory under ambient conditions. In particular, unfolded globular proteins tend to be more collapsed under the same conditions than charged disordered sequences of the same length. However, inclusion of explicit solvent in addition naturally captures temperature-dependent solvation effects, which results in an initial collapse of the chains as temperature is increased, in qualitative agreement with experiment. There is a universal origin to the collapse, revealed in the change of hydration of individual residues as a function of temperature: namely, that the initial collapse is driven by unfavorable solvation free energy of individual residues, which in turn has a strong temperature dependence. We also observe that in unfolded globular proteins, increased temperature also initially favors formation of native-like (rather than non-native-like) structure. Our results help to establish how sequence encodes the degree of intrinsic disorder or order as well as its response to changes in environmental conditions.
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