ArticleStructure (London, England : 1993)2014
Computing the relative stabilities and the per-residue components in protein conformational changes.
Article in Structure (London, England : 1993), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 29 citations in OpenAlex.
- Exploring the structural acrobatics of fold-switching proteins using simplified structure-based models.Biophysical reviews · 2023Review
- Illuminating the "Twilight Zone": Advances in Difficult Protein Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Dimer dissociation is a key energetic event in the fold-switch pathway of KaiB.Biophysical journal · 2022Article
- Article
- Differential Local Stability Governs the Metamorphic Fold Switch of Bacterial Virulence Factor RfaH.Biophysical journal · 2020Article
- Allosterism and signal transfer in DNA.Nucleic acids research · 2018Article
- Computation of Hemagglutinin Free Energy Difference by the Confinement Method.The journal of physical chemistry. B · 2017Article
- Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches.PLoS computational biology · 2016Article
- Constraint methods that accelerate free-energy simulations of biomolecules.The Journal of chemical physics · 2015Review
- Residue-level global and local ensemble-ensemble comparisons of protein domains.Protein science : a publication of the Protein Society · 2015Article
- Biophysics of protein evolution and evolutionary protein biophysics.Journal of the Royal Society, Interface · 2014Article
- Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Protein molecules often undergo conformational changes. In order to gain insights into the forces that drive such changes, it would be useful to have a method that computes the per-residue contributions to the conversion free energy. Here, we describe the "confine-convert-release" (CCR) method, which is applicable to large conformational changes. We show that CCR correctly predicts the stable states of several "chameleon" sequences that have previously been challenging for molecular simulations. CCR can often discriminate better from worse predictions of native protein models in critical assessment of protein structure prediction (CASP). We show how the total conversion free energies can be parsed into per-residue free-energy components. Such parsing gives insights into which amino acids are most responsible for given transformations. For example, here we are able to "reverse-engineer" the known design principles of the chameleon proteins. This opens up the possibility for systematic improvements in structure-prediction scoring functions, in the design of protein conformational switches, and in interpreting protein mechanisms at the amino-acid level.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.