ArticleJournal of molecular biology2013
Impact of mutations on the allosteric conformational equilibrium.
Article in Journal of molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
27 citing papers in PubMed, 56 citations in OpenAlex.
- Article
- Thermostability Enhancement of GH 62 α-l-Arabinofuranosidase by Directed Evolution and Rational Design.Journal of agricultural and food chemistry · 2024Article
- Machine learning and protein allostery.Trends in biochemical sciences · 2023Review
- Article
- Evolution of tunnels in α/β-hydrolase fold proteins-What can we learn from studying epoxide hydrolases?PLoS computational biology · 2022Article
- AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations.Nucleic acids research · 2020Article
- Congenital myasthenic syndrome due to mutations in MUSK suggests that the level of MuSK phosphorylation is crucial for governing synaptic structure.Human mutation · 2020Article
- Influence of Disease-Causing Mutations on Protein Structural Networks.Frontiers in molecular biosciences · 2020Article
- The importance of the quaternary structure to represent conformational ensembles of the major Mycobacterium tuberculosis drug target.Scientific reports · 2019Article
- Association of BUD13-ZNF259-APOA5-APOA1-SIK3 cluster polymorphism in 11q23.3 and structure of APOA5 with increased plasma triglyceride levels in a Korean population.Scientific reports · 2019Article
- Article
- C1q and Mannose-Binding Lectin Interact with CR1 in the Same Region on CCP24-25 Modules.Frontiers in immunology · 2018Article
- Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS.Journal of chemical theory and computation · 2017Article
- Classifying kinase conformations using a machine learning approach.BMC bioinformatics · 2017Article
- Rapid Characterization of Allosteric Networks with Ensemble Normal Mode Analysis.The journal of physical chemistry. B · 2016Article
- CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.Journal of molecular biology · 2016Article
- Allosteric Dynamic Control of Binding.Biophysical journal · 2015Article
- Oncogenic mutations weaken the interactions that stabilize the p110α-p85α heterodimer in phosphatidylinositol 3-kinase α.The FEBS journal · 2015Article
- Biophysics of protein evolution and evolutionary protein biophysics.Journal of the Royal Society, Interface · 2014Article
- Allosteric activation of Bordetella pertussis adenylyl cyclase by calmodulin: molecular dynamics and mutagenesis studies.The Journal of biological chemistry · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Allostery in a protein involves effector binding at an allosteric site that changes the structure and/or dynamics at a distant, functional site. In addition to the chemical equilibrium of ligand binding, allostery involves a conformational equilibrium between one protein substate that binds the effector and a second substate that less strongly binds the effector. We run molecular dynamics simulations using simple, smooth energy landscapes to sample specific ligand-induced conformational transitions, as defined by the effector-bound and effector-unbound protein structures. These simulations can be performed using our web server (http://salilab.org/allosmod/). We then develop a set of features to analyze the simulations and capture the relevant thermodynamic properties of the allosteric conformational equilibrium. These features are based on molecular mechanics energy functions, stereochemical effects, and structural/dynamic coupling between sites. Using a machine-learning algorithm on a data set of 10 proteins and 179 mutations, we predict both the magnitude and the sign of the allosteric conformational equilibrium shift by the mutation; the impact of a large identifiable fraction of the mutations can be predicted with an average unsigned error of 1k(B)T. With similar accuracy, we predict the mutation effects for an 11th protein that was omitted from the initial training and testing of the machine-learning algorithm. We also assess which calculated thermodynamic properties contribute most to the accuracy of the prediction.
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Registered trials
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.