ArticlePLoS computational biology2013
Designing molecular dynamics simulations to shift populations of the conformational states of calmodulin.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Multiply Perturbed Response: A Computational Protocol to Identify Cooperative Allosteric Residue Combinations Driving Protein Conformational Transitions.Bio-protocol · 2026Article
- Functional Calmodulin States Are Selected from an Electrostatically Tuned Free Energy Landscape.Journal of chemical information and modeling · 2026Article
- Metamorphic Proteins to Achieve Conformationally Selective Material Surface Binding.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- Ranking Single Fluorescent Protein-Based Calcium Biosensor Performance by Molecular Dynamics Simulations.Journal of chemical information and modeling · 2025Article
- Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT3 as case study.Journal of computer-aided molecular design · 2023Article
- Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions inJournal of chemical information and modeling · 2023Article
- The structural basis of Akt PH domain interaction with calmodulin.Biophysical journal · 2021Article
- Predicting Genetic Variation Severity Using Machine Learning to Interpret Molecular Simulations.Biophysical journal · 2021Article
- The mechanism of complex formation between calmodulin and voltage gated calcium channels revealed by molecular dynamics.PloS one · 2021Article
- Structural analysis of the PATZ1 BTB domain homodimer.Acta crystallographica. Section D, Structural biology · 2020Article
- A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs.Frontiers in molecular biosciences · 2020Article
- Bayesian inference of protein conformational ensembles from limited structural data.PLoS computational biology · 2018Article
- Aqueous solution interactions with sex hormone-binding globulin and estradiol: a theoretical investigation.Journal of biological physics · 2018Article
- Effect of Ca2+ on the promiscuous target-protein binding of calmodulin.PLoS computational biology · 2018Article
- Combining molecular dynamics simulation and ligand-receptor contacts analysis as a new approach for pharmacophore modeling: beta-secretase 1 and check point kinase 1 as case studies.Journal of computer-aided molecular design · 2016Article
- ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution.Journal of chemical theory and computation · 2016Article
- Molecular Basis of S100A1 Activation at Saturating and Subsaturating Calcium Concentrations.Biophysical journal · 2016Article
- Detailed molecular dynamics simulations of human transferrin provide insights into iron release dynamics at serum and endosomal pH.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2015Article
- Effect of Calcium Ion Removal, Ionic Strength, and Temperature on the Conformation Change in Calmodulin Protein at Physiological pH.Journal of biophysics (Hindawi Publishing Corporation : Online) · 2014Article
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3 authors.
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Abstract
We elucidate the mechanisms that lead to population shifts in the conformational states of calcium-loaded calmodulin (Ca(2+)-CaM). We design extensive molecular dynamics simulations to classify the effects that are responsible for adopting occupied conformations available in the ensemble of NMR structures. Electrostatic interactions amongst the different regions of the protein and with its vicinal water are herein mediated by lowering the ionic strength or the pH. Amino acid E31, which is one of the few charged residues whose ionization state is highly sensitive to pH differences in the physiological range, proves to be distinctive in its control of population shifts. E31A mutation at low ionic strength results in a distinct change from an extended to a compact Ca(2+)-CaM conformation within tens of nanoseconds, that otherwise occur on the time scales of microseconds. The kinked linker found in this particular compact form is observed in many of the target-bound forms of Ca(2+)-CaM, increasing the binding affinity. This mutation is unique in controlling C-lobe dynamics by affecting the fluctuations between the EF-hand motif helices. We also monitor the effect of the ionic strength on the conformational multiplicity of Ca(2+)-CaM. By lowering the ionic strength, the tendency of nonspecific anions in water to accumulate near the protein surface increases, especially in the vicinity of the linker. The change in the distribution of ions in the vicinal layer of water allows N- and C- lobes to span a wide variety of relative orientations that are otherwise not observed at physiological ionic strength. E31 protonation restores the conformations associated with physiological environmental conditions even at low ionic strength.
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