ArticleBiophysical journal2004
A molecular dynamics study of Ca(2+)-calmodulin: evidence of interdomain coupling and structural collapse on the nanosecond timescale.
Article in Biophysical journal, 2004. 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, 62 citations in OpenAlex.
- Metamorphic Proteins to Achieve Conformationally Selective Material Surface Binding.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- Decreased Interactions between Calmodulin and a Mutant Huntingtin Model Might Reduce the Cytotoxic Level of Intracellular CaInternational journal of molecular sciences · 2021Article
- The mechanism of complex formation between calmodulin and voltage gated calcium channels revealed by molecular dynamics.PloS one · 2021Article
- Coarse-Grained Modeling and Molecular Dynamics Simulations of CaFrontiers in molecular biosciences · 2021Article
- Bayesian inference of protein conformational ensembles from limited structural data.PLoS computational biology · 2018Article
- Effect of Ca2+ on the promiscuous target-protein binding of calmodulin.PLoS computational biology · 2018Article
- Conformational heterogeneity of the calmodulin binding interface.Nature communications · 2016Article
- Internal coordinate molecular dynamics: a foundation for multiscale dynamics.The journal of physical chemistry. B · 2015Article
- Distinguishing unfolding and functional conformational transitions of calmodulin using ultraviolet resonance Raman spectroscopy.Protein science : a publication of the Protein Society · 2014Article
- 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
- Mapping conformational dynamics of proteins using torsional dynamics simulations.Biophysical journal · 2013Article
- Computational investigation of the key factors affecting the second stage activation mechanisms of domain II m-calpain.Journal of molecular modeling · 2013Article
- Retention of conformational entropy upon calmodulin binding to target peptides is driven by transient salt bridges.Biophysical journal · 2012Article
- Article
- The use of ESI-MS to probe the binding of divalent cations to calmodulin.Journal of the American Society for Mass Spectrometry · 2009Article
- Caldendrin-Jacob: a protein liaison that couples NMDA receptor signalling to the nucleus.PLoS biology · 2008Article
- A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides.Biophysical journal · 2006Article
- A molecular dynamics study of the effect of Ca2+ removal on calmodulin structure.Biophysical journal · 2006Article
- Protein grabs a ligand by extending anchor residues: molecular simulation for Ca2+ binding to calmodulin loop.Biophysical journal · 2006Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A 20-ns molecular dynamics simulation of Ca(2+)-calmodulin (CaM) in explicit solvent is described. Within 5 ns, the extended crystal structure adopts a compact shape similar in dimension to complexes of CaM and target peptides but with a substantially different orientation between the N- and C-terminal domains. Significant interactions are observed between the terminal domains in this compact state, which are mediated through the same regions of CaM that bind to target peptides derived from protein kinases and most other target proteins. The process of compaction is driven by the loss of helical structure in two separate regions between residues 75-79 and 82-86, the latter being driven by unfavorable electrostatic interactions between acidic residues. In the first 5 ns of the simulation, a substantial number of contacts are observed between the first helix of the N-terminal domain and residues 74-77 of the central linker. These contacts are correlated with the closing of the second EF-hand, indicating a mechanism by which they can lower calcium affinity in the N-terminal domain.
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