ArticleBiophysical journal2006
Protein grabs a ligand by extending anchor residues: molecular simulation for Ca2+ binding to calmodulin loop.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 35 citations in OpenAlex.
- Exonic splicing code and protein binding sites for calcium.Nucleic acids research · 2022Article
- Molecular dynamics provides new insights into the mechanism of calcium signal transduction and interdomain interactions in cardiac troponin.FEBS open bio · 2021Article
- Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif.The Journal of chemical physics · 2021Article
- Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Calcium induced regulation of skeletal troponin--computational insights from molecular dynamics simulations.PloS one · 2013Article
- The effect of macromolecular crowding, ionic strength and calcium binding on calmodulin dynamics.PLoS computational biology · 2011Article
- Activation of the edema factor of Bacillus anthracis by calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding.Biophysical journal · 2010Article
- Estimating affinities of calcium ions to proteins.Advances and applications in bioinformatics and chemistry : AABC · 2010Article
- Critical role of heparin binding domains of ameloblastin for dental epithelium cell adhesion and ameloblastoma proliferation.The Journal of biological chemistry · 2009Article
- An altered mode of calcium coordination in methionine-oxidized calmodulin.Biophysical journal · 2008Article
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
The structural difference in proteins between unbound and bound forms directly suggests the importance of the conformational plasticity of proteins. However, pathways that connect two-end structures and how they are coupled to the binding reaction are not well understood at atomic resolution. Here, we analyzed the free-energy landscape, explicitly taking into account coupling between binding and conformational change by performing atomistic molecular dynamics simulations for Ca2+ binding to a calmodulin loop. Using the AMBER force field with explicit water solvent, we conducted umbrella sampling for the free-energy surface and steered molecular dynamics for the pathway search. We found that, at an early stage of binding, some key residue side chains extend their "arms" to catch Ca2+ and, after catching, they carry the Ca2+ to the center of the binding pocket. This grabbing motion resulted in smooth and stepwise exchange in coordination partners of Ca2+ from water oxygen to atoms in the calmodulin loop. The key residue that first caught the ion was one of the two acidic residues, which are highly conserved. In the pathway simulations, different pathways were observed between binding and dissociation reactions: The former was more diverse than the latter.
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