ArticleBiophysical journal2005
Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 96 citations in OpenAlex.
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- Structural Communication between theInternational journal of molecular sciences · 2021Article
- Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding.Biophysical journal · 2020Article
- Allosteric communication in molecular machines via information exchange: what can be learned from dynamical modeling.Biophysical reviews · 2020Review
- Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Normal Mode Analysis as a Routine Part of a Structural Investigation.Molecules (Basel, Switzerland) · 2019Review
- Simple mechanics of protein machines.Journal of the Royal Society, Interface · 2019Article
- Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members.Journal of chemical information and modeling · 2019Article
- Dissecting conformational changes in APP's transmembrane domain linked to ε-efficiency in familial Alzheimer's disease.PloS one · 2018Article
- Protein dynamics and the all-ferrous [Fe4 S4 ] cluster in the nitrogenase iron protein.Protein science : a publication of the Protein Society · 2016Article
- Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.Nucleic acids research · 2015Article
- Cooperative Dynamics of Intact AMPA and NMDA Glutamate Receptors: Similarities and Subfamily-Specific Differences.Structure (London, England : 1993) · 2015Article
- WEBnm@ v2.0: Web server and services for comparing protein flexibility.BMC bioinformatics · 2014Article
- Counterbalance of ligand- and self-coupled motions characterizes multispecificity of ubiquitin.Protein science : a publication of the Protein Society · 2013Article
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
Based on the elastic network model, we develop a new analysis for protein complexes, which probes the local dynamics of a subsystem that is elastically coupled to a fluctuating environment. This method is applied to a comparative dynamical analysis of the nucleotide-binding pocket of two motor proteins-myosins and kinesins. In myosins, the observed structural changes in the nucleotide-pocket from the transition state to the rigorlike state are dominated by the lowest normal mode that involves significant movements in both switch I and switch II; in kinesins, the measured conformational changes in the nucleotide-pocket are also dominated by the lowest mode, which, however, only involves large movement in switch I. We then compute the global structural changes induced by the nucleotide-pocket deformations as described by the dominant pocket-mode, which yield encouraging results: in myosins, multiple hinge motions involving the opening/closing of the cleft between the upper and lower 50 -kDa subdomains and the swinging movement of the converter are induced, which are dominated by precisely the same global mode that has been recently identified by us as important to the dynamical correlations among the nucleotide-pocket, the actin-binding site, and the converter; in kinesins, the induced global conformational changes are well described by a highly collective global mode which hints for a dynamical pathway spanning from the nucleotide-pocket to the neck-linker via the H6 helix.
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