ArticleProceedings of the National Academy of Sciences of the United States of America2003
A comparative study of motor-protein motions by using a simple elastic-network model.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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92 citing papers in PubMed, 221 citations in OpenAlex.
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- Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes.International journal of molecular sciences · 2021Article
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- Allosteric communication in molecular machines via information exchange: what can be learned from dynamical modeling.Biophysical reviews · 2020Review
- Delineating elastic properties of kinesin linker and their sensitivity to point mutations.Scientific reports · 2020Article
- A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs.Frontiers in molecular biosciences · 2020Article
- 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
- Analyzing Fluctuation Properties in Protein Elastic Networks with Sequence-Specific and Distance-Dependent Interactions.Biomolecules · 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
- Revealing evolutionary constraints on proteins through sequence analysis.PLoS computational biology · 2019Article
- Heat activation mechanism of TRPV1: New insights from molecular dynamics simulation.Temperature (Austin, Tex.) · 2019Review
- Interface Residues That Drive Allosteric Transitions Also Control the Assembly of l-Lactate Dehydrogenase.The journal of physical chemistry. B · 2018Article
- Coarse-Grained Protein Dynamics Studies Using Elastic Network Models.International journal of molecular sciences · 2018Review
32 more citing papers are in PubMed but not listed here.
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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
In this work, we report on a study of the structure-function relationships for three families of motor proteins, including kinesins, myosins, and F1-ATPases, by using a version of the simple elastic-network model of large-scale protein motions originally proposed by Tirion [Tirion, M. (1996) Phys. Rev. Lett. 77, 1905-1908]. We find a surprising dichotomy between kinesins and the other motor proteins (myosins and F1-ATPase). For the latter, there exist one or two dominant lowest-frequency modes (one for myosin, two for F1-ATPase) obtained from normal-mode analysis of the elastic-network model, which overlap remarkably well with the measured conformational changes derived from pairs of solved crystal structures in different states. Furthermore, we find that the computed global conformational changes induced by the measured deformation of the nucleotide-binding pocket also overlap well with the measured conformational changes, which is consistent with the "nucleotide-binding-induced power-stroke" scenario. In contrast, for kinesins, this simplicity breaks down. Multiple modes are needed to generate the measured conformational changes, and the computed displacements induced by deforming the nucleotide-binding pocket also overlap poorly with the measured conformational changes, and are insufficient to explain the large-scale motion of the relay helix and the linker region. This finding may suggest the presence of two different mechanisms for myosins and kinesins, despite their strong evolutionary ties and structural similarities.
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