ArticleJournal of molecular biology2007
Predicting allosteric communication in myosin via a pathway of conserved residues.
Article in Journal of molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Article
- A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins.PLoS computational biology · 2018Article
- Energy transport pathway in proteins: Insights from non-equilibrium molecular dynamics with elastic network model.Scientific reports · 2018Article
- Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank.Biophysical reviews · 2017Review
- Design of Elastic Networks with Evolutionary Optimized Long-Range Communication as Mechanical Models of Allosteric Proteins.Biophysical journal · 2017Article
- Dynamical persistence of active sites identified in maltose-binding protein.Journal of molecular modeling · 2017Article
- Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.PLoS computational biology · 2017Article
- Dependence of prevalence of contiguous pathways in proteins on structural complexity.PloS one · 2017Article
- A Failure to Communicate: MYOSIN RESIDUES INVOLVED IN HYPERTROPHIC CARDIOMYOPATHY AFFECT INTER-DOMAIN INTERACTION.The Journal of biological chemistry · 2015Article
- Article
- The ensemble nature of allostery.Nature · 2014Review
- A unified view of "how allostery works".PLoS computational biology · 2014Article
- Allosteric regulation of the Hsp90 dynamics and stability by client recruiter cochaperones: protein structure network modeling.PloS one · 2014Article
- MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues.Nucleic acids research · 2013Article
- Multiple pathways promote dynamical coupling between catalytic domains in Escherichia coli prolyl-tRNA synthetase.Biochemistry · 2013Article
- Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.Pharmacology & therapeutics · 2013Review
- Homology model of nonmuscle myosin heavy chain IIA and binding mode analysis with its inhibitor blebbistatin.Journal of molecular modeling · 2013Article
- Normal-mode-analysis-guided investigation of crucial intersubunit contacts in the cAMP-dependent gating in HCN channels.Biophysical journal · 2012Article
- Alternative relay and converter domains tune native muscle myosin isoform function in Drosophila.Journal of molecular biology · 2012Article
- Myosin I links PIP3 signaling to remodeling of the actin cytoskeleton in chemotaxis.Science signaling · 2012Article
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Authors and funding
6 authors.
Funding
Abstract
We present a computational method that predicts a pathway of residues that mediate protein allosteric communication. The pathway is predicted using only a combination of distance constraints between contiguous residues and evolutionary data. We applied this analysis to find pathways of conserved residues connecting the myosin ATP binding site to the lever arm. These pathway residues may mediate the allosteric communication that couples ATP hydrolysis to the lever arm recovery stroke. Having examined pre-stroke conformations of Dictyostelium, scallop, and chicken myosin II as well as Dictyostelium myosin I, we observed a conserved pathway traversing switch II and the relay helix, which is consistent with the understood need for allosteric communication in this conformation. We also examined post-rigor and rigor conformations across several myosin species. Although initial residues of these paths are more heterogeneous, all but one of these paths traverse a consistent set of relay helix residues to reach the beginning of the lever arm. We discuss our results in the context of structural elements and reported mutational experiments, which substantiate the significance of the pre-stroke pathways. Our method provides a simple, computationally efficient means of predicting a set of residues that mediate allosteric communication. We provide a refined, downloadable application and source code (on https://simtk.org) to share this tool with the wider community (https://simtk.org/home/allopathfinder).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.