ArticlePloS one2010
Optimal identification of semi-rigid domains in macromolecules from molecular dynamics simulation.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 21 citations in OpenAlex.
- Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins.Journal of chemical information and modeling · 2023Article
- Molecular dynamics identifies semi-rigid domains in the PD-1 checkpoint receptor bound to its natural ligand PD-L1.Frontiers in bioengineering and biotechnology · 2022Article
- Unifying view of mechanical and functional hotspots across class A GPCRs.PLoS computational biology · 2017Article
- Relative Movements of Domains in Large Molecules of the Immune System.Journal of immunology research · 2015Article
- Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation.PloS one · 2015Article
- Dynamic architecture of a protein kinase.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Finding semirigid domains in biomolecules by clustering pair-distance variations.BioMed research international · 2014Article
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
Biological function relies on the fact that biomolecules can switch between different conformations and aggregation states. Such transitions involve a rearrangement of parts of the biomolecules involved that act as dynamic domains. The reliable identification of such domains is thus a key problem in biophysics. In this work we present a method to identify semi-rigid domains based on dynamical data that can be obtained from molecular dynamics simulations or experiments. To this end the average inter-atomic distance-deviations are computed. The resulting matrix is then clustered by a constrained quadratic optimization problem. The reliability and performance of the method are demonstrated for two artificial peptides. Furthermore we correlate the mechanical properties with biological malfunction in three variants of amyloidogenic transthyretin protein, where the method reveals that a pathological mutation destabilizes the natural dimer structure of the protein. Finally the method is used to identify functional domains of the GroEL-GroES chaperone, thus illustrating the efficiency of the method for large biomolecular machines.
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