ArticleBiophysical journal2009
Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- The energetics of subunit rotation in the ribosome.Biophysical reviews · 2021Review
- Comparative Analysis of Structural and Dynamical Features of Ribosome Upon Association With mRNA Reveals Potential Role of Ribosomal Proteins.Frontiers in molecular biosciences · 2021Article
- Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems.Proteins · 2020Article
- A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs.Frontiers in molecular biosciences · 2020Article
- Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.International journal of molecular sciences · 2018Review
- Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change.Biophysical journal · 2017Article
- Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states.PloS one · 2017Article
- ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution.Journal of chemical theory and computation · 2016Article
- Ribosome Mechanics Informs about Mechanism.Journal of molecular biology · 2016Review
- Article
- Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids.Frontiers in molecular biosciences · 2016Article
- Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.PLoS computational biology · 2015Article
- How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics.Biophysical journal · 2015Article
- The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality.Protein science : a publication of the Protein Society · 2014Article
- Exploring the dynamics of four RNA-dependent RNA polymerases by a coarse-grained model.The journal of physical chemistry. B · 2012Article
- Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis.Journal of the American Chemical Society · 2011Article
- MAVENs: motion analysis and visualization of elastic networks and structural ensembles.BMC bioinformatics · 2011Article
- Mechanism of cohesin loading onto chromosomes: a conformational dynamics study.Biophysical journal · 2010Article
- Global dynamics of proteins: bridging between structure and function.Annual review of biophysics · 2010Review
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Authors and funding
5 authors.
Funding
Abstract
The mixed-resolution elastic network model was introduced previously for computing the motions of a structure, which is described at different levels of detail in different parts, for example, with atomistic and residue-level regions. This method has proved to be an efficient tool to explore the collective dynamics of proteins with some atomistic details, which would be difficult to obtain with either conventional full-atom approaches or fully coarse-grained models. Understanding function often requires atomic detail, but not necessarily for the entire structure. In this study, the calculation of the interaction forces between different resolution regions for the hierarchical levels of coarse-graining is further elaborated on in the new approach by considering explicitly the atomic contacts in the crystal structure. The collective dynamics of the enzyme triosephosphate isomerase and its active site together with loop 6 motions are considered in detail. The supramolecular assemblage ribosome and local atomic motions in its "interesting" functional part-the decoding center-are investigated for the low frequency range of the spectrum with high computational efficiency. This new atom-based mixed coarse-graining approach can be effectively used to generate realistic high-resolution conformations of extremely large protein-DNA or RNA complexes by performing energy minimization on structures deformed along the normal modes of the elastic network model. The new model permits focusing on specific functional parts that move in coordination and response to the remainder of the entire structure.
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