ArticleProteins2009
Iterative cluster-NMA: A tool for generating conformational transitions in proteins.
Article in Proteins, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Attenuating dependence on structural data in computing protein energy landscapes.BMC bioinformatics · 2019Article
- Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.International journal of molecular sciences · 2018Review
- Using Spectral Representation to Classify Proteins' Conformational States.International journal of molecular sciences · 2018Article
- Computing energy landscape maps and structural excursions of proteins.BMC genomics · 2016Article
- Evolutionary Conserved Positions Define Protein Conformational Diversity.PLoS computational biology · 2016Article
- Ribosome Mechanics Informs about Mechanism.Journal of molecular biology · 2016Review
- Insights into mechanism kinematics for protein motion simulation.BMC bioinformatics · 2014Article
- Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model.PLoS computational biology · 2014Article
- Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.BMC structural biology · 2013Article
- Polymer uncrossing and knotting in protein folding, and their role in minimal folding pathways.PloS one · 2013Article
- Biomolecular dynamics: order-disorder transitions and energy landscapes.Reports on progress in physics. Physical Society (Great Britain) · 2012Article
- Article
- Protein folding pathways and state transitions described by classical equations of motion of an elastic network model.Protein science : a publication of the Protein Society · 2010Article
- Group theory and biomolecular conformation: I. Mathematical and computational models.Journal of physics. Condensed matter : an Institute of Physics journal · 2010Review
- Tracing conformational changes in proteins.BMC structural biology · 2010Article
- Computational methods for predicting sites of functionally important dynamics.The journal of physical chemistry. B · 2009Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Computational models provide insight into the structure-function relationship in proteins. These approaches, especially those based on normal mode analysis, can identify the accessible motion space around a given equilibrium structure. The large magnitude, collective motions identified by these methods are often well aligned with the general direction of the expected conformational transitions. However, these motions cannot realistically be extrapolated beyond the local neighborhood of the starting conformation. In this article, the iterative cluster-NMA (icNMA) method is presented for traversing the energy landscape from a starting conformation to a desired goal conformation. This is accomplished by allowing the evolving geometry of the intermediate structures to define the local accessible motion space, and thus produce an appropriate displacement. Following the derivation of the icNMA method, a set of sample simulations are performed to probe the robustness of the model. A detailed analysis of beta1,4-galactosyltransferase-T1 is also given, to highlight many of the capabilities of icNMA. Remarkably, during the transition, a helix is seen to be extended by an additional turn, emphasizing a new unknown role for secondary structures to absorb slack during transitions. The transition pathway for adenylate kinase, which has been frequently studied in the literature, is also discussed.
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