ArticleProceedings of the National Academy of Sciences of the United States of America2009
Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase.
Article in Proceedings of the National Academy of Sciences of the United States of America, 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.
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- Phytoconstituents of Withania somnifera (L.) Dunal (Ashwagandha) unveiled potential cerebroside sulfotransferase inhibitors: insight through virtual screening, molecular dynamics, toxicity, and reverse pharmacophore analysis.Journal of biological engineering · 2024Article
- Tackling Hysteresis in Conformational Sampling: How to Be Forgetful with MEMENTO.Journal of chemical theory and computation · 2023Article
- Generating conformational transition paths with low potential-energy barriers for proteins.Journal of computer-aided molecular design · 2018Article
- Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case.Biophysical journal · 2015Article
- Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.BMC structural biology · 2013Article
- A generic force field for protein coarse-grained molecular dynamics simulation.International journal of molecular sciences · 2012Article
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- Biomolecular dynamics: order-disorder transitions and energy landscapes.Reports on progress in physics. Physical Society (Great Britain) · 2012Article
- Structural distributions from single-molecule measurements as a tool for molecular mechanics.Chemical physics · 2012Article
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- Structural plasticity and conformational transitions of HIV envelope glycoprotein gp120.PloS one · 2012Article
- 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
- Integrating ion mobility mass spectrometry with molecular modelling to determine the architecture of multiprotein complexes.PloS one · 2010Article
- Multiscale coarse-graining of the protein energy landscape.PLoS computational biology · 2010Article
- A force field for virtual atom molecular mechanics of proteins.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
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2 authors.
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Abstract
Many proteins function through conformational transitions between structurally disparate states, and there is a need to explore transition pathways between experimentally accessible states by computation. The sizes of systems of interest and the scale of conformational changes are often beyond the scope of full atomic models, but appropriate coarse-grained approaches can capture significant features. We have designed a comprehensive knowledge-based potential function based on a C alpha representation for proteins that we call the virtual atom molecular mechanics (VAMM) force field. Here, we describe an algorithm for using the VAMM potential to describe conformational transitions, and we validate this algorithm in application to a transition between open and closed states of adenylate kinase (ADK). The VAMM algorithm computes normal modes for each state and iteratively moves each structure toward the other through a series of intermediates. The move from each side at each step is taken along that normal mode showing greatest engagement with the other state. The process continues to convergence of terminal intermediates to within a defined limit--here, a root-mean-square deviation of 1 A. Validations show that the VAMM algorithm is highly effective, and the transition pathways examined for ADK are compatible with other structural and biophysical information. We expect that the VAMM algorithm can address many biological systems.
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