ArticleJournal of chemical theory and computation2014
Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Protonation- and substrate-regulated dimer opening couples brain-type creatine kinase to vesicular and actin-remodeling membranes.Research square · 2026Article
- Impact of anionic lipids on the energy landscape of conformational transition in anion exchanger 1 (AE1).Nature communications · 2025Article
- Structural dynamics of sphingosine kinase 1 regulation and inhibition.bioRxiv : the preprint server for biology · 2025Article
- Voltage sensor conformations induced by LQTS-associated mutations in hERG potassium channels.Nature communications · 2025Article
- Molecular dynamics simulations of biological membranes and membrane-associated phenomena across scales.Current opinion in structural biology · 2025Review
- Comparative Study of the Bending Free Energies of C- and G-Based DNA: A-, B-, and Z-DNA and Associated Mismatched Trinucleotide Repeats.Journal of chemical information and modeling · 2025Article
- Structural dynamics of sphingosine kinase 1 regulation and inhibition.Research square · 2025Article
- Dissecting Large-Scale Structural Transitions in Membrane Transporters Using Advanced Simulation Technologies.The journal of physical chemistry. B · 2025Review
- Conformational free energy landscape of a glutamate transporter and microscopic details of its transport mechanism.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Recent Applications of In Silico Approaches for Studying Receptor Mutations Associated with Human Pathologies.Molecules (Basel, Switzerland) · 2024Review
- Mechanism of proton-powered c-ring rotation in a mitochondrial ATP synthase.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The Alternating Access Mechanism in Mammalian Multidrug Resistance Transporters and Their Bacterial Homologs.Membranes · 2023Article
- Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes.The Journal of biological chemistry · 2022Article
- Proton-driven alternating access in a spinster lipid transporter.Nature communications · 2022Article
- Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins.Chemical science · 2022Article
- A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.Journal of chemical theory and computation · 2022Article
- Role of internal loop dynamics in antibiotic permeability of outer membrane porins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge.Chemical science · 2021Article
- Defining the Energetic Basis for a Conformational Switch Mediating Ligand-Independent Activation of Mutant Estrogen Receptors in Breast Cancer.Molecular cancer research : MCR · 2021Article
- Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein.Chemical science · 2021Article
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Authors and funding
2 authors.
Funding
Abstract
Characterizing large-scale structural transitions in biomolecular systems poses major technical challenges to both experimental and computational approaches. On the computational side, efficient sampling of the configuration space along the transition pathway remains the most daunting challenge. Recognizing this issue, we introduce a knowledge-based computational approach toward describing large-scale conformational transitions using (i) nonequilibrium, driven simulations combined with work measurements and (ii) free energy calculations using empirically optimized biasing protocols. The first part is based on designing mechanistically relevant, system-specific reaction coordinates whose usefulness and applicability in inducing the transition of interest are examined using knowledge-based, qualitative assessments along with nonequilirbrium work measurements which provide an empirical framework for optimizing the biasing protocol. The second part employs the optimized biasing protocol resulting from the first part to initiate free energy calculations and characterize the transition quantitatively. Using a biasing protocol fine-tuned to a particular transition not only improves the accuracy of the resulting free energies but also speeds up the convergence. The efficiency of the sampling will be assessed by employing dimensionality reduction techniques to help detect possible flaws and provide potential improvements in the design of the biasing protocol. Structural transition of a membrane transporter will be used as an example to illustrate the workings of the proposed approach.
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Registered trials
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