ArticlePLoS computational biology2011
Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 119 citations in OpenAlex.
- Dissecting mechanisms of ligand binding and conformational changes in the glutamine-binding protein.eLife · 2026Article
- Microscopic Insights into a Ligand Escape Pathway and Energetics in Leucine-Isoleucine-Valine Binding Protein.ACS omega · 2026Article
- Two-conformer equilibrium of maltose-binding protein in the absence of ligand from residual dipolar coupling analysis.Protein science : a publication of the Protein Society · 2026Article
- Functional protein dynamics in a crystal.Nature communications · 2024Article
- Functional Protein Dynamics in a Crystal.bioRxiv : the preprint server for biology · 2024Article
- Computational insights into the mechanisms underlying structural destabilization and recovery in trafficking-deficient hERG mutants.Frontiers in molecular biosciences · 2024Article
- An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes.Journal of chemical theory and computation · 2023Article
- Neutralizing Antibodies Against Allosteric Proteins: Insights From a Bacterial Adhesin.Journal of molecular biology · 2022Review
- What have molecular simulations contributed to understanding of Gram-negative bacterial cell envelopes?Microbiology (Reading, England) · 2022Review
- Enhanced sampling without borders: on global biasing functions and how to reweight them.Physical chemistry chemical physics : PCCP · 2022Review
- Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives.Advances and applications in bioinformatics and chemistry : AABC · 2022Review
- A novel RNA pol II CTD interaction site on the mRNA capping enzyme is essential for its allosteric activation.Nucleic acids research · 2021Article
- Toggle switch residues control allosteric transitions in bacterial adhesins by participating in a concerted repacking of the protein core.PLoS pathogens · 2021Article
- The structural changes in the signaling mechanism of bacteriophytochromes in solution revealed by a multiscale computational investigation.Chemical science · 2021Article
- Ligand binding and global adaptation of the GlnPQ substrate binding domain 2 revealed by molecular dynamics simulations.Protein science : a publication of the Protein Society · 2020Article
- Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein.PLoS computational biology · 2020Article
- Ligand-bound glutamine binding protein assumes multiple metastable binding sites with different binding affinities.Communications biology · 2020Article
- A role for actin flexibility in thin filament-mediated contractile regulation and myopathy.Nature communications · 2020Article
- Structure dictates the mechanism of ligand recognition in the histidine and maltose binding proteins.Current research in structural biology · 2020Article
- Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: insights from accelerated molecular dynamics simulations.Nucleic acids research · 2019Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Periplasmic binding proteins (PBPs) are a large family of molecular transporters that play a key role in nutrient uptake and chemotaxis in Gram-negative bacteria. All PBPs have characteristic two-domain architecture with a central interdomain ligand-binding cleft. Upon binding to their respective ligands, PBPs undergo a large conformational change that effectively closes the binding cleft. This conformational change is traditionally viewed as a ligand induced-fit process; however, the intrinsic dynamics of the protein may also be crucial for ligand recognition. Recent NMR paramagnetic relaxation enhancement (PRE) experiments have shown that the maltose binding protein (MBP) - a prototypical member of the PBP superfamily - exists in a rapidly exchanging (ns to µs regime) mixture comprising an open state (approx 95%), and a minor partially closed state (approx 5%). Here we describe accelerated MD simulations that provide a detailed picture of the transition between the open and partially closed states, and confirm the existence of a dynamical equilibrium between these two states in apo MBP. We find that a flexible part of the protein called the balancing interface motif (residues 175-184) is displaced during the transformation. Continuum electrostatic calculations indicate that the repacking of non-polar residues near the hinge region plays an important role in driving the conformational change. Oscillations between open and partially closed states create variations in the shape and size of the binding site. The study provides a detailed description of the conformational space available to ligand-free MBP, and has implications for understanding ligand recognition and allostery in related proteins.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.