ArticlePLoS computational biology2012
Exploration of multi-state conformational dynamics and underlying global functional landscape of maltose binding protein.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Disrupting virulence: in silico discovery of MexL inhibitors to block pyocyanin biosynthesis in Pseudomonas aeruginosa.Archives of microbiology · 2026Article
- Dissecting mechanisms of ligand binding and conformational changes in the glutamine-binding protein.eLife · 2026Article
- Generation of Pathway Signatures by Combining Normal Modes with Weighted Ensemble Simulations.bioRxiv : the preprint server for biology · 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
- Article
- Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations.The journal of physical chemistry. B · 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
- Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase.eLife · 2020Article
- Ligand-bound glutamine binding protein assumes multiple metastable binding sites with different binding affinities.Communications biology · 2020Article
- Investigations of the underlying mechanisms of HIF-1α and CITED2 binding to TAZ1.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Structure dictates the mechanism of ligand recognition in the histidine and maltose binding proteins.Current research in structural biology · 2020Article
- Quantifying the Intrinsic Conformation Energy Landscape Topography of Proteins with Large-Scale Open-Closed Transition.ACS central science · 2018Article
- Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Molecular mechanism of multispecific recognition of Calmodulin through conformational changes.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Molecular dynamics simulation reveals how phosphorylation of tyrosine 26 of phosphoglycerate mutase 1 upregulates glycolysis and promotes tumor growth.Oncotarget · 2017Article
- Mapping transiently formed and sparsely populated conformations on a complex energy landscape.eLife · 2016Article
- Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations.PloS one · 2015Article
- Probing protein multidimensional conformational fluctuations by single-molecule multiparameter photon stamping spectroscopy.The journal of physical chemistry. B · 2014Article
- Dynamic conformational change regulates the protein-DNA recognition: an investigation on binding of a Y-family polymerase to its target DNA.PLoS computational biology · 2014Article
- Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An increasing number of biological machines have been revealed to have more than two macroscopic states. Quantifying the underlying multiple-basin functional landscape is essential for understanding their functions. However, the present models seem to be insufficient to describe such multiple-state systems. To meet this challenge, we have developed a coarse grained triple-basin structure-based model with implicit ligand. Based on our model, the constructed functional landscape is sufficiently sampled by the brute-force molecular dynamics simulation. We explored maltose-binding protein (MBP) which undergoes large-scale domain motion between open, apo-closed (partially closed) and holo-closed (fully closed) states responding to ligand binding. We revealed an underlying mechanism whereby major induced fit and minor population shift pathways co-exist by quantitative flux analysis. We found that the hinge regions play an important role in the functional dynamics as well as that increases in its flexibility promote population shifts. This finding provides a theoretical explanation of the mechanistic discrepancies in PBP protein family. We also found a functional "backtracking" behavior that favors conformational change. We further explored the underlying folding landscape in response to ligand binding. Consistent with earlier experimental findings, the presence of ligand increases the cooperativity and stability of MBP. This work provides the first study to explore the folding dynamics and functional dynamics under the same theoretical framework using our triple-basin functional model.
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