ArticleBiophysical journal2009
Collective dynamics of periplasmic glutamine binding protein upon domain closure.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 40 citations in OpenAlex.
- Revealing Allosteric Mechanism of Amino Acid Binding Proteins from Open to Closed State.Molecules (Basel, Switzerland) · 2023Article
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- Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations.Technology and health care : official journal of the European Society for Engineering and Medicine · 2021Article
- Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling.International journal of molecular sciences · 2020Article
- 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
- Altered conformational sampling along an evolutionary trajectory changes the catalytic activity of an enzyme.Nature communications · 2020Article
- Phosphite binding by the HtxB periplasmic binding protein depends on the protonation state of the ligand.Scientific reports · 2019Article
- Building a macro-mixing dual-basin Gō model using the Multistate Bennett Acceptance Ratio.Biophysics and physicobiology · 2019Article
- Combining multi-scale modelling methods to decipher molecular motions of a branching sucrase from glycoside-hydrolase family 70.PloS one · 2018Article
- A consistent force field parameter set for zwitterionic amino acid residues.Journal of molecular modeling · 2014Article
- Conformational state distributions and catalytically relevant dynamics of a hinge-bending enzyme studied by single-molecule FRET and a coarse-grained simulation.Biophysical journal · 2014Article
- Ligand binding and dynamics of the monomeric epidermal growth factor receptor ectodomain.Proteins · 2013Article
- Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics.Journal of molecular modeling · 2013Article
- Mechanism of displacement of a catalytically essential loop from the active site of mammalian fructose-1,6-bisphosphatase.Biochemistry · 2013Article
- Analysis of conformational motions and residue fluctuations for Escherichia coli ribose-binding protein revealed with elastic network models.International journal of molecular sciences · 2013Article
- Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein.Biochemistry · 2011Article
- A role for both conformational selection and induced fit in ligand binding by the LAO protein.PLoS computational biology · 2011Article
- Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics.PLoS computational biology · 2011Article
- Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The glutamine binding protein is a vital component of the associated ATP binding cassette transport systems responsible for the uptake of glutamine into the cell. We have investigated the global movements of this protein by molecular dynamics simulations and principal component analysis (PCA). We confirm that the most dominant mode corresponds to the biological function of the protein, i.e., a hinge-type motion upon ligand binding. The closure itself was directly observed from two independent trajectories whereby PCA was used to elucidate the nature of this closing reaction. Two intermediary states are identified and described in detail. The ligand binding induces the structural change of the hinge regions from a discontinuous beta-sheet to a continuous one, which also enhances softness of the hinge and modifies the direction of hinge motion to enable closing. We also investigated the convergence behavior of PCA modes, which were found to converge rather quickly when the associated magnitudes of the eigenvalues are well separated.
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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.