ArticleBiophysical journal2007
Analysis of domain movements in glutamine-binding protein with simple models.
Article in Biophysical journal, 2007. 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, 41 citations in OpenAlex.
- Dissecting mechanisms of ligand binding and conformational changes in the glutamine-binding protein.eLife · 2026Article
- 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
- Ligand-bound glutamine binding protein assumes multiple metastable binding sites with different binding affinities.Communications biology · 2020Article
- Energy transport pathway in proteins: Insights from non-equilibrium molecular dynamics with elastic network model.Scientific reports · 2018Article
- The Intrinsic Dynamics and Unfolding Process of an Antibody Fab Fragment Revealed by Elastic Network Model.International journal of molecular sciences · 2015Article
- Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics.Journal of molecular modeling · 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
- Article
- Stability and folding behavior analysis of zinc-finger using simple models.International journal of molecular sciences · 2010Article
- Ligand-free open-closed transitions of periplasmic binding proteins: the case of glutamine-binding protein.Biochemistry · 2010Article
- A luminescence lifetime assisted ratiometric fluorimeter for biological applications.The Review of scientific instruments · 2009Article
- Collective dynamics of periplasmic glutamine binding protein upon domain closure.Biophysical journal · 2009Article
- Article
- Protein unfolding behavior studied by elastic network model.Biophysical journal · 2008Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this work, the mechanism of domain movements of glutamine-binding protein (GlnBP), especially the influence of the ligand on GlnBP dynamic behavior is investigated with the aid of a Gaussian network model (GNM) and an anisotropy elastic network model. The results show that the "open-closed" transition mainly appears as the large movement of the small domain, especially the top region including two alpha-helices and two beta-strands. The slowest mode of each three forms of GlnBP--ligand-free open, ligand-bound closed, and ligand-free closed GlnBP--shows that the open-closed motion of the two domains has a common hinge axis centered on Lys-87 and Gln-183. Accompanying the conformational transition, the residues within both large and small domains move in a highly coupled way. The peaks of the fast modes correspond to residues that were thought, in the GNM, to be important for the stability of the protein, and these residues may be involved in the interactions with the membrane-bound components. With the contacts between the large domain and the small domain increasing, the ability of the "open-closed" motion is decreased. All the results agree well with those of molecular dynamics simulations, and it is thought that the open-closed conformation transition is the nature of the topology structure of GlnBP. Also, the influence of the ligand on GlnBP is studied with a modified GNM method. The results obtained show that the ligand does not influence the closed-to-open transition tendency.
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