Dynamics and allostery of the ionotropic glutamate receptors and the ligand binding domain

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


The dynamics of the ligand-binding domain (LBD) and the intact ionotropic glutamate receptor (iGluR) were studied using Gaussian Network Model (GNM) analysis. The dynamics of LBDs with various allosteric modulators is compared using a novel method of multiple alignment of GNM modes of motion. The analysis reveals that allosteric effectors change the dynamics of amino acids at the upper lobe interface of the LBD dimer as well as at the hinge region between the upper- and lower- lobes. For the intact glutamate receptor the analysis show that the clamshell-like movement of the LBD upper and lower lobes is coupled to the bending of the trans-membrane domain (TMD) helices which may open the channel pore. The results offer a new insight on the mechanism of action of allosteric modulators on the iGluR and support the notion of TMD helices bending as a possible mechanism for channel opening. In addition, the study validates the methodology of multiple GNM modes alignment as a useful tool to study allosteric effect and its relation to proteins dynamics.

Original languageEnglish
Pages (from-to)267-277
Number of pages11
JournalProteins: Structure, Function and Bioinformatics
Issue number2
StatePublished - 1 Feb 2016


  • Allostery
  • Gaussian network model
  • Ionotropic glutamate receptors
  • Multiple modes alignment
  • Normal mode analysis


Dive into the research topics of 'Dynamics and allostery of the ionotropic glutamate receptors and the ligand binding domain'. Together they form a unique fingerprint.

Cite this