Related ArticlesStructural mobility of the extracellular ligand-binding core of an ionotropic glutamate receptor. Analysis of NMR relaxation dynamics.
Biochemistry. 2002 Aug 20;41(33):10472-81
Authors: McFeeters RL, Oswald RE
Ionotropic glutamate receptors play important roles in a variety of neuronal processes and have been implicated in multiple neurodegenerative diseases. The extracellular ligand-binding (S1S2) core of the GluR2 subtype can be expressed in bacteria as a soluble, monomeric protein with binding properties essentially identical to those of the intact receptor. The crystal structure of this protein has been determined in the presence and absence of various agonists and antagonists [Armstrong, N., Sun, Y., Chen, G. Q., and Gouaux, E. (1998) Nature 395, 913-917; Armstrong, N., and Gouaux, E. (2000) Neuron 28, 165-181]. The protein consists of two lobes, with the S1 segment composing the majority of lobe 1 and the S2 segment composing most of lobe 2. A domain closure upon ligand binding has been postulated, but details of intradomain motions have not been investigated. In this paper, the backbone motions of the ligand-binding core of GluR2 bound to glutamate were studied using (15)N longitudinal (T1) and transverse (T2) relaxation measurements as well as [1H]-15N nuclear Overhauser effects at 500 and 600 MHz. Residues in the agonist-binding pocket exhibited two main classes of motion. Those contacting the alpha-substituents of the ligand glutamate exhibited minimal internal motion, while those contacting the gamma-constituents exhibited exchange dynamics, indicating two dynamically distinct portions of the binding pocket. Also, two residues in transdomain linkers between lobes 1 and 2 show exchange, lending new insight into the previously proposed domain closure hypothesis. Finally, concerted motion of helix F suggests a pathway for ligand dissociation without the necessity of domain reopening.
An NMR-Based Structural Rationale for Contrasting Stoichiometry and Ligand Binding Site(s) in Fatty Acid-binding Proteins.
An NMR-Based Structural Rationale for Contrasting Stoichiometry and Ligand Binding Site(s) in Fatty Acid-binding Proteins.
An NMR-Based Structural Rationale for Contrasting Stoichiometry and Ligand Binding Site(s) in Fatty Acid-binding Proteins.
Biochemistry. 2011 Jan 12;
Authors: He Y, Estephan R, Yang X, Vela A, Wang H, Bernard C, Stark RE
Liver fatty acid-binding protein (LFABP) is a 14-kDa cytosolic polypeptide, differing from other family members in number of ligand binding sites, diversity of bound ligands, and transfer of fatty acid(s) to...
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01-14-2011 12:05 PM
[NMR paper] NMR structure and peptide hormone binding site of the first extracellular domain of a
NMR structure and peptide hormone binding site of the first extracellular domain of a type B1 G protein-coupled receptor.
Related Articles NMR structure and peptide hormone binding site of the first extracellular domain of a type B1 G protein-coupled receptor.
Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12836-41
Authors: Grace CR, Perrin MH, DiGruccio MR, Miller CL, Rivier JE, Vale WW, Riek R
The corticotropin-releasing factor (CRF) ligand family has diverse effects on the CNS, including the modulation of the stress response. The ligands'...
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11-24-2010 10:01 PM
[NMR paper] Structural characterization by NMR of the natively unfolded extracellular domain of b
Structural characterization by NMR of the natively unfolded extracellular domain of beta-dystroglycan: toward the identification of the binding epitope for alpha-dystroglycan.
Related Articles Structural characterization by NMR of the natively unfolded extracellular domain of beta-dystroglycan: toward the identification of the binding epitope for alpha-dystroglycan.
Biochemistry. 2003 Nov 25;42(46):13717-24
Authors: Bozzi M, Bianchi M, Sciandra F, Paci M, Giardina B, Brancaccio A, Cicero DO
Dystroglycan (DG) is an adhesion molecule playing a...
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11-24-2010 09:16 PM
[NMR paper] Structural analysis of the extracellular domain of vaccinia virus envelope protein, A
Structural analysis of the extracellular domain of vaccinia virus envelope protein, A27L, by NMR and CD spectroscopy.
Related Articles Structural analysis of the extracellular domain of vaccinia virus envelope protein, A27L, by NMR and CD spectroscopy.
J Biol Chem. 2002 Jun 7;277(23):20949-59
Authors: Lin TH, Chia CM, Hsiao JC, Chang W, Ku CC, Hung SC, Tzou DL
This study presents the molecular structure of the extracellular domain of vaccinia virus envelope protein, A27L, determined by NMR and CD spectroscopy. A recombinant protein, eA27L-aa,...
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11-24-2010 08:49 PM
[NMR paper] Ligand-induced structural changes to maltodextrin-binding protein as studied by solut
Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy.
Related Articles Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy.
J Mol Biol. 2001 Jun 15;309(4):961-74
Authors: Evenäs J, Tugarinov V, Skrynnikov NR, Goto NK, Muhandiram R, Kay LE
Solution NMR studies on the physiologically relevant ligand-free and maltotriose-bound states of maltodextrin-binding protein (MBP) are presented. Together with existing data on MBP in complex with...
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11-19-2010 08:32 PM
[NMR paper] Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein
Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange.
Biochemistry. 1997 Feb 25;36(8):2278-90
Authors: Hodsdon ME, Cistola DP
The backbone dynamics of the liganded (holo) and unliganded (apo) forms of Escherichia...
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08-22-2010 03:31 PM
[NMR paper] Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein
Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange.
Biochemistry. 1997 Feb 25;36(8):2278-90
Authors: Hodsdon ME, Cistola DP
The backbone dynamics of the liganded (holo) and unliganded (apo) forms of Escherichia...
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08-22-2010 03:03 PM
Installation of GROMACS 3.3.1 on Dell Inspiron 6400 with Fedora Core 6, Test 3, Dual Core processor
This is not really a "hard-core NMR topic" but it could be useful for people who try to complement dynamics data from NMR relaxation experiments with MD simulations.
I had really hard time trying to install the newer versions of Gromacs 3.3 and 3.3.1 on my laptop (Dell Inspiron 6400 Dual Core processor) . The laptop used to run Suse 10.1 that was recently replaced with Fedora Core 6 Test 3 (that finally supports Intel integrated mobile 945 video cards). With both OS, Gromacs 3.3.x could be installed, however, its sub-program "genion" failed (the program never ends while consuming 100%...
Structural mobility of the extracellular ligand-binding core of an ionotropic glutama
Linear Mode
