Intrinsic motions in the N-terminal domain of an ionotropic glutamate receptor detected by fluorescence correlation spectroscopy.

Abstract:

:Ionotropic glutamate receptors (iGluRs) mediate excitatory neurotransmission in the central nervous system and play key roles in brain development and disease. iGluRs have two distinct extracellular domains, but the functional role of the distal N-terminal domain (NTD) is poorly understood. Crystal structures of the NTD from some non-N-methyl-d-aspartate (NMDA) iGluRs are consistent with a rigid body that facilitates receptor assembly but suggest an additional dynamic role that could modulate signaling. Here, we moved beyond spatial and temporal limitations of conventional protein single-molecule spectroscopy by employing correlation analysis of extrinsic oxazine fluorescence fluctuations. We observed nanosecond (ns)-to-microsecond (μs) motions of loop segments and helices within a region of an AMPA-type iGluR NTD, which has been identified previously to be structurally variable. Our data reveal that the AMPA receptor NTD undergoes rapid conformational fluctuations, suggesting an inherent allosteric capacity for this domain in addition to its established assembly function.

journal_name

J Mol Biol

authors

Jensen MH,Sukumaran M,Johnson CM,Greger IH,Neuweiler H

doi

10.1016/j.jmb.2011.09.037

subject

Has Abstract

pub_date

2011-11-18 00:00:00

pages

96-105

issue

1

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(11)01077-1

journal_volume

414

pub_type

杂志文章
  • Derivation of a structural model for the c-myc IRES.

    abstract::We have derived a secondary structure model for the c-myc internal ribosome entry segment (IRES) by using information from chemical probing of the c-myc IRES RNA to constrain structure prediction programs. Our data suggest that the IRES is modular in nature, and can be divided into two structural domains linked by a l...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4745

    authors: Le Quesne JP,Stoneley M,Fraser GA,Willis AE

    更新日期:2001-06-29 00:00:00

  • Determinants of intra versus intermolecular self-association within the regulatory domains of Rlk and Itk.

    abstract::A protein fragment from the Tec family member Rlk (also known as Txk) containing a single proline-rich ligand adjacent to a Src homology 3 (SH3) domain has been investigated by nuclear magnetic resonance (NMR) spectroscopy. Analysis of the concentration dependence of the chemical shifts, NMR linewidths and self-diffus...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00531-x

    authors: Laederach A,Cradic KW,Fulton DB,Andreotti AH

    更新日期:2003-06-20 00:00:00

  • Surface topographies at subnanometer-resolution reveal asymmetry and sidedness of aquaporin-1.

    abstract::Aquaporin-1 (AQP1) is an abundant protein in human erythrocyte membranes which functions as a specific and constitutively active water conducting pore. Solubilized and isolated as tetramer, it forms well-ordered two-dimensional (2D) crystals when reconstituted in the presence of lipids. Several high resolution project...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0686

    authors: Walz T,Tittmann P,Fuchs KH,Müller DJ,Smith BL,Agre P,Gross H,Engel A

    更新日期:1996-12-20 00:00:00

  • Three-dimensional structure-activity relationship modeling of cocaine binding to two monoclonal antibodies by comparative molecular field analysis.

    abstract::Successful immunotherapy of cocaine addiction and overdoses requires cocaine-binding antibodies with specific properties, such as high affinity and selectivity for cocaine. We have determined the affinities of two cocaine-binding murine monoclonal antibodies (mAb: clones 3P1A6 and MM0240PA) for cocaine and its metabol...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)01235-4

    authors: Paula S,Tabet MR,Keenan SM,Welsh WJ,Ball WJ Jr

    更新日期:2003-01-17 00:00:00

  • FLP protein of 2 mu circle plasmid of yeast induces multiple bends in the FLP recognition target site.

    abstract::The FLP recombinase of the 2 mu plasmid of Saccharomyces cerevisiae binds to a target containing three 13 base-pair symmetry elements called a, b and c. The symmetry elements b and c are in direct orientation while the a element is in inverted orientation with respect to b and c on the opposite side of an eight base-p...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(05)80320-1

    authors: Schwartz CJ,Sadowski PD

    更新日期:1990-11-20 00:00:00

  • Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering.

    abstract::A systematic classification of beta-hairpin structures which takes into account the polypeptide chain length and hydrogen bonding between the two antiparallel beta-strands is described. We have used this classification of beta-hairpin structures and their specific sequence pattern to derive rules which demonstrate its...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90583-4

    authors: Sibanda BL,Blundell TL,Thornton JM

    更新日期:1989-04-20 00:00:00

  • Crystallization of p68 on lipid monolayers and as three-dimensional single crystals.

    abstract::Two-dimensional crystals of p68, a Ca2+ -binding protein that has homology with members of the lipocortin/calpactin family, were obtained by interaction with a phospholipid monolayer. By measuring surface pressure at constant surface area, p68 was found to interact in a Ca2+ -dependent manner specifically with phospha...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90534-2

    authors: Newman R,Tucker A,Ferguson C,Tsernoglou D,Leonard K,Crumpton MJ

    更新日期:1989-03-05 00:00:00

  • Modulator of drug activity B from Escherichia coli: crystal structure of a prokaryotic homologue of DT-diaphorase.

    abstract::Modulator of drug activity B (MdaB) is a putative member of the DT-diaphorase family of NAD(P)H:oxidoreductases that afford cellular protection against quinonoid compounds. While there have been extensive investigations of mammalian homologues, putative prokaryotic members of this enzyme family have received little at...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.03.053

    authors: Adams MA,Jia Z

    更新日期:2006-06-02 00:00:00

  • C--H...O hydrogen bond involving proline residues in alpha-helices.

    abstract::Despite proline being assumed to be a helix-breaker, a large number of alpha-helices are found to contain Pro in globular as well as membrane proteins. Proline has no free NH group and therefore cannot form the conventional intra-helical NH.O=C hydrogen bond. An analysis of known protein structures has shown that the ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2199

    authors: Chakrabarti P,Chakrabarti S

    更新日期:1998-12-11 00:00:00

  • Structural bases for sulfide recognition in Lucina pectinata hemoglobin I.

    abstract::The X-ray crystal structure of the sulfide derivative of ferric Lucina pectinata hemoglobin component I (HbI) has been determined at 1.9 A resolution (R-factor 0.186). The heme pocket structural organization of HbI is in keeping with its ligand binding properties. The fast sulfide association rate constant can be rela...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0228

    authors: Rizzi M,Wittenberg JB,Coda A,Ascenzi P,Bolognesi M

    更新日期:1996-04-26 00:00:00

  • Organization of the R family and other interspersed repetitive DNA sequences in the mouse genome.

    abstract::Six R sequences have been described as members of a new family of dispersed repetitive DNA in the mouse genome (Gebhard et al., 1982). Several sequenced regions were extended in the 5' direction (R1, R2 and R6) and two new sequences were determined (R7 and R8). On the basis of our sequence and blot hybridization data ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80147-8

    authors: Gebhard W,Zachau HG

    更新日期:1983-10-25 00:00:00

  • Sequence dependence of translational positioning of core nucleosomes.

    abstract::The basis for the choice of translational position of a histone octamer on DNA is poorly understood. To gain further insights into this question we have studied the translational and rotational settings of core particles assembled on a simple repeating 20 bp positioning sequence. We show that the translational positio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4546

    authors: Negri R,Buttinelli M,Panetta G,De Arcangelis V,Di Mauro E,Travers A

    更新日期:2001-04-06 00:00:00

  • Genomic analysis of sequence variation in tandemly repeated DNA. Evidence for localized homogeneous sequence domains within arrays of alpha-satellite DNA.

    abstract::As a model to examine the local distribution of sequence variation within large arrays of tandemly repeated DNA in complex genomes, the long-range organization of alpha-satellite DNA from human chromosome 17 was investigated. Three individual chromosomes, representing different alpha-satellite haplotypes, were segrega...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(05)80056-7

    authors: Warburton PE,Willard HF

    更新日期:1990-11-05 00:00:00

  • Angular disorder in actin: is it consistent with general principles of protein structure?

    abstract::Harold Erickson has recently provided a useful analysis of helical structures having one class versus two classes of intersubunit bonds. His analysis is based upon an assumption that the subunits themselves are essentially unchanged upon bond formation (polymerization). He shows that such a structure having two classe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90743-p

    authors: Egelman EH,DeRosier DJ

    更新日期:1991-02-05 00:00:00

  • An objective assessment of conformational variability in complexes of hepatitis C virus polymerase with non-nucleoside inhibitors.

    abstract::A major target for antiviral therapy against hepatitis C virus (HCV) is the HCV polymerase nonstructural protein 5B (NS5B). Huge efforts have been devoted to the development of nucleoside and non-nucleoside inhibitors (NNIs) of NS5B. An offshoot of these efforts has been the structural characterization of the interact...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.10.001

    authors: Caillet-Saguy C,Simister PC,Bressanelli S

    更新日期:2011-12-02 00:00:00

  • Concerning the axial rotational flexibility of the Fab regions of immunoglobulin G.

    abstract::By electron microscopy, we have observed immunocomplexes with both negative stain and in amorphous ice using monoclonal antibodies directed against one of the 24 subunits of scorpion haemocyanin. A copy of this subunit occurs at each of the corners of the square-shaped haemocyanin molecule. Three distinct orientations...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90484-1

    authors: Wade RH,Taveau JC,Lamy JN

    更新日期:1989-03-20 00:00:00

  • Characterization of preferred deoxyribonuclease I cleavage sites.

    abstract::The preferred DNase I cleavage sites within the 160 bp tyrT DNA fragment were identified by studying the initial rate of cleavage of individual bonds. The results show that there is no correlation between the rate of cleavage and the identity of the dinucleotide sequence that is cleaved. Examination of the sequences s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1152

    authors: Herrera JE,Chaires JB

    更新日期:1994-02-18 00:00:00

  • The RecB nuclease domain binds to RecA-DNA filaments: implications for filament loading.

    abstract::The E. coli RecBCD enzyme facilitates the loading of RecA onto single-stranded DNA produced by the combined helicase/nuclease activity of RecBCD. The nuclease domain of RecB protein, RecB(nuc), has been previously shown to bind RecA. Surprisingly, RecB(nuc) also binds to phage and eukaryotic homologs of RecA, leading ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.06.042

    authors: Lucarelli D,Wang YA,Galkin VE,Yu X,Wigley DB,Egelman EH

    更新日期:2009-08-14 00:00:00

  • Three-state model for lysozyme folding: triangular folding mechanism with an energetically trapped intermediate.

    abstract::We investigated the role of a partially folded intermediate that transiently accumulates during lysozyme folding. Previous studies had shown that the partially folded intermediate is located on a slow-folding pathway and that an additional fast direct pathway from the unfolded state to the native state exists. Kinetic...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1030

    authors: Wildegger G,Kiefhaber T

    更新日期:1997-07-11 00:00:00

  • Reconstituted and native iron-cores of bacterioferritin and ferritin.

    abstract::The structural and magnetic properties of the iron-cores of reconstituted horse spleen ferritin and Azotobacter vinelandii bacterioferritin have been investigated by high-resolution transmission electron microscopy, electron diffraction and Mossbauer spectroscopy. The structural properties of native horse spleen ferri...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90290-7

    authors: Mann S,Williams JM,Treffry A,Harrison PM

    更新日期:1987-12-05 00:00:00

  • A Distinct Motif in a Prokaryotic Small Ras-Like GTPase Highlights Unifying Features of Walker B Motifs in P-Loop NTPases.

    abstract::A hallmark of the catalytically essential Walker B motif of P-loop NTPases is the presence of an acidic residue (aspartate/glutamate) for efficient Mg2+ coordination. Although the Walker B motif has been identified in well-studied examples of P-loop NTPases, its identity is ambiguous in many families, for example, in ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.07.024

    authors: Kanade M,Chakraborty S,Shelke SS,Gayathri P

    更新日期:2020-09-18 00:00:00

  • Crystal structure and comparative functional analyses of a Mycobacterium aldo-keto reductase.

    abstract::Aldo-keto reductases (AKRs) are a large superfamily of NADPH-dependent enzymes that catalyze the reduction of aldehydes, aldoses, dicarbonyls, steroids, and monosaccharides. While their precise physiological role is generally unknown, AKRs are nevertheless involved in the detoxification of a broad range of toxic metab...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.02.021

    authors: Scoble J,McAlister AD,Fulton Z,Troy S,Byres E,Vivian JP,Brammananth R,Wilce MC,Le Nours J,Zaker-Tabrizi L,Coppel RL,Crellin PK,Rossjohn J,Beddoe T

    更新日期:2010-04-23 00:00:00

  • Position-specific inhibition of yeast mitochondrial transcription by a poly(T) sequence.

    abstract::The 3' flanking nucleotide(s) of the octanucleotide promoter sequence regulates transcriptional efficiency of some mitochondrial genes in Saccharomyces cerevisiae. To understand this regulation the in vitro transcriptional activity of various synthetic mitochondrial promoters carrying different 3' flanking sequences w...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1483

    authors: Biswas TK,Getz GS

    更新日期:1998-01-30 00:00:00

  • Conformational changes in phosphoglucose isomerase induced by ligand binding.

    abstract::Phosphoglucose isomerase (PGI; EC 5.3.1.9) is the second enzyme in glycolysis, where it catalyzes the isomerization of D-glucose-6-phosphate to D-fructose-6-phosphate. It is the same protein as autocrine motility factor, differentiation and maturation mediator, and neuroleukin. Here, we report a new X-ray crystal stru...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00892-6

    authors: Arsenieva D,Jeffery CJ

    更新日期:2002-10-11 00:00:00

  • The oligomeric distribution of SecYEG is altered by SecA and translocation ligands.

    abstract::The multimeric membrane protein complex translocase mediates the transport of preproteins across and integration of membrane proteins into the inner membrane of Escherichia coli. The translocase consists of the peripheral membrane-associated ATPase SecA and the heterotrimeric channel-forming complex consisting of SecY...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.09.058

    authors: Scheuring J,Braun N,Nothdurft L,Stumpf M,Veenendaal AK,Kol S,van der Does C,Driessen AJ,Weinkauf S

    更新日期:2005-11-25 00:00:00

  • High-resolution structure of the major periplasmic domain from the cell shape-determining filament MreC.

    abstract::Bacterial cell shape is dictated by the cell wall, a plastic structure that must adapt to growth and division whilst retaining its function as a selectively permeable barrier. The modulation of cell wall structure is achieved by a variety of enzymatic functions, all of which must be spatially regulated in a precise ma...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.07.022

    authors: Lovering AL,Strynadka NCJ

    更新日期:2007-09-28 00:00:00

  • Ribonuclease T1 with free recognition and catalytic site: crystal structure analysis at 1.5 A resolution.

    abstract::The free form of ribonuclease T1 (RNase T1) has been crystallized at neutral pH, and the three-dimensional structure of the enzyme has been determined at 1.5 A nominal resolution. Restrained least-squares refinement yielded an R value of 14.3% for 12,623 structure amplitudes. The high resolution of the structure analy...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90215-r

    authors: Martinez-Oyanedel J,Choe HW,Heinemann U,Saenger W

    更新日期:1991-11-20 00:00:00

  • DNA combing reveals intrinsic temporal disorder in the replication of yeast chromosome VI.

    abstract::It is generally believed that DNA replication in most eukaryotes proceeds according to a precise program in which there is a defined temporal order by which each chromosomal region is duplicated. However, the regularity of this program at the level of individual chromosomes, in terms of both the relative timing and th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2007.10.046

    authors: Czajkowsky DM,Liu J,Hamlin JL,Shao Z

    更新日期:2008-01-04 00:00:00

  • Alanine scan of core positions in ubiquitin reveals links between dynamics, stability, and function.

    abstract::Mutations at solvent-inaccessible core positions in proteins can impact function through many biophysical mechanisms including alterations to thermodynamic stability and protein dynamics. As these properties of proteins are difficult to investigate, the impacts of core mutations on protein function are poorly understo...

    journal_title:Journal of molecular biology

    pub_type: 评论,杂志文章

    doi:10.1016/j.jmb.2013.10.042

    authors: Lee SY,Pullen L,Virgil DJ,Castañeda CA,Abeykoon D,Bolon DN,Fushman D

    更新日期:2014-04-03 00:00:00

  • The refined structures of goose lysozyme and its complex with a bound trisaccharide show that the "goose-type" lysozymes lack a catalytic aspartate residue.

    abstract::The structure of goose egg-white lysozyme (GEWL) has been refined to an R-value of 15.9% at 1.6 A resolution. Details of the structure determination, the refinement and the structure itself are presented. The structure of a complex of the enzyme with the trisaccharide of N-acetyl glucosamine has also been determined a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(95)80038-7

    authors: Weaver LH,Grütter MG,Matthews BW

    更新日期:1995-01-06 00:00:00