Voltage-gating of Escherichia coli porin: a cystine-scanning mutagenesis study of loop 3.

Abstract:

:Porins, such as Escherichia coli OmpF, provide the only reported example of a voltage-gated channel where the three-dimensional structure is known to high resolution. Mutations that affect voltage-gating are clustered around the eyelet region, which is a mid-channel constriction caused by a polypeptide loop (L3) folding inside the lumen of this beta-barrel pore. These data, combined with molecular dynamics simulations, indicate that voltage-gating may involve L3 displacement. We have constructed six double cysteine OmpF mutants, five of which form disulphide bonds fixing L3 in the conformation determined by X-ray crystallography. These channels have altered single-channel conductances but unimpaired voltage-gating. The data show that L3 movement is not required for voltage-gating.

journal_name

J Mol Biol

authors

Bainbridge G,Mobasheri H,Armstrong GA,Lea EJ,Lakey JH

doi

10.1006/jmbi.1997.1474

subject

Has Abstract

pub_date

1998-01-16 00:00:00

pages

171-6

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(97)91474-1

journal_volume

275

pub_type

杂志文章
  • Structural Basis for the Interaction between the IUS-SPRY Domain of RanBPM and DDX-4 in Germ Cell Development.

    abstract::RanBPM and RanBP10 are non-canonical members of the Ran binding protein family that lack the Ran binding domain and do not associate with Ran GTPase in vivo. Rather, they have been shown to be scaffolding proteins that are important for a variety of cellular processes, and both of these proteins contain a SPRY domain,...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.09.004

    authors: Hong SK,Kim KH,Song EJ,Kim EE

    更新日期:2016-10-23 00:00:00

  • Early events in the binding of the pPS10 replication protein RepA to single iteron and operator DNA sequences.

    abstract::RepA protein, encoded in the Pseudomonas pPS10 replicon, is a stable dimer in solution (dRepA), acting as a self-repressor of repA transcription through binding to an inverted repeat operator. However, RepA monomers (mRepA) are required to initiate plasmid replication upon binding to four directly repeated DNA sequenc...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.09.013

    authors: Díaz-López T,Dávila-Fajardo C,Blaesing F,Lillo MP,Giraldo R

    更新日期:2006-12-15 00:00:00

  • V-shaped scaffold: a new architectural motif identified in an A x (G x G x G x G) pentad-containing dimeric DNA quadruplex involving stacked G(anti) x G(anti) x G(anti) x G(syn) tetrads.

    abstract::We report the results of an NMR study of unlabeled and uniformly (13)C,(15)N-labeled d(G(3)AG(2)T(3)G(3)AT) in 100 mM NaCl, conditions under which it forms a dimeric quadruplex containing several new topological features. The DNA oligomer chain in each symmetry-related monomer subunit undergoes three sharp turns to fo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4916

    authors: Zhang N,Gorin A,Majumdar A,Kettani A,Chernichenko N,Skripkin E,Patel DJ

    更新日期:2001-08-31 00:00:00

  • Structural comparison of cuticle and interstitial collagens from annelids living in shallow sea-water and at deep-sea hydrothermal vents.

    abstract::Two types of annelid collagens of different sizes were purified, one from acetic acid extracts of the cuticle (length 2.5 microns) and the other, after pepsin digestion, from interstitial spaces of the body wall (0.3 micron). They were obtained from Alvinella pompejana, Alvinella caudata and Paralvinella grasslei coll...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.0084

    authors: Gaill F,Mann K,Wiedemann H,Engel J,Timpl R

    更新日期:1995-02-17 00:00:00

  • Two distinct binding modes of a protein cofactor with its target RNA.

    abstract::Like most cellular RNA enzymes, the bI5 group I intron requires binding by a protein cofactor to fold correctly. Here, we use single-molecule approaches to monitor the structural dynamics of the bI5 RNA in real time as it assembles with its CBP2 protein cofactor. These experiments show that CBP2 binds to the target RN...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.06.048

    authors: Bokinsky G,Nivón LG,Liu S,Chai G,Hong M,Weeks KM,Zhuang X

    更新日期:2006-08-25 00:00:00

  • Partitioning of plasmid R1. Ten direct repeats flanking the parA promoter constitute a centromere-like partition site parC, that expresses incompatibility.

    abstract::The parA partitioning system of plasmid R1 consists of three different components: the cis-acting centromere-like parC site, and the two trans-acting proteins ParM and ParR. These three components are contained within a region of 1.6 kb. The parC site is located upstream of the two genes, parM and parR, which are expr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(94)90058-2

    authors: Dam M,Gerdes K

    更新日期:1994-03-11 00:00:00

  • GTP-dependent conformational changes associated with the functional switch between Galpha and cross-linking activities in brain-derived tissue transglutaminase.

    abstract::GTP and Ca2+, two well-known modulators of intracellular signaling pathways, control a structural/functional switch between two vital and mutually exclusive activities, cross-linking and Galpha activity, in the same enzyme. The enzyme, a brain-derived tissue-type transglutaminase (TGase), was recently cloned by us in ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2052

    authors: Monsonego A,Friedmann I,Shani Y,Eisenstein M,Schwartz M

    更新日期:1998-10-02 00:00:00

  • An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints.

    abstract::A novel approach aiding in the prediction of RNA secondary structures is presented. Although phylogenetic methods are the most successful at deriving RNA secondary structures, the are not applicable when the number of sequences or the sequence variability is too low. Methods based on energy minimization are therefore ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0608

    authors: Gaspin C,Westhof E

    更新日期:1995-11-24 00:00:00

  • Pseudo 2-fold symmetry in the copper-binding domain of arthropodan haemocyanins. Possible implications for the evolution of oxygen transport proteins.

    abstract::Investigation of the copper-binding centre of Panulirus interruptus haemocyanin led to the discovery of a pseudo 2-fold axis relating two helical pairs surrounding and co-ordinating the two copper ions. The pseudo 2-fold symmetry relating one helical pair, co-ordinating Cu-A, to the second helical pair co-ordinating C...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90499-3

    authors: Volbeda A,Hol WG

    更新日期:1989-04-05 00:00:00

  • Molecular evolution of multisubunit RNA polymerases: sequence analysis.

    abstract::Transcription in all cellular organisms is performed by multisubunit, DNA-dependent RNA polymerases that synthesize RNA from DNA templates. Previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit RNA polymerases. In addition, RNA polymerases contain multiple...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.10.062

    authors: Lane WJ,Darst SA

    更新日期:2010-01-29 00:00:00

  • Quaternary re-arrangement analysed by spectral enhancement: the interaction of a sporulation repressor with its antagonist.

    abstract::The protein/protein interaction between SinI and SinR has been studied by analytical ultracentrifugation and gel electrophoresis in an attempt to understand how these proteins contribute to developmental control of sporulation in Bacillus subtilis. SinR was found to be tetrameric, while SinI was found to exist as mono...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3221

    authors: Scott DJ,Leejeerajumnean S,Brannigan JA,Lewis RJ,Wilkinson AJ,Hoggett JG

    更新日期:1999-11-12 00:00:00

  • Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II.

    abstract::Human RNA polymerase II recognizes a strong transcriptional pause signal in the initially transcribed region of HIV-1. We report the use of a limited-step transcription assay to dissect the mechanism underlying recognition of and escape from this HIV-1 pause. Our results suggest that the primary determinant of transcr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4842

    authors: Palangat M,Landick R

    更新日期:2001-08-10 00:00:00

  • A model of Cdc25 phosphatase catalytic domain and Cdk-interaction surface based on the presence of a rhodanese homology domain.

    abstract::Mammalian Cdc25 phosphatase is responsible for the dephosphorylation of Cdc2 and other cyclin-dependent kinases at Thr14 and Tyr15, thus activating the kinase and allowing cell cycle progression. The catalytic domain of this dual-specificity phosphatase has recently been mapped to the 180 most C-terminal amino acids. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1998

    authors: Hofmann K,Bucher P,Kajava AV

    更新日期:1998-09-11 00:00:00

  • Molecular Organization of Soluble Type III Secretion System Sorting Platform Complexes.

    abstract::Many medically relevant Gram-negative bacteria use the type III secretion system (T3SS) to translocate effector proteins into the host for their invasion and intracellular survival. A multi-protein complex located at the cytosolic interface of the T3SS is proposed to act as a sorting platform by selecting and targetin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.07.004

    authors: Bernal I,Börnicke J,Heidemann J,Svergun D,Horstmann JA,Erhardt M,Tuukkanen A,Uetrecht C,Kolbe M

    更新日期:2019-09-06 00:00:00

  • Site-directed mutations in motif VI of Escherichia coli DNA helicase II result in multiple biochemical defects: evidence for the involvement of motif VI in the coupling of ATPase and DNA binding activities via conformational changes.

    abstract::Two site-directed mutants of Escherichia coli DNA helicase II (UvrD) were constructed to examine the functional significance of motif VI in a superfamily I helicase. Threonine 604 and arginine 605, representing two of the most highly conserved residues in motif VI, were replaced with alanine, generating the mutant all...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1614

    authors: Hall MC,Ozsoy AZ,Matson SW

    更新日期:1998-03-27 00:00:00

  • Solution structure of the SH2 domain of Grb2 complexed with the Shc-derived phosphotyrosine-containing peptide.

    abstract::The solution structure of growth factor receptor-bound protein 2 (Grb2) SH2 complexed with a Shc-derived phosphotyrosine (pTyr)-containing peptide was determined by nuclear magnetic resonance (NMR) spectroscopy. The pTyr binding site of Grb2 SH2 was similar to those of other SH2 domains. In contrast, the amino acid re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2792

    authors: Ogura K,Tsuchiya S,Terasawa H,Yuzawa S,Hatanaka H,Mandiyan V,Schlessinger J,Inagaki F

    更新日期:1999-06-11 00:00:00

  • Cation transport: an example of structural based selectivity.

    abstract::Through the high-resolution structure of the gramicidin A channel in lamellar phase lipids and the characterization of specific ion peptide interactions, fundamental principles for ion channel selectivity and conductance efficiency are illustrated with atomic resolution detail. Delocalized cation binding in the first ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2434

    authors: Tian F,Cross TA

    更新日期:1999-02-05 00:00:00

  • Conserved structural features are found upstream from the three co-ordinately regulated discoidin I genes of Dictyostelium discoideum.

    abstract::The discoidin I genes of Dictyostelium form a small, co-ordinately regulated multigene family. We have sequenced and compared the upstream regions of the DiscI-alpha, -beta and -gamma genes. For the most part the upstream regions of the three genes are non-homologous. The upstream sequences of the beta and gamma genes...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(84)80038-8

    authors: Poole SJ,Firtel RA

    更新日期:1984-01-15 00:00:00

  • Group II chaperonins: new TRiC(k)s and turns of a protein folding machine.

    abstract::In the past decade, the eubacterial group I chaperonin GroEL became the paradigm of a protein folding machine. More recently, electron microscopy and X-ray crystallography offered insights into the structure of the thermosome, the archetype of the group II chaperonins which also comprise the chaperonin from the eukary...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1006/jmbi.1999.3008

    authors: Gutsche I,Essen LO,Baumeister W

    更新日期:1999-10-22 00:00:00

  • Crystal structure of the dog lipocalin allergen Can f 2: implications for cross-reactivity to the cat allergen Fel d 4.

    abstract::The dog lipocalin allergen Can f 2 is an important cause of allergic sensitization in humans worldwide. Here, the first crystal structure of recombinant rCan f 2 at 1.45 A resolution displays a classical lipocalin fold with a conserved Gly-Xaa-Trp motif, in which Trp19 stabilizes the overall topology of the monomeric ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.05.043

    authors: Madhurantakam C,Nilsson OB,Uchtenhagen H,Konradsen J,Saarne T,Högbom E,Sandalova T,Grönlund H,Achour A

    更新日期:2010-08-06 00:00:00

  • Sigma competition: the contest between bacteriophage T4 middle and late transcription.

    abstract::In bacterial transcription, diverse sigma-family promoter recognition proteins compete for a common RNA polymerase core. Bacteriophage T4 infection ultimately reduces this competition to a duel between activated viral middle and enhanced late transcription, involving two sigma proteins, two phage-encoded activator pro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2953

    authors: Kolesky S,Ouhammouch M,Brody EN,Geiduschek EP

    更新日期:1999-08-13 00:00:00

  • Solution Conformation of Bovine Leukemia Virus Gag Suggests an Elongated Structure.

    abstract::Bovine leukemia virus (BLV) is a deltaretrovirus that infects domestic cattle. The structural protein Gag, found in all retroviruses, is a polyprotein comprising three major functional domains: matrix (MA), capsid (CA), and nucleocapsid (NC). Previous studies have shown that both mature BLV MA and NC are able to bind ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.01.036

    authors: Qualley DF,Cooper SE,Ross JL,Olson ED,Cantara WA,Musier-Forsyth K

    更新日期:2019-03-15 00:00:00

  • Preliminary crystallographic study of the Fab fragment of a monoclonal antibody directed against a cobra cardiotoxin.

    abstract::We report on the preparation, crystallization and preliminary X-ray crystallographic study of the Fab fragments from a murine monoclonal anti-cardiotoxin antibody M gamma 2-3 directed against a cobra cardiotoxin. The Fab fragment has been crystallized from polyethylene glycol 8000 solutions in a form suitable for high...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(86)90503-6

    authors: Guillon V,Alzari PM,Grognet JM

    更新日期:1986-06-20 00:00:00

  • RNA binding, packaging and polymerase activities of the different incomplete polymerase complex particles of dsRNA bacteriophage phi 6.

    abstract::phi 6 is an enveloped dsRNA bacterial virus. Its segmented genome resides inside the virion associated polymerase complex which is formed by four proteins (P1, P2, P4 and P7) encoded by the viral L segment. Complete and incomplete polymerase complex particles can be produced using cDNA copies of this largest genome se...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0317

    authors: Juuti JT,Bamford DH

    更新日期:1995-06-09 00:00:00

  • X-ray diffraction and electron microscopy from Lethocerus flight muscle partially relaxed by adenylylimidodiphosphate and ethylene glycol.

    abstract::The low-angle X-ray diffraction pattern from Lethocerus flight muscle fibres was recorded in rigor or under two conditions that modify crossbridge structure and behaviour, aqueous adenylylimidodiphosphate (AMPPNP) and AMPPNP + calcium in an ethylene glycol-water mixture. The effects on the 38.7 nm layer-line peaks (hk...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90152-C

    authors: Tregear RT,Wakabayashi K,Tanaka H,Iwamoto H,Reedy MC,Reedy MK,Sugi H,Amemiya Y

    更新日期:1990-07-05 00:00:00

  • The nature of ligand-induced conformational change in transferrin in solution. An investigation using X-ray scattering, XAFS and site-directed mutants.

    abstract::Ligand-induced conformational change in transferrins has been studied by site-directed mutagenesis of human serum half molecule (N-lobe), X-ray absorption fine structure (XAFS) spectroscopy and X-ray solution scattering. Use of recent advances in data analysis has been made for extracting model-independent molecular s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1787

    authors: Grossmann JG,Crawley JB,Strange RW,Patel KJ,Murphy LM,Neu M,Evans RW,Hasnain SS

    更新日期:1998-06-05 00:00:00

  • Human T cell cyclophilin18 binds to thiol-specific antioxidant protein Aop1 and stimulates its activity.

    abstract::Cyclophilins (CyPs) define a family of proteins binding to the immunosuppressive drug cyclosporin A (CsA). They are evolutionary highly conserved proteins being present in both pro- and eukaryotes and in different subcellular locations. CyPs possess enzymatic activity, namely peptidyl-prolyl cis-trans isomerase (PPIas...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1644

    authors: Jäschke A,Mi H,Tropschug M

    更新日期:1998-04-10 00:00:00

  • Energetics of lesion recognition by a DNA repair protein: thermodynamic characterization of formamidopyrimidine-glycosylase (Fpg) interactions with damaged DNA duplexes.

    abstract::As part of an overall effort to map the energetic landscape of the base excision repair pathway, we report the first thermodynamic characterization of repair enzyme binding to lesion-containing duplexes. Isothermal titration calorimetry (ITC) in conjunction with spectroscopic measurements and protease protection assay...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00365-6

    authors: Minetti CA,Remeta DP,Zharkov DO,Plum GE,Johnson F,Grollman AP,Breslauer KJ

    更新日期:2003-05-16 00:00:00

  • Functional analysis of the glucocorticoid regulatory elements present in the mouse mammary tumor virus long terminal repeat. A synthetic distal binding site can replace the proximal binding domain.

    abstract::Transcription of mouse mammary tumor virus DNA is stimulated by steroid hormones. The DNA sequences involved in this regulation are located in the viral long terminal repeat between positions -200 and -50 with respect to the transcription initiation site. In this region four, one distal and three proximal, in vitro bi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(86)90008-2

    authors: Kühnel B,Buetti E,Diggelmann H

    更新日期:1986-08-05 00:00:00

  • Direct visualization of dynamics and co-operative conformational changes within RecA filaments that appear to be associated with the hydrolysis of adenosine 5'-O-(3-thiotriphosphate).

    abstract::Highly co-operative structural transitions and conformational changes can be directly observed in bundles of filaments formed by the RecA protein of Escherichia coli. These filaments have been formed with RecA protein, DNA and the ATP analog adenosine 5'-O-(3-thiotriphosphate) (ATP-gamma-S). We show that while ATP-gam...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)91036-o

    authors: Yu X,Egelman EH

    更新日期:1992-05-05 00:00:00