Two-dimensional crystallization of the light-harvesting complex from Rhodospirillum rubrum.

Abstract:

:Homogeneous detergent-solubilized B873 light-harvesting complexes from a carotenoid-less mutant of the purple non-sulfur bacterium, Rhodospirillum rubrum G9, were reassembled spontaneously into two-dimensional (2D) hexagonal arrays during extensive and controlled dialysis. As the complexes contain only 1 to 2 mol phospholipid per mol alpha beta dimer, the arrays formed by a self assembly process are primary due to protein-protein interactions. The hexagonal lattices were analyzed by negative stain electron microscopy and digital image processing. They exhibited a unit cell size of 12.3 nm, in close agreement with the particle diameter of the active photo-unit in native chromatophore membranes. The unit cell contains a central 5 nm stain-filled depression, embraced by a ring with an outer diameter of 10 nm.

journal_name

J Mol Biol

authors

Ghosh R,Hoenger A,Hardmeyer A,Mihailescu D,Bachofen R,Engel A,Rosenbusch JP

doi

10.1006/jmbi.1993.1298

subject

Has Abstract

pub_date

1993-05-20 00:00:00

pages

501-4

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(83)71298-2

journal_volume

231

pub_type

杂志文章
  • Mutations within a conserved region of vaccinia topoisomerase affect the DNA cleavage-religation equilibrium.

    abstract::The segment of the vaccinia DNA topoisomerase from residues 143 to 167 (VGLLTLKNKHIEISPDEIVIKFVGK) is conserved in other members of the eukaryotic type I topoisomerase family. In order to gauge the function of this region, we performed a mutational analysis in which 23 of 25 positions were substituted by alanine. Seve...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0568

    authors: Petersen BO,Wittschieben J,Shuman S

    更新日期:1996-10-25 00:00:00

  • NMR structure of the HIV-1 regulatory protein VPR.

    abstract::The human immunodeficiency virus type 1 (HIV-1) genome encodes a highly conserved regulatory gene product, Vpr (96 residues, 14kDa), which is incorporated into virions. In the infected cells, Vpr, expressed late in the virus cycle, is believed to function in the early phases of HIV-1 replication, such as nuclear migra...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00060-3

    authors: Morellet N,Bouaziz S,Petitjean P,Roques BP

    更新日期:2003-03-14 00:00:00

  • Solution structure by NMR of circulin A: a macrocyclic knotted peptide having anti-HIV activity.

    abstract::The three-dimensional solution structure of circulin A, a 30 residue polypeptide from the African plant Chassalia parvifolia, has been determined using two-dimensional 1H-NMR spectroscopy. Circulin A was originally identified based upon its inhibition of the cytopathic effects and replication of the human immunodefici...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2276

    authors: Daly NL,Koltay A,Gustafson KR,Boyd MR,Casas-Finet JR,Craik DJ

    更新日期:1999-01-08 00:00:00

  • Crystal structure of the two N-terminal domains of g3p from filamentous phage fd at 1.9 A: evidence for conformational lability.

    abstract::Infection of Escherichia coli by filamentous bacteriophages is mediated by the minor phage coat protein g3p and involves two distinct cellular receptors, the F' pilus and the periplasmic protein TolA. Recently we have shown that the two receptors are contacted in a sequential manner, such that binding of TolA by the N...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2720

    authors: Holliger P,Riechmann L,Williams RL

    更新日期:1999-05-14 00:00:00

  • Preliminary crystallographic studies of the Fab fragment of an anti-azophenylarsonate antibody.

    abstract::Single crystals of the Fab fragment of a murine A/J anti-azophenylarsonate monoclonal antibody have been prepared by the vapor diffusion method. Antibody 3A7 uses the same combination of variable region gene segments (VK, JK, VH, JH) as do anti-azophenylarsonate antibodies bearing a predominant cross-reactive idiotype...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90587-1

    authors: Lin SF,Coll M,Gefter ML,Margolies MN,Wang AH

    更新日期:1989-04-20 00:00:00

  • Effects of mutations in the polymerase domain on the polymerase, RNase H and strand transfer activities of human immunodeficiency virus type 1 reverse transcriptase.

    abstract::Based on structural analyses and on the behavior of mutants, we suggest that the polymerase domain of HIV-1 reverse transcriptase (RT) plays a critical role in holding and appropriately positioning the template-primer both at the polymerase active site and at the RNase H active site. For RT to successfully copy the vi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1624

    authors: Gao HQ,Boyer PL,Arnold E,Hughes SH

    更新日期:1998-04-03 00:00:00

  • The binding of 2-deoxy-D-glucose 6-phosphate to glycogen phosphorylase b: kinetic and crystallographic studies.

    abstract::Kinetic and crystallographic studies have characterized the effect of 2-deoxy-glucose 6-phosphate on the catalytic and structural properties of glycogen phosphorylase b. Previous work on the binding of glucose 6-phosphate, a potent physiological inhibitor of the enzyme, to T state phosphorylase b in the crystal showed...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0665

    authors: Oikonomakos NG,Zographos SE,Johnson LN,Papageorgiou AC,Acharya KR

    更新日期:1995-12-15 00:00:00

  • Molecular requirements for duplex recognition and cleavage by eukaryotic RNase III: discovery of an RNA-dependent DNA cleavage activity of yeast Rnt1p.

    abstract::Members of the double-stranded RNA (dsRNA) specific RNase III family are known to use a conserved dsRNA-binding domain (dsRBD) to distinguish RNA A-form helices from DNA B-form ones, however, the basis of this selectivity and its effect on cleavage specificity remain unknown. Here, we directly examine the molecular re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.02.059

    authors: Lamontagne B,Hannoush RN,Damha MJ,Abou Elela S

    更新日期:2004-04-23 00:00:00

  • Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCI.

    abstract::The restriction enzyme R.BbvCI cleaves duplex DNA within a seven base-pair asymmetric recognition sequence, thus: CCTCAGC/GCTGAGG-->CC--TCAGC/GC--TGAGG. We show that R.BbvCI comprises two different subunits, R(1) and R(2); that each subunit contains a catalytic site for DNA strand hydrolysis; and that these sites act ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.02.034

    authors: Heiter DF,Lunnen KD,Wilson GG

    更新日期:2005-05-06 00:00:00

  • A measure for the angle between projections based on the extent of correlation between corresponding central sections.

    abstract::A pre-condition for the ab initio assignment of Euler angles to a set of projections from an asymmetric object is that at least three of the available projections correspond to rotations about different axes. For symmetric objects this condition may be relaxed. There are some applications of single-particle electron m...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.09.068

    authors: Patwardhan A,Paul D,Al-Khayat HA,Morris EP

    更新日期:2004-11-26 00:00:00

  • High affinity of endonuclease VII for the Holliday structure containing one nick ensures productive resolution.

    abstract::During homologous recombination, genetic information is physically exchanged between parental DNAs via crossing single strands of the same polarity within a four-way DNA junction called a Holliday structure. This process is terminated by the endonucleolytic activity of resolvases, which convert the four-way DNA back t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00594-6

    authors: Birkenbihl RP,Kemper B

    更新日期:2002-08-02 00:00:00

  • Mutational analysis of the conserved bases C1402 and A1500 in the center of the decoding domain of Escherichia coli 16 S rRNA reveals an important tertiary interaction.

    abstract::Interactions within the decoding center of the 30 S ribosomal subunit have been investigated by constructing all 15 possible mutations at nucleotides C1402 and A1500 in helix 44 of 16 S rRNA. As expected, most of the mutations resulted in highly deleterious phenotypes, consistent with the high degree of conservation o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4576

    authors: Vila-Sanjurjo A,Dahlberg AE

    更新日期:2001-05-04 00:00:00

  • Oligosaccharide preferences of beta1,4-galactosyltransferase-I: crystal structures of Met340His mutant of human beta1,4-galactosyltransferase-I with a pentasaccharide and trisaccharides of the N-glycan moiety.

    abstract::beta-1,4-Galactosyltransferase-I (beta4Gal-T1) transfers galactose from UDP-galactose to N-acetylglucosamine (GlcNAc) residues of the branched N-linked oligosaccharide chains of glycoproteins. In an N-linked biantennary oligosaccharide chain, one antenna is attached to the 3-hydroxyl-(1,3-arm), and the other to the 6-...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.07.050

    authors: Ramasamy V,Ramakrishnan B,Boeggeman E,Ratner DM,Seeberger PH,Qasba PK

    更新日期:2005-10-14 00:00:00

  • Slowing bacterial translation speed enhances eukaryotic protein folding efficiency.

    abstract::The mechanisms for de novo protein folding differ significantly between bacteria and eukaryotes, as evidenced by the often observed poor yields of native eukaryotic proteins upon recombinant production in bacterial systems. Polypeptide synthesis rates are faster in bacteria than in eukaryotes, but the effects of gener...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.12.042

    authors: Siller E,DeZwaan DC,Anderson JF,Freeman BC,Barral JM

    更新日期:2010-03-12 00:00:00

  • TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions.

    abstract::The COG database was used for a comparative genome analysis with genomes from anaerobic and aerobic microorganisms with the aim of identifying proteins specific to the anaerobic way of life. A total of 33 COGs were identified, five of which correspond to proteins of unknown function. We focused our study on TM0486 fro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.05.014

    authors: Dermoun Z,Foulon A,Miller MD,Harrington DJ,Deacon AM,Sebban-Kreuzer C,Roche P,Lafitte D,Bornet O,Wilson IA,Dolla A

    更新日期:2010-07-16 00:00:00

  • Functionally important correlated motions in the single-stranded DNA-binding protein encoded by filamentous phage Pf3.

    abstract::To elucidate the interplay between different parts of dimeric single-stranded DNA-binding proteins we have studied the correlated motions in the protein encoded by filamentous phage Pf3 via the combined use of 15N-NMR relaxation experiments, molecular dynamics simulations and essential dynamics calculations. These stu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2629

    authors: Horstink LM,Abseher R,Nilges M,Hilbers CW

    更新日期:1999-04-02 00:00:00

  • Tripodal Lipoprotein Variants with C-Terminal Hydrophobic Residues Allosterically Modulate Activity of the DegP Protease.

    abstract::DegP, a member of the highly conserved HtrA family of proteases, performs a regulated proteolysis of toxic misfolded proteins in the periplasm of Gram-negative bacteria. The allosteric switch between inactive and active conformations is a central mechanism to carefully control proteolytic activity of DegP and to maint...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2017.09.011

    authors: Park H,Kim YT,Choi C,Kim S

    更新日期:2017-10-13 00:00:00

  • The molecular and crystal structure of dextrans: a combined electron and X-ray diffraction study. II. A low temperature, hydrated polymorph.

    abstract::The crystal and molecular structure of a dextran hydrate has been determined through combined electron and X-ray diffraction analysis, aided by stereochemical model refinement. A total of 65 hk0 electron diffraction intensities were measured on frozen single crystals held at the temperature of liquid nitrogen, to a re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90010-5

    authors: Guizard C,Chanzy H,Sarko A

    更新日期:1985-06-05 00:00:00

  • Biochemical Differences and Similarities between the DEAD-Box Helicase Orthologs DDX3X and Ded1p.

    abstract::DDX3X is a conserved DEAD-box RNA helicase involved in translation initiation and other processes of RNA metabolism. Mutations in human DDX3X and deregulation of its expression are linked to tumorigenesis and intellectual disability. The protein is also targeted by diverse viruses. Previous studies demonstrated helica...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2017.10.008

    authors: Sharma D,Putnam AA,Jankowsky E

    更新日期:2017-11-24 00:00:00

  • A group of repetitive human DNA families that is characterized by extrachromosomal oligomers and restriction-fragment length polymorphism.

    abstract::We have recently reported a novel human repetitive DNA (Sau3A family) that exists both in the chromosomes and in the extrachromosomal fraction. Several more clones that hybridized with the Sau3A family were isolated from the extrachromosomal fraction of HeLa cells. Use of these clones as probes has revealed that at le...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90342-1

    authors: Kiyama R,Matsui H,Okumura K,Oishi M

    更新日期:1987-02-20 00:00:00

  • FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.

    abstract::FUGUE, a program for recognizing distant homologues by sequence-structure comparison (http://www-cryst.bioc.cam.ac.uk/fugue/), has three key features. (1) Improved environment-specific substitution tables. Substitutions of an amino acid in a protein structure are constrained by its local structural environment, which ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4762

    authors: Shi J,Blundell TL,Mizuguchi K

    更新日期:2001-06-29 00:00:00

  • The chromatin of active genes is not in a permanently open conformation.

    abstract::Quantitative measurements of local chromatin accessibility to DNase I in 15-day chicken embryo erythrocyte nuclei have been performed using a range of nuclease concentrations and real-time TaqMan PCR to monitor the loss of short ( approximately 80 bp) amplicons. At the beta-globin locus, well-established DNase I hyper...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.12.048

    authors: Sapojnikova N,Thorne A,Myers F,Staynov D,Crane-Robinson C

    更新日期:2009-02-20 00:00:00

  • Targeting of adenovirus serotype 5 pseudotyped with short fiber from serotype 41 to c-erbB2-positive cells using bispecific single-chain diabody.

    abstract::The purpose of the current study was to alter the broad native tropism of human adenovirus for virus targeting to c-erbB2-positive cancer cells. First, we engineered a single-chain antibody (scFv) against the c-erbB2 oncoprotein into minor capsid protein IX (pIX) of adenovirus serotype 5 (Ad5) in a manner commensurate...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.03.016

    authors: Kashentseva EA,Douglas JT,Zinn KR,Curiel DT,Dmitriev IP

    更新日期:2009-05-08 00:00:00

  • Asymmetric dimeric structure of ferredoxin-NAD(P)+ oxidoreductase from the green sulfur bacterium Chlorobaculum tepidum: implications for binding ferredoxin and NADP+.

    abstract::Ferredoxin-NAD(P)(+) oxidoreductase (FNR) catalyzes the reduction of NAD(P)(+) to NAD(P)H with the reduced ferredoxin (Fd) during the final step of the photosynthetic electron transport chain. FNR from the green sulfur bacterium Chlorobaculum tepidum is functionally analogous to plant-type FNR but shares a structural ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.06.024

    authors: Muraki N,Seo D,Shiba T,Sakurai T,Kurisu G

    更新日期:2010-08-20 00:00:00

  • Detecting patterns in protein sequences.

    abstract::The detection of conserved sequence patterns (motifs) in related proteins often yields valuable structural and functional insights. We describe a method that utilizes rigorous statistics and a depth-first search procedure to efficiently and exhaustively search a set of proteins for significant patterns up to a specifi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1407

    authors: Neuwald AF,Green P

    更新日期:1994-06-24 00:00:00

  • Long-range electrostatic interactions influence the orientation of Fos-Jun binding at AP-1 sites.

    abstract::Heterodimeric transcription regulatory proteins that bind palindromic DNA sequences can potentially bind their recognition sites in two opposite orientations. The orientation of transcription factor binding can control transcriptional activity by altering interactions with proteins that bind to adjacent regulatory ele...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4286

    authors: Ramirez-Carrozzi VR,Kerppola TK

    更新日期:2001-01-19 00:00:00

  • Conformational changes during the assembly of factor B from its domains by (1)H NMR spectroscopy and molecular modelling: their relevance to the regulation of factor B activity.

    abstract::Factor B is a key component of the alternative pathway of complement and is cleaved by factor D into the Ba and Bb fragments in the presence of activated C3 (C3b or C3(H(2)O)). The Ba fragment contains three short consensus/complement repeat domains, while the Bb fragment contains a von Willebrand factor type A (vWF-A...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4044

    authors: Hinshelwood J,Perkins SJ

    更新日期:2000-09-01 00:00:00

  • Protein-induced conformational changes of RNA during the assembly of human signal recognition particle.

    abstract::The human signal recognition particle (SRP) is a large RNA-protein complex that targets secretory and membrane proteins to the endoplasmic reticulum membrane. The S domain of SRP is composed of roughly half of the 7SL RNA and four proteins (SRP19, SRP54, and the SRP68/72 heterodimer). In order to understand how the bi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.12.056

    authors: Menichelli E,Isel C,Oubridge C,Nagai K

    更新日期:2007-03-16 00:00:00

  • Crystal structure of zebrafish hatching enzyme 1 from the zebrafish Danio rerio.

    abstract::Fish hatching enzymes are zinc metalloproteases that digest the egg envelope (chorion) at the time of hatching. The crystal structure of zebrafish hatching enzyme 1 (ZHE1) has been solved at 1.10 Å resolution. ZHE1 is monomeric, is mitten shaped, and has a cleft at the center of the molecule. ZHE1 consists of three 3(...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.08.023

    authors: Okada A,Sano K,Nagata K,Yasumasu S,Ohtsuka J,Yamamura A,Kubota K,Iuchi I,Tanokura M

    更新日期:2010-10-08 00:00:00

  • The structure of LL-diaminopimelate aminotransferase from Chlamydia trachomatis: implications for its broad substrate specificity.

    abstract::We have previously reported the structures of the native holo and substrate-bound forms of LL-diaminopimelate aminotransferase from Arabidopsis thaliana (AtDAP-AT). Here, we report the crystal and molecular structures of the LL-diaminopimelate aminotransferase from Chlamydia trachomatis (CtDAP-AT) in the apo-form and ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.06.023

    authors: Watanabe N,Clay MD,van Belkum MJ,Fan C,Vederas JC,James MN

    更新日期:2011-08-19 00:00:00