The importance of somatic mutations in the V(lambda) gene 2a2 in human monoclonal anti-DNA antibodies.

Abstract:

:2a2 is the most commonly rearranged gene in the human V(lambda )locus. It has been postulated that certain immunoglobulin genes (including 2a2) are rearranged preferentially because their germline sequences encode structures capable of binding to a range of antigens. Somatic mutation could then increase the specificity and affinity of binding to a particular antigen. We studied the properties of five IgG molecules in which the same heavy chain was paired with different light chains derived from 2a2. The pattern of somatic mutations in 2a2 was shown to be crucial in conferring the ability to bind DNA, but two different patterns of mutation each conferred this ability.Computer-generated models of the three-dimensional structures of these antibodies illustrate the ability of 2a2 to form a DNA binding site in different ways. Somatic mutations at the periphery of the DNA binding site were particularly important. In two different light chains, mutations to arginine at different sites in the complementarity determining regions (CDRs) enhanced binding to DNA. In a third light chain, however, mutation to arginine at a different site blocked binding to DNA.

journal_name

J Mol Biol

authors

Rahman A,Haley J,Radway-Bright E,Nagl S,Low DG,Latchman DS,Isenberg DA

doi

10.1006/jmbi.2000.4491

keywords:

subject

Has Abstract

pub_date

2001-03-16 00:00:00

pages

149-60

issue

1

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(00)94491-7

journal_volume

307

pub_type

杂志文章
  • DNA double-strand break in vivo at the 3' extremity of exons located upstream of group II introns. Senescence and circular DNA introns in Podospora mitochondria.

    abstract::In the filamentous fungus Podospora anserina, the unavoidable phenomenon of senescence is associated with the amplification of the first intron of the mitochondrial cox1 that accumulates as circular DNA molecules consisting of tandem repeats. This group II intron (cox1-i1 or alpha) is able to transpose and contains an...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1613

    authors: Sainsard-Chanet A,Begel O,Belcour L

    更新日期:1994-10-07 00:00:00

  • Infrared dichroism of twisted beta-sheet barrels. The structure of E. coli outer membrane proteins.

    abstract::The infrared dichroic ratios of the amide bands from oriented beta-barrels yield an experimental value for the mean orientation, beta, of the beta-strands, relative to the barrel axis. For a barrel of n strands, this then gives the shear number, S, that characterizes the stagger of the beta-sheet. Combining values of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3557

    authors: Marsh D

    更新日期:2000-03-31 00:00:00

  • Native and non-native structure in a protein-folding intermediate: spectroscopic studies of partially reduced IGF-I and an engineered alanine model.

    abstract::The structure of a metastable folding intermediate of human insulin-like growth factor I (IGF-I) and an engineered model are investigated by circular dichroism and two-dimensional 1H NMR spectroscopy. The intermediate, which contains two of three native disulfide bonds, was trapped by acid quenching and isolated by re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0320

    authors: Hua QX,Narhi L,Jia W,Arakawa T,Rosenfeld R,Hawkins N,Miller JA,Weiss MA

    更新日期:1996-06-07 00:00:00

  • Origin of ultraviolet damage in DNA.

    abstract::A novel ultraviolet (u.v.) footprinting technique has been used to analyze the formation of u.v. photoproducts at 250 bases of a 5 S rRNA gene under conditions where the gene is either double or single-stranded. Because many more types of u.v. damage can be detected by the u.v. footprinting technique than has been pre...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90120-4

    authors: Becker MM,Wang Z

    更新日期:1989-12-05 00:00:00

  • The 29.9 kDa subunit of mitochondrial complex I is involved in the enzyme active/de-active transitions.

    abstract::Mitochondrial respiratory chain complex I undergoes transitions from active to de-activated forms. We have investigated the phenomenon in sub-mitochondrial particles from Neurospora crassa wild-type and a null-mutant lacking the 29.9 kDa nuclear-coded subunit of complex I. Based on enzymatic activities, genetic crosse...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.06.005

    authors: Ushakova AV,Duarte M,Vinogradov AD,Videira A

    更新日期:2005-08-12 00:00:00

  • Immunoglobulin G1 Fc domain motions: implications for Fc engineering.

    abstract::The fragment crystallizable (Fc) region links the key pathogen identification and destruction properties of immunoglobulin G (IgG). Pathogen opsonization positions Fcs to activate pro-inflammatory Fcγ receptors (FcγRs) on immune cells. The cellular response and committal to a damaging, though protective, immune respon...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.01.011

    authors: Frank M,Walker RC,Lanzilotta WN,Prestegard JH,Barb AW

    更新日期:2014-04-17 00:00:00

  • Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength.

    abstract::The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA that resides in the HDV genome and regulates its replication. The native fold of the ribozyme is complex, having two pseudoknots. Earlier work implicated four non-native pairings in slowing pseudoknot formation: Alt 1, Alt 2, Alt 3, and Alt P1. The goal o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.05.071

    authors: Brown TS,Chadalavada DM,Bevilacqua PC

    更新日期:2004-08-13 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

  • Structural Basis for p53 Lys120-Acetylation-Dependent DNA-Binding Mode.

    abstract::Normal cellular homeostasis depends on tight regulation of gene expression, which requires the modulation of transcription factors' DNA-binding specificity. That said, the mechanisms that allow transcription factors to distinguish between closely related response elements following different cellular signals are not f...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.06.009

    authors: Vainer R,Cohen S,Shahar A,Zarivach R,Arbely E

    更新日期:2016-07-31 00:00:00

  • Analysis and prediction of functional sub-types from protein sequence alignments.

    abstract::The increasing number and diversity of protein sequence families requires new methods to define and predict details regarding function. Here, we present a method for analysis and prediction of functional sub-types from multiple protein sequence alignments. Given an alignment and set of proteins grouped into sub-types ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4036

    authors: Hannenhalli SS,Russell RB

    更新日期:2000-10-13 00:00:00

  • X-ray structure of a dihydropyrimidinase from Thermus sp. at 1.3 A resolution.

    abstract::Dihydropyrimidinases (hydantoinases) catalyse the reversible hydrolytic ring-opening of cyclic diamides such as dihydropyrimidines in the catabolism of pyrimidines. In biotechnology, these enzymes find application in the enantiospecific production of amino acids from racemic hydantoins. The crystal structure of a D-en...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(02)00422-9

    authors: Abendroth J,Niefind K,Schomburg D

    更新日期:2002-06-28 00:00:00

  • The chromosome of Shigella flexneri bacteriophage Sf6: complete nucleotide sequence, genetic mosaicism, and DNA packaging.

    abstract::Shigella flexneri temperate bacteriophage Sf6 is of interest in part because its prophage expresses the oac gene that alters the antigenic properties of the surface O-antigen polysaccharide of its host bacterium. We have determined the complete sequence of its 39,044 bp genome. The sequence shows that Sf6 is a member ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.03.068

    authors: Casjens S,Winn-Stapley DA,Gilcrease EB,Morona R,Kühlewein C,Chua JE,Manning PA,Inwood W,Clark AJ

    更新日期:2004-05-28 00:00:00

  • Synthesis and degradation of the mRNA of the Tn21 mer operon.

    abstract::The mercury resistance locus encoded by Tn21 on the monocopy IncFII plasmid R100 (merTn21) consists of a metal-responsive activator/repressor, merR, which controls initiation of a polycistronic message that includes genes for the uptake (merTPC) and reduction (merA) of Hg2+ and merD, which may also play a minor regula...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90919-b

    authors: Gambill BD,Summers AO

    更新日期:1992-05-20 00:00:00

  • X-ray structure of a water-soluble analog of the membrane protein phospholamban: sequence determinants defining the topology of tetrameric and pentameric coiled coils.

    abstract::Phospholamban (PLB) is a pentameric transmembrane protein that regulates the Ca(2+)-dependent ATPase SERCA2a in sarcoplasmic reticulum membranes. We previously described the computational design of a water-soluble variant of phospholamban, WSPLB, which reproduced many of the structural and functional properties of the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.02.040

    authors: Slovic AM,Stayrook SE,North B,Degrado WF

    更新日期:2005-05-06 00:00:00

  • Relative flexibility of DNA and RNA: a molecular dynamics study.

    abstract::State of the art molecular dynamics simulations are used to study the structure, dynamics, molecular interaction properties and flexibility of DNA and RNA duplexes in aqueous solution. Special attention is paid to the deformability of both types of structures, revisiting concepts on the relative flexibility of DNA and...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.07.048

    authors: Noy A,Pérez A,Lankas F,Javier Luque F,Orozco M

    更新日期:2004-10-22 00:00:00

  • Crystallographic studies on damaged DNAs. II. N(6)-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis.

    abstract::In a previous paper, 2'-deoxy-N(6)-methoxyadenosine (mo(6)A) was shown to form a mismatch base-pair with 2'-deoxycytidine with a Watson-Crick-type geometry. To fully understand the structural basis of genetic mutations with damaged DNA, it is necessary to examine whether the methoxylated adenine residue still has the ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3304

    authors: Chatake T,Hikima T,Ono A,Ueno Y,Matsuda A,Takénaka A

    更新日期:1999-12-17 00:00:00

  • Structural basis for oligosaccharide recognition by Pyrococcus furiosus maltodextrin-binding protein.

    abstract::A maltodextrin-binding protein from Pyrococcus furiosus (PfuMBP) has been overproduced in Escherichia coli, purified, and crystallized. The crystal structure of the protein bound to an oligosaccharide ligand was determined to 1.85 A resolution. The fold of PfuMBP is very similar to that of the orthologous MBP from E. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4202

    authors: Evdokimov AG,Anderson DE,Routzahn KM,Waugh DS

    更新日期:2001-01-26 00:00:00

  • Effect of antibiotics on large ribosomal subunit assembly reveals possible function of 5 S rRNA.

    abstract::Functional large ribosomal subunits of Thermus aquaticus can be reconstituted from ribosomal proteins and either natural or in vitro transcribed 23 S and 5 S rRNA. Omission of 5 S rRNA during subunit reconstitution results in dramatic decrease of the peptidyl transferase activity of the assembled subunits. However, th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3030

    authors: Khaitovich P,Mankin AS

    更新日期:1999-09-03 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

  • Transferrins: iron release from lactoferrin.

    abstract::Iron loss in vitro by the iron scavenger bovine lactoferrin was investigated in acidic media in the presence of three different monoanions (NO(3)(-), Cl(-) and Br(-)) and one dianion (SO(4)(2-)). Holo and monoferric C-site lactoferrins lose iron in acidic media (pH< or =3.5) by a four-step mechanism. The first two ste...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4101

    authors: Abdallah FB,El Hage Chahine JM

    更新日期:2000-10-20 00:00:00

  • Crystal structure of the factor for inversion stimulation FIS at 2.0 A resolution.

    abstract::The factor for inversion stimulation (FIS) binds as a homodimeric molecule to a loose 15 nucleotide consensus sequence in DNA. It stimulates DNA-related processes, such as DNA inversion and excision, it activates transcription of tRNA and rRNA genes and it regulates its own synthesis. FIS crystallizes as a homodimer, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90134-6

    authors: Kostrewa D,Granzin J,Stock D,Choe HW,Labahn J,Saenger W

    更新日期:1992-07-05 00:00:00

  • Tunicate muscle actin genes. Structure and organization as a gene cluster.

    abstract::We have isolated and determined the complete nucleotide sequences of two genes, HrMA4a and HrMA2, which encode the same muscle actin protein of the tunicate Halocynthia roretzi. HrMA4a and HrMA2 contain three exons, and the genes have intron-exon splice junctions at the same positions. The 5' flanking region of HrMA4a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90237-e

    authors: Kusakabe T,Makabe KW,Satoh N

    更新日期:1992-10-05 00:00:00

  • Vibrio cholerae YaeO is a Structural Homologue of RNA Chaperone Hfq that Inhibits Rho-dependent Transcription Termination by Dissociating its Hexameric State.

    abstract::Rho-dependent transcription termination is a well-conserved process in bacteria. The Psu and YaeO proteins are the two established inhibitors of the ATP-dependent RNA helicase Rho protein of Escherichia coli. Here, we show a detailed sequence and phylogenetic analysis demonstrating that Vibrio cholerae YaeO (VcYaeO) i...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.09.019

    authors: Pal K,Yadav M,Jain S,Ghosh B,Sen R,Sen U

    更新日期:2019-12-06 00:00:00

  • A direct estimation of the context effect on the efficiency of termination.

    abstract::An in vitro assay in which terminating Escherichia coli ribosomes with different stop signals in the A-site compete for a limited amount of a release factor (RF1 or RF2) has been used to estimate the relative termination efficiencies at stop codons with different adjacent downstream nucleotides. The assay allows direc...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2220

    authors: Pavlov MY,Freistroffer DV,Dincbas V,MacDougall J,Buckingham RH,Ehrenberg M

    更新日期:1998-12-04 00:00:00

  • Targeted Killing of Pseudomonas aeruginosa by Pyocin G Occurs via the Hemin Transporter Hur.

    abstract::Pseudomonas aeruginosa is a priority pathogen for the development of new antibiotics, particularly because multi-drug-resistant strains of this bacterium cause serious nosocomial infections and are the leading cause of death in cystic fibrosis patients. Pyocins, bacteriocins of P. aeruginosa, are potent and diverse pr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.04.020

    authors: Atanaskovic I,Mosbahi K,Sharp C,Housden NG,Kaminska R,Walker D,Kleanthous C

    更新日期:2020-06-12 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

  • Regulation of prion protein expression by noncoding regions of the Prnp gene.

    abstract::Expression of the cellular prion protein is necessary for the transmission and propagation of prion diseases. Increasing the level of prion protein expression decreases the incubation period for these diseases. Therefore, understanding the regulation of prion protein expression could be critical for treating or preven...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.02.086

    authors: Haigh CL,Wright JA,Brown DR

    更新日期:2007-05-11 00:00:00

  • Molecular crowding limits the role of fetal hemoglobin in therapy for sickle cell disease.

    abstract::The dominant assumption central to most treatments for sickle cell anemia has been that replacement of sickle hemoglobin (HbS) by fetal hemoglobin (HbF) would have major clinical benefit. Using laser photolysis, we have measured polymerization kinetics including rates of homogeneous and heterogeneous nucleation on mix...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.02.006

    authors: Rotter M,Aprelev A,Adachi K,Ferrone FA

    更新日期:2005-04-15 00:00:00

  • Sub-atomic resolution crystal structure of cholesterol oxidase: what atomic resolution crystallography reveals about enzyme mechanism and the role of the FAD cofactor in redox activity.

    abstract::The crystal structure of cholesterol oxidase, a 56kDa flavoenzyme was anisotropically refined to 0.95A resolution. The final crystallographic R-factor and R(free) value is 11.0% and 13.2%, respectively. The quality of the electron density maps has enabled modeling of alternate conformations for 83 residues in the enzy...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00054-8

    authors: Lario PI,Sampson N,Vrielink A

    更新日期:2003-03-07 00:00:00

  • RasIns: Genetically Encoded Intrabodies of Activated Ras Proteins.

    abstract::K- and H-Ras are the most commonly mutated genes in human tumors and are critical for conferring and maintaining the oncogenic phenotype in tumors with poor prognoses. Here, we design genetically encoded antibody-like ligands (intrabodies) that recognize active, GTP-bound K- and H-Ras. These ligands, which use the 10t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.11.008

    authors: Cetin M,Evenson WE,Gross GG,Jalali-Yazdi F,Krieger D,Arnold D,Takahashi TT,Roberts RW

    更新日期:2017-02-17 00:00:00