当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Canonical antigen-binding loop structures in immunoglobulins: more structures, more canonical classes?

Canonical antigen-binding loop structures in immunoglobulins: more structures, more canonical classes?

Abstract：

:Grafting the antigen-binding loops onto a human antibody scaffold is a widely used technique to humanise murine antibodies. The success of this approach depends largely on the observation that the antigen-binding loops adopt only a limited number of canonical structures. Identification of the correct canonical structure is therefore essential. Algorithms that predict the main-chain conformation of the hypervariable loops using only the amino acid sequence often provide this information. Here, we describe new canonical loop conformations for the hypervariable regions H1 and H2 as found in single-domain antibody fragments of dromedaries or llama. Although the occurrence of these new loop conformations was not predicted by the algorithms used, it seems that they could occur in human or mouse antigen-binding loops. Their discovery indicates that the currently used set of canonical structures is incomplete and that the prediction algorithms should be extended to include these new structures.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Decanniere K,Muyldermans S,Wyns L

doi

10.1006/jmbi.2000.3839

keywords:

subject

Has Abstract

pub_date

2000-06-30 00:00:00

pages

83-91

issue

1

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(00)93839-7

journal_volume

300

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Structures of DegQ from Legionella pneumophila Define Distinct ON and OFF States.

    abstract：:HtrA (high-temperature requirement A) family proteins play important roles in protein-quality control processes in the bacterial periplasm. A common feature of all members of this family is their modular organization comprising a chymotrypsin-like protease domain and at least one PDZ (postsynaptic density of 95 kDa, d...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2015.06.023

    authors： Schubert A,Wrase R,Hilgenfeld R,Hansen G

    更新日期：2015-08-28 00:00:00

  • Positioning membrane proteins by novel protein engineering and biophysical approaches.

    abstract：:Membrane proteins are unique, in that they can function properly only when they are bound to cellular membranes in a distinct manner. Therefore, positioning of membrane proteins with respect to the membrane is required in addition to the three-dimensional structures in order to understand their detailed molecular mech...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.06.080

    authors： Tatulian SA,Qin S,Pande AH,He X

    更新日期：2005-09-02 00:00:00

  • The homologous pairing domain of RecA also mediates the allosteric regulation of DNA binding and ATP hydrolysis: a remarkable concentration of functional residues.

    abstract：:Switching between the active (ATP and DNA bound) and inactive conformations of the homologous recombination RecA protein is regulated by ATP hydrolysis. First, we use the homologous pairing domain of RecA derived from its mobile loop L2 to show that the interaction of this random coil peptide with the gamma-phosphate ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4163

    authors： Voloshin ON,Wang L,Camerini-Otero RD

    更新日期：2000-11-10 00:00:00

  • HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins.

    abstract：:We describe a hidden Markov model, HMMSTR, for general protein sequence based on the I-sites library of sequence-structure motifs. Unlike the linear hidden Markov models used to model individual protein families, HMMSTR has a highly branched topology and captures recurrent local features of protein sequences and struc...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3837

    authors： Bystroff C,Thorsson V,Baker D

    更新日期：2000-08-04 00:00:00

  • High affinity cooperative DNA binding by the yeast Mlh1-Pms1 heterodimer.

    abstract：:We demonstrate here that the Saccharomyces cerevisiae Mlh1-Pms1 heterodimer required for DNA mismatch repair and other cellular processes is a DNA binding protein. Binding was evaluated using a variety of single and double-stranded DNA molecules. Mlh1-Pms1 bound short substrates with low affinity and showed a slight p...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4958

    authors： Hall MC,Wang H,Erie DA,Kunkel TA

    更新日期：2001-09-28 00:00:00

  • Virtual interaction profiles of proteins.

    abstract：:We have developed a new method for the prediction of peptide sequences that bind to a protein, given a three-dimensional structure of the protein in complex with a peptide. By applying a recently developed sequence prediction algorithm and a novel ensemble averaging calculation, we generate a diverse collection of pep...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5035

    authors： Wollacott AM,Desjarlais JR

    更新日期：2001-10-19 00:00:00

  • Complementary recognition in condensed DNA: accelerated DNA renaturation.

    abstract：:The functional consequences of DNA condensation are investigated. The recognition of complementary strands is profoundly modified by this critical phenomenon. (1) Condensation of denatured DNA greatly accelerates the kinetics of DNA renaturation. We propose a unifying explanation for the effects of several acceleratin...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90595-w

    authors： Sikorav JL,Church GM

    更新日期：1991-12-20 00:00:00

  • Involvement of C-terminal structural elements of equine infectious anemia virus reverse transcriptase in DNA polymerase and ribonuclease H activities.

    abstract：:In order to investigate the modes of DNA synthesis supported by the 66 and 51 kDa subunits of equine infectious anemia virus reverse transcriptase (EIAV RT), recombinant p66 polypeptides containing a modified ribonuclease H (RNase H) domain were purified and evaluated. Defined heteropolymeric template-primer combinati...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0181

    authors： Rausch JW,Arts EJ,Wöhrl BM,Le Grice SF

    更新日期：1996-04-05 00:00:00

  • Thermus thermophilus cytochrome-c552: A new highly thermostable cytochrome-c structure obtained by MAD phasing.

    abstract：:The three-dimensional structure of cytochrome-c552 from Thermus thermophilus has been determined by the multiple anomalous dispersion technique using synchrotron radiation and refined to a resolution of 1.28 A. Data collection at 90 K and the recording of three data sets (f'-minimum: 7125 eV, f"-maximum: 7138 eV and r...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1181

    authors： Than ME,Hof P,Huber R,Bourenkov GP,Bartunik HD,Buse G,Soulimane T

    更新日期：1997-08-29 00:00:00

  • Requirement of 3'-terminal guanosine in (-)-stranded RNA for in vitro replication of cucumber mosaic virus satellite RNA by viral RNA-dependent RNA polymerase.

    abstract：:The 3' terminus of the (-) RNA strand in the replicative forms of several (+)-stranded RNA viruses possesses an unpaired guanosine with unknown function. This unpaired guanosine is also found at the 3' terminus of the (-) strand in the double-stranded form of two cucumoviral satellite RNAs. Using a cucumber mosaic vir...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1326

    authors： Wu G,Kaper JM

    更新日期：1994-05-20 00:00:00

  • Folding transitions during assembly of the eukaryotic mRNA cap-binding complex.

    abstract：:The cap-binding protein eIF4E is the first in a chain of translation initiation factors that recruit 40S ribosomal subunits to the 5' end of eukaryotic mRNA. During cap-dependent translation, this protein binds to the 5'-terminal m(7)Gppp cap of the mRNA, as well as to the adaptor protein eIF4G. The latter then intera...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.12.034

    authors： von der Haar T,Oku Y,Ptushkina M,Moerke N,Wagner G,Gross JD,McCarthy JE

    更新日期：2006-03-03 00:00:00

  • Mechanism of codon recognition by transfer RNA and codon-induced tRNA association.

    abstract：:The steps of UUC recognition by tRNAPhe were analysed by temperature-jump measurements. At ion concentrations close to physiological conditions we found three relaxation processes, which we assigned to (1) formation of codon-anticodon complexes, (2) a conformational change of the anticodon loop coupled with Mg2+ bindi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(84)90085-8

    authors： Labuda D,Striker G,Porschke D

    更新日期：1984-04-25 00:00:00

  • Detection of Escherichia coli ribosome binding at translation initiation sites in the absence of tRNA.

    abstract：:Binary complexes between messenger RNA and E. coli ribosomes were examined. A ribosome-mRNA binary complex on T4 gene 32 mRNA withstood inhibition by antibodies against ribosomal protein S1. Anti-S1 blocks ternary complex formation, as measured by "extension inhibition" or "toeprinting" analysis, only when preincubate...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90876-8

    authors： Hartz D,McPheeters DS,Green L,Gold L

    更新日期：1991-03-05 00:00:00

  • Defining the peptide nucleic acids (PNA) length requirement for PNA binding-induced transcription and gene expression.

    abstract：:Induction of gene expression has great potential in the treatment of many human diseases. Peptide nucleic acid (PNA) as a novel DNA-binding reagent provides an ideal system to induce gene-specific expression. In our recent studies, we have demonstrated that PNA bound to double-stranded DNA targets and, therefore, gene...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5109

    authors： Wang G,Jing K,Balczon R,Xu X

    更新日期：2001-11-09 00:00:00

  • Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer.

    abstract：:Many proteins are composed of independently-folded domains connected by flexible linkers. The primary sequence and length of such linkers can set the effective concentration for the tethered domains, which impacts rates of association and enzyme activity. The length of such linkers can be sensitive to environmental co...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.166793

    authors： Basak S,Sakia N,Dougherty L,Guo Z,Wu F,Mindlin F,Lary JW,Cole JL,Ding F,Bowen ME

    更新日期：2021-01-01 00:00:00

  • Microscopy in Infectious Disease Research-Imaging Across Scales.

    abstract：:A comprehensive understanding of host-pathogen interactions requires quantitative assessment of molecular events across a wide range of spatiotemporal scales and organizational complexities. Due to recent technical developments, this is currently only achievable with microscopy. This article is providing a general per...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2018.06.018

    authors： Laketa V

    更新日期：2018-08-17 00:00:00

  • FOXO4 Transactivation Domain Interaction with Forkhead DNA Binding Domain and Effect on Selective DNA Recognition for Transcription Initiation.

    abstract：:Forkhead box O4 (FOXO4) is a human transcription factor (TF) that participates in cell homeostasis. While the structure and DNA binding properties of the conserved forkhead domain (FHD) have been thoroughly investigated, how the transactivation domain (TAD) regulates the DNA binding properties of the protein remains e...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2021.166808

    authors： Kim J,Ahn D,Park CJ

    更新日期：2021-01-13 00:00:00

  • Functional reconstitution of purified human Hv1 H+ channels.

    abstract：:Voltage-dependent H(+) (Hv) channels mediate proton conduction into and out of cells under the control of membrane voltage. Hv channels are unusual compared to voltage-dependent K(+), Na(+), and Ca(2+) channels in that Hv channel genes encode a voltage sensor domain (VSD) without a pore domain. The H(+) currents obser...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.02.034

    authors： Lee SY,Letts JA,MacKinnon R

    更新日期：2009-04-17 00:00:00

  • Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein-Protein Interaction Data.

    abstract：:Protein interactions play a crucial role among the different functions of a cell and are central to our understanding of cellular processes both in health and disease. Here we present Galaxy InteractoMIX (http://galaxy.interactomix.com), a platform composed of 13 different computational tools each addressing specific ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.09.015

    authors： Mirela-Bota P,Aguirre-Plans J,Meseguer A,Galletti C,Segura J,Planas-Iglesias J,Garcia-Garcia J,Guney E,Oliva B,Fernandez-Fuentes N

    更新日期：2020-09-23 00:00:00

  • Ribosomal protein L9: a structure determination by the combined use of X-ray crystallography and NMR spectroscopy.

    abstract：:The structure of protein L9 from the Bacillus stearothernophilus ribosome has been determined at 2.5 A resolution by refinement against single crystal X-ray diffraction data with additional constraints provided by NMR data. This highly elongated protein consists of two domains separated by a nine-turn connecting helix...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0696

    authors： Hoffman DW,Cameron CS,Davies C,White SW,Ramakrishnan V

    更新日期：1996-12-20 00:00:00

  • Bypass of DNA heterologies during RuvAB-mediated three- and four-strand branch migration.

    abstract：:During general genetic recombination and recombinational DNA repair, DNA damages and heterologies are often encountered which must be efficiently processed by the cellular recombination machinery. In RecA-mediated three-strand exchange reactions between single-stranded circular and linear duplex DNA, or four-strand ex...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0600

    authors： Adams DE,West SC

    更新日期：1996-11-08 00:00:00

  • The structure of Sif2p, a WD repeat protein functioning in the SET3 corepressor complex.

    abstract：:In Saccharomyces cerevisiae, the SIF2 gene product is an integral component of the Set3 complex (SET3C), an assembly of proteins with some homology to the human SMRT and N-CoR corepressor complexes. SET3C has histone deacetylase activity that is responsible for repressing a set of meiotic genes. We have determined the...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.06.025

    authors： Cerna D,Wilson DK

    更新日期：2005-08-26 00:00:00

  • Interdomain contact regions and angles between adjacent short consensus repeat domains.

    abstract：:The short consensus repeat domain (SCR, complement control protein module, sushi-domain) is a structural unit found in multiple adjacent copies in more than 40 human proteins. Each bead-like domain is composed of approximately 60 residues and the adjacent domains are connected in a head-to-tail fashion with linkers th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.10.017

    authors： Lehtinen MJ,Meri S,Jokiranta TS

    更新日期：2004-12-10 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

  • Structure-function analysis of the acyl carrier protein synthase (AcpS) from Mycobacterium tuberculosis.

    abstract：:We have solved the crystal structure of the acyl carrier protein synthase (AcpS) from Mycobacterium tuberculosis (Mtb) at 1.95 A resolution. AcpS, a 4-phosphopantetheinyl transferase, activates two distinct acyl carrier proteins (ACPs) that are present in fatty acid synthase (FAS) systems FAS-I and FAS-II, the ACP-I d...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.08.065

    authors： Dym O,Albeck S,Peleg Y,Schwarz A,Shakked Z,Burstein Y,Zimhony O

    更新日期：2009-11-06 00:00:00

  • Protein folding kinetics provides a context-independent assessment of beta-strand propensity in the Fyn SH3 domain.

    abstract：:Structural database-derived propensities for amino acids to adopt particular local protein structures, such as alpha-helix and beta-strand, have long been recognized and effectively exploited for the prediction of protein secondary structure. However, the experimental verification of database-derived propensities usin...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.07.059

    authors： Zarrine-Afsar A,Dahesh S,Davidson AR

    更新日期：2007-10-26 00:00:00

  • A single tyrosine prevents insertion of ribonucleotides in the eukaryotic-type phi29 DNA polymerase.

    abstract：:Three conserved motifs (named A, B and C) have been proposed to form the polymerization active site in all classes of DNA-dependent polymerases. In eukaryotic-type (alpha-like) DNA polymerases, motif A is characterized by the consensus "Dx2SLYP". Mutants in phi29 DNA polymerase residue Tyr254 of this conserved motif h...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2900

    authors： Bonnin A,Lázaro JM,Blanco L,Salas M

    更新日期：1999-07-02 00:00:00

  • The external alternative NAD(P)H dehydrogenase NDE3 is localized both in the mitochondria and in the cytoplasm of Neurospora crassa.

    abstract：:The filamentous fungus Neurospora crassa has a branched respiratory chain. Several alternative dehydrogenases, aside from the canonical complex I enzyme, are involved in the oxidation of NAD(P)H substrates. Based on homology searches in the fungal genome, we have tentatively identified one of these proteins. The corre...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.02.080

    authors： Carneiro P,Duarte M,Videira A

    更新日期：2007-05-11 00:00:00

  • Crystallization and subunit structure of canine myeloperoxidase.

    abstract：:Three crystal forms of canine myeloperoxidase are described. An orthorhombic form in space group P2(1)2(1)2(1) has unit cell dimensions: a = 108.3 A (1 A = 0.1 nm) b = 205.9 A and c = 139.9 A. A trigonal form in space group P3(1)21 or P3(2)21 has unit cell dimensions: a = b = 138.9 A and c = 145.2 A. A monoclinic form...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90413-x

    authors： Fenna RE

    更新日期：1987-08-20 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