Journal of Molecular Biology

Items from 1 to 20 out of 30 results

article

Mutational analysis of o29 DNA polymerase residues acting as ssDNA ligands for 3'-5' exonucleolysis

Miguel de Vega, José M. Lázaro, Margarita Salas, Luis Blanco

Journal of Molecular Biology > 1998 > 279 > 4 > 807-822

Here, three highly conserved amino acid residues have been characterized to function as ssDNA binding ligands at the 3'-5' exonuclease active site of o29 DNA polymerase. One of these residues, Phe65, belongs to motif Exo II, previously described to contain an invariant aspartate and an invariant asparagine involved in catalysis and ssDNA binding, respectively. The other two residues, Ser122 and Leu123,...

article

Two large subunits of the fission yeast RNA polymerase II provide platforms for the assembly of small subunits

Akira Ishiguro, Makoto Kimura, Kiyoshi Yasui, Akira Iwata, more

Journal of Molecular Biology > 1998 > 279 > 4 > 703-712

The subunit-subunit contact network was analyzed for the Schizosaccharomyces pombe RNA polymerase II consisting of ten putative subunits. Previously we carried out far-Western blot analysis of bimolecular interaction with radio-labeled subunit 3 and 5 probes. Here we extended the analysis using another six small-sized subunits as probes. Taking the results together the subunit-subunit interaction...

article

Catapult mechanism renders the chaperone action of hsp70 unidirectional

Serge M. Gisler, Ezra V. Pierpaoli, Philipp Christen

Journal of Molecular Biology > 1998 > 279 > 4 > 833-840

Molecular chaperones of the Hsp70 type promote the folding and membrane translocation of proteins. The interaction of Hsp70s with polypeptides is linked to ATP binding and hydrolysis. We formed complexes of seven different fluorescence-labeled peptides with DnaK, the Hsp70 homolog of Escherichia coli, and determined the rate of peptide release under two different sets of conditions. (1) Upon addition...

article

A partial HPRT gene duplication generated by non-homologous recombination in V79 chinese hamster cells is eliminated by homologous recombination

Thomas Helleday, Catherine Arnaudeau, Dag Jenssen

Journal of Molecular Biology > 1998 > 279 > 4 > 687-694

Here, the sequence in the hprt gene of the duplication mutant SPD8 originating from V79 Chinese hamster cells was determined. The duplication arose after non-homologous recombination between exon 6 and intron 7, resulting in an extra copy of the 3' portion of exon 6, of exon 7 and of flanking intron regions. Only a duplication of exon 7 is present in the mRNA, since the duplicated exon 6 lacks its...

article

Solution structure and dynamics of the bioactive retroviral M domain from rous sarcoma virus

James M. McDonnell, David Fushman, Sean M. Cahill, Wenjun Zhou, more

Journal of Molecular Biology > 1998 > 279 > 4 > 921-928

A biologically active construct of the retroviral M domain from the avian Rous sarcoma virus is defined and its solution structure described. This M domain is fully active in budding and infectivity without myristylation. In spite of a sequence homology level that suggests no relationship among M domains and the family of matrix proteins in mammalian retroviruses, the conserved structural elements...

article

Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis

Christian Massire, Luc Jaeger, Eric Westhof

Journal of Molecular Biology > 1998 > 279 > 4 > 773-793

The secondary structure of bacterial RNase P RNA, a ribozyme responsible for the maturation of the 5' end of tRNAs, is well established on the basis of sequence comparison analysis. RNase P RNA secondary structures fall into two types, A and B, which share a common core formed by the assembly of two main folding domains, but differ in their peripheral elements.A revised alignment of 137 available...

article

tRNA imbalance promotes -1 frameshifting via near-cognate decoding

Michael O’Connor

Journal of Molecular Biology > 1998 > 279 > 4 > 727-736

tRNA ₁ ^G ^l ^y is the Escherichia coli glycine tRNA specific for GGG codons. A genetic selection for multicopy suppressors of a frameshift mutation has shown that increased levels of wild-type tRNA ₁ ^G ^l ^y causes -1 frameshifting. Analysis of the suppression spectrum of this multicopy suppressor and peptide sequencing of the suppressed protein product showed that...

article

The muscle thin filament as a classical Cooperative/Allosteric regulatory system

Journal of Molecular Biology > 1998 > 279 > 4 > 1024

article

A superrepressor mutant of the arginine repressor with a correctly predicted alteration of ligand binding specificity

Helmut Niersbach, Robert Lin, Gregory D. Van Duyne, Werner K. Maas

Journal of Molecular Biology > 1998 > 279 > 4 > 753-760

Arginine biosynthesis in Escherichia coli is negatively regulated by the hexameric repressor protein ArgR and the corepressor l-arginine. l-Arginine binds to ArgR in the C-terminal domain of the repressor. Binding to operator DNA occurs in the N-terminal domain. The molecular structures of both domains have recently been elucidated. The known stereochemistry of the arginine binding pocket was used...

article

New insights for dinucleotide backbone binding in conserved C5' H...O hydrogen bonds

Pei-Ying Chu, Ming-Jing Hwang

Journal of Molecular Biology > 1998 > 279 > 4 > 695-701

Most enzymes that utilize dinucleotide NAD or NADP are known to comprise a glycine-rich loop segment (e.g. the GXGXXG signature motif of Rossman fold) which binds the cofactor's diphosphate moiety. Through analysis of a set of diverse NAD(P)-bound protein structures, we show here that with few exceptions this diphosphate binding is complemented by a second loop segment interacting from a different...

article

Analyzing the functional organization of a novel restriction modification system, the BcgI system

Huimin Kong

Journal of Molecular Biology > 1998 > 279 > 4 > 823-832

BcgI is a novel, multi-subunit, restriction-modification (R-M) system that differs from all the other types of R-M system in its genetic and functional organization. The holoenzyme contains two different subunits,BcgI A and BcgI B. Both are required for endonuclease and methyltransferase activities. Here, we show that the endonuclease activity is mediated by the N-terminal portion of the A subunit...

article

Design, synthesis and structure of a zinc finger with an artificial β-turn

John H. Viles, Sunil U. Patel, John B.O. Mitchell, Claire M. Moody, more

Journal of Molecular Biology > 1998 > 279 > 4 > 973-986

We have incorporated a bicyclic β-turn mimetic (BTD; β-turn dipeptide) into a zinc finger, creating a zinc finger with an artificial β-turn. The designed peptide chelates zinc and has the same fold as the unmodified native zinc finger (finger 3 of the human YY1 protein). A combination of ¹ H NMR and structure calculations reveals that, in solution, this zinc finger has a fold similar to the...

article

The transcriptional activator GvpE for the halobacterial gas vesicle genes resembles a basic region leucine-zipper regulatory protein

Kerstin Krüger, Thomas Hermann, Vanessa Armbruster, Felicitas Pfeifer

Journal of Molecular Biology > 1998 > 279 > 4 > 761-771

The GvpE protein involved in the regulation of gas vesicles synthesis in halophilic archaea has been identified as the transcriptional activator for the promoter located upstream of the gvpA gene encoding the major gas vesicle structural protein GvpA. A closer inspection of the GvpE protein sequence revealed that GvpE resembles basic leucine-zipper proteins typically involved in the gene regulation...

article

Purified lens major intrinsic protein (MIP) forms highly ordered tetragonal two-dimensional arrays by reconstitution

Lorenz Hasler, Thomas Walz, Peter Tittmann, Heinz Gross, more

Journal of Molecular Biology > 1998 > 279 > 4 > 855-864

Lens major intrinsic protein (MIP) is the founding member of the MIP family of membrane channel proteins. Its isolation from ovine lens fibre cell membranes and its two-dimensional crystallization are described. Membranes were solubilized with n-octyl-β-d-glucoside and proteins fractionated by sucrose gradient centrifugation containing decyl-β-d-maltoside. MIP was purified by cation exchange chromatography,...

article

Are there non-trivial dynamic cross-correlations in proteins?

Roger Abseher, Michael Nilges

Journal of Molecular Biology > 1998 > 279 > 4 > 911-920

The analysis of internal motion in ensembles of flexible molecules in coordinate space requires the removal of overall motion by a least-squares fitting procedure of the Cartesian coordinates. It has been demonstrated that the choice of the atom set used for fitting influences the picture of the internal motion of BPTI. We have performed essential dynamics analyses of a 1 ns molecular dynamics trajectory...

article

Structural basis for the high affinity of amino-aromatic SH2 phosphopeptide ligands

Joseph Rahuel, Carlos Garcı́a-Echeverrı́a, Pascal Furet, André Strauss, more

Journal of Molecular Biology > 1998 > 279 > 4 > 1013-1022

An anthranyl moiety placed at the N terminus of a phosphotyrosine peptide potentiates the inhibitory effect of this small peptide on the binding of the Grb2 SH2 domain to the EGF receptor. Using molecular modeling procedures based on the Lck SH2 domain structure, this observation was rationalized in terms of a suitably favorable π-π stacking interaction between the anthranyl moiety and the arginine...

article

Dimer-to-tetramer transformation: loop excision dramatically alters structure and stability of the ROP four α-helix bundle protein

Michael W. Lassalle, Hans-Jürgen Hinz, Herbert Wenzel, Metaxia Vlassi, more

Journal of Molecular Biology > 1998 > 279 > 4 > 987-1000

The ROP loop excision mutant RM6 shows dramatic changes in structure and stability in comparison to the wild-type protein. Removal of the five amino acids (Asp30, Ala31, Asp32, Glu33, Gln34) from the loop results in a complete reorganization of the protein as evidenced by single crystal X-ray analysis and thermodynamic unfolding studies. The homodimeric four-α-helix motif of the wild-type structure...

article

Engineering bidentate macromolecular inhibitors for trypsin and urokinase-type plasminogen activator

Steve Q. Yang, Charles S. Craik

Journal of Molecular Biology > 1998 > 279 > 4 > 1001-1011

Ecotin, a dimeric serine protease inhibitor from Escherichia coli, is a novel platform for inhibitor design. An approach using the three-dimensional structure of the ecotin-trypsin complex to guide combinatiorial design efforts was taken to create potent bidentate ecotin inhibitors for trypsin and human urokinase-type plasminogen activator (uPA). The ecotin surface loop that was redesigned is composed...

article

Three-dimensional structures of single-chain Fv-neuraminidase complexes

Robyn L. Malby, Airlie J. McCoy, Alexander A. Kortt, Peter J. Hudson, more

Journal of Molecular Biology > 1998 > 279 > 4 > 901-910

The structure of the complex between a recombinant single-chain Fv construct of antibody NC10 with a five-residue peptide linker between V _H and V _L (termed scFv(5)), and its antigen, tetrameric neuraminidase from influenza virus (NA), has been determined and refined at 2.5 A resolution. The antibody-antigen binding interface is very similar to that of a similar NC10 scFv-NA complex...

article

Effects of reaction conditions on RNA secondary structure and on the helicase activity of Escherichia coli transcription termination factor rho

Katherine M. Walstrom, Jody M. Dozono, Peter H. von Hippel

Journal of Molecular Biology > 1998 > 279 > 4 > 713-726

The ATPase and helicase activities of the Escherichia coli transcription termination protein rho have been studied under a variety of reaction conditions that alter its transcription termination activity. These conditions include KCl, KOAc, or KGlu concentrations from 50 to 150 mM and Mg(OAc) ₂ concentrations from 1 to 5 mM (in the presence of 1 mM ATP). In higher KCl or higher Mg(OAc) ...

Number:
4
Volume:
279
Year:
1998

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Keywords

DNAK (2)
ECOTIN (2)
PROTEASE INHIBITOR (2)
UPA (2)
X-RAY CRYSTALLOGRAPHY (2)
1H NMR (1)
2D CRYSTALLIZATION (1)
3'-5' EXONUCLEASE (1)
ANTHRANYL (1)
ANTIBODY DOMAIN (1)
ANTIGEN-ANTIBODY COMPLEX (1)
ARCHAEA (1)
ARGININE REPRESSOR PROTEIN (1)
ASSEMBLY (1)
ATPASE ACTIVITY (1)
BCGI (1)
BRANCH MIGRATION (1)
BZIP PROTEIN (1)
C H...O HYDROGEN BONDS (1)
CAPSID PROTEIN (1)
CHAPERONE (1)
CHAPERONE CYCLE (1)
CHEMICAL CROSSLINKING (1)
CITRULLINE (1)
COFACTOR-FREE CHLOROPEROXIDASE (1)
COILED COIL (1)
COOPERATIVITY (1)
COUPLING ENERGY (1)
CRYSTAL STRUCTURE (1)
DECODING (1)
DEOXYRIBONUCLEASE (1)
DIMERIC INHIBITOR (1)
DISTANCE SPACE (1)
DNA BINDING (1)
DNA-BINDING PROTEIN (1)
DNAJ (1)
DYNAMICS (1)
ELECTRON CRYSTALLOGRAPHY (1)
ELECTROSTATIC INTERACTIONS (1)
ENDONUCLEASE (1)
ESCHERICHIA COLI (1)
ESSENTIAL DYNAMICS (1)
FAR-WESTERN BLOTTING (1)
FLUORESCENCE (1)
FRAMESHIFTING (1)
GAS VESICLES (1)
GENOME ORGANIZATION (1)
GRB2 (1)
GRPE (1)
HETERONUCLEAR NMR SPECTROSCOPY (1)
HOLLIDAY JUNCTION (1)
HOMOLOGOUS RECOMBINATION (1)
HSP70 (1)
HYDROLASE SEQUENCE COMPARISON (1)
HYPERTHERMOPHILIC STABILITY (1)
HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE (1)
LEUCINE ZIPPER (1)
LOOP EXCISION (1)
MAJOR INTRINSIC PROTEIN (1)
MEMBRANE PROTEIN (1)
METHYLTRANSFERASE (1)
MISMATCHES (1)
MOLECULAR DYNAMICS (1)
MUTAGENESIS (1)
N-TERMINAL DOMAIN (1)
NA (1)
NAD (1)
NADP (1)
NEURAMINIDASE (1)
NMR SPIN RELAXATION (1)
NON-HOMOLOGOUS RECOMBINATION (1)
NUCLEASE HYPERSENSITIVITY (1)
NUCLEIC ACID CONFORMATION (1)
O29 DNA POLYMERASE (1)
PARTIAL GENE DUPLICATION (1)
PEPTIDE DESIGN (1)
PHAGE DISPLAY (1)
PHOSPHATE BACKBONE (1)
PRESTEADY STATE KINETICS (1)
PRINCIPAL COMPONENT ANALYSIS (1)
PROCESSIVITY (1)
PROTEASE (1)
PROTEIN DESIGN (1)
PROTEIN DYNAMICS (1)
PROTEIN EVOLUTION (1)
PROTEIN FOLDING (1)
PROTEIN-NUCLEOTIDE RECOGNITION (1)
PROTEIN-RNA INTERACTIONS (1)
REACTION MECHANISM (1)
RECOMBINANT DNA (1)
RECOMBINATION (1)
RESTRICTION-MODIFICATION (1)
RIBONUCLEASE P RNA (1)
RIBOSOME ARCHITECTURE (1)
RIBOZYME (1)
RNA FOLDING (1)
RNA MODELLING (1)
RNA POLYMERASE (1)
RNA SECONDARY STRUCTURE (1)
RNA-DNA HELICASE ACTIVITY (1)
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Journal of Molecular Biology

Mutational analysis of o29 DNA polymerase residues acting as ssDNA ligands for 3'-5' exonucleolysis

Two large subunits of the fission yeast RNA polymerase II provide platforms for the assembly of small subunits

Catapult mechanism renders the chaperone action of hsp70 unidirectional

A partial HPRT gene duplication generated by non-homologous recombination in V79 chinese hamster cells is eliminated by homologous recombination

Solution structure and dynamics of the bioactive retroviral M domain from rous sarcoma virus

Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis

tRNA imbalance promotes -1 frameshifting via near-cognate decoding

The muscle thin filament as a classical Cooperative/Allosteric regulatory system

A superrepressor mutant of the arginine repressor with a correctly predicted alteration of ligand binding specificity

New insights for dinucleotide backbone binding in conserved C5' H...O hydrogen bonds

Analyzing the functional organization of a novel restriction modification system, the BcgI system

Design, synthesis and structure of a zinc finger with an artificial β-turn

The transcriptional activator GvpE for the halobacterial gas vesicle genes resembles a basic region leucine-zipper regulatory protein

Purified lens major intrinsic protein (MIP) forms highly ordered tetragonal two-dimensional arrays by reconstitution

Are there non-trivial dynamic cross-correlations in proteins?

Structural basis for the high affinity of amino-aromatic SH2 phosphopeptide ligands

Dimer-to-tetramer transformation: loop excision dramatically alters structure and stability of the ROP four α-helix bundle protein

Engineering bidentate macromolecular inhibitors for trypsin and urokinase-type plasminogen activator

Three-dimensional structures of single-chain Fv-neuraminidase complexes

Effects of reaction conditions on RNA secondary structure and on the helicase activity of Escherichia coli transcription termination factor rho

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