Journal of Molecular Biology

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Characterization of Ceap-11 and Ceap-16, Two Novel Splicing–Variant–Proteins, Associated with Centrosome, Microtubule Aggregation and Cell Proliferation

Zhaoqing Wang, Handong Wei, Yongtao Yu, Jing Sun, more

Journal of Molecular Biology > 2004 > 343 > 1 > 71-82

A novel human gene, encoding two polypeptide-isoforms, has been identified from human fetal liver cDNA library. These two alternatively spliced polypeptide-variants are associated with centrosomes, and are designated Ceap-11 and Ceap-16, respectively, according to the acronym Ceap for centrosomal-associated protein and the approximate relative molecular mass. The high degree of sequence similarity...

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Erratum to ''Unification of the Folding Mechanisms of Non-two-state and Two-state Proteins'' [J. Mol. Biol. (2004) 339, 951-965]

Kiyoto Kamagata, Munehito Arai, Kunihiro Kuwajima

Journal of Molecular Biology > 2004 > 343 > 1 > 279

article

Specific and Non-specific Purine Trap in the T-loop of Normal and Suppressor tRNAs

Félix R. Doyon, Ekaterina I. Zagryadskaya, Jianhong Chen, Sergey V. Steinberg

Journal of Molecular Biology > 2004 > 343 > 1 > 55-69

To elucidate the general constraints imposed on the structure of the D and T-loops in functional tRNAs, active suppressor tRNAs were selected in vivo from a combinatorial tRNA gene library in which several nucleotide positions in these loops were randomized. Analysis of the nucleotide sequences of the selected clones demonstrates that most of them contain combination U54-A58 allowing the formation...

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Unzipping Mechanism of the Double-stranded DNA Unwinding by a Hexameric Helicase: Quantitative Analysis of the Rate of the dsDNA Unwinding, Processivity and Kinetic Step-size of the Escherichia coli DnaB Helicase Using Rapid Quench-flow Method

Roberto Galletto, Maria J. Jezewska, Wlodzimierz Bujalowski

Journal of Molecular Biology > 2004 > 343 > 1 > 83-99

Kinetics of the double-stranded (ds) DNA unwinding by the Escherichia coli replicative helicase DnaB protein has been examined under single-turnover conditions using the chemical quench-flow technique. The unwinding reaction proceeds through an initial conformational transition followed by the unwinding catalytic steps and the release of the single-stranded (ss) DNA. Analyses of the reaction as a...

article

Structural Basis for the Variation in Triclosan Affinity to Enoyl Reductases

Lakshmi Swarnamukhi Pidugu, Mili Kapoor, Namita Surolia, Avadhesha Surolia, more

Journal of Molecular Biology > 2004 > 343 > 1 > 147-155

Bacteria synthesize fatty acids in a dissociated type pathway different from that in humans. Enoyl acyl carrier protein reductase, which catalyzes the final step of fatty acid elongation, has been validated as a potential anti-microbial drug target. Triclosan is known to inhibit this enzyme effectively. Precise characterization of the mode of triclosan binding is required to develop highly specific...

article

Inventory and Comparative Analysis of Rice and Arabidopsis ATP-binding Cassette (ABC) Systems

Olivier Garcia, Philippe Bouige, Cyrille Forestier, Elie Dassa

Journal of Molecular Biology > 2004 > 343 > 1 > 249-265

ATP-binding cassette (ABC) proteins constitute a large superfamily found in all kingdoms of living organisms. The recent completion of two draft sequences of the rice (Oryza sativa) genome allowed us to analyze and classify its ABC proteins and to compare to those in Arabidopsis thaliana. We identified a similar number of ABC proteins in rice and Arabidopsis (121 versus 120), despite the rice genome...

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Optimal Combination of Theory and Experiment for the Characterization of the Protein Folding Landscape of S6: How Far Can a Minimalist Model Go?

Silvina Matysiak, Cecilia Clementi

Journal of Molecular Biology > 2004 > 343 > 1 > 235-248

The detailed characterization of the overall free energy landscape associated with the folding process of a protein is the ultimate goal in protein folding studies. Modern experimental techniques provide accurate thermodynamic and kinetic measurements on restricted regions of a protein landscape. Although simplified protein models can access larger regions of the landscape, they are oftentimes built...

article

Conformational Flexibility of the C Terminus with Implications for Substrate Binding and Catalysis Revealed in a New Crystal Form of Deacetoxycephalosporin C Synthase

Linda M. Öster, Anke C. Terwisscha van Scheltinga, Karin Valegård, Alasdair MacKenzie Hose, more

Journal of Molecular Biology > 2004 > 343 > 1 > 157-171

Deacetoxycephalosporin C synthase (DAOCS) from Streptomyces clavuligerus catalyses the oxidative ring expansion of the penicillin nucleus into the nucleus of cephalosporins. The reaction requires dioxygen and 2-oxoglutarate as co-substrates to create a reactive iron–oxygen intermediate from a ferrous iron in the active site. The active enzyme is monomeric in solution. The structure of DAOCS was determined...

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X-ray Scattering Study of Pike Olfactory Nerve: Intensity of the Axonal Membrane, Solution of the Phase Problem and Electron Density Profile††We owe more than can be said to Ray Kado's unfailing interest for the structural aspects of electrophysiology. His untimely death put a cruel end to our collaboration. Let these papers be a tribute to his memory.

Vittorio Luzzati, Patrice Vachette, Evelyne Benoit, Gilles Charpentier

Journal of Molecular Biology > 2004 > 343 > 1 > 187-197

Synchrotron radiation X-ray scattering experiments were performed on unmyelinated pike olfactory nerves. The difference between the meridional and the equatorial traces of the 2-D spectra yielded the 1-D equatorial intensity of the macromolecular components oriented with respect to the nerve: axonal membranes, microtubules and other cytoskeletal filaments. These 1-D spectra display a diffuse band...

article

Author Index

Journal of Molecular Biology > 2004 > 343 > 1 > 281

article

Interactions of the RepA Helicase Hexamer of Plasmid RSF1010 with the ssDNA. Quantitative Analysis of Stoichiometries, Intrinsic Affinities, Cooperativities, and Heterogeneity of the Total ssDNA-binding Site

Maria J. Jezewska, Roberto Galletto, Wlodzimierz Bujalowski

Journal of Molecular Biology > 2004 > 343 > 1 > 115-136

Interactions between the replicative RepA helicase hexamer of plasmid RSF1010 with the single-stranded DNA (ssDNA) have been studied, using the quantitative fluorescence titration, analytical sedimentation velocity, and sedimentation equilibrium techniques. Experiments were performed with fluorescein-labeled ssDNA oligomers. Studies with unmodified ssDNA oligomers were accomplished using the macromolecular...

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Contents list

Journal of Molecular Biology > 2004 > 343 > 1 > iii-v

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Evolution of Vitamin B2 Biosynthesis. A Novel Class of Riboflavin Synthase in Archaea††This paper is dedicated to the memory of Dr Justus Henatsch, Europa Fachhochschule Fresenius Idstein.

Markus Fischer, Anne-Kathrin Schott, Werner Römisch, Arne Ramsperger, more

Journal of Molecular Biology > 2004 > 343 > 1 > 267-278

The open reading frame MJ1184 of Methanococcus jannaschii with similarity to riboflavin synthase of Methanothermobacter thermoautotrophicus was cloned into an expression vector but was poorly expressed in an Escherichia coli host strain. However, a synthetic open reading frame that was optimized for expression in E.coli directed the synthesis of abundant amounts of a protein with an apparent subunit...

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Genetics

Journal of Molecular Biology > 2004 > 343 > 1 > VIII

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The Reconstitution and Activity of the Small Multidrug Transporter EmrE is Modulated by Non-bilayer Lipid Composition

Paul Curnow, Mark Lorch, Kalypso Charalambous, Paula J. Booth

Journal of Molecular Biology > 2004 > 343 > 1 > 213-222

The ability of multidrug transport proteins within biological membranes to recognise a diverse array of substrates is a fundamental aspect of antibiotic resistance. Detailed information on the mechanisms of recognition and transport can be provided only by in vitro studies in reconstituted bilayer systems. We describe the controlled, efficient reconstitution of the small multidrug transporter EmrE...

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STAND, a Class of P-Loop NTPases Including Animal and Plant Regulators of Programmed Cell Death: Multiple, Complex Domain Architectures, Unusual Phyletic Patterns, and Evolution by Horizontal Gene Transfer

Detlef D. Leipe, Eugene V. Koonin, L. Aravind

Journal of Molecular Biology > 2004 > 343 > 1 > 1-28

Using sequence profile analysis and sequence-based structure predictions, we define a previously unrecognized, widespread class of P-loop NTPases. The signal transduction ATPases with numerous domains (STAND) class includes the AP-ATPases (animal apoptosis regulators CED4/Apaf-1, plant disease resistance proteins, and bacterial AfsR-like transcription regulators) and NACHT NTPases (e.g. NAIP, TLP1,...

article

The Crystal Structure of an EST2 Mutant Unveils Structural Insights on the H Group of the Carboxylesterase/Lipase Family

Giuseppina De Simone, Valeria Menchise, Vincenzo Alterio, Luigi Mandrich, more

Journal of Molecular Biology > 2004 > 343 > 1 > 137-146

Esterase 2 (EST2) from the thermophilic eubacterium Alicyclobacillus acidocaldarius is a thermostable serine hydrolase belonging to the H group of the esterase/lipase family. This enzyme hydrolyzes monoacylesters of different acyl-chain length and various compounds with industrial interest. EST2 displays an optimal temperature at 70°C and maximal activity with pNP-esters having acyl-chain bearing...

article

CALLADINE

Journal of Molecular Biology > 2004 > 343 > 1 > VII

article

The C Terminus of Fragile X Mental Retardation Protein Interacts with the Multi-domain Ran-binding Protein in the Microtubule-organising Centre

Rajesh P. Menon, Toby J. Gibson, Annalisa Pastore

Journal of Molecular Biology > 2004 > 343 > 1 > 43-53

Absence of the fragile X mental retardation protein (FMRP) causes fragile X syndrome, the most common form of hereditary mental retardation. FMRP is a mainly cytoplasmic protein thought to be involved in repression of translation, through a complex network of protein–protein and protein–RNA interactions. Most of the currently known protein partners of FMRP recognise the conserved N terminus of the...

article

Crystal Structure and Kinetics Identify Escherichia coli YdcW Gene Product as a Medium-chain Aldehyde Dehydrogenase

Arnaud Gruez, Véronique Roig-Zamboni, Sacha Grisel, Aurélia Salomoni, more

Journal of Molecular Biology > 2004 > 343 > 1 > 29-41

In the context of a medium-scaled structural genomics program aiming at solving the structures of as many as possible bacterial unknown open reading frame products from Escherichia coli (Y prefix), we have solved the structure of YdcW at 2.1Å resolution, using molecular replacement. According to its sequence identity, YdcW has been classified into the betaine aldehyde dehydrogenases family (EC 1.2...

INFONA - science communication portal

Journal of Molecular Biology

Characterization of Ceap-11 and Ceap-16, Two Novel Splicing–Variant–Proteins, Associated with Centrosome, Microtubule Aggregation and Cell Proliferation

Erratum to ''Unification of the Folding Mechanisms of Non-two-state and Two-state Proteins'' [J. Mol. Biol. (2004) 339, 951-965]

Specific and Non-specific Purine Trap in the T-loop of Normal and Suppressor tRNAs

Unzipping Mechanism of the Double-stranded DNA Unwinding by a Hexameric Helicase: Quantitative Analysis of the Rate of the dsDNA Unwinding, Processivity and Kinetic Step-size of the Escherichia coli DnaB Helicase Using Rapid Quench-flow Method

Structural Basis for the Variation in Triclosan Affinity to Enoyl Reductases

Inventory and Comparative Analysis of Rice and Arabidopsis ATP-binding Cassette (ABC) Systems

Optimal Combination of Theory and Experiment for the Characterization of the Protein Folding Landscape of S6: How Far Can a Minimalist Model Go?

Conformational Flexibility of the C Terminus with Implications for Substrate Binding and Catalysis Revealed in a New Crystal Form of Deacetoxycephalosporin C Synthase

Author Index

Interactions of the RepA Helicase Hexamer of Plasmid RSF1010 with the ssDNA. Quantitative Analysis of Stoichiometries, Intrinsic Affinities, Cooperativities, and Heterogeneity of the Total ssDNA-binding Site

Contents list

Evolution of Vitamin B2 Biosynthesis. A Novel Class of Riboflavin Synthase in Archaea††This paper is dedicated to the memory of Dr Justus Henatsch, Europa Fachhochschule Fresenius Idstein.

Genetics

The Reconstitution and Activity of the Small Multidrug Transporter EmrE is Modulated by Non-bilayer Lipid Composition

STAND, a Class of P-Loop NTPases Including Animal and Plant Regulators of Programmed Cell Death: Multiple, Complex Domain Architectures, Unusual Phyletic Patterns, and Evolution by Horizontal Gene Transfer

The Crystal Structure of an EST2 Mutant Unveils Structural Insights on the H Group of the Carboxylesterase/Lipase Family

CALLADINE

The C Terminus of Fragile X Mental Retardation Protein Interacts with the Multi-domain Ran-binding Protein in the Microtubule-organising Centre

Crystal Structure and Kinetics Identify Escherichia coli YdcW Gene Product as a Medium-chain Aldehyde Dehydrogenase

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