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1.
Methods Mol Biol ; 899: 1-26, 2012.
Article in English | MEDLINE | ID: mdl-22735943

ABSTRACT

Protein-based therapeutics are highly successful in clinic and currently enjoy unprecedented recognition of their potential. More than 100 genuine and similar number of modified therapeutic proteins are approved for clinical use in the European Union and the USA with 2010 sales of US$108 bln; monoclonal antibodies (mAbs) accounted for almost half (48%) of the sales. Based on their pharmacological activity, they can be divided into five groups: (a) replacing a protein that is deficient or abnormal; (b) augmenting an existing pathway; (c) providing a novel function or activity; (d) interfering with a molecule or organism; and (e) delivering other compounds or proteins, such as a radionuclide, cytotoxic drug, or effector proteins. Therapeutic proteins can also be grouped based on their molecular types that include antibody-based drugs, Fc fusion proteins, anticoagulants, blood factors, bone morphogenetic proteins, engineered protein scaffolds, enzymes, growth factors, hormones, interferons, interleukins, and thrombolytics. They can also be classified based on their molecular mechanism of activity as (a) binding non-covalently to target, e.g., mAbs; (b) affecting covalent bonds, e.g., enzymes; and (c) exerting activity without specific interactions, e.g., serum albumin. Most protein therapeutics currently on the market are recombinant and hundreds of them are in clinical trials for therapy of cancers, immune disorders, infections, and other diseases. New engineered proteins, including bispecific mAbs and multispecific fusion proteins, mAbs conjugated with small molecule drugs, and proteins with optimized pharmacokinetics, are currently under development. However, in the last several decades, there are no conceptually new methodological developments comparable, e.g., to genetic engineering leading to the development of recombinant therapeutic proteins. It appears that a paradigm change in methodologies and understanding of mechanisms is needed to overcome major challenges, including resistance to therapy, access to targets, complexity of biological systems, and individual variations.


Subject(s)
Antibodies, Monoclonal/therapeutic use , Immunoglobulin Fc Fragments/therapeutic use , Protein Engineering , Recombinant Fusion Proteins/therapeutic use , Antibodies, Monoclonal/adverse effects , Antibodies, Monoclonal/classification , Antibodies, Monoclonal/economics , Antithrombin III/therapeutic use , European Union , Humans , Immune System Diseases/drug therapy , Molecular Targeted Therapy/economics , Molecular Targeted Therapy/methods , Neoplasms/drug therapy , Protein Engineering/economics , Recombinant Fusion Proteins/classification , United States
2.
Article in English | MEDLINE | ID: mdl-21301094

ABSTRACT

Phospholipases D are the major dermonecrotic component of Loxosceles venom and catalyze the hydrolysis of phospholipids, resulting in the formation of lipid mediators such as ceramide-1-phosphate and lysophosphatidic acid which can induce pathological and biological responses. Phospholipases D can be classified into two classes depending on their catalytic efficiency and the presence of an additional disulfide bridge. In this work, both wild-type and H12A-mutant forms of the class II phospholipase D from L. intermedia venom were crystallized. Wild-type and H12A-mutant crystals were grown under very similar conditions using PEG 200 as a precipitant and belonged to space group P12(1)1, with unit-cell parameters a = 50.1, b = 49.5, c = 56.5 Å, ß = 105.9°. Wild-type and H12A-mutant crystals diffracted to maximum resolutions of 1.95 and 1.60 Å, respectively.


Subject(s)
Phospholipase D/chemistry , Phospholipase D/classification , Spider Venoms/enzymology , Spiders/enzymology , Amino Acid Sequence , Animals , Crystallization , Crystallography, X-Ray/methods , Diffusion , Disulfides/chemistry , Escherichia coli/genetics , Histidine/chemistry , Hot Temperature , Hydrogen Bonding , Hydrogen-Ion Concentration , Molecular Sequence Data , Molecular Weight , Mutation , Phospholipase D/genetics , Phospholipase D/isolation & purification , Phosphoric Diester Hydrolases , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/isolation & purification , Sequence Homology, Amino Acid , Transformation, Bacterial , X-Ray Diffraction
3.
J Biol Chem ; 285(30): 23165-76, 2010 Jul 23.
Article in English | MEDLINE | ID: mdl-20498364

ABSTRACT

The correct localization of integral membrane proteins to subcellular compartments is important for their functions. Synaptotagmin contains a single transmembrane domain that functions as a type I signal-anchor sequence in its N terminus and two calcium-binding domains (C(2)A and C(2)B) in its C terminus. Here, we demonstrate that the localization of an Arabidopsis synaptotagmin homolog, SYT1, to the plasma membrane (PM) is modulated by tandem C2 domains. An analysis of the roots of a transformant-expressing green fluorescent protein-tagged SYT1 driven by native SYT1 promoter suggested that SYT1 is synthesized in the endoplasmic reticulum, and then delivered to the PM via the exocytotic pathway. We transiently expressed a series of truncated proteins in protoplasts, and determined that tandem C(2)A-C(2)B domains were necessary for the localization of SYT1 to the PM. The PM localization of SYT1 was greatly reduced following mutation of the calcium-binding motifs of the C(2)B domain, based on sequence comparisons with other homologs, such as endomembrane-localized SYT5. The localization of SYT1 to the PM may have been required for the functional divergence that occurred in the molecular evolution of plant synaptotagmins.


Subject(s)
Arabidopsis/cytology , Arabidopsis/metabolism , Cell Membrane/metabolism , Synaptotagmin I/chemistry , Synaptotagmin I/metabolism , Amino Acid Motifs , Amino Acid Sequence , Endoplasmic Reticulum/metabolism , Gene Deletion , Models, Molecular , Molecular Sequence Data , Phylogeny , Plant Leaves/cytology , Plant Leaves/metabolism , Plant Roots/cytology , Plant Roots/metabolism , Protein Structure, Tertiary , Protein Transport , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Synaptotagmin I/classification , Synaptotagmin I/genetics
4.
J Proteome Res ; 9(6): 3311-8, 2010 Jun 04.
Article in English | MEDLINE | ID: mdl-20405931

ABSTRACT

A straightforward method using mild enzymatic digestions combined with MALDI mass spectrometry (MS) was used to enhance determination of the multiple phosphorylation sites of a set of recombinant nucleotide-binding proteins in Escherichia coli, including kinases and cystathionine beta-synthase (CBS) domain containing proteins. The protein kinases reveal abundant phosphorylations in the kinase domains and relatively low phosphogluconoylation (258 Da) at the N-terminal His-tag. In contrast, the CBS domain-containing proteins possess a highly conserved phosphorylation in vivo at Ser-2 of the His-tag. Multistage MS/MS and selected reaction monitoring established that the CBS domain proteins also contain a combined modification of gluconoylation (178 Da) and phosphorylation (80 Da) at two different sites, instead of an isobaric phosphogluconoylation (258 Da) event at the N-terminus. Functional analysis of 20 recombinant proteins as identified by mass spectrometry has shown the phosphorylation at the N-terminal His-tag is relevant to nucleotide binding and phosphotransfer reaction catalyzed by a serine protein kinase.


Subject(s)
Escherichia coli/chemistry , Peptide Fragments/chemistry , Recombinant Fusion Proteins/chemistry , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Amino Acid Sequence , Carrier Proteins/chemistry , Carrier Proteins/classification , Carrier Proteins/metabolism , Escherichia coli/metabolism , Histidine/chemistry , Molecular Sequence Data , Oligopeptides/chemistry , Peptide Fragments/metabolism , Phosphorylation , Protein Structure, Tertiary , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/metabolism , Tandem Mass Spectrometry , Trypsin/metabolism
5.
Article in English | MEDLINE | ID: mdl-20077575

ABSTRACT

BACKGROUND: CNTO 530is a biopharmaceutical consisting of a novel peptide that mimics the actions of erythropoietin, fused to the Fc fragment of human IgG4. Pharmacokinetic and pharmacodynamic studies showed that CNTO 530 produced sustained increases in red blood cell parameters in rats and rabbits and that the serum half life of CNTO 530 was 2 days in rabbits and 3 days in rats. METHODS: For the evaluation of embryofetal development, CNTO 530 was injected at loading doses of 0, 0.9/1, 6, or 60 mg/kg subcutaneously (SC) on gestation day (GD)7 followed by maintenance doses of 0, 0.3, 2, or 20 mg/kg SC every 3 days through GD16 in rats and every 2 days through GD19 in rabbits (GD0 was the day of mating). Rats were Caesarean sectioned on GD21, rabbits on GD29. RESULTS: Administration of CNTO 530 was associated with an increase in hematocrit at all dose levels and a decrease in maternal body weight gains. Fetuses exhibited reduced body weight and delayed ossification. Soft tissue changes were limited to cardiovascular alterations in the high-dose rabbits only. Rat and rabbit fetuses were exposed to CNTO 530 in all dose groups. CONCLUSIONS: These studies show that the embryo/fetal development effects observed following CNTO 530 treatment during organogenesis are qualitatively similar to those seen with other erythropoietin agonists and are likely a secondary consequence of increased hematocrit in the dams. Unlike other erythropoietin receptor agonists, CNTO 530 was able to cross the placental barrier, which was considered likely the result of FcRn-mediated transcytosis.


Subject(s)
Embryo, Mammalian/drug effects , Embryonic Development/drug effects , Fetal Development/drug effects , Receptors, Erythropoietin/agonists , Recombinant Fusion Proteins/toxicity , Teratogens/toxicity , Abnormalities, Drug-Induced/etiology , Animals , Body Weight/drug effects , Bone and Bones/drug effects , Bone and Bones/embryology , Embryo, Mammalian/embryology , Female , Fetal Weight/drug effects , Injections, Subcutaneous , Osteogenesis/drug effects , Polycythemia/chemically induced , Pregnancy , Rabbits , Rats , Recombinant Fusion Proteins/classification , Teratogens/classification
6.
J Mol Biol ; 392(3): 701-22, 2009 Sep 25.
Article in English | MEDLINE | ID: mdl-19616556

ABSTRACT

Translation initiation is down-regulated in eukaryotes by phosphorylation of the alpha-subunit of eIF2 (eukaryotic initiation factor 2), which inhibits its guanine nucleotide exchange factor, eIF2B. The N-terminal S1 domain of phosphorylated eIF2alpha interacts with a subcomplex of eIF2B formed by the three regulatory subunits alpha/GCN3, beta/GCD7, and delta/GCD2, blocking the GDP-GTP exchange activity of the catalytic epsilon-subunit of eIF2B. These regulatory subunits have related sequences and have sequences in common with many archaeal proteins, some of which are involved in methionine salvage and CO(2) fixation. Our sequence analyses however predicted that members of one phylogenetically distinct and coherent group of these archaeal proteins [designated aIF2Bs (archaeal initiation factor 2Bs)] are functional homologs of the alpha, beta, and delta subunits of eIF2B. Three of these proteins, from different archaea, have been shown to bind in vitro to the alpha-subunit of the archaeal aIF2 from the cognate archaeon. In one case, the aIF2B protein was shown further to bind to the S1 domain of the alpha-subunit of yeast eIF2 in vitro and to interact with eIF2Balpha/GCN3 in vivo in yeast. The aIF2B-eIF2alpha interaction was however independent of eIF2alpha phosphorylation. Mass spectrometry has identified several proteins that co-purify with aIF2B from Thermococcus kodakaraensis, and these include aIF2alpha, a sugar-phosphate nucleotidyltransferase with sequence similarity to eIF2Bvarepsilon, and several large-subunit (50S) ribosomal proteins. Based on this evidence that aIF2B has functions in common with eIF2B, the crystal structure established for an aIF2B was used to construct a model of the eIF2B regulatory subcomplex. In this model, the evolutionarily conserved regions and sites of regulatory mutations in the three eIF2B subunits in yeast are juxtaposed in one continuous binding surface for phosphorylated eIF2alpha.


Subject(s)
Archaea/chemistry , Archaeal Proteins/metabolism , Eukaryotic Initiation Factor-2/metabolism , Prokaryotic Initiation Factor-2/metabolism , Amino Acid Sequence , Archaea/metabolism , Archaeal Proteins/chemistry , Archaeal Proteins/classification , Archaeal Proteins/genetics , Binding Sites , Eukaryotic Initiation Factor-2/chemistry , Eukaryotic Initiation Factor-2/genetics , Models, Molecular , Molecular Sequence Data , Mutation , Phylogeny , Prokaryotic Initiation Factor-2/chemistry , Prokaryotic Initiation Factor-2/classification , Prokaryotic Initiation Factor-2/genetics , Protein Structure, Tertiary , Protein Subunits/chemistry , Protein Subunits/genetics , Protein Subunits/metabolism , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Ribosome Subunits, Large, Archaeal/genetics , Ribosome Subunits, Large, Archaeal/metabolism , Sequence Alignment
7.
J Virol ; 82(17): 8476-86, 2008 Sep.
Article in English | MEDLINE | ID: mdl-18524818

ABSTRACT

C-terminal binding protein (CtBP) binds to adenovirus early region 1A (AdE1A) through a highly conserved PXDLS motif close to the C terminus. We now have demonstrated that CtBP1 also interacts directly with the transcriptional activation domain (conserved region 3 [CR3]) of adenovirus type 5 E1A (Ad5E1A) and requires the integrity of the entire CR3 region for optimal binding. The interaction appears to be at least partially mediated through a sequence ((161)RRNTGDP(167)) very similar to a recently characterized novel CtBP binding motif in ZNF217 as well as other regions of CR3. Using reporter assays, we further demonstrated that CtBP1 represses Ad5E1A CR3-dependent transcriptional activation. Ad5E1A also appears to be recruited to the E-cadherin promoter through its interaction with CtBP. Significantly, Ad5E1A, CtBP1, and ZNF217 form a stable complex which requires CR3 and the PLDLS motif. It has been shown that Ad513SE1A, containing the CR3 region, is able to overcome the transcriptional repressor activity of a ZNF217 polypeptide fragment in a GAL4 reporter assay through recruitment of CtBP1. These results suggest a hitherto-unsuspected complexity in the association of Ad5E1A with CtBP, with the interaction resulting in transcriptional activation by recruitment of CR3-bound factors to CtBP1-containing complexes.


Subject(s)
Adenovirus E1A Proteins/chemistry , Adenovirus E1A Proteins/metabolism , Adenovirus E1A Proteins/genetics , Alcohol Oxidoreductases/metabolism , Amino Acid Motifs , Amino Acid Sequence , Antibodies, Monoclonal/metabolism , Binding Sites , Carcinoma, Small Cell/metabolism , Cell Line, Tumor , Conserved Sequence , DNA-Binding Proteins/metabolism , Genes, Reporter , Glutathione Transferase/metabolism , Green Fluorescent Proteins/metabolism , HCT116 Cells , HT29 Cells , HeLa Cells , Humans , Luciferases/analysis , Lung Neoplasms/metabolism , Molecular Sequence Data , Mutation , Osteosarcoma/metabolism , Plasmids , Protein Binding , Protein Structure, Tertiary , RNA, Small Interfering/metabolism , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/metabolism , Time Factors , Transfection
8.
Mol Cell ; 30(3): 381-92, 2008 May 09.
Article in English | MEDLINE | ID: mdl-18471983

ABSTRACT

Phosphoinositide 3-kinase (PI3K) and its product phosphatidylinositol(3,4,5)-trisphosphate (PIP3) control cell growth, migration, and other processes by recruiting proteins with pleckstrin homology (PH) domains and possibly other domains to the plasma membrane (PM). However, previous experimental and structural work with PH domains left conflicting evidence about which ones are PIP3 regulated. Here we used live-cell confocal imaging of 130 YFP-conjugated mouse PH domains and found that 20% translocated to the PM in response to receptor-generated PIP3 production. We developed a recursive-learning algorithm to predict PIP3 regulation of 1200 PH domains from different eukaryotes and validated that it accurately predicts PIP3 regulation. Strikingly, this algorithm showed that PIP3 regulation is specified by amino acids across the PH domain, not just the PIP3-binding pocket, and must have evolved several times independently from PIP3-insensitive ancestral PH domains. Finally, our algorithm and live-cell experiments provide a functional survey of PH domains in different species, showing that PI3K regulation increased from approximately two C. elegans and four Drosophila to 40 vertebrate proteins.


Subject(s)
Algorithms , Caenorhabditis elegans Proteins/metabolism , Microscopy, Confocal/methods , Models, Theoretical , Phosphatidylinositol Phosphates/metabolism , Recombinant Fusion Proteins/metabolism , Amino Acid Sequence , Animals , Caenorhabditis elegans , Caenorhabditis elegans Proteins/chemistry , Caenorhabditis elegans Proteins/genetics , Humans , Mice , Models, Molecular , Molecular Sequence Data , NIH 3T3 Cells , Phosphatidylinositol 3-Kinases/metabolism , Phosphatidylinositol 4,5-Diphosphate , Phylogeny , Protein Binding , Protein Conformation , Proteome/analysis , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/genetics , Sequence Alignment
9.
Protein Expr Purif ; 45(2): 393-9, 2006 Feb.
Article in English | MEDLINE | ID: mdl-16112872

ABSTRACT

Malonyl coenzyme A (CoA)-acyl carrier protein (ACP) transacylase (MCAT) is an essential enzyme in fatty acid and mycolic acid biosynthesis of Mycobacterium tuberculosis. fabd2 is a novel gene coding MCAT in M. tuberculosis besides another known fabd. In our study, fabd2 was inserted into a bacterial expression vector pET28a resulting in a 6x Histidine-tag fabd2 fusion gene construction. The protein was purified by nickel affinity chromatography and the characterizations of FabD2 have been investigated. The molecular weight of FabD2 was estimated to be 26 kDa by MALDI-TOF. Consistent with the biosynthesis specialty of reported MCATs, FabD2 resulted in a typical activity of bacterial MCATs, which catalyzes the transacylation of malonate from malonyl-CoA to activated holo-ACP. Some physical and chemical differences between FabD2 and FabD also have been found. FabD2 shows dissimilarity with FabD in secondary structure in different pH buffer and MCAT genes RT-PCR results reveal different transcript condition with each other. Furthermore, FabD2 shows low similarity in protein sequence when alignment with other MCATs.


Subject(s)
Acyl-Carrier Protein S-Malonyltransferase/isolation & purification , Acyl-Carrier Protein S-Malonyltransferase/metabolism , Bacterial Proteins/isolation & purification , Bacterial Proteins/metabolism , Fatty Acid Synthases/chemistry , Mycobacterium tuberculosis/enzymology , Acyl-Carrier Protein S-Malonyltransferase/classification , Acyl-Carrier Protein S-Malonyltransferase/genetics , Bacterial Proteins/classification , Bacterial Proteins/genetics , Cations, Divalent/chemistry , Fatty Acid Synthases/isolation & purification , Fatty Acid Synthases/metabolism , Hydrogen-Ion Concentration , Molecular Weight , Mycobacterium tuberculosis/genetics , Phylogeny , Protein Structure, Secondary , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/isolation & purification , Recombinant Fusion Proteins/metabolism
10.
Biophys J ; 84(4): 2306-18, 2003 Apr.
Article in English | MEDLINE | ID: mdl-12668439

ABSTRACT

ClC-4 and ClC-5 are mammalian ClC isoforms with unique ion conduction and gating properties. Macroscopic current recordings in heterologous expression systems revealed very small currents at negative potentials, whereas a substantially larger instantaneous current amplitude and a subsequent activation were observed upon depolarization. Neither the functional basis nor the physiological impact of these channel features are currently understood. Here, we used whole-cell recordings to study pore properties of human ClC-4 channels heterologously expressed in tsA201 or HEK293 cells. Variance analysis demonstrated that the prominent rectification of the instantaneous macroscopic current amplitude is due to a voltage-dependent unitary current conductance. The single channel amplitudes are very small, i.e., 0.10 +/- 0.02 pA at +140 mV for external Cl(-) and internal I(-). Conductivity and permeability sequences were determined for various external and internal anions, and both values increase for anions with lower dehydration energies. ClC-4 exhibits pore properties that are distinct from other ClC isoforms. These differences can be explained by assuming differences in the size of the pore narrowing and the electrostatic potentials within the ion conduction pathways.


Subject(s)
Cell Membrane Permeability/physiology , Chloride Channels/classification , Chloride Channels/physiology , Chlorine/physiology , Kidney/embryology , Membrane Potentials/physiology , Anions/pharmacokinetics , Cell Line , Electric Conductivity , Humans , Ion Channel Gating/physiology , Kidney/physiology , Porosity , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/physiology , Species Specificity
11.
Biophys J ; 84(4): 2655-63, 2003 Apr.
Article in English | MEDLINE | ID: mdl-12668474

ABSTRACT

Skeletal-type E-C coupling is thought to require a direct interaction between RyR1 and the alpha(1S)-DHPR. Most available evidence suggests that the cytoplasmic II-III loop of the dihydropyridine receptor (DHPR) is the primary source of the orthograde signal. However, identification of the region(s) of RyR1 involved in bidirectional signaling with the alpha(1S)-DHPR remains elusive. To identify these regions we have designed a series of chimeric RyR cDNAs in which different segments of RyR1 were inserted into the corresponding region of RyR3 and expressed in dyspedic 1B5 myotubes. RyR3 provides a preferable background than RyR2 for defining domains essential for E-C coupling because it possesses less sequence homology to RyR1 than the RyR2 backbone used in previous studies. Our data show that two regions of RyR1 (chimera Ch-10 aa 1681-2641 and Ch-9 aa 2642-3770), were independently able to restore skeletal-type E-C coupling to RyR3. These two regions were further mapped and the critical RyR1 residues were 1924-2446 (Ch-21) and 2644-3223 (Ch-19). These results both support and refine the previous hypothesis that multiple domains of RyR1 combine to functionally interact with the DHPR during E-C coupling.


Subject(s)
Calcium/metabolism , Muscle Contraction/physiology , Muscle Fibers, Skeletal/chemistry , Muscle Fibers, Skeletal/physiology , Ryanodine Receptor Calcium Release Channel/chemistry , Ryanodine Receptor Calcium Release Channel/physiology , Action Potentials/physiology , Animals , Caffeine/pharmacology , Humans , Muscle Contraction/drug effects , Muscle Fibers, Skeletal/drug effects , Muscle, Skeletal/chemistry , Muscle, Skeletal/drug effects , Muscle, Skeletal/physiology , Protein Isoforms , Protein Structure, Tertiary , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/deficiency , Recombinant Fusion Proteins/physiology , Ryanodine Receptor Calcium Release Channel/classification , Ryanodine Receptor Calcium Release Channel/deficiency
12.
Nat Biotechnol ; 21(5): 539-45, 2003 May.
Article in English | MEDLINE | ID: mdl-12692560

ABSTRACT

The specificity of biological regulatory mechanisms relies on selective interactions between different proteins in different cell types and in response to different extracellular signals. We describe a bimolecular fluorescence complementation (BiFC) approach for the simultaneous visualization of multiple protein interactions in the same cell. This approach is based on complementation between fragments of fluorescent proteins with different spectral characteristics. We have identified 12 bimolecular fluorescent complexes that correspond to 7 different spectral classes. Bimolecular complex formation between fragments of different fluorescent proteins did not differentially affect the dimerization efficiency of the bZIP domains of Fos and Jun or the subcellular sites of interactions between these domains. Multicolor BiFC enables visualization of interactions between different proteins in the same cell and comparison of the efficiencies of complex formation with alternative interaction partners.


Subject(s)
DNA-Binding Proteins/chemistry , DNA-Binding Proteins/metabolism , Fluorescent Dyes , Microscopy, Fluorescence/methods , Transcription Factors/chemistry , Transcription Factors/metabolism , Animals , Basic-Leucine Zipper Transcription Factors , COS Cells , Chlorocebus aethiops , Color , DNA-Binding Proteins/analysis , DNA-Binding Proteins/classification , G-Box Binding Factors , Recombinant Fusion Proteins/analysis , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/metabolism , Reproducibility of Results , Sensitivity and Specificity , Transcription Factors/analysis , Transcription Factors/classification , Zinc Fingers
13.
J Biotechnol ; 101(3): 253-65, 2003 Mar 20.
Article in English | MEDLINE | ID: mdl-12615394

ABSTRACT

The production of hybrid enzymes with novel properties and the research for new methods for enzyme immobilization in bioreactors are of major interest in biotechnology. We report here the second part of a study concerning the improvement of the properties of the endoxylanase XYN3A4 from the anaerobic fungi Neocallimastix frontalis. The effects of gene fusion and immobilization on metal-chelate matrix are also compared for the reference enzymes XYN3, XYN3A, XYN4 used for the construction of the fusion protein XYN3A4. The influence of the metal ion in the immobilization process was first investigated and best immobilization yields were obtained with the Cu(II) ion whereas best coupling efficiencies were reached with the Ni(II) ion. It was also observed that XYN3, XYN3A and XYN34 had a lower rate of hydrolysis when immobilized on Ni(II)-IDA and more difficulties to accomodate small substrates than the soluble enzymes. Nevertheless, a major difference was noted during the hydrolysis of birchwood xylan and it appears that the reaction using the immobilized XYN3A4 chimeric enzyme leads to the accumulation of a specific product.


Subject(s)
Chelating Agents , Metals/chemistry , Neocallimastix/enzymology , Xylosidases/biosynthesis , Xylosidases/chemistry , Catalysis , Endo-1,4-beta Xylanases , Enzyme Activation , Enzymes, Immobilized/chemistry , Escherichia coli/enzymology , Escherichia coli/genetics , Gene Expression Regulation, Enzymologic , Gene Expression Regulation, Fungal , Neocallimastix/genetics , Nickel/chemistry , Recombinant Fusion Proteins/biosynthesis , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/genetics , Substrate Specificity , Transfection/methods , Xylosidases/classification , Xylosidases/genetics
14.
Appl Microbiol Biotechnol ; 60(5): 523-33, 2003 Jan.
Article in English | MEDLINE | ID: mdl-12536251

ABSTRACT

In response to the rapidly growing field of proteomics, the use of recombinant proteins has increased greatly in recent years. Recombinant hybrids containing a polypeptide fusion partner, termed affinity tag, to facilitate the purification of the target polypeptides are widely used. Many different proteins, domains, or peptides can be fused with the target protein. The advantages of using fusion proteins to facilitate purification and detection of recombinant proteins are well-recognized. Nevertheless, it is difficult to choose the right purification system for a specific protein of interest. This review gives an overview of the most frequently used and interesting systems: Arg-tag, calmodulin-binding peptide, cellulose-binding domain, DsbA, c-myc-tag, glutathione S-transferase, FLAG-tag, HAT-tag, His-tag, maltose-binding protein, NusA, S-tag, SBP-tag, Strep-tag, and thioredoxin.


Subject(s)
Recombinant Fusion Proteins/chemistry , Recombinant Proteins/isolation & purification , Amino Acid Sequence , Binding Sites , Calmodulin/chemistry , Carrier Proteins/chemistry , Cellulose/chemistry , Glutathione Transferase/chemistry , Histidine/chemistry , Industry , Maltose-Binding Proteins , Oligopeptides/chemistry , Peptide Fragments/chemical synthesis , Peptides/chemistry , Protein Binding , Protein Engineering , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/genetics , Ribonucleases/chemical synthesis
15.
Infect Immun ; 70(6): 2869-76, 2002 Jun.
Article in English | MEDLINE | ID: mdl-12010974

ABSTRACT

Group B streptococci (GBS) are a major cause of pneumonia, sepsis, and meningitis in newborns and infants. GBS initiate infection of the lung by colonizing mucosal surfaces of the respiratory tract; adherence of the bacteria to host cells is presumed to be the initial step in and prerequisite for successful colonization (G. S. Tamura, J. M. Kuypers, S. Smith, H. Raff, and C. E. Rubens, Infect. Immun. 62:2450-2458, 1994). We have performed a genome-wide screen to identify novel genes of GBS that mediate adherence to fibronectin. A shotgun phage display library was constructed from chromosomal DNA of a serotype Ia GBS strain and affinity selected on immobilized fibronectin. DNA sequence analysis of different clones identified 19 genes with homology to known bacterial adhesin genes, virulence genes, genes involved in transport or metabolic processes, and genes with yet-unknown function. One of the isolated phagemid clones showed significant homology to the gene (scpB) for the GBS C5a peptidase, a surface-associated serine protease that specifically cleaves the complement component C5a, a chemotaxin for polymorphonuclear leukocytes. In this work we have demonstrated that affinity-purified recombinant ScpB and a peptide ScpB fragment (ScpB-PDF), similar to the peptide identified in the phagemid, bound fibronectin in a concentration-dependent manner. Adherence assays to fibronectin were performed, comparing an isogenic scpB mutant to the wild-type strain. Approximately 50% less binding was observed with the mutant than with the wild-type strain. The mutant phenotype could be fully restored by in trans complementation of the mutant with the cloned wild-type scpB gene, providing further evidence for the role of ScpB in fibronectin adherence. Our results suggest that C5a peptidase is a bifunctional protein, which enzymatically cleaves C5a and mediates adherence to fibronectin. Since binding of fibronectin has been implicated in attachment and invasion of eukaryotic cells by streptococci, our results may imply a second important role for this surface protein in the pathogenesis of GBS infections.


Subject(s)
Adhesins, Bacterial/metabolism , Endopeptidases/metabolism , Fibronectins/metabolism , Membrane Glycoproteins/metabolism , Serine Endopeptidases/metabolism , Streptococcus agalactiae/metabolism , Adhesins, Bacterial/classification , Adhesins, Bacterial/genetics , Endopeptidases/classification , Endopeptidases/genetics , Genetic Complementation Test , Genome, Bacterial , Membrane Glycoproteins/classification , Membrane Glycoproteins/genetics , Mutagenesis , Peptide Library , Peptides/metabolism , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Serine Endopeptidases/classification , Serine Endopeptidases/genetics , Streptococcus agalactiae/genetics
16.
EMBO J ; 21(7): 1811-20, 2002 Apr 02.
Article in English | MEDLINE | ID: mdl-11927565

ABSTRACT

The genome of Saccharomyces cerevisiae encodes three close homologues of the Escherichia coli 2'-O-rRNA methyltransferase FtsJ/RrmJ, designated Trm7p, Spb1p and Mrm2p. We present evidence that Trm7p methylates the 2'-O-ribose of nucleotides at positions 32 and 34 of the tRNA anticodon loop, both in vivo and in vitro. In a trm7Delta strain, which is viable but grows slowly, translation is impaired, thus indicating that these tRNA modifications could be important for translation efficiency. We discuss the emergence of a family of three 2'-O-RNA methyltransferases in Eukaryota and one in Prokaryota from a common ancestor. We propose that each eukaryotic enzyme is located in a different cell compartment, in which it would methylate a different RNA that can adopt a very similar secondary structure.


Subject(s)
Anticodon/metabolism , RNA, Fungal/metabolism , RNA, Transfer/metabolism , Ribose/biosynthesis , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/enzymology , tRNA Methyltransferases/metabolism , Amino Acid Sequence , Animals , Base Sequence , Catalysis , Cell Cycle Proteins/chemistry , Escherichia coli/enzymology , Eukaryotic Cells , Humans , Methyltransferases/chemistry , Molecular Sequence Data , Mutagenesis , Nucleic Acid Conformation , Protein Biosynthesis , Protein Structure, Tertiary , RNA, Messenger , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Ribose/analogs & derivatives , S-Adenosylmethionine/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/classification , Saccharomyces cerevisiae Proteins/genetics , Sequence Homology, Amino Acid , tRNA Methyltransferases/chemistry , tRNA Methyltransferases/classification , tRNA Methyltransferases/genetics
17.
J Bacteriol ; 184(2): 540-6, 2002 Jan.
Article in English | MEDLINE | ID: mdl-11751833

ABSTRACT

We report here the molecular cloning and expression of a hemolytic sphingomyelinase from an aquatic bacterium, Pseudomonas sp. strain TK4. The sphingomyelinase gene was found to consist of 1,548 nucleotides encoding 516 amino acid residues. The recombinant 57.7-kDa enzyme hydrolyzed sphingomyelin but not phosphatidylcholine, phosphatidylserine, phosphatidylglycerol, phosphatidic acid, or phosphatidylethanolamine, indicating that the enzyme is a sphingomyelin-specific sphingomyelinase C. The hydrolysis of sphingomyelin by the enzyme was found to be most efficient at pH 8.0 and activated by Mn(2+). The enzyme shows quite a broad specificity, i.e., it hydrolyzed 4-nitrobenz-2-oxa-1,3-diazole (NBD)-sphingomyelin with short-chain fatty acids and NBD-sphingosylphosphorylcholine, the latter being completely resistant to hydrolysis by any sphingomyelinase reported so far. Significant sequence similarities were found in sphingomyelinases from Bacillus cereus, Staphylococcus aureus, Listeria ivanovii, and Leptospira interrogans, as well as a hypothetical protein encoded in Chromobacterium violaceum, although the first three lacked one-third of the sequence corresponding to that from the C terminus of the TK4 enzyme. Interestingly, the deletion mutant of strain TK4 lacking 186 amino acids at the C-terminal end hydrolyzed sphingomyelin, whereas it lost all hemolytic activity, indicating that the C-terminal region of the TK4 enzyme is indispensable for the hemolytic activity.


Subject(s)
Gene Expression , Hemolysin Proteins/genetics , Manganese/metabolism , Pseudomonas/enzymology , Sphingomyelin Phosphodiesterase/genetics , Amino Acid Sequence , Animals , Base Sequence , Cloning, Molecular , DNA, Bacterial , Escherichia coli/metabolism , Genetic Vectors/metabolism , Hemolysin Proteins/classification , Hemolysin Proteins/isolation & purification , Hemolysin Proteins/metabolism , Hydrolysis , Molecular Sequence Data , Mutagenesis , Pseudomonas/genetics , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/isolation & purification , Recombinant Fusion Proteins/metabolism , Sequence Analysis, DNA , Sequence Homology, Amino Acid , Sheep , Sphingomyelin Phosphodiesterase/classification , Sphingomyelin Phosphodiesterase/isolation & purification , Sphingomyelin Phosphodiesterase/metabolism , Sphingomyelins/metabolism , Substrate Specificity
18.
Proc Natl Acad Sci U S A ; 98(19): 10960-5, 2001 Sep 11.
Article in English | MEDLINE | ID: mdl-11553816

ABSTRACT

In Arabidopsis, monogalactosyldiacylglycerol (MGDG) is synthesized by a multigenic family of MGDG synthases consisting of two types of enzymes differing in their N-terminal portion: type A (atMGD1) and type B (atMGD2 and atMGD3). The present paper compares type B isoforms with the enzymes of type A that are known to sit in the inner membrane of plastid envelope. The occurrence of types A and B in 16:3 and 18:3 plants shows that both types are not specialized isoforms for the prokaryotic and eukaryotic glycerolipid biosynthetic pathways. Type A atMGD1 gene is abundantly expressed in green tissues and along plant development and encodes the most active enzyme. Its mature polypeptide is immunodetected in the envelope of chloroplasts from Arabidopsis leaves after cleavage of its transit peptide. atMGD1 is therefore likely devoted to the massive production of MGDG required to expand the inner envelope membrane and build up the thylakoids network. Transient expression of green fluorescent protein fusions in Arabidopsis leaves and in vitro import experiments show that type B precursors are targeted to plastids, owing to a different mechanism. Noncanonical addressing peptides, whose processing could not be assessed, are involved in the targeting of type B precursors, possibly to the outer envelope membrane where they might contribute to membrane expansion. Expression of type B enzymes was higher in nongreen tissues, i.e., in inflorescence (atMGD2) and roots (atMGD3), where they conceivably influence the eukaryotic structure prominence in MGDG. In addition, their expression of type B enzymes is enhanced under phosphate deprivation.


Subject(s)
Galactosyltransferases/genetics , Glycolipids/biosynthesis , Photosynthesis/physiology , Amino Acid Sequence , Arabidopsis/enzymology , Arabidopsis/genetics , Base Sequence , Chemical Fractionation , Chloroplasts , DNA, Plant , Diglycerides/metabolism , Escherichia coli , Eukaryotic Cells , Galactolipids , Galactosyltransferases/classification , Galactosyltransferases/isolation & purification , Galactosyltransferases/metabolism , Gene Expression , Genes, Plant , Green Fluorescent Proteins , Luminescent Proteins/genetics , Luminescent Proteins/metabolism , Molecular Sequence Data , Phosphates/metabolism , Phylogeny , Prokaryotic Cells , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/isolation & purification , Recombinant Fusion Proteins/metabolism , Substrate Specificity , Tissue Distribution
19.
FEBS Lett ; 480(2-3): 255-60, 2000 Sep 01.
Article in English | MEDLINE | ID: mdl-11034340

ABSTRACT

P67, a new protein binding to a specific RNA probe, was purified from radish seedlings [Echeverria, M. and Lahmy, S. (1995) Nucleic Acids Res. 23, 4963-4970]. Amino acid sequence information obtained from P67 microsequencing allowed the isolation of genes encoding P67 in radish and Airabidopsis thaliana. Immunolocalisation experiments in transfected protoplasts demonstrated that this protein is addressed to the chloroplast. The RNA-binding activity of recombinant P67 was found to be similar to that of the native protein. A significant similarity with the maize protein CRP1 [Fisk, D.G., Walker, M.B. and Barkan, A. (1999) EMBO J. 18, 2621-2630] suggests that P67 belongs to the PPR family and could be involved in chloroplast RNA processing.


Subject(s)
Chloroplasts/metabolism , Plant Proteins/metabolism , RNA-Binding Proteins/metabolism , Amino Acid Motifs , Amino Acid Sequence , Arabidopsis , Base Sequence , Brassica , Cloning, Molecular , DNA, Plant , Gene Expression , Genes, Plant , Molecular Sequence Data , Plant Proteins/classification , Plant Proteins/genetics , RNA, Messenger , RNA-Binding Proteins/classification , RNA-Binding Proteins/genetics , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Subcellular Fractions
20.
Oncogene ; 19(32): 3656-64, 2000 Jul 27.
Article in English | MEDLINE | ID: mdl-10951572

ABSTRACT

The tumour suppressor p53 protein integrates multiple signals regulating cell cycle progression and apoptosis. This regulation is mediated by several kinases that phosphorylate specific residues in the different functional domains of the p53 molecule. The human VRK1 protein is a new kinase related to a poxvirus kinase, and more distantly to the casein kinase 1 family. We have characterized the biochemical properties of human VRK1 from HeLa cells. VRK1 has a strong autophosphorylating activity in several Ser and Thr residues. VRK-1 phosphorylates acidic proteins, such as phosvitin and casein, and basic proteins such as histone 2b and myelin basic protein. Because some transcription factors are regulated by phosphorylation, we tested as substrates the N-transactivation domains of p53 and c-Jun fused to GST. Human c-Jun is not phosphorylated by VRK1. VRK1 phosphorylates murine p53 in threonine 18. This threonine is within the p53 hydrophobic loop (residues 13-23) required for the interaction of p53 with the cleft of its inhibitor mdm-2. The VRK1 C-terminus domain (residues 268-396) that contains a nuclear localization signal targets the protein to the nucleus, as determined by using fusion proteins with the green fluorescent protein. We conclude that VRK1 is an upstream regulator of p53 that belongs to a new signalling pathway.


Subject(s)
Nuclear Proteins/metabolism , Protein Serine-Threonine Kinases/metabolism , Proteins , Proto-Oncogene Proteins/metabolism , Threonine/metabolism , Tumor Suppressor Protein p53/metabolism , Viral Proteins/metabolism , 3T3 Cells , Amino Acid Sequence , Animals , Base Sequence , Binding Sites , Casein Kinases , Catalytic Domain , Cell Nucleus/metabolism , HeLa Cells , Humans , Intracellular Signaling Peptides and Proteins , Mice , Molecular Sequence Data , Nuclear Proteins/classification , Nuclear Proteins/genetics , Phosphorylation , Protein Kinases/classification , Protein Kinases/metabolism , Protein Serine-Threonine Kinases/classification , Protein Serine-Threonine Kinases/genetics , Proto-Oncogene Proteins c-mdm2 , Recombinant Fusion Proteins/classification , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Serine/metabolism , Substrate Specificity , Threonine/genetics , Transcription Factors/metabolism , Tumor Suppressor Protein p53/genetics , Viral Proteins/classification , Viral Proteins/genetics
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