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PubMed2002

Importance of secondary structural specificity determinants in protein folding: insertion of a native beta-sheet sequence into an alpha-helical coiled-coil.

To examine how a short secondary structural element derived from a native protein folds when in a different protein environment, we inserted an 11-residue beta-sheet segment (cassette) from human immunoglobulin fold, Fab new, into an alpha-helical coiled-coil host protein (cassette holder). This de novo design protein model, the structural cassette mutagenesis (SCM) model, allows us to study protein folding principles involving both short- and long-range interactions that affect secondary structure stability and conformation. In this study, we address whether the insertion of this beta-sheet cassette into the alpha-helical coiled-coil protein would result in conformational change nucleated by the long-range tertiary stabilization of the coiled-coil, therefore overriding the local propensity of the cassette to form beta-sheet, observed in its native immunoglobulin fold. The results showed that not only did the nucleating helices of the coiled-coil on either end of the cassette fail to nucleate the beta-sheet cassette to fold with an alpha-helical conformation, but also the entire chimeric protein became a random coil. We identified two determinants in this cassette that prevented coiled-coil formation: (1) a tandem dipeptide NN motif at the N-terminal of the beta-sheet cassette, and (2) the hydrophilic Ser residue, which would be buried in the hydrophobic core if the coiled-coil structure were to fold. By amino acid substitution of these helix disruptive residues, that is, either the replacement of the NN motif with high helical propensity Ala residues or the substitution of Ser with Leu to enhance hydrophobicity, we were able to convert the random coil chimeric protein into a fully folded alpha-helical coiled-coil. We hypothesized that this NN motif is a "secondary structural specificity determinant" which is very selective for one type of secondary structure and may prevent neighboring residues from adopting an alternate protein fold. These sequences with secondary structural specificity determinants have very strong local propensity to fold into a specific secondary structure and may affect overall protein folding by acting as a folding initiation site.

Amino Acid Motifs↗

PubMed1991

Phosphotyrosine as a specificity determinant for casein kinase-2, a growth related Ser/Thr-specific protein kinase.

The motif Ser-Ser-Ser-Glu-Glu is readily phosphorylated by casein kinase-2 (CK-2), a growth-related protein kinase whose consensus sequence is Ser(Thr)-Xaa-Xaa-Glu(Asp) [(1990) Biochim. Biophys. Acta 1054, 267-283]. Here we show that phosphotyrosine can replace carboxylic acids as specificity determinant for CK-2 phosphorylation, the phosphotyrosyl peptide Ser-Ser-Ser-TyrP-TyrP actually being a substrate more efficient than Ser-Ser-Ser-Glu-Glu itself both in terms of Km (0.69 vs 2.43 mM) and Vmax. Prior dephosphorylation of phosphotyrosine entirely prevents the subsequent phosphorylation of serine by CK-2. While Ser-Ser-Ser-TyrP-TyrP is a better substrate than Ser-Ser-Ser-SerP-SerP, which in turn is better than Ser-Ser-Ser-Glu-Glu, Ser-Ser-Ser-ThrP-ThrP is a less efficient substrate than Ser-Ser-Ser-Glu-Glu. Thus the order of efficiency of phosphoamino acids as specificity determinants for CK-2 appears to be TyrP greater than SerP much greater than ThrP.

Amino Acid Sequence↗

PubMed1993

Phosphorylated residues as specificity determinants for an acidophilic protein tyrosine kinase. A study with src and cdc2 derived phosphopeptides.

Spleen TPK-IIB is an acidophilic protein tyrosine kinase, devoid of autophosphorylation activity, whose phosphorylation of the src-peptide NEYTA is crucially specified by Glu-2[(1991) J. Biol. Chem. 266, 17798-17803]. We show that phosphothreonine, phosphotyrosine and phosphoserine are, in this order, specificity determinants even more effective than glutamic acid if they are replacing Glu-2, to give the phosphopeptides NTpYTA, NYpYTA, NSpYTA, respectively. Non-phosphorylated threonine, tyrosine and serine are conversely ineffective. Consequently also the heptapeptide GEGTYGV reproducing the phosphoacceptor and inhibitory site of p34cdc2 is not appreciably affected by TPK-IIB, unless its threonyl residue is previously phosphorylated, the phosphoderivative GEGTpYGV being readily phosphorylated at its tyrosyl residue. Such a behaviour is unique for TPK-IIB among the protein tyrosine kinases tested (lyn-TPK, fgr-TPK and EGF-receptor, besides TPK-IIB). These data provide the first evidence that, in some instances, the targeting by protein tyrosine kinases can be specifically determined by the previous phosphorylation of the peptide substrate, thus extending the concept of 'hierarchal phosphorylation' [(1991) J. Biol. Chem. 266, 14139-14142] to tyrosyl residues as well.

Amino Acid Sequence↗

PubMed2005

A family 10 Thermoascus aurantiacus xylanase utilizes arabinose decorations of xylan as significant substrate specificity determinants.

Xylan, which is a key component of the plant cell wall, consists of a backbone of beta-1,4-linked xylose residues that are decorated with arabinofuranose, acetyl, 4-O-methyl d-glucuronic acid and ferulate. The backbone of xylan is hydrolysed by endo-beta1,4-xylanases (xylanases); however, it is unclear whether the various side-chains of the polysaccharide are utilized by these enzymes as significant substrate specificity determinants. To address this question we have determined the crystal structure of a family 10 xylanase from Thermoascus aurantiacus, in complex with xylobiose containing an arabinofuranosyl-ferulate side-chain. We show that the distal glycone subsite of the enzyme makes extensive direct and indirect interactions with the arabinose side-chain, while the ferulate moiety is solvent-exposed. Consistent with the 3D structural data, the xylanase displays fourfold more activity against xylotriose in which the non-reducing moiety is linked to an arabinose side-chain, compared to the undecorated form of the oligosacchairde. These data indicate that the sugar decorations of xylans in the T.aurantiacus family 10 xylanase, rather than simply being accommodated, can be significant substrate specificity determinants.

Arabinose↗

PubMed1992

Reversed-phase chromatographic method for specific determination of glutathione in cultured malignant cells.

A chromatographic method for the specific determination of glutathione in malignant cell lines is described. The method is based on the ability of glutathione-S-transferase to specifically and quantitatively conjugate glutathione to 1-chloro-2,4-dinitrobenzene and chromatographic quantitation of the resultant conjugate, dinitrophenyl-S-glutathione, by reversed-phase liquid chromatography. The assay can be performed on 20,000 g supernatants of cell homogenates without acid extraction. 2-Mercaptoethanol, a sulfhydryl compound often used as a thiol-protective agent to preserve enzymatic activities of a number of enzymes, did not interfere with glutathione determination by this method. The dinitrophenyl-S-glutathione isolated from either standard glutathione samples or from cell homogenates was shown to be identical to authentic dinitrophenyl-S-glutathione using mass spectrometry. Recovery of glutathione in standard samples by the current method was identical to that determined using 5,5'-dithiobis(2-nitrobenzoic acid). Exogenous glutathione added to supernatants of cell homogenate in the presence or absence of 2-mercaptoethanol was also completely recovered.

Chromatography, High Pressure Liquid↗

PubMed1999

In vitro scanning saturation mutagenesis of all the specificity determining residues in an antibody binding site.

For the first time, each specificity determining residue (SDR) in the binding site of an antibody has been replaced with every other possible single amino acid substitution, and the resulting mutants analyzed for binding affinity and specificity. The studies were conducted on a variant of the 26-10 antidigoxin single chain Fv (scFv) using in vitro scanning saturation mutagenesis, a new process that allows the high throughput production and characterization of antibody mutants [Burks,E.A., Chen,G., Georgiou,G. and Iverson,B.L. (1997) Proc. Natl Acad. Sci. USA, 94, 412-417]. Single amino acid mutants of 26-10 scFv were identified that modulated specificity in dramatic fashion. The overall plasticity of the antibody binding site with respect to amino acid replacement was also evaluated, revealing that 86% of all mutants retained measurable binding activity. Finally, by analyzing the physical properties of amino acid substitutions with respect to their effect on hapten binding, conclusions were drawn regarding the functional role played by the wild-type residue at each SDR position. The reported results highlight the value of in vitro scanning saturation mutagenesis for engineering antibody binding specificity, for evaluating the plasticity of proteins, and for comprehensive structure-function studies and analysis.

Amino Acids↗

PubMed2000

Location of the epoxide function determines specificity of the allelic variants of human glutathione transferase Pi toward benzo[c]chrysene diol epoxide isomers.

Carcinogenic activity of many polycyclic aromatic hydrocarbons (PAHs) is mainly attributed to their respective diol epoxides, which can be classified as either bay or fjord region depending upon the location of the epoxide function. The Pi class human glutathione (GSH) transferase (hGSTP1-1), which is polymorphic in humans with respect to amino acid residues in positions 104 (isoleucine or valine) and/or 113 (alanine or valine), plays an important role in the detoxification of PAH-diol epoxides. Here, we report that the location of the epoxide function determines specificity of allelic variants of hGSTP1-1 toward racemic anti-diol epoxide isomers of benzo[c]chrysene (B[c]C). The catalytic efficiency (k(cat)/K(m)) of V104,A113 (VA) and V104,V113 (VV) variants of hGSTP1-1 was approximately 2.3- and 1.7-fold higher, respectively, than that of the I104,A113 (IA) isoform toward bay region isomer (+/-)-anti-B[c]C-1,2-diol-3,4-epoxide. On the other hand, the IA variant was approximately 1.6- and 3.5-fold more efficient than VA and VV isoforms, respectively, in catalyzing the GSH conjugation of fjord region isomer (+/-)-anti-B[c]C-9,10-diol-11,12-epoxide. The results of the present study clearly indicate that the location of the epoxide function determines specificity of the allelic variants of hGSTP1-1 in the GSH conjugation of activated diol epoxide isomers of B[c]C.

Alleles↗

PubMed2000

Specificity determinants for bacteriophage Hong Kong 022 integrase: analysis of mutants with relaxed core-binding specificities.

The integrase (Int) proteins encoded by bacteriophages HK022 and lambda catalyse similar site-specific integration and excision reactions between specific DNA regions known as attachment (att) sites. However, the Int proteins of HK022 and lambda are unable to catalyse recombination between non-cognate att sites. The att sites of both phages contain weak binding sites for Int, known as 'core-type' sites. Negatively acting nucleotide determinants associated with specific core sites (lambda B', HK022 B', HK022 C) are responsible for the barrier to non-cognate recombination. In this study, we used challenge phages to demonstrate that the lambda and HK022 Ints cannot bind to core sites containing non-cognate specificity determinants in vivo. We isolated mutants of the HK022 Int, which bind the lambda B' core site. Two mutants, D99N and D99A, have changed a residue in the core-binding (CB) domain, which may be directly contacting the core site DNA. We suggest that binding to the lambda B' site was accomplished by removing the negatively charged aspartate residue, which normally participates in a conflicting interaction with the G4 nucleotide of the lambda B' site. We showed that, although our mutants retain the ability to recombine their cognate att sites, they are unable to recombine lambda att sites.

Amino Acid Sequence↗

PubMedDate not supplied

Recombinant fibre proteins of human adenoviruses Ad9, Ad15 and Ad19: localization of the haemagglutination properties and the type-specific determinant.

The adenovirus fibre carries the type-specific gamma determinant the existence of which was suggested by haemagglutination inhibition tests. Furthermore, the fibre is thought to be responsible for the agglutination of monkey, rat and human erythrocytes. In order to verify that the haemagglutination properties and the type-specific gamma determinant are located on the fibre knob domain, several recombinant fibre proteins of subgenus D adenoviruses were constructed, expressed in HeLa cells and tested in haemagglutination and haemagglutination inhibition tests. Our data showed that the epitopes responsible for the interaction with erythrocytes and the gamma determinant are located on the fibre knob domain.

Adenoviruses, Human↗

PubMed1997

Cephalosporin substrate specificity determinants of TEM-1 beta-lactamase.

beta-lactamase is a bacterial enzyme that catalyzes the hydrolysis of beta-lactam antibiotics such as penicillins and cephalosporins. TEM-1 beta-lactamase is a prevalent beta-lactamase found in Gram-negative bacteria and is capable of hydrolyzing both penicillins and cephalosporins, except for the extended-spectrum cephalosporins. To identify the sequence determinants in the active site for a given antibiotic substrate, random libraries were constructed that each contain all possible amino acid combinations for the designated region of TEM-1 beta-lactamase. To establish the determinants of substrate specificity for cephalosporins versus those for penicillins, these active site libraries have been screened for mutants with high levels of activity for the second generation cephalosporin cephaloridine. Based on the sequence results, substitutions of W165S, A237T, and E240C were identified as cephalosporin-specific. Kinetic analysis of these mutants was done to determine whether each is capable of distinguishing between the two classes of antibiotics. Both the A237T and E240C substitutions, alone or in combination, exhibited increased cephalosporinase activity and decreased penicillinase activity relative to the wild-type enzyme. A sequence comparison between functional mutants selected for cephaloridine hydrolytic activity and functional mutants previously selected for ampicillin hydrolytic activity suggests that TEM-1 beta-lactamase has greater restrictions in maintaining cephalosporinase activity versus maintaining penicillinase activity.

Amino Acid Sequence↗

PubMed1996

The use of magnetic beads coated with soluble HLA class I or class II proteins in antibody screening and for specificity determinations of donor-reactive antibodies.

An adequate method that will permit rapid specificity determination of donor reactive antibodies is urgently needed. Such a method could also be used for monitoring the presence of HLA antibodies in panel scanning. We here describe a method using magnetic beads coated with soluble HLA antigens that can be directly added to patient serum for efficient absorption of HLA antibodies. The entire procedure takes 45 min, and can therefore be easily adopted for use in acute crossmatching situations. Furthermore since no live cells are required for identification of alloantibodies in the screening for HLA specific panel-reactive antibodies, it can be used as an ideal complement for screening of panel-reactive antibodies. Binding of antibodies to the antigen-coated beads is easily visualized using flow cytometry. A new method for quick purification of soluble MA antigens from a pool of lymphocytes or thrombocytes is also presented.

Antibodies, Monoclonal↗

PubMed2002

Differences in the use of health services among people with and without epilepsy in the United Kingdom: socio-economic and disease-specific determinants.

We aim to examine the socio-economic, demographic and disease-specific determinants in the use of health services by patients with epilepsy, compared to people without epilepsy. We used data from the fourth national survey of morbidity in general practice, carried out in 1991-1992. Overall mean annual number of consultations with general practitioners, home visits and referrals to secondary care per person were calculated for people with epilepsy, stratified by age, sex and socio-economic status. The proportion of patients consulting for certain diseases or disease groups were also calculated for patients with epilepsy. Results were compared to these in people without epilepsy, and rate ratios were calculated. Patients with epilepsy consulted twice as often, required three to four times more home visits, and were referred to secondary care three times more often than people without epilepsy, irrespective of age, sex and social class. Among patients with epilepsy, consultation rates and home visits were higher in females, older people and people from the manual social classes. A higher proportion of patients with epilepsy consulted for neoplasms, haematological and mental health disorders, dementia, stroke and gastrointestinal bleeding. Older age and low social class were less strongly associated with health service utilisation than in people without epilepsy, indicating that people with epilepsy lose much of the protective effect of young age and high social class on health. Factors contributing to the higher utilisation of health services in people with epilepsy need to be studied further and their effects taken into account in the organisation of health services for people with epilepsy.

Adolescent↗

PubMed1982

Immunochemical characterization of Candida albicans cell wall antigens: specific determinant of Candida albicans serotype A mannan.

We investigated the chemical structure of the specific determinant in the mannan of Candida albicans M-1012 (serotype A) strain. Acetolysis of the mannan, obtained by alkali extraction and purified as the copper complex, gave mannose and six oligosaccharides (from di- to hexasaccharide) and a small amount of a heptasaccharide. We examined the inhibition by these oligosaccharides up to hexaose of the precipitin reaction between anti-factor 6 serum specific for serotype A and homologous mannan, and found that the mannohexaose was the most effective inhibitor. These, and results obtained by proton magnetic resonance (PMR) spectroscopy, methylation analysis, and other structural studies, suggest that the main component of this hexaose consists of one terminal alpha (1-3) linkage in addition to four alpha (1-2) linkages, and that this alpha (1-3)-containing mannohexaose may be responsible for the specificity of antigenic factor 6. Further results obtained by analyses of polarimetry, PMR spectroscopy, and chromium trioxide oxidation-methylation of C. albicans M-1012 mannan has a beta-linkage in addition to alpha-linkages, and that the mode of the beta-linkage is mainly (1-6) linkage. Further evidence obtained by Smith degradation-methylation analysis and by quantitative precipitin reactions of intact and acid-degraded mannan suggests that the antigenic determinant of antigenic factor 6 may be bound, via the beta (1-6) linkage, to C-6 of mannose residues involved in oligosaccharide side chains of serotype A mannan.

Antigens, Fungal↗

PubMed1993

Anion-exchange analysis of ribulose-bisphosphate carboxylase/oxygenase reactions: CO2/O2 specificity determination and identification of side products.

An improved anion-exchange chromatographic method for determining the carboxylation/oxygenation specificity (tau) of ribulose 1,5-bisphosphate carboxylase/oxygenase is presented. This assay, which entails radiometric detection of [1-3H]ribulose-bisphosphate turnover products separated on MonoQ anion-exchange resin, is more convenient, less error-prone, and more generally applicable than previous methods of tau determination. It is suitable for both wild-type and site-directed mutant enzymes of widely varying activity and specificity levels and allows simultaneous visualization of various side products of ribulose-bisphosphate processing. A facile method for scrubbing dissolved O2 from carboxylase reaction solutions, which does not require extensive purging and exchange of dissolved gases, is also described.

Anion Exchange Resins↗

PubMed1987

A linear method for determining specific activity of tracers in radioimmunoassays.

I describe a rapid and objective method for graphically determining specific activity of radioactive tracers by self-displacement. Two sets of results are plotted on the same graph: total/bound counts vs concentration of unlabeled analyte (for the standard curve results) or quantity of radioactivity (for tracer self-displacement results). Because these plots are linear, not only are the difficulties of curve fitting and the need for numerous data points avoided, but also how well the data fit the lines can be assessed by calculating the standard deviation of the slope of the lines. This method minimizes uncertainty between data points, allows easier interpolation, and often yields more precise results than do previously published procedures.

Half-Life↗

PubMed1985

Synthesis of sigma 29, an RNA polymerase specificity determinant, is a developmentally regulated event in Bacillus subtilis.

Using an immunological probe, we have determined that the synthesis of the Bacillus subtilis RNA polymerase promoter specificity determinant sigma 29 is a developmentally regulated event. sigma 29 is absent from vegetatively growing cells but is abundant in sporulating cells for a restricted (2-h) period during differentiation (hour 2 to hour 4 into the sporeforming process). The narrowness of this period suggests that sigma 29 is a regulatory factor that directs the transcription of a subpopulation of genes at a precise, intermediate stage of spore formation. This view predicts that sigma 29 should be dispensable for early sporulation events. We verified this prediction by an analysis of sigma 29 accumulation in mutants that are blocked at different stages of sporulation in which we show that cells can advance to at least an intermediate point in development (stage III) in the absence of detectable sigma 29. Lastly, our anti-sigma 29 antibody probe detected a second, previously unrecognized protein in Bacillus cell extracts that may be a precursor to sigma 29. This protein, P31 (molecular weight, 31,000) is synthesized earlier in sporulation than is sigma 29. It has a peptide profile that is similar to sigma 29 and is present in all Bacillus subtilis Spo- mutants that were tested and found to still be able to accumulate sigma 29.

Antibodies, Monoclonal↗

PubMed2006

A comprehensive structure-function map of the intracellular surface of the human C5a receptor. II. Elucidation of G protein specificity determinants.

Within any given cell many G protein-coupled receptors are expressed in the presence of multiple G proteins, yet most receptors couple to a specific subset of G proteins to elicit their programmed response. Numerous studies demonstrate that the carboxyl-terminal five amino acids of the Galpha subunits are a major determinant of specificity, however the receptor determinants of specificity are less clear. We have used a collection of 133 functional mutants of the C5a receptor obtained in a mutagenesis screen targeting the intracellular loops and the carboxyl terminus (Matsumoto, M. L., Narzinski, K., Kiser, P. D., Nikiforovich, G. V., and Baranski, T. J. (2007) J. Biol. Chem. 282, 3105-3121) to investigate how specificity is encoded. Each mutant, originally selected for its ability to signal through a nearly full-length Galpha(i) in yeast, was tested to see whether it could activate three versions of chimeric Galpha subunits consisting of Gpa1 fused to the carboxyl-terminal five amino acids of Galpha(i), Galpha(q), or Galpha(s) in yeast. Surprisingly the carboxyl-terminal tail of the C5a receptor is the most important specificity determinant in that nearly all mutants in this region showed a gain in coupling to Galpha(q) and/or Galpha(s). More than half of the receptors mutated in the second intracellular loop also demonstrated broadened G protein coupling. Given a lack of selective advantage for this broadened signaling in the initial screen, we propose a model in which the carboxyl-terminal tail acts together with the intracellular loops to generate a specificity filter for receptor-G protein interactions that functions primarily to restrict access of incorrect G proteins to the receptor.

Amino Acid Sequence↗

PubMed1977

Lipoxygenic micromethod for specific determination of lipase activity in serum and duodenal fluid.

We propose a rapid enzymatic micromethod for the specific determination of lipase (EC 3.1.1.3) activity in serum and duodenal fluid. Free linoleic acid produced during 10-min incubation of 10 mul of sample with 1 ml of substrate (trillinolein emulsion) at 30 degrees C is converted by lipoxygenase (EC 1.99.2.1), in a coupled reaction, to its hydroperoxide, which is measured photometrically after solubilizing the reaction mixture in ethanol. Lipase activity is calculated from the rate of hydroperoxide formation, with linoleic acid as primary standard. The velocity of the reaction is greatest at pH 8.8, 35-37 degrees C, and a deoxycholate concentration of 3.6 mmol/liter. The energy of activation is 6.7 kcal/mol. The differing "apparent" Km values obtained for lipase in undiluted serum (4 X 10(-5) mol/liter) and in albumin-based diluents (1 X 10(-5) mol/liter) indicate the presence of a competitive inhibitor in the serum matrix. We detected no lipase activity in urine. Results by the proposed method correlate well with those by a copper soap extraction method (r = 0.95), but values are significantly higher for pancreatitis patients' sera (slope 1.6). The linear dynamic range extends to 1000 U/liter. Hemolysis, lipemia, and hyperbilirubinemia do not interfere. The normal range is 40-60 U/liter. Lipase activity of pancreatitis patients generally exceed 1000 U/liter during the acute phase and 250 U/liter for as long as 10 days after it.

Amylases↗