MacProMass: A computer program to correlate mass spectral data to peptide and protein structures

Lee, Terry D.; Vemuri, Sunil

doi:10.1002/bms.1200191103

Cited by 46 publications

(13 citation statements)

References 10 publications

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“…Calculation of molecular mass from the series of multiply charged ions found in the protein was achieved with the MacSpec TM computer program (version 3.3, PE Sciex, Ontario, Canada). Calculation of theoretical protein average (chemical) molecular mass was achieved with the MacBiospec TM computer program (version 1.0.1, PE Sciex) based on the MacProMAss computer program of Lee and Vermuri (35).…”

Section: Methodsmentioning

confidence: 99%

Cloning and Characterization of a New Member of the Nudix Hydrolases from Human and Mouse

Yang

Slupska

Yue

et al. 2000

Journal of Biological Chemistry

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Proteins containing the Nudix box "GX 5 EX 7 REUXE-EXGU" (where U is usually Leu, Val, or Ile) are Nudix hydrolases, which catalyze the hydrolysis of a variety of nucleoside diphosphate derivatives. Here we report cloning and characterization of a human cDNA encoding a novel nudix hydrolase NUDT5 for the hydrolysis of ADP-sugars. The deduced amino acid sequence of NUDT5 contains 219 amino acids, including a conserved Nudix box sequence. The recombinant NUDT5 was expressed in Escherichia coli and purified to near homogeneity. At the optimal pH of 7, the purified recombinant NUDT5 catalyzed hydrolysis of two major substrates ADP-ribose and ADP-mannose with K m values of 32 and 83 M, respectively; the V max for ADP-mannose was about 1.5 times that with ADP-ribose. The murine NUDT5 homolog was also cloned and characterized. mNudT5 has 81% amino acid identity to NUDT5 with catalytic activities similar to NUDT5 under the optimal pH of 9. Both NUDT5 and mNudT5 transcripts were ubiquitously expressed in tissues analyzed with preferential abundance in liver. The genomic structures of both NUDT5 and mNudT5 were determined and located on human chromosome 10 and mouse chromosome 2, respectively. The role of NUDT5 in maintaining levels of free ADP-ribose in cells is discussed.

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Section: Methodsmentioning

confidence: 99%

Cloning and Characterization of a New Member of the Nudix Hydrolases from Human and Mouse

Yang

Slupska

Yue

et al. 2000

Journal of Biological Chemistry

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“…Full-scan mass spectra were recorded at mass-to-charge ratios (m/z) of from 50 to 1,999. To correlate mass spectral data to the peptide sequence, the computer program MacProMass (version 1.05) was used (22).…”

Section: Methodsmentioning

confidence: 99%

The extracellular PI-type proteinase of Lactococcus lactis hydrolyzes beta-casein into more than one hundred different oligopeptides

et al. 1995

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The peptides released from ␤-casein by the action of P I -type proteinase (PrtP) from Lactococcus lactis subsp. cremoris Wg2 have been identified by on-line coupling of liquid chromatography to mass spectrometry. After 24 h of incubation of ␤-casein with purified PrtP, a stable mixture of peptides was obtained. The trifluoroacetic acid-soluble peptides of this ␤-casein hydrolysate were fractionated by high-performance liquid chromatography and introduced into the liquid chromatography-ion spray mass spectrometry interface. Multiply charged ions were generated from trifluoroacetic acid-soluble peptides under low nozzle voltage conditions, yielding the MH ؉ mass of each eluted peptide. All peptides corresponding to each of the MH ؉ calculated masses were determined. In those cases in which different peptides were possible, further identification was achieved by collision-induced dissociation under higher nozzle voltage conditions. Hydrolysis of ␤-casein by PrtP was observed to proceed much further than reported previously. More than 40% of the peptide bonds are cleaved by PrtP, resulting in the formation of more than 100 different oligopeptides. With the exception of Phe, significant release of amino acids or di-and tripeptides could not be observed. Interestingly, one-fifth of the identified oligopeptides are small enough to be taken up by the oligopeptide transport system. Uptake of these peptides could supply L. lactis with all amino acids, including the essential ones, indicating that growth of L. lactis might be possible on peptides released from ␤-casein by proteinase only.Lactococci have very limited capacities of synthesizing amino acids and therefore must utilize exogenous nitrogen sources for optimal growth. The amino acid requirement is strain dependent, but Glu or Gln, Ile, Leu, His, Met, and Val are essential for the growth of most Lactococcus lactis strains (6). The addition of several other amino acids was found to be growth stimulatory (34,25). The concentrations of essential amino acids in milk are very low, especially those of Ile and Leu (less than 1 mg/liter) (27). Moreover, the concentrations of other free amino acids are too low to explain the growth of L. lactis to the cell densities normally reached in coagulated milk (27,44). Thus, for optimal growth in milk, lactococci depend on the utilization of milk proteins, such as caseins. Casein hydrolysis by lactococci is mediated by a complex proteolytic system which includes a cell envelope-located proteinase (P I -or P III -type proteinase [PrtP]) and several peptidases (for recent reviews, see references 31, 32, and 42).According to proposed models, PrtP is involved in the first step of casein degradation (32, 39). The action of purified PrtP on ␤-casein has been studied extensively (28,29,33,46,47). After separation of the proteolytic products by reverse-phase high-performance liquid chromatography (HPLC), the different peptides are collected, purified when needed, and identified by biochemical methods (i.e., amino acid composition, determina...

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“…DNA sequences were submitted to the National Center for Biotechnology Information for homology searches and comparisons with other sequences in GenBank. The molecular weights and pIs of deduced amino acid sequences were determined by using MacProMass computer software (18).…”

Section: Methodsmentioning

confidence: 99%

Purification, characterization, and genetic analysis of Mycobacterium tuberculosis urease, a potentially critical determinant of host-pathogen interaction

1995

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Mycobacterium tuberculosis urease (urea amidohydrolase [EC 3.5.1.5]) was purified and shown to contain three subunits: two small subunits, each approximately 11,000 Da, and a large subunit of 62,000 Da. The N-terminal sequences of the three subunits were homologous to those of the A, B, and C subunits, respectively, of other bacterial ureases. M. tuberculosis urease was specific for urea, with a K m of 0.3 mM, and did not hydrolyze thiourea, hydroxyurea, arginine, or asparagine. The enzyme was active over a broad pH range (optimal activity at pH 7.2) and was remarkably stable against heating to 60؇C and resistant to denaturation with urea. The enzyme was not inhibited by 1 mM EDTA but was inhibited by N-ethylmaleimide, hydroxyurea, acetohydroxamate, and phenylphosphorodiamidate. Urease activity was readily detectable in M. tuberculosis growing in nitrogen-rich broth, but expression increased 10-fold upon nitrogen deprivation, which is consistent with a role for the enzyme in nitrogen acquisition by the bacterium. The gene cluster encoding urease was shown to have organizational similarities to urease gene clusters of other bacteria. The nucleotide sequence of the M. tuberculosis urease gene cluster revealed open reading frames corresponding to the urease A, B, and C subunits, as well as to the urease accessory molecules F and G.Tuberculosis is a global health problem of escalating proportions. Mycobacterium tuberculosis, the main etiologic agent of tuberculosis, is a facultative intracellular bacterial pathogen that parasitizes host mononuclear phagocytes. Throughout its life cycle within the mononuclear phagocyte, M. tuberculosis resides in a membrane-bound phagosome which is only mildly acidified (5) and which does not fuse with lysosomes (1, 4, 41). However, the mechanisms underlying these phenomena are unknown.Previous studies have demonstrated that NH 4 Cl added exogenously to mouse mononuclear phagocytes blocks phagosome-lysosome fusion (6) and promotes phagosome endosome fusion (8). Hence, ammonia production by intracellular M. tuberculosis may partly underlie the inhibition of phagosomelysosome fusion. M. tuberculosis is able to produce ammonia from urea by the action of urease, and thus this enzyme may play a role in phagosome-lysosome fusion inhibition. In addition, urease may modulate the pH of the phagosome and provide a source of nitrogen for biosynthesis. However, urease of M. tuberculosis has not been purified or characterized previously. To learn more about M. tuberculosis urease, we have purified and characterized the enzyme and cloned and sequenced the urease gene cluster. MATERIALS AND METHODSBiochemicals and chemicals. Bacillus pasteurii urease, jack bean urease, urea, ␣-ketoglutarate, NADPH, glutamate dehydrogenase, thiourea, hydryoxylurea, N-ethylmaleimide, and acetohydroxamate were obtained from Sigma Chemical Co. (St. Louis, Mo.). Phenylphosphorodiamidate was obtained from Lancaster Chemical Co. (Windham, N.H.). Q-Sepharose fast-flow, Superdex-75, and phenyl-Sepharose were purchased from ...

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MacProMass: A computer program to correlate mass spectral data to peptide and protein structures

Cited by 46 publications

References 10 publications

Cloning and Characterization of a New Member of the Nudix Hydrolases from Human and Mouse

Cloning and Characterization of a New Member of the Nudix Hydrolases from Human and Mouse

The extracellular PI-type proteinase of Lactococcus lactis hydrolyzes beta-casein into more than one hundred different oligopeptides

Purification, characterization, and genetic analysis of Mycobacterium tuberculosis urease, a potentially critical determinant of host-pathogen interaction

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