Computer program for calculation of kinetic and pharmacologic parameters using a ‘direct linear plot’ derived algorithm

Kamiński, Zbigniew; Domino, Edward F.

doi:10.1016/0169-2607(87)90064-2

Cited by 10 publications

(9 citation statements)

References 10 publications

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“…DNA was precipitated and liberated bases measured as above. Kinetic constants were calculated using a program based on the Eisenthall-Cornish-Bowden nonparametric algorithm (Kamiński & Domino, 1987). The K i value was calculated from replots of ordinate and abscissa intercepts.…”

Section: Estimation Of K I For Fpg Glycosylase Activity Inhibition Bymentioning

confidence: 99%

Inhibition of DNA repair glycosylases by base analogs and tryptophan pyrolysate, Trp-P-1.

Speina

Cieśla²,

Gra̧ziewicz³

et al. 2005

Acta Biochim Pol

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DNA base analogs, 2,4,5,6-substituted pyrimidines and 2,6-substituted purines were tested as potential inhibitors of E. coli Fpg protein (formamidopyrimidine -DNA glycosylase). Three of the seventeen compounds tested revealed inhibitory properties. 2-Thioxanthine was the most efficient, inhibiting 50% of 2,6-diamino-4-hydroxy-5N-methyl-formamidopyrimidine (Fapy-7MeG) excision activity at 17.1 mM concentration. The measured K i was 4.44 ± 0.15 mM. Inhibition was observed only when the Fpg protein was first challenged to its substrate followed by the addition of the base analog, suggesting uncompetitive (catalytic) inhibition. For two other com-Vol. 52 No. 1/2005 167-178 QUARTERLY . ; [ 3 H]MNU-DNA, DNA alkylated with [ 3 H]methylnitrosourea; 8-oxoG, 8-oxoguanine; Trp-P-1, 3-amino-1,4-dimethyl-5H-pyrido[4,3-b]indole. pounds, 2-thio-or 2-oxo-4,5,6-substituted pyrimidines, IC 50 was only 343.3 ± 58.6 and 350 ± 24.4 mM, respectively. No change of the Fpg glycosylase activity was detected in the presence of Fapy-7MeG, up to 5 mM. We also investigated the effect of DNA structure modified by tryptophan pyrolysate (Trp-P-1) on the activity of base excision repair enzymes: Escherichia coli and human DNA glycosylases of oxidized (Fpg, Nth) and alkylated bases (TagA, AlkA, and ANPG), and for bacterial AP endonuclease (Xth protein). Trp-P-1, which changes the secondary DNA structure into non-B, non-Z most efficiently inhibited excision of alkylated bases by the AlkA glycosylase (IC 50 = 1 mM). The ANPG, TagA, and Fpg proteins were also inhibited although to a lesser extent (IC 50 = 76.5 mM, 96 mM, and 187.5 mM, respectively). Trp-P-1 also inhibited incision of DNA at abasic sites by the b-lyase activity of the Fpg and Nth proteins, and to a lesser extent by the Xth AP endonuclease. Thus, DNA conformation is critical for excision of damaged bases and incision of abasic sites by DNA repair enzymes.

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Section: Estimation Of K I For Fpg Glycosylase Activity Inhibition Bymentioning

confidence: 99%

Inhibition of DNA repair glycosylases by base analogs and tryptophan pyrolysate, Trp-P-1.

Speina

Cieśla²,

Gra̧ziewicz³

et al. 2005

Acta Biochim Pol

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“…For determination of kinetic parameters, the gel autoradiographs were scanned on an Ultroscan XL LKB Bromma Densitometer and band intensities were evaluated with the Gelscan XL Pharmacia Data System. The K m and V max values were calculated using the Eisenthal and Cornish-Bowden direct linear plot algorithm [24,25].…”

Section: Taq Polymerase Reactions and Determination Of Kinetic Paramementioning

confidence: 99%

Neighbouring bases in template influence base-pairing of isoguanine

Maciejewska

Lichota

Kuśmierek

2003

Biochemical Journal

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Assuming that the efficiency of the incorporation of 5-methyl-2h-deoxyisocytosine-5h triphosphate (dMiCTP) and dTTP opposite isoguanine (iG) is a measure of the proportion of the keto and enol tautomers of iG in the Thermus aquaticus DNA polymerase active centre, we studied the influence of temperature and iGneighbouring bases in the template on base-pairing of iG. On the basis of experiments with four sequences (3h-TXT-5h, 3h-GXG-5h, 3h-CXC-5h, 3h-CXT-5h, where X l iG) at 37, 50, 65 and 80 mC, we found that 3h-neighbours decrease the fraction of the keto tautomer in the order C G T, whereas temperature apparently does not influence the tautomeric equilibrium of iG. The variability of the ratio of incorporation of dMiCTP versus dTTP (5-20) primarily reflects the variability of K m values, since

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“…(29). V max and K m values were calculated by two methods: a program using the Eisenthall-Cornish-Bowden nonparametric algorithm (30) and direct fitting of the hyperbolic MichaelisMenten equation to the data points in Microcal Origin. Values obtained by both methods differed usually by no more than 3-6%.…”

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confidence: 99%

The Pyrimidine Ring-opened Derivative of 1,N 6-Ethenoadenine Is Excised from DNA by theEscherichia coli Fpg and Nth Proteins

Speina

Cieśla

Wójcik

et al. 2001

Journal of Biological Chemistry

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It was previously shown that 1,N 6 -ethenoadenine (⑀A) in DNA rearranges into a pyrimidine ring-opened derivative of 20-fold higher mutagenic potency in Escherichia coli (AB1157 lac⌬U169) than the parental ⑀A (Basu, A. K., Wood, M. L., Niedernhofer, L. J., Ramos, L. A., and Essigmann, J. M. (1993) Biochemistry 32, 12793-12801). We have found that at pH 7.0, the stability of the N-glycosidic bond in ⑀dA is 20-fold lower than in dA. In alkaline conditions, but also at neutrality, ⑀dA depurinates or converts into products: ⑀dA 3 B 3 C 3 D. Compound B is a product of water molecule addition to the C(2)-N(3) bond, which is in equilibrium with a product of N(1)-C(2) bond rupture in ⑀dA. Compound C is a deformylated derivative of ring-opened compound B, which further depurinates yielding compound D. Ethenoadenine degradation products are not recognized by human N-alkylpurine-DNA glycosylase, which repairs ⑀A. Product B is excised from oligodeoxynucleotides by E. coli formamidopyrimidine-DNA glycosylase (Fpg) and endonuclease III (Nth). Repair by the Fpg protein is as efficient as that of 7,8-dihydro-8-oxoguanine when the excised base is paired with dT and dC but is less favorable when paired with dG and dA. Ethenoadenine rearrangement products are formed in oligodeoxynucleotides also at neutral pH at the rate of about 2-3% per week at 37°C, and therefore they may contribute to ⑀A mutations.

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Computer program for calculation of kinetic and pharmacologic parameters using a ‘direct linear plot’ derived algorithm

Cited by 10 publications

References 10 publications

Inhibition of DNA repair glycosylases by base analogs and tryptophan pyrolysate, Trp-P-1.

Inhibition of DNA repair glycosylases by base analogs and tryptophan pyrolysate, Trp-P-1.

Neighbouring bases in template influence base-pairing of isoguanine

The Pyrimidine Ring-opened Derivative of 1,N 6-Ethenoadenine Is Excised from DNA by theEscherichia coli Fpg and Nth Proteins

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