Alkylation of cysteinyl residues of pig heart NAD-specific isocitrate dehydrogenase by iodoacetate

Mauck, Linda; Colman, Roberta F.

doi:10.1016/0005-2744(76)90278-3

Cited by 12 publications

(14 citation statements)

References 23 publications

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“…same pH) (Mauck & Colman, 1976), but is much more specific. With 16% residual activity, 2.8 mol of [14C]acetate/subunit is incorporated as a result of reaction with iodoacetate (Mauck & Colman, 1976).…”

Section: Discussionmentioning

confidence: 95%

“…EC 1.1.1.41] by chemical modification. By the use of a variety of "group-specific" reagents, several amino acid residues have been determined to be critical to the function of isocitrate dehydrogenase: lysyl (Shen & Colman, 1975;Hayman & Colman, 1977), cysteinyl (Mauck & Colman, 1976), argininyl (Hayman & Colman, 1978), and glutamyl or aspartyl residues (Ramachandran & Colman, 1977).…”

mentioning

confidence: 99%

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3-Bromo-2-ketoglutarate: a substrate and affinity label for DPN-dependent isocitrate dehydrogenase

Bednar¹,

Hartman²,

Colman³

1982

Biochemistry

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Section: Discussionmentioning

confidence: 95%

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confidence: 99%

3-Bromo-2-ketoglutarate: a substrate and affinity label for DPN-dependent isocitrate dehydrogenase

Bednar¹,

Hartman²,

Colman³

1982

Biochemistry

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“…Indirectly mentioned values like "... a value that is 50 times higher than the K M for this substrate." [27] will therefore not be recognized. However, we are not aware of an algorithm that is capable of gathering such numerical values from sentences.…”

Section: Discussionmentioning

confidence: 99%

KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes

2010

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BackgroundThe amount of available biological information is rapidly increasing and the focus of biological research has moved from single components to networks and even larger projects aiming at the analysis, modelling and simulation of biological networks as well as large scale comparison of cellular properties. It is therefore essential that biological knowledge is easily accessible. However, most information is contained in the written literature in an unstructured way, so that methods for the systematic extraction of knowledge directly from the primary literature have to be deployed.DescriptionHere we present a text mining algorithm for the extraction of kinetic information such as KM, Ki, kcat etc. as well as associated information such as enzyme names, EC numbers, ligands, organisms, localisations, pH and temperatures. Using this rule- and dictionary-based approach, it was possible to extract 514,394 kinetic parameters of 13 categories (KM, Ki, kcat, kcat/KM, Vmax, IC50, S0.5, Kd, Ka, t1/2, pI, nH, specific activity, Vmax/KM) from about 17 million PubMed abstracts and combine them with other data in the abstract.A manual verification of approx. 1,000 randomly chosen results yielded a recall between 51% and 84% and a precision ranging from 55% to 96%, depending of the category searched.The results were stored in a database and are available as "KID the KInetic Database" via the internet.ConclusionsThe presented algorithm delivers a considerable amount of information and therefore may aid to accelerate the research and the automated analysis required for today's systems biology approaches. The database obtained by analysing PubMed abstracts may be a valuable help in the field of chemical and biological kinetics. It is completely based upon text mining and therefore complements manually curated databases.The database is available at http://kid.tu-bs.de. The source code of the algorithm is provided under the GNU General Public Licence and available on request from the author.

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“…The BrKG-modified cysteine or its PTH derivative may either decompose under the acidic conditions encountered in the gas-phase sequencer or be insoluble in the solvents used so that it is not detected. The NAD+-specific isocitrate dehydrogenase of pig heart has previously been reported to be inactivated by reaction at pH 6.0 of iodoacetate with 1-2 cysteines/average peptide chain (Mauck & Colman, 1976). In that case also, the inactivation rate was markedly decreased by the combined addition of Mn2+ and isocitrate, but not by NAD+.…”

Section: Separation By Hplc Of [Hc\{carboxymethyl)cysteinementioning

confidence: 95%

“…However, in neither of these studies were the cysteine peptides identified. A critical cysteine of NAD+dependent isocitrate dehydrogenase, which is attacked by BrKG and has now been identified, was probably included among those modified in the earlier studies (Fan & Plaut, 1974;Mauck & Colman, 1976).…”

Section: Separation By Hplc Of [Hc\{carboxymethyl)cysteinementioning

confidence: 96%

Cysteinyl peptide labeled by 3-bromo-2-ketoglutarate in the active site of pig heart NAD+-dependent isocitrate dehydrogenase

Saha

Huang²,

Colman³

1989

Biochemistry

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The substrate affinity label 3-bromo-2-ketoglutarate (BrKG) reacts covalently with pig heart NAD+-specific isocitrate dehydrogenase with complete inactivation and incorporation of about 0.8 mol of reagent/mol of average enzyme subunit [Bednar, R.A., Hartman, F.C., & Colman, R.F. (1982) Biochemistry 21, 3681-3689]. Protection against inactivation is provided by isocitrate and Mn2+. We have now identified a critical modified peptide by comparison of the peptides labeled by BrKG at pH 6.1 in the absence and presence of isocitrate and Mn2+. Modified enzyme, isolated from unreacted BrKG, was incubated with [3H]NaBH4 to reduce the keto group of protein-bound 2-ketoglutarate and thereby introduce a radioactive tracer into the modified amino acid. Following carboxymethylation and digestion with trypsin, the specific modified peptide was isolated by reverse-phase HPLC, first in 0.1% trifluoroacetic acid with a gradient in acetonitrile and then in 20 mM ammonium acetate, pH 5.8, with an acetonitrile gradient. Gas-phase sequencing gave the modified peptide: Ser-Ala-X-Val-Pro-Val-Asp-Phe-Glu-Glu-Val-Val-Val-Ser-Ser-Asn-Ala-Asp-Gl u-Glu- Asp-Ile-Arg. The corresponding tryptic peptide that was isolated from unmodified enzyme yielded the same sequence except for (carboxymethyl)cysteine at position 3, suggesting that cysteine is the target of 3-bromo-2-ketoglutarate. Pig heart NAD+-dependent isocitrate dehydrogenase is composed of three distinct subunits (alpha, beta, and gamma) that can be separated by chromatofocusing in urea and identified by analytical gel isoelectric focusing. The peptide modified by 3-bromo-2-ketoglutarate, which is in or near the substrate site, is derived only from the separated gamma subunit.(ABSTRACT TRUNCATED AT 250 WORDS)

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Alkylation of cysteinyl residues of pig heart NAD-specific isocitrate dehydrogenase by iodoacetate

Cited by 12 publications

References 23 publications

3-Bromo-2-ketoglutarate: a substrate and affinity label for DPN-dependent isocitrate dehydrogenase

3-Bromo-2-ketoglutarate: a substrate and affinity label for DPN-dependent isocitrate dehydrogenase

KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes

Cysteinyl peptide labeled by 3-bromo-2-ketoglutarate in the active site of pig heart NAD+-dependent isocitrate dehydrogenase

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