pKa calculations for class C ?-lactamases: The role of tyr-150

Lamotte‐Brasseur, Josette; Dubus, Alain; Wade, Rebecca C.

doi:10.1002/(sici)1097-0134(20000701)40:1<23::aid-prot40>3.0.co;2-7

Cited by 40 publications

(36 citation statements)

References 30 publications

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“…Tyrosines with abnormally low pKa values are involved directly or indirectly in the catalytic activity of a number of enzymes including glutathione S-transferase [38], asparaginase [39], beta-lactamases [40], and albumin [41]. A lysine at the active center of acetoacetate decarboxylase was implicated in a 3.7 unit decrease in the pKa of a phenolic reporter group [42].…”

Section: Resultsmentioning

confidence: 99%

Mass spectral characterization of organophosphate-labeled, tyrosine-containing peptides: Characteristic mass fragments and a new binding motif for organophosphates

Schopfer

Grigoryan

et al. 2010

Journal of Chromatography B

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We have identified organophosphorus agent (OP)-tyrosine adducts on 12 different proteins labeled with 6 different OP. Labeling was achieved by treating pure proteins with up to 40-fold molar excess of OP at pH 8-8.6. OP-treated proteins were digested with trypsin, and peptides were separated by HPLC. Fragmentation patterns for 100 OP-peptides labeled on tyrosine were determined in the mass spectrometer. The goals of the present work were 1) to determine the common features of the OP-reactive tyrosines, and 2) to describe non-sequence MSMS fragments characteristic of OP-tyrosine peptides. Characteristic ions at 272 amu and 244 amu for tyrosine-OP immonium ions were nearly always present in the MSMS spectrum of peptides labeled on tyrosine by chlorpyrifos oxon. Characteristic fragments also appeared from the parent ions that had been labeled with diisopropylfluorophosphate (216 amu), sarin (214 amu), soman (214 amu) or 312, 329, 691 and 708 amu). In contrast to OP-reactive serines, which lie in the consensus sequence GXSXG, the OP-reactive tyrosines have no consensus sequence. Their common feature is the presence of nearby positively charged residues that activate the phenolic hydroxyl group. The significance of these findings is the recognition of a new binding motif for OP to proteins that have no active site serine. Modified peptides are difficult to find when the OP bears no radiolabel and no tag. The characteristic MSMS fragment ions are valuable because they are identifiers for OP-tyrosine, independent of the peptide.

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Section: Resultsmentioning

confidence: 99%

Mass spectral characterization of organophosphate-labeled, tyrosine-containing peptides: Characteristic mass fragments and a new binding motif for organophosphates

Schopfer

Grigoryan

et al. 2010

Journal of Chromatography B

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“…This analysis provides apparent titration behavior for the ionizable groups involved in the cleavage reaction. This approach of comparing pK a prediction results with kinetic data has literature precedent [20, 43, 44]. For a couple of related metallonucleases, one limb of the profile has been assigned to the attacking water molecule [8, 37].…”

Section: Resultsmentioning

confidence: 99%

Nucleophile activation in PD…(D/E)xK metallonucleases: An experimental and computational pKa study

Xie

Briggs

Dupureur

2010

Journal of Inorganic Biochemistry

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Metallonucleases conduct metal dependent nucleic acid hydrolysis. While metal ions serve in multiple mechanistic capacities in these enzymes, precisely how the attacking water is activated remains unclear for those lacking an obvious general base. All arguments hinge on appropriate pK a 's for active site moieties very close to this species, and measurement of the pK a of a specific water molecule is difficult to access experimentally. Here we describe a computational approach for exploring the local electrostatic influences on the water-derived nucleophile in metallonucleases featuring the common PD…(D/E)xK motif. We utilized UHBD to predict the pK a 's of active site groups, including that of a water molecule positioned to act as a nucleophile. The pK a of a Mg(II)-ligated water molecule hydrogen bonded to the conserved Lys70 in a Mg(II)-PvuII enzyme complex was calculated to be 6.5. The metal and the charge on the Lys group were removed in separate experiments; both resulted in the elevation of the pK a of this water molecule, consistent with contributions from both moieties to lowering this pK a . This behavior is preserved among other PD…(D/E)xK metallonucleases. pK a 's extracted from the pH dependence of the single turnover rate constant are compared to previous experimental data and the above predicted pK a 's.

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“…The first important step in determining a number of properties for a protein, such as its solubility, catalytic function, binding and folding behavior, is determining the p K a values of ionizable residues 1, 2. There are a wide variety of programs available for predicting p K a s, and a number of studies have been done benchmarking their results 3–5.…”

Section: Introductionmentioning

confidence: 99%

Weekly docetaxel versus docetaxel/gemcitabine in the treatment of elderly or poor performance status patients with advanced nonsmall cell lung cancer

Hainsworth

Spigel

Farley

et al. 2007

Cancer

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Objectives: The aims of this study were to investigate the long‐term clinical outcomes of patients with successful versus unsuccessful revascularization with drug‐eluting stents (DES) for chronic total occlusion (CTO). Background: The benefits of successful revascularization of CTO remain unclear. Methods: Consecutive patients (n = 333) with “true” CTO, defined as Thrombolysis In Myocardial Infarction (TIMI) flow grade 0 on angiography and duration ≥3 months, were divided into two groups, those with successful (CTO success group, n = 251) and unsuccessful (CTO failure group, n = 82) revascularization with DES for CTO lesions. The primary endpoint was defined as major adverse cardiac events (MACE) the composite of death, Q‐wave myocardial infarction (MI), or target vessel revascularization (TVR). Results: The CTO success group was significantly younger, with a higher involvement of LAD, and lower incidences of renal failure, previous myocardial infarction, and previous coronary intervention than the CTO failure group. After a median follow up of 1,317 days (interquartile range, 1,059–1,590 days), there were no significant between‐group differences in rate of MACE, both after crude analysis (9.4% vs. 11.8%, log‐rank P = 0.16) and after adjustment (HR 1.17; 95% CI 0.47–2.88, P = 0.53). On multivariate analysis, major predictors of MACE were left ventricle ejection fraction (LVEF) <40% (HR 3.14; 95% CI 1.39–7.09, P = 0.005) and multiple CTO (HR 2.38; 95% CI 1.01–5.71, P = 0.049). Conclusions: Long‐term clinical outcomes were similar in the CTO success and failure groups. Multiple CTOs and LVEF <40% in CTO patients were independent predictors of MACE. © 2011 Wiley‐Liss, Inc.

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pKa calculations for class C ?-lactamases: The role of tyr-150

Cited by 40 publications

References 30 publications

Mass spectral characterization of organophosphate-labeled, tyrosine-containing peptides: Characteristic mass fragments and a new binding motif for organophosphates

Mass spectral characterization of organophosphate-labeled, tyrosine-containing peptides: Characteristic mass fragments and a new binding motif for organophosphates

Nucleophile activation in PD…(D/E)xK metallonucleases: An experimental and computational pKa study

Weekly docetaxel versus docetaxel/gemcitabine in the treatment of elderly or poor performance status patients with advanced nonsmall cell lung cancer

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