Dataset Information

Nucleophile activation in PD...(D/E)xK metallonucleases: an experimental and computational pK(a) study.

ABSTRACT: 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.

SUBMITTER: Xie F

PROVIDER: S-EPMC2913505 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Nucleophile activation in PD...(D/E)xK metallonucleases: an experimental and computational pK(a) study.

Xie Fuqian F Briggs James M JM Dupureur Cynthia M CM

Journal of inorganic biochemistry 20100306 6

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 ...[more]

PMID: 20347155

Similar Datasets

Project description:BACKGROUND:Coronary heart disease (CHD) is a common cardiovascular disease accounting for 10-20% mortality by heart disease worldwide. The gold standard treatment to manage CHD is aspirin, which may prevent myocardial infarction and sudden death; however, long-term use of aspirin may increase its side effects. Currently, more and more clinicians are exploring different approaches to use the right combination of medicine to enhance the efficacy and reduce side effects. Salvianolate can significantly inhibit the aggregation and activation of platelets in patients with CHD; however, its optimum combination with western medicine is not established or supported by clinical trial results. METHODS/DESIGN:This trial is a prospectively planned, open-labeled, parallel-grouped, single-centered clinical trial with aggregated pharmacodynamics-pharmacokinetics (PK-PD) data. All treatment courses will last for 10 days and blood sample will be acquired before administration on days 8, 9, and 10, and after administration at 5 min, 15 min, 30 min, 45 min, 1 h, 2 h, 4 h, 8 h, 12 h, and 24 h on day 10. This trial uses PK-PD modeling to provide a description of the concentration-effect relationship and an estimate of pharmacological potency of the medicine. The primary outcome will be changes in aspirin esterase and catechol-o-methyltransferase (COMT) activity at different blood concentrations to determine the PK-PD characteristics of the combination of salvianolate and aspirin, followed by analysis of the correlation between exposure level and pharmacodynamic index of the medicines. DISCUSSION:This trial will aim to evaluate the relationship between changes in the pharmacokinetics and therapeutic effect index in the combined use of salvianolate and aspirin. It also discusses the possible mechanism of medicine combination in the treatment for CHD and provides an experimental basis for a clinically rational medicine combination. TRIAL REGISTRATION:ClinicalTrials.gov, NCT03306550 . Registered on 9 October 2017. ClinicalTrials.gov https://register.clinicaltrials.gov/prs/app/action/SelectProtocol?sid=S0007D8H&selectaction=Edit&uid=U0003QY8&ts=2&cx=oiuc9g.

Project description:Inter- and intramolecular C-H bond activations by thorium metallacyclopropene complexes were comprehensively studied. The reduction of [?5-1,2,4-(Me3C)3C5H2]2ThCl2 (1) with potassium graphite (KC8) in the presence of internal alkynes (PhC 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 CR) yields the corresponding thorium metallacyclopropenes [?5-1,2,4-(Me3C)3C5H2]2Th(?2-C2Ph(R)) (R = Ph (2), Me (3), iPr (4), C6H11 (5)). Complexes 3-5 derived from phenyl(alkyl)acetylenes are very reactive resulting in an intramolecular C-H bond activation of the 1,2,4-(Me3C)3C5H2 ligand. In contrast, no intramolecular C-H bond activation is observed for the diphenylacetylene derived complex 2, but it does activate ?-C-H bonds in pyridine or carbonyl derivatives upon coordination. Density functional theory (DFT) studies complement the experimental studies and provide additional insights into the observed reactivity.

Dataset Information

Nucleophile activation in PD...(D/E)xK metallonucleases: an experimental and computational pK(a) study.

Publications

Nucleophile activation in PD...(D/E)xK metallonucleases: an experimental and computational pK(a) study.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure