Browse
Submit Data
Databases
API
Help

Dataset Information

5 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction.

ABSTRACT: DNA synthesis by polymerases is essential for life. Deprotonation of the nucleophile 3'-OH is thought to be the obligatory first step in the DNA synthesis reaction. We have examined each entity surrounding the nucleophile 3'-OH in the reaction catalyzed by human DNA polymerase (Pol) η and delineated the deprotonation process by combining mutagenesis with steady-state kinetics, high-resolution structures of in crystallo reactions, and molecular dynamics simulations. The conserved S113 residue, which forms a hydrogen bond with the primer 3'-OH in the ground state, stabilizes the primer end in the active site. Mutation of S113 to alanine destabilizes primer binding and reduces the catalytic efficiency. Displacement of a water molecule that is hydrogen bonded to the 3'-OH using the 2'-OH of a ribonucleotide or 2'-F has little effect on catalysis. Moreover, combining the S113A mutation with 2'-F replacement, which removes two potential hydrogen acceptors of the 3'-OH, does not reduce the catalytic efficiency. We conclude that the proton can leave the O3' via alternative paths, supporting the hypothesis that binding of the third Mg²⁺ initiates the reaction by breaking the α-β phosphodiester bond of an incoming deoxyribonucleoside triphosphate (dNTP).

SUBMITTER: Gregory MT

PROVIDER: S-EPMC8201771 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State.

Project description:Steric constraints imposed by the active sites of protein and RNA enzymes pose major challenges to the investigation of structure-function relationships within these systems. As a strategy to circumvent such constraints in the HDV ribozyme, we have synthesized phosphoramidites from propanediol derivatives and incorporated them at the 5'-termini of RNA and DNA oligonucleotides to generate a series of novel substrates with nucleophiles perturbed electronically through geminal fluorination. In nonenzymatic, hydroxide-catalyzed intramolecular transphosphorylation of the DNA substrates, pH-rate profiles revealed that fluorine substitution reduces the maximal rate and the kinetic p Ka, consistent with the expected electron-withdrawing effect. In HDV ribozyme reactions, we observed that the RNA substrates undergo transphosphorylation relatively efficiently, suggesting that the conformational constraints imposed by a ribofuranose ring are not strictly required for ribozyme catalysis. In contrast to the nonenzymatic reactions, however, substrate fluorination modestly increases the ribozyme reaction rate, consistent with a mechanism in which (1) the 2'-hydroxyl nucleophile exists predominantly in its neutral, protonated form in the ground state and (2) the 2'-hydroxyl bears some negative charge in the rate-determining step, consistent with a transition state in which the extent of 2'-OH deprotonation exceeds the extent of P-O bond formation.

| S-EPMC6693346 | biostudies-literature

Stereoselective RNA Reaction with Chiral 2'-OH Acylating Agents

Project description:The reactivity of RNA 2'-OH groups with acylating agents has recently been investigated for high-yield conjugation of RNA strands. To date, only achiral molecules have been studied for this reaction, despite the complex chiral structure of RNA. Here we prepare a set of chiral acylimidazoles and study their stereoselectivity in RNA reactions. Reactions performed with unfolded and folded RNAs reveal that positional selectivity and reactivity vary widely with local RNA macro-chirality. We further document remarkable effects of chirality on reagent reactivity, identifying an asymmetric reagent with 1000-fold greater reactivity than prior achiral reagents. In addition, we identify a chiral compound with higher RNA structural selectivity than any previously reported RNA-mapping species. Further, azide-containing homologs of a chiral dimethylalanine reagent were synthesized and applied to local RNA labeling, displaying 92% yield and 16:1 diastereoselectivity. The results establish that reagent stereochemistry and chiral RNA structure are critical elements of small molecule-RNA reactions, and demonstrate new chemical strategies for selective RNA modification and probing.

2023-11-14 | GSE247565 | GEO

Reaction coordinates and rates from transition paths.

Project description:The molecular mechanism of a reaction in solution is reflected in its transition-state ensemble and transition paths. We use a Bayesian formula relating the equilibrium and transition-path ensembles to identify transition states, rank reaction coordinates, and estimate rate coefficients. We also introduce a variational procedure to optimize reaction coordinates. The theory is illustrated with applications to protein folding and the dipole reorientation of an ordered water chain inside a carbon nanotube. To describe the folding of a simple model of a three-helix bundle protein, we variationally optimize the weights of a projection onto the matrix of native and nonnative amino acid contacts. The resulting one-dimensional reaction coordinate captures the folding transition state, with formation and packing of helix 2 and 3 constituting the bottleneck for folding.

| S-EPMC1100744 | biostudies-literature

Optimizing reaction paths for methanol synthesis from CO<sub>2</sub> hydrogenation via metal-ligand cooperativity.

Project description:As diversified reaction paths exist over practical catalysts towards CO2 hydrogenation, it is highly desiderated to precisely control the reaction path for developing efficient catalysts. Herein, we report that the ensemble of Pt single atoms coordinated with oxygen atoms in MIL-101 (Pt1@MIL) induces distinct reaction path to improve selective hydrogenation of CO2 into methanol. Pt1@MIL achieves the turnover frequency number of 117 h-1 in DMF under 32 bar at 150 °C, which is 5.6 times that of Ptn@MIL. Moreover, the selectivity for methanol is 90.3% over Pt1@MIL, much higher than that (13.3%) over Ptn@MIL with CO as the major product. According to mechanistic studies, CO2 is hydrogenated into HCOO* as the intermediate for Pt1@MIL, whereas COOH* serves as the intermediate for Ptn@MIL. The unique reaction path over Pt1@MIL not only lowers the activation energy for the enhanced catalytic activity, but also contributes to the high selectivity for methanol.

| S-EPMC6478740 | biostudies-literature

Synthesis of Ni3Si4O10(OH)2 Porous Microspheres as Support of Pd Catalyst for Hydrogenation Reaction.

Project description:Nickel phyllosilicates have attracted much attention owing to their potential applications in various fields. Herein, Ni3Si4O10(OH)2 porous microspheres (NiSi-PMs) with a diameter of 1.2 to 3.2 μm were successfully fabricated via a urea-assisted hydrothermal method, and subsequently used to prepare supported Pd catalyst. Characterizations of the NiSi-PMs and the obtained catalyst, combined with the catalytic performance for the hydrogenation reaction, are presented and discussed. The BET surface area and pore volume of the NiSi-PMs were 196.2 m2 g-1 and 0.70 cm3 g-1, respectively. The Pd/NiSi-PMs catalyst exhibited remarkable catalytic activity for the hydrogenation of styrene under mild conditions, with a turnover frequency of 5234 h-1, and the catalyst was recovered and recycled for six consecutive cycles without any discernible loss of activity. H2-TPR and H2-TPD revealed that the activity of the catalysts was closely related to the adsorption property for hydrogen. The present Ni3Si4O10(OH)2 supported Pd catalyst afforded a promising and competitive candidate for heterogeneous catalysis.

| S-EPMC6669689 | biostudies-literature

Tyrosine deprotonation and associated hydrogen bond rearrangements in a photosynthetic reaction center.

Project description:Photosynthetic reaction centers from Blastochloris viridis possess Tyr-L162 located mid-way between the special pair chlorophyll (P) and the heme (heme3). While mutation of the tyrosine does not affect the kinetics of electron transfer from heme3 to P, recent time-resolved Laue diffraction studies reported displacement of Tyr-L162 in response to the formation of the photo-oxidized P(+•), implying a possible tyrosine deprotonation event. pK(a) values for Tyr-L162 were calculated using the corresponding crystal structures. Movement of deprotonated Tyr-L162 toward Thr-M185 was observed in P(+•) formation. It was associated with rearrangement of the H-bond network that proceeds to P via Thr-M185 and His-L168.

| S-EPMC3200362 | biostudies-literature

New Insights into the Reaction Paths of Hydroxyl Radicals with Purine Moieties in DNA and Double-Stranded Oligodeoxynucleotides.

Project description:The reaction of hydroxyl radical (HO•) with DNA produces many primary reactive species and many lesions as final products. In this study, we have examined the optical spectra of intermediate species derived from the reaction of HO• with a variety of single- and double-stranded oligodeoxynucleotides and ct-DNA in the range of 1 ?s to 1 ms by pulse radiolysis using an Intensified Charged Coupled Device (ICCD) camera. Moreover, we applied our published analytical protocol based on an LC-MS/MS system with isotopomeric internal standards to enable accurate and precise measurements of purine lesion formation. In particular, the simultaneous measurement of the four purine 5',8-cyclo-2'-deoxynucleosides (cPu) and two 8-oxo-7,8-dihydro-2'-deoxypurine (8-oxo-Pu) was obtained upon reaction of genetic material with HO• radicals generated either by ?-radiolysis or Fenton-type reactions. Our results contributed to the debate in the literature regarding absolute level of lesions, method of HO• radical generation, 5'R/5'S diastereomeric ratio in cPu, and relative abundance between cPu and 8-oxo-Pu.

| S-EPMC6865195 | biostudies-literature

Multiple paths to cold tolerance

Project description:Multiple paths to cold tolerance: the role of environmental cues, morphological traits and the circadian clock gene vrille

| PRJEB45370 | ENA

A nucleophile-catalyzed cycloisomerization permits a concise synthesis of (+)-harziphilone.

Project description:Substantial structural transformations of much use in complex chemical synthesis can be achieved by channeling the reactivity of highly unsaturated molecules. This report describes the direct conversion of an acyclic polyunsaturated diketone to the HIV-1 Rev/Rev-responsive element inhibitor harziphilone under mild reaction conditions.

| S-EPMC514435 | biostudies-literature

Efficient prediction of reaction paths through molecular graph and reaction network analysis.

Project description:Despite remarkable advances in computational chemistry, prediction of reaction mechanisms is still challenging, because investigating all possible reaction pathways is computationally prohibitive due to the high complexity of chemical space. A feasible strategy for efficient prediction is to utilize chemical heuristics. Here, we propose a novel approach to rapidly search reaction paths in a fully automated fashion by combining chemical theory and heuristics. A key idea of our method is to extract a minimal reaction network composed of only favorable reaction pathways from the complex chemical space through molecular graph and reaction network analysis. This can be done very efficiently by exploring the routes connecting reactants and products with minimum dissociation and formation of bonds. Finally, the resulting minimal network is subjected to quantum chemical calculations to determine kinetically the most favorable reaction path at the predictable accuracy. As example studies, our method was able to successfully find the accepted mechanisms of Claisen ester condensation and cobalt-catalyzed hydroformylation reactions.

| S-EPMC5887236 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data