scholarly journals Epoxidation and late-stage C-H functionalization by P450 TamI is mediated by variant heme-iron oxidizing species

2021 ◽  
Author(s):  
Rosa V. Espinoza ◽  
Mark A. Maskeri ◽  
Aneta Turlik ◽  
Anjanay Nangia ◽  
Yogan Khatri ◽  
...  
Keyword(s):  
Density Functional ◽  
Isotope Effects ◽  
Heme Iron ◽  
Site Directed Mutagenesis ◽  
Compound I ◽  
Iron Species ◽  
Epoxide Opening ◽  
Catalytically Active ◽  
Common Substrate ◽  
Solvent Isotope

P450-catalyzed hydroxylation reactions are well understood mechanistically including the identity of the active oxidizing species. However, the catalytically active heme-iron species in P450 iterative oxidation cascades that involve mechanistically divergent pathways and distinct carbon atoms within a common substrate remains unexplored. Recently, we reported the enzymatic synthesis of tri-functionalized tirandamycin O (9) and O’ (10) using a bacterial P450 TamI variant and developed mechanistic hypotheses to explore their formation. Here, we report the ability of bacterial P450 TamI L295A to shift between different oxidizing species as it catalyzes the sequential epoxidation, hydroxylation and radical-catalyzed epoxide-opening cascade to create new tirandamycin antibiotics. We also provide evidence that the TamI peroxo-iron species could be a viable catalyst to enable nucleophilic epoxide opening in the absence of iron-oxo Compound I. Using site-directed mutagenesis, kinetic solvent isotope effects, artificial oxygen surrogates, end-point assays, and density functional theory (DFT) calculations, we provide new insights into the active oxidant species that P450 TamI employs to introduce its unique pattern of oxidative decorations.

scholarly journals On the role of Brønsted catalysis in Pseudomonas fluorescens mannitol 2-dehydrogenase

2003 ◽  
Vol 375 (1) ◽  
pp. 141-149 ◽  
Author(s):  
Mario KLIMACEK ◽  
Kathryn L. KAVANAGH ◽  
David K. WILSON ◽  
Bernd NIDETZKY
Keyword(s):  
Pseudomonas Fluorescens ◽  
Time Course ◽  
Isotope Effects ◽  
Secondary Alcohol ◽  
Molecular Size ◽  
Order Rate Constant ◽  
Site Directed Mutagenesis ◽  
Linear Slope ◽  
Solvent Isotope ◽  
Relationship Of

X-ray structure of the Pseudomonas fluorescens mannitol 2-dehydrogenase ternary complex with NAD+ and d-mannitol suggests that Lys-295 provides catalytic base assistance to secondary alcohol group oxidation. We have replaced Lys-295 by site-directed mutagenesis with alanine or methionine and evaluated the catalytic significance of side-chain substitution by kinetic analysis of restoration of activity with external amines, and from pH and solvent isotope effects on the reaction catalysed by K295A (Lys-295→Ala mutant). K295A and K295M (Lys-295→Met mutants) show 3×104- and 2×106-fold lower turnover numbers respectively for d-mannitol oxidation (kcatO) at pH 10.0 than the wild-type. The second-order rate constant for non-covalent rescue of activity (kB) by free methylamine base is 31 M−1·s−1 for K295A, but only 0.021 M−1·s−1 for K295M. A Brønsted relationship of log kB (corrected for molecular size effects) and pKa of the external amine is linear (slope β=0.66±0.16; r2=0.99) for K295A-catalysed d-mannitol oxidation at pH 10.0. The kcatO values of K295A in H2O and 2H2O are linearly dependent on [OL−] in the pL range 7.5–10.5 (where L is 1H or 2H). The solvent isotope effect on kcatO is 0.69. The time course of d-fructose reduction by K295A at pH 8.2 displays a pre-steady-state burst of NADH consumption. These data support a mechanism in which the ε-NH2 group of Lys-295 participates in an obligatory pH-dependent, pre-catalytic equilibrium which may control alcohol/alkoxide equilibration of enzyme-bound d-mannitol and activates the C2 atom for subsequent catalytic oxidation by NAD+.

Vapour Pressure Isotope Effect on Evaporation from Pure Organic Phases - a PIMD Approach

2020 ◽  
Author(s):  
Luis Vasquez ◽  
Agnieszka Dybala-Defratyka
Keyword(s):  
Path Integral ◽  
Vapour Pressure ◽  
Density Functional ◽  
Isotope Effects ◽  
Tight Binding ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Special Importance ◽  
Non Covalent Interactions ◽  
Covalent Interactions

<p></p><p>Very often in order to understand physical and chemical processes taking place among several phases fractionation of naturally abundant isotopes is monitored. Its measurement can be accompanied by theoretical determination to provide a more insightful interpretation of observed phenomena. Predictions are challenging due to the complexity of the effects involved in fractionation such as solvent effects and non-covalent interactions governing the behavior of the system which results in the necessity of using large models of those systems. This is sometimes a bottleneck and limits the theoretical description to only a few methods.<br> In this work vapour pressure isotope effects on evaporation from various organic solvents (ethanol, bromobenzene, dibromomethane, and trichloromethane) in the pure phase are estimated by combining force field or self-consistent charge density-functional tight-binding (SCC-DFTB) atomistic simulations with path integral principle. Furthermore, the recently developed Suzuki-Chin path integral is tested. In general, isotope effects are predicted qualitatively for most of the cases, however, the distinction between position-specific isotope effects observed for ethanol was only reproduced by SCC-DFTB, which indicates the importance of using non-harmonic bond approximations.<br> Energy decomposition analysis performed using the symmetry-adapted perturbation theory (SAPT) revealed sometimes quite substantial differences in interaction energy depending on whether the studied system was treated classically or quantum mechanically. Those observed differences might be the source of different magnitudes of isotope effects predicted using these two different levels of theory which is of special importance for the systems governed by non-covalent interactions.</p><br><p></p>

scholarly journals NMR of Natural Products as Potential Drugs

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3763
Author(s):  
Poul Erik Hansen
Keyword(s):  
Natural Products ◽  
Hydrogen Bonding ◽  
Density Functional ◽  
Chemical Shifts ◽  
Isotope Effects ◽  
Density Functional Theory Calculations ◽  
Intramolecular Hydrogen Bonding ◽  
Chemical Equilibria ◽  
Nmr Techniques ◽  
Intramolecular Hydrogen

This review outlines methods to investigate the structure of natural products with emphasis on intramolecular hydrogen bonding, tautomerism and ionic structures using NMR techniques. The focus is on 1H chemical shifts, isotope effects on chemical shifts and diffusion ordered spectroscopy. In addition, density functional theory calculations are performed to support NMR results. The review demonstrates how hydrogen bonding may lead to specific structures and how chemical equilibria, as well as tautomeric equilibria and ionic structures, can be detected. All these features are important for biological activity and a prerequisite for correct docking experiments and future use as drugs.

scholarly journals Rate and Product Studies with 1-Adamantyl Chlorothioformate under Solvolytic Conditions

2021 ◽  
Vol 22 (14) ◽  
pp. 7394
Author(s):  
Kyoung Ho Park ◽  
Mi Hye Seong ◽  
Jin Burm Kyong ◽  
Dennis N. Kevill
Keyword(s):  
Rate Constants ◽  
Isotope Effects ◽  
Ion Pairs ◽  
Carbonyl Sulfide ◽  
Activation Parameters ◽  
Chloride Ions ◽  
Reaction Channels ◽  
Decomposition Pathway ◽  
Solvent Isotope ◽  
Solvent Isotope Effects

A study was carried out on the solvolysis of 1-adamantyl chlorothioformate (1-AdSCOCl, 1) in hydroxylic solvents. The rate constants of the solvolysis of 1 were well correlated using the Grunwald–Winstein equation in all of the 20 solvents (R = 0.985). The solvolyses of 1 were analyzed as the following two competing reactions: the solvolysis ionization pathway through the intermediate (1-AdSCO)+ (carboxylium ion) stabilized by the loss of chloride ions due to nucleophilic solvation and the solvolysis–decomposition pathway through the intermediate 1-Ad+Cl− ion pairs (carbocation) with the loss of carbonyl sulfide. In addition, the rate constants (kexp) for the solvolysis of 1 were separated into k1-Ad+Cl− and k1-AdSCO+Cl− through a product study and applied to the Grunwald–Winstein equation to obtain the sensitivity (m-value) to change in solvent ionizing power. For binary hydroxylic solvents, the selectivities (S) for the formation of solvolysis products were very similar to those of the 1-adamantyl derivatives discussed previously. The kinetic solvent isotope effects (KSIEs), salt effects and activation parameters for the solvolyses of 1 were also determined. These observations are compared with those previously reported for the solvolyses of 1-adamantyl chloroformate (1-AdOCOCl, 2). The reasons for change in reaction channels are discussed in terms of the gas-phase stabilities of acylium ions calculated using Gaussian 03.

scholarly journals Dual role of CO in the stability of subnano Pt clusters at the Fe3O4(001) surface

2016 ◽  
Vol 113 (32) ◽  
pp. 8921-8926 ◽  
Author(s):  
Roland Bliem ◽  
Jessi E. S. van der Hoeven ◽  
Jan Hulva ◽  
Jiri Pavelec ◽  
Oscar Gamba ◽  
...  
Keyword(s):  
Density Functional ◽  
Elevated Temperatures ◽  
Time Lapse ◽  
Dual Role ◽  
Oxidation Catalyst ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Active Metal ◽  
Catalytically Active ◽  
The Stability

Interactions between catalytically active metal particles and reactant gases depend strongly on the particle size, particularly in the subnanometer regime where the addition of just one atom can induce substantial changes in stability, morphology, and reactivity. Here, time-lapse scanning tunneling microscopy (STM) and density functional theory (DFT)-based calculations are used to study how CO exposure affects the stability of Pt adatoms and subnano clusters at the Fe3O4(001) surface, a model CO oxidation catalyst. The results reveal that CO plays a dual role: first, it induces mobility among otherwise stable Pt adatoms through the formation of Pt carbonyls (Pt1–CO), leading to agglomeration into subnano clusters. Second, the presence of the CO stabilizes the smallest clusters against decay at room temperature, significantly modifying the growth kinetics. At elevated temperatures, CO desorption results in a partial redispersion and recovery of the Pt adatom phase.

scholarly journals Spectroscopic evidence for direct flavin-flavin contact in a bifurcating electron transfer flavoprotein

2020 ◽  
Vol 295 (36) ◽  
pp. 12618-12634
Author(s):  
H. Diessel Duan ◽  
Nishya Mohamed-Raseek ◽  
Anne-Frances Miller
Keyword(s):  
Electron Transfer ◽  
Density Functional ◽  
Protein Denaturation ◽  
Rhodopseudomonas Palustris ◽  
Density Functional Theory Calculations ◽  
Site Directed Mutagenesis ◽  
Functional Theory ◽  
Electron Transfer Flavoprotein ◽  
Midpoint Potential ◽  
Ct Complex

A remarkable charge transfer (CT) band is described in the bifurcating electron transfer flavoprotein (Bf-ETF) from Rhodopseudomonas palustris (RpaETF). RpaETF contains two FADs that play contrasting roles in electron bifurcation. The Bf-FAD accepts electrons pairwise from NADH, directs one to a lower-reduction midpoint potential (E°) carrier, and the other to the higher-E° electron transfer FAD (ET-FAD). Previous work noted that a CT band at 726 nm formed when ET-FAD was reduced and Bf-FAD was oxidized, suggesting that both flavins participate. However, existing crystal structures place them too far apart to interact directly. We present biochemical experiments addressing this conundrum and elucidating the nature of this CT species. We observed that RpaETF missing either FAD lacked the 726 nm band. Site-directed mutagenesis near either FAD produced altered yields of the CT species, supporting involvement of both flavins. The residue substitutions did not alter the absorption maximum of the signal, ruling out contributions from residue orbitals. Instead, we propose that the residue identities modulate the population of a protein conformation that brings the ET-flavin and Bf-flavin into direct contact, explaining the 726 nm band based on a CT complex of reduced ET-FAD and oxidized Bf-FAD. This is corroborated by persistence of the 726 nm species during gentle protein denaturation and simple density functional theory calculations of flavin dimers. Although such a CT complex has been demonstrated for free flavins, this is the first observation of such, to our knowledge, in an enzyme. Thus, Bf-ETFs may optimize electron transfer efficiency by enabling direct flavin-flavin contact.

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