A theoretical study of the mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase II

The mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase II has been investigated using molecular mechanics and quantum mechanics methods.Molecular dynamics(MD) simulations were carried out using the TIP3 water model and generalized solvent boundary potential(GSBP) by CHARMM based on the X-ray crystal structure.Two models of the ternary elongation complex were constructed based on CHARMM MD calculations.All the species including reactants,transition states,intermediates,and products were optimized using the DFT-PBE method coupled with the basis set DZVP and the auxiliary basis set GEN-A2.Three pathways were explored using the DFT method.The most favorable reaction pathway involves indirect proton migration from the RNA primer 3’-OH to the oxygen atom of-phosphate via a solvent water molecule,proton rotation from the oxygen atom of-phosphate to the-phosphate side,the RNA primer 3’-O nucleophilic attack on the-phosphorus atom,and P-O bond breakage.The corresponding reaction potential profile was obtained.The rate limiting step,with a barrier height of 21.5 kcal/mol,is the RNA primer 3’-O nucleophilic attack,rather than the commonly considered proton transfer process.A high-resolution crystal structure including crystallographic water molecules is required for further studies.     

Characterization of novel isobenzofuranones by DFT calculations and 2D NMR analysis

Phthalides are frequently found in naturally occurring substances and exhibit a broad spectrum of biological activities. In the search for compounds with insecticidal activity, phthalides have been used as versatile building blocks for the syntheses of novel potential agrochemicals. In our work, the Diels–Alder reaction between furan‐2(5H)‐one and cyclopentadiene was used successfully to obtain (3aR,4S,7R,7aS)‐3a,4,7,7a‐tetrahydro‐4,7‐methanoisobenzofuran‐1(3H)‐one and (3aS,4R,7S,7aR)‐3a,4,7,7a‐tetrahydro‐4,7‐methanoisobenzofuran‐1(3H)‐one ( 2 ) and (3aS,4S,7R,7aR)‐3a,4,7,7a‐tetrahydro‐4,7‐methanoisobenzofuran‐1(3H)‐one and (3aR,4R,7S,7aS)‐3a,4,7,7a‐tetrahydro‐4,7‐methanoisobenzofuran‐1(3H)‐one ( 3 ). The endo adduct ( 2 ) was brominated to afford (3aR,4R,5R,7R,7aS,8R)‐5,8‐dibromohexahydro‐4,7‐methanoisobenzofuran‐1(3H)‐one and (3aS,4S,5S,7S,7aR,8S)‐5,8‐dibromohexahydro‐4,7‐methanoisobenzofuran‐1(3H)‐one ( 4 ) and (3aS,4R,5R,6S,7S,7aR)‐5,6‐dibromohexahydro‐4,7‐methanoisobenzofuran‐1(3H)‐one and (3aR,4S,5S,6R,7R,7aS)‐5,6‐dibromohexahydro‐4,7‐methanoisobenzofuran‐1(3H)‐one ( 5 ). Following the initial analysis of the NMR spectra and the proposed two novel unforeseen products, we have decided to fully analyze the classical and non‐classical assay structures with the aid of computational calculations. Computation to predict the ¹³C and ¹H chemical shifts for mean absolute error analyses have been carried out by gauge‐including atomic orbital method at M06‐2X/6‐31+G(d,p) and B3LYP/6‐311+G(2d,p) levels of theory for all viable conformers. Characterization of the novel unforeseen compounds ( 4 ) and ( 5 ) were not possible by employing only the experimental NMR data; however, a more conclusive structural identification was performed by comparing the experimental and theoretical ¹H and ¹³C chemical shifts by mean absolute error and DP4 probability analyses. Copyright © 2016 John Wiley & Sons, Ltd.     

Sulfur K-edge XAS and DFT calculations on nitrile hydratase: geometric and electronic structure of the non-heme iron active site

The geometric and electronic structure of the active site of the non-heme iron enzyme nitrile hydratase (NHase) is studied using sulfur K-edge XAS and DFT calculations. Using thiolate (RS(-))-, sulfenate (RSO(-))-, and sulfinate (RSO(2)(-))-ligated model complexes to provide benchmark spectral parameters, the results show that the S K-edge XAS is sensitive to the oxidation state of S-containing ligands and that the spectrum of the RSO(-) species changes upon protonation as the S-O bond is elongated (by approximately 0.1 A). These signature features are used to identify the three cysteine residues coordinated to the low-spin Fe(III) in the active site of NHase as CysS(-), CysSOH, and CysSO(2)(-) both in the NO-bound inactive form and in the photolyzed active form. These results are correlated to geometry-optimized DFT calculations. The pre-edge region of the X-ray absorption spectrum is sensitive to the Z(eff) of the Fe and reveals that the Fe in [FeNO](6) NHase species has a Z(eff) very similar to that of its photolyzed Fe(III) counterpart. DFT calculations reveal that this results from the strong pi back-bonding into the pi antibonding orbital of NO, which shifts significant charge from the formally t(2)(6) low-spin metal to the coordinated NO.     

The origin of the stereochemically active Pb(II) lone pair: DFT calculations on PbO and PbS

The concept of a chemically inert but stereochemically active 6s² lone pair is commonly associated with Pb(II). We have performed density functional theory calculations on PbO and PbS in both the rocksalt and litharge structures which show anion dependence of the stereochemically active lone pair. PbO is more stable in litharge while PbS is not, and adopts the symmetric rocksalt structure showing no lone pair activity. Analysis of the electron density, density of states and crystal orbital overlap populations shows that the asymmetric electron density formed by Pb(II) is a direct result of anion-cation interactions. The formation has a strong dependence on the electronic states of the anion and while oxygen has the states required for interaction with Pb 6s, sulphur does not. This explains for the first time why PbO forms distorted structures and possesses an asymmetric density and PbS forms symmetric structures with no lone pair activity. This analysis shows that distorted Pb(II) structures are not the result of chemically inert, sterically active lone pairs, but instead result from asymmetric electron densities that rely on direct electronic interaction with the coordinated anions.     

Characterization of paramagnetic species in N-doped TiO2 powders by EPR spectroscopy and DFT calculations

Electron paramagnetic resonance (EPR), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations are combined for the first time in an effort to characterize the paramagnetic species present in N-doped anatase TiO2 powders obtained by sol-gel synthesis. The experimental hyperfine coupling constants are well reproduced by two structurally different nitrogen impurities: substitutional and interstitial N atoms in the TiO2 anatase matrix. DFT calculations show that the nitrogen impurities induce the formation of localized states in the band gap. Substitutional nitrogen states lie just above the valence band, while interstitial nitrogen states lie higher in the gap. Excitations from these localized states to the conduction band may account for the absorption edge shift toward lower energies (visible region) observed in the case of N-doped TiO2 with respect to pure TiO2 (UV region). Calculations also show that nitrogen doping leads to a substantial reduction of the energy cost to form oxygen vacancies in bulk TiO2. This suggests that nitrogen doping is likely to be accompanied by oxygen vacancy formation. Finally, we propose that the relative abundance of the two observed nitrogen-doping species depends on the preparation conditions, such as the oxygen concentration in the atmosphere and the annealing temperature during synthesis.     

High level ab initio and DFT calculations of models of the catalytically active Ni-Fe hydrogenases

Multi-reference M?ller-Plesset calculations of a model of the Ni-SI state of nickel-iron hydrogenase predict a singlet rather than a triplet state for this species, and show that it is better described with a BP86 rather than a B3LYP functional.     

Characterization of the monovalent ion position and hydrogen-bond network in guanine quartets by DFT calculations of NMR parameters

Conformational stability of G-quartets found in telomeric DNA quadruplex structures requires the coordination of monovalent ions. Here, an extensive Hartree-Fock and density functional theory analysis of the energetically favored position of Li+, Na+, and K+ ions is presented. The calculations show that at quartet-quartet distances observed in DNA quadruplex structures (3.3 A), the Li+ and Na+ ions favor positions of 0.55 and 0.95 A outside the plane of the G-quartet, respectively. The larger K+ ion prefers a central position between successive G-quartets. The energy barrier separating the minima in the quartet-ion-quartet model are much smaller for the Li+ and Na+ ions compared with the K+ ion; this suggests that K+ ions will not move as freely through the central channel of the DNA quadruplex. Spin-spin coupling constants and isotropic chemical shifts in G-quartets extracted from crystal structures of K+- and Na+-coordinated DNA quadruplexes were calculated with B3LYP/6-311G(d). The results show that the sizes of the trans-hydrogen-bond couplings are influenced primarily by the hydrogen bond geometry and only slightly by the presence of the ion. The calculations show that the R(N2N7) distance of the N2-H2...N7 hydrogen bond is characterized by strong correlations to both the chemical shifts of the donor group atoms and the (h2)J(N2N7) couplings. In contrast, weaker correlations between the (h3)J(N1C6') couplings and single geometric factors related to the N1-H1...O6=C6 hydrogen bond are observed. As such, deriving geometric information on the hydrogen bond through the use of trans-hydrogen-bond couplings and chemical shifts is more complex for the N1-H1...O6=C6 hydrogen bond than for the N2-H2...N7 moiety. The computed trans-hydrogen-bond couplings are shown to correlate with the experimentally determined couplings. However, the experimental values do not show such strong geometric dependencies.     

Characterization of the CYP3A4 active site by homology modeling

Human microsomal cytochrome P450s participate in drug metabolism and detoxification. Among them, CYP3A4 is the most important isoform for drug-drug interactions. To gain a better understanding of the active site, a homology model of CYP3A4 was constructed based on the crystallographic coordinates of mammalian CYP2C5. The putative active site is much larger than that of CYP2C5 and is divided into three parts (i.e. a proximal and two distal sites from the heme). Most residues reported to be important for ligand-binding are located in the active site of the model. Moreover, some inhibitors (paclitaxel etc.) docked into the model have complementary shapes to the pocket. Pharmacophore docking of 14 substrates was also performed using Ph4Dock of MOE. Calculated interaction energies showed a moderate correlation with the logarithm of apparent K(m) values. These results suggest that this model is reliable enough to be used in the design of compounds for removing undesirable CYP3A4 inhibition.     

Characterization of an RNA active site: interactions between a Diels-Alderase ribozyme and its substrates and products

Ribozymes have recently been shown to catalyze the stereoselective formation of carbon-carbon bonds between small organic molecules. The interactions of these Diels-Alderase ribozymes with their substrates and products have now been elucidated by chemical substitution analysis by using 44 different, systematically varied analogues. RNA-diene interaction is governed by stacking interactions, while hydrogen bonding and metal ion coordination appear to be less important. The diene has to be an anthracene derivative, and substituents at defined positions are permitted, thereby shedding light on the geometry of the binding site. The dienophile must be a five-membered maleimidyl ring with an unsubstituted reactive double bond, and a hydrophobic side chain makes a major contribution to RNA binding. The ribozyme distinguishes between different enantiomers of chiral substrates and accelerates cycloadditions with both enantio- and diastereoselectivity. The stereochemistry of the reaction is controlled by RNA-diene interactions. The RNA interacts strongly and stereoselectively with the cycloaddition products, requiring several structural features to be present. Taken together, the results highlight the intricacy of ribozyme active sites which can control chemical reaction pathways based on minute differences in substrate stereochemistry and substitution pattern.     

Molecular orbital calculations of the active site complex of two iron ferredoxins

In this report we present further results of molecular orbital calculations for a model of the active site complex of two iron ferredoxins, using the Iterative Extended Hückel Method for our calculations. In the first paper of this series we dealt mainly with energy-conformation calculations which helped establish the salient chemical and conformational features of the lowest energy forms for such a complex. Presented here are the nature and energy ordering of the 70 molecular orbitals in the active site model, a calculation of room temperature magnetic moment, of the electric field gradient at the Fe nucleus and an assignment of the optical absorption spectra in the one electron approximation for the lowest energy conformer of the oxidized state of these proteins. For each property, we compare our calculated results with experiment whenever possible, and with the results of previous correlations. In addition, we indicate the sensitivity of these properties to variations in conformation about the Fe atoms.

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Zusammenfassung In der vorliegenden Arbeit werden weitere Resultate der Untersuchung eines Modells des an der aktiven Stelle gebildeten Komplexes von zwei Eisen-ferredoxinen mitgeteilt, die mit Hilfe der iterativen erweiterten Hückel-Methode gewonnen wurden. In der ersten Veröffentlichung dieser Reihe wurden hauptsächlich die Ergebnisse der Berechnungen von Konformationsenergien angegeben, die dazu beitrugen, die wichtigsten chemischen Eigenschaften sowie die Konformationen solcher Komplexe mit der niedrigsten Energie zu ermitteln. Hier werden nun die Eigenschaften der 70 niedrigsten Molekülorbitale des Modells, eine Berechnung des magnetischen Moments bei Raumtemperatur und des elektrischen Feldgradienten am Fe-Kern sowie die Zuordnung des optischen Absorptionsspektrums in der Einelektronennäherung für die Konformation niedrigster Energie des oxydierten Zustandes dieser Proteine veröffentlicht. Die Ergebnisse werden soweit möglich mit dem Experiment und früheren Interpretationen verglichen. Zusätzlich wird auf die Empfindlichkeit dieser Eigenschaften bezüglich einer Variation der Konformation in der Nähe des Fe-Atoms hingewiesen.

     

Molecular orbital calculations of the active site complex of two iron ferredoxins

The results presented here are the first part of a systematic theoretical study of some of the physical and biochemical properties of two iron ferredoxins obtained by the use of an Extended Hückel Self-Consistent Charge iteration method of molecular orbital calculations. In this initial study, attention is focused on the calculation of electronic energies as a function of molecular geometry and the nature of the bonding ligands at the active site in order to determine the most stable form of the active site complex. Included in the active site complex are two iron atoms, two acid labile sulfur atoms of unknown inorganic origin and four sulfur atoms presumably from nearby cysteine residues. Fifteen chemical-conformational variations of this basic active site complex were considered. Among these conformational variations of the sulfur ligands, Fe-Fe distances, bond lengths and angles and chemical variations such as the effect of axial ligands, disulfide bonds and added protons were included. Our results indicate that that with all reasonable variations of the ligands, the preferred molecular geometry about 4-coordinated Fe is tetrahedral rather than planar. The planar conformation is somewhat stabilized by the addition of axial ligands, but is still less favorable than the tetrahedral conformation. In this model, interactions between the two iron atoms occur automatically since they are both part of the same active site complex. Hence the absence of low temperature paramagnetism in the oxidized state is readily explained. Preliminary investigations of the reduced state with one additional electron indicate that the odd electron is delocalized, as observed in both ESR and ENDOR. Its presence apparently substantially destabilizes all of the molecular orbital energies in accord with the observation that only one electron can be added to these proteins without decomposing them.

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Zusammenfassung Die vorliegenden Ergebnisse stellen den ersten Teil einer systematischen theoretischen Untersuchung einiger physikalischer und biochemischer Eigenschaften des Fe₂-Ferredoxins mit Hilfe einer selbstkonsistenten erweiterten Hückelmethode dar. In diesem ersten Teil wird besonders die elektronische Energie in Abhängigkeit von der Molekülgeometrie und der Art der Liganden an der aktiven Stelle untersucht, um die stabilste Form des Komplexes der aktiven Stelle zu finden. Dieser Komplex enthält zwei Eisenatome, zwei saure, nicht fest gebundene Schwefelatome unbekannter anorganischer Herkunft sowie vier Schwefelatome, vermutlich aus nahegelegenen Cysteinresten. Bei den 15 untersuchten Konformationen der Schwefelliganden wurden Änderungen der Fe-Fe-Abstände, Bindungslängen und -winkel sowie chemische Variationen wie die Einwirkung der axialen Liganden, der Disulfidbindungen und zusätzlicher Protonen berücksichtigt. Es ergibt sich, daß das Eisen vierfach tetraedrisch koordiniert ist und nicht planar, selbst bei der Addition axialer Liganden. In diesem Modell ergeben sich Wechselwirkungen zwischen den beiden Eisenatomen zwanglos, da sie zum gleichen aktiven Komplex gehören. Dadurch wird das Fehlen eines Tieftemperatur-Paramagnetismus im oxydierten Zustand hinreichend erklärt. Eine vorläufige Untersuchung des reduzierten Zustandes mit einem zusätzlichen Elektron zeigt, daß dieses delokalisiert ist, genau wie es mit ESR und ENDOR beobachtet wird. seine Gegenwart destabilisiert offenbar alle MO-Energien, was in Übereinstimmung mit der Beobachtung steht, daß nur ein Elektron von diesen Proteinen addiert werden kann, ohne sie zu zerstören.

     

Vibrational assignment of the Raman active modes of 1,10-phenanthroline-5,6-dione using DFT calculations

A complete assignment of the Raman active modes of 1,10-phenanthroline-5,6-dione in the 100-4000 cm(-1) spectral region is reported. Intense well resolved spectra of solid phendione with high S/N are reported. Assignment of the normal modes with appropriate symmetry representation symbols was achieved by employing density functional theory calculations. Our calculations were modeled on results previously reported for phenanthroline. Results of the B3LYP calculations were consistent and established that phendione possess sixty fundamentals.     

Implications of active site constraints on varied DNA polymerase selectivity

DNA polymerase selectivity often varies significantly depending on the DNA polymerase. The origin of this varying error propensity is elusive. It is assumed that DNA polymerases form nucleotide binding pockets that differ in properties such as shape and tightness. We tested this prediction and studied HIV-1 RT by employment of size-augmented nucleotides and site-directed mutagenesis of the enzyme. New valuable insights into the mechanism of DNA polymerase fidelity were obtained. The presented study provides experimental evidence that variations of steric constraints within the nucleotide binding pocket of at least two DNA polymerases cause variations in nucleotide incorporation selectivity. Thus, our results support the concept of active site tightness as a causative in differential fidelity among DNA polymerases.     

Sequential assembly of an active RNA polymerase molecule at the air-water interface

At the heart of understanding cellular processes lies our ability to explore the specific nature of communication between sequential information carrying biopolymers. However, the data extracted from conventional solution phase studies may not reflect the dynamics of communication between recognized partners as they occur in the crowded cellular milieu. We use the principle of immobilization of histidine-tagged biopolymers at a Ni(II)-encoded Langmuir monolayer to study sequence-specific protein-protein interactions in an artificially crowded environment. The advantage of this technique lies in increasing the surface density of one of the interacting partners that allows us to study macromolecular interactions in a controlled crowded environment, but without compromising the speed of the reactions. We have taken advantage of this technique to follow the sequential assembly process of the multiprotein complex Escherichia coli RNA polymerase at the interface and also deciphered the role of one of the proteins, omega (ω), in the assembly pathway. Our reconstitution studies indicate that in the absence of molecular chaperones or other cofactors, omega (ω) plays a decisive role in refolding the largest protein beta prime (β') and its recruitment into the multimeric assembly to reconstitute an active RNA polymerase. It was also observed that the monolayer had the ability to distinguish between sequence-specific and -nonspecific interactions despite the immobilization of one of the biomacromolecules. The technique provides a universal two-dimensional template for studying protein-ligand interactions while mimicking molecular crowding.     

DFT analysis of the active site in catalytic metabolic redox reactions of mononuclear molybdenum enzymes

Abstract

Model complexes [Mo^VIO₂(S₂C₂Me₂)SMe]^? (A, derived from the X-ray crystal structure of native sulfite oxidase (SO)) and [Mo^VIO₂(mnt)₂]^2? (B, coordination mode similar to the active site of selenate reductase (SeR)) were computed at the COSMO-B3LYP/SDDp//B3LYP/Lanl2DZ(p) energy level of Density Functional Theory in order to study their behavior in oxidation of selenite (Se^IV) and sulfite (S^IV) to selenate (Se^VI) and sulfate (S^VI), respectively. For the oxidation of sulfite, computational model A, which resembles the SO active site, is clearly the best choice (lowest barrier, minor exothermicity). For the reduction of selenate, a smaller activation is computed for model A; however, the reaction is less exothermic with model B, which resembles the SeR active site.     

Vibrational study of tolazoline hydrochloride by using FTIR-Raman and DFT calculations

Quantum mechanical (QM) calculations have been carried out in order to study the tolazoline hydrochloride theoretical structure and vibrational properties. This compound was characterized by infrared and Raman spectroscopies in the solid phase. For a complete assignment of the IR and Raman spectra, the density functional theory (DFT) calculations were combined with Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology in order to fit the theoretical frequency values to the experimental ones. An agreement between theoretical and available experimental results was found. Three intense bands in the infrared spectrum characteristic of the protonated species of the compound were detected. Also, the possible charge-transfer and the topological properties for both benzyl and imidazoline rings were studied by means of Natural Bond Orbital (NBO) and Atoms in Molecules theory (AIM) investigation.     

S K-edge XAS and DFT calculations on square-planar NiII-thiolate complexes: effects of active and passive H-bonding

S K-edge XAS for a low-spin NiII-thiolate complex shows a 0.2 eV shift to higher pre-edge energy but no change in Ni-S bond covalency upon H-bonding. This is different from the H-bonding effect we observed in high-spin FeIII-thiolate complexes where there is a significant decrease in Fe-S bond covalency but no change in energy due to H-bonding (Dey, A.; Okamura, T.-A.; Ueyama, N.; Hedman, B.; Hodgson, K. O.; Solomon, E. I. J. Am. Chem. Soc. 2005, 127, 12046-12053). These differences were analyzed using DFT calculations, and the results indicate that two different types of H-bonding interactions are possible in metal-thiolate systems. In the high-spin FeIII-thiolate case, the H-bonding involves a thiolate donor orbital which is also involved in bonding with the metal (active), while in the low-spin NiII-thiolate, the orbital involved in H-bonding is nonbonding with respect to the M-S bonding (passive). The contributions of active and passive H-bonds to the reduction potential and Lewis acid properties of a metal center are evaluated.