SPECIFIC BINDING OF A SHORT miRNA SEQUENCE BY ZINC KNUCKLES OF Lin28: A MOLECULAR DYNAMICS SIMULATION STUDY

Protein Lin28 recognizes pre-let-7 microRNAs (miRNAs) through direct interactions between its zinc-knuckle type zinc-finger (ZnF) domains and the terminal loop of pre-let-7, resulting in the inhibition of the synthesis of mature let-7 miRNAs. Despite the physiological importance, the involved conformational changes and energetic factors contributing to the binding affinity and specificity remain unclear. We conducted molecular dynamics (MD) simulations in conjunction with molecular mechanics/generalized born surface area (MM/GBSA) and energy decomposition calculations to investigate the RNA binding-induced conformational changes of the ZnFs and the residual level energetic factors that influence the binding affinity and specificity. We showed that the binding of the RNA results in the inter-domain conformational changes of the two ZnF domains, including changes of the spatial relationships of several nucleobase-binding amino acids. We also observed mutation-induced weakening of the affinity of the Lin28–pre-let-7 binding, which reveals the importance of the stacking interactions between the side-chains of Tyr140, His148, His162 and the bases of nucleic acid G2 and G5 in the specific recognition of pre-let-7 by the ZnFs of Lin28.

WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

MOLECULAR STRUCTURE, NATURAL BOND ORBITAL, SUBSTITUENT EFFECT AND CHEMICAL REACTIVITY ANALYSIS OF TERMINAL BORYLENE RUTHENIUM COMPLEXES: Ru(PH3)2HCl(BC6H4X)

The structure and properties of a terminal borylene ruthenium complexes Ru ( PH 3)2 HCl ( BC 6 H 4X) have been investigated using theoretical methods. Frontier orbital analysis indicates the HOMO is distributed on the Ru and Cl ligand. On the other hand, LUMO is distributed on the Ru and phenyl ligand. The influence of solvent on the structure and properties of X = H structure has been studied. Time-dependent density functional theory (TD-DFT) is used to calculate the energy, oscillatory strength and wavelength absorption maxima (λmax) of various electronic transitions and their nature within molecules. Nonlinear optical (NLO) behavior of title compounds is investigated by the computed value of first hyperpolarizability (βtotal).

MODELING OF INTERFACIAL BEHAVIOR OF WATER AND ORGANICS

Modeling of water structure at a surface of different adsorbents, as well as an influence of dissolved compounds or co-adsorbates on bound water, is of importance to understand the temperature dependence of the characteristics of bound water, especially at T < 273 K, in comparison with bulk water. 1 H NMR spectra giving useful information on the water structure can be obtained using different ways such as experimental measurements, direct ab initio and density functional theory (DFT) calculations or estimation using semiempirical calculations and appropriate calibration functions. Here, application of the last approach is analyzed with respect to a variety of relatively large hydrated systems. Despite the simplicity of this approach, it gives quantitative characterization of structural features of interfacial water and effects of different co-adsorbates and adsorbent surfaces on bound water.

THEORETICAL INVESTIGATION OF SUBSTITUTION EFFECT ON THE PROTON TRANSFER MECHANISM IN 3-MERCAPTO-PROPENETHIAL

We present detailed theoretical studies of the proton transfer (PT) in the 3-Mercapto-propenethial (MP) and in some of its derivatives. The effect of substitution on the transition state structures corresponding to the PT in R2 or R1(3) positions is studied by using B3LYP/6-311++G** level of theory in gas phase and water solution. The following substituents have been taken into consideration: Cl, F, OH, SH, OCH3, SCH3, CHO, NO2, CCH and OCF3 . For the different derivatives of 3-MP, we have computed geometries and potential energy curves for the intramolecular PT in their ground. Also, the excited-state properties of intramolecular hydrogen bonding in substituted systems have been investigated theoretically using the time-dependent density functional theory method. The π-electron delocalization parameter (Q) and HOMA index as a geometrical indicator of a local aromaticity are investigated. Natural bond orbital (NBO) analysis was also performed for better understanding the nature of intramolecular interactions. The results of analysis by Quantum theory of "Atoms in Molecules" and NBO method fairly support the DFT results. Correlations between the PT reaction barrier versus topological parameters, ν(S–H) and γ(S–H) are also probed. The obtained results showed a strong influence of the R substituent on the PT reaction barrier changes. Numerous correlations between topological, geometrical, thermodynamic properties and energetic parameters were also found.

THEORETICAL INVESTIGATION ON THE STRUCTURE AND PROPERTIES OF ALUMAZINE⋯M COMPLEXES (M = Li+, Na+, K+, Be2+, Mg2+, AND Ca2+)

The nature of alumazine⋯M ( M = Li+ , Na+ , K+ , Be2+ , Mg2+ , AND Ca2+ ) interactions was studied by ab initio calculations. The interaction energies were calculated at MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) level. The calculations suggest that the size and charge of cation are two important factors that affect the interaction energy, charge transfer values and the variation in aromaticity of alumazine ring upon complexation. The theory of atoms in molecules (AIM) and natural bond orbital (NBO) analyses of complexes indicate that the variation of densities and the extent of charge shifts upon complexation correlate well with the obtained interaction energies. Finally, nucleus independent chemical shift (NICS) method was applied for evaluating the variation in aromaticity of alumazine ring upon complexation.

COMPUTATIONAL MODELING STUDY ON METABOLISM MECHANISM OF OSELTAMIVIR

Oseltamivir (OTV) is widely used in the treatment of both influenza virus A and B infections. Additionally, OTV is an effective antiviral drug in treating the 2009 A ( H1N1 ) influenza virus. Clinical studies concluded that OTV is readily extensively converted to the active carboxylate metabolite after oral administration. In order to investigate the metabolism mechanism of OTV, we carried out density functional theory (DFT) quantum mechanical calculations. The molecule orbital (MO) theory and natural population analysis (NPA) were also employed to help understanding the reaction mechanism. All possible reaction pathways for OTV metabolism are considered, involving hydrolysis of ester and amide. Two mechanisms were considered in this work, viz. concerted mechanism and stepwise mechanism. Our results indicate the stepwise mechanism is more favorable in both hydrolysis reactions and the rate-determining stage is the formation of the tetrahedral intermediate. In addition, the hydrolysis reactions can be assisted by substrate NH2 group and solvent water molecules. The substrate-assisted mechanism for the formation of the carboxylate metabolite is the most favorable one.

THE MECHANISM OF ACID-CATALYZED DECARBOXYLATION OF PYRROLE-2-CARBOXYLIC ACID: INSIGHTS FROM CLUSTER-CONTINUUM MODEL CALCULATIONS

The decarboxylation of pyrrole-2-carboxylic acid comprises the addition of water to the carboxyl group and the C–C bond cleavage leading to the protonated carbonic acid. Herein possible concerted and stepwise mechanisms for the C-protonated and O-protonated pathways were extensively investigated by using the cluster-continuum model. The calculated results indicate that the initial hydration or the nucleophilic attack of water at the carbonyl group of both C- and O-protonated derivatives is the rate-determining step for the overall reaction, and the O-protonated pathway will dominate the whole reaction. The predicted activation Gibbs energies for the overall reaction initialized by the O-protonated species fall in the range of 83.3 ∼ 123.0 kJ/mol, showing good agreement with experimental values of 91.6 ∼ 101.3 kJ/mol. On the basis of extensive calculations, the remarkable dependence of the predicted mechanisms and thermodynamic values on the number of explicit water molecules in the cluster-continuum model was discussed.