Effect of Y220C mutation on p53 and its rescue mechanism: a computer chemistry approach.

Mutation causes inactivation of 'p53' tumor suppressor protein in almost fifty percent of cancers in humans. Outside the DNA-binding surface of p53, Y220C is the most common cancerous mutation. Previous studies have shown that a surface cavity is created by this mutation which destabilizes p53. PhiKan083, a carbazole derivative capable of binding with that cavity, and slows down its thermal denaturation rate. We investigated, theoretically, on mechanisms of structural stability loss due to Y220C mutation and mechanisms of stability restoration by PhiKan083 at the atomic level. From this study it is found that in Tp53C, Tyr220 has five electrostatic interactions with residues Val 147, Prol51, Pro153 and Pro223 located on S3/S4 loop and S7/S8 loop. The S7/S8 loop is stabilized by these electrostatic interactions. Due to the Y220C mutation all these electrostatic interactions are lost. As a result the structural fluctuation occurs at S7/S8 loop, and the loop is displaced from its original position after 6 ns MD simulation. When PhiKan083 is present (inserted) at the mutation site it provides five electrostatic interactions with Pro155, Glu221 and Thr230, and two hydrogen bonds with Leu145 and Asp228, respectively. These interactions provided by Pkikan083 stabilized the S7/S8 loop, and as a result it couldn't be displaced. Our results showed that due to Y220C mutation p53 became destabilized through structural fluctuations surrounding the mutation site. When PhiKan083 is present at the Y220C mutation site (in 2vuk), it provides electrostatic and hydrogen bonding interactions among residue-220, its neighboring residues and PhiKan08. These interactions give additional stability to Y220C mutant p53, thus Y220C mutant p53 doesn't destabilize.

A computational chemistry study on friction of h-MoS2. Part II. Friction anisotropy.

In this work, the friction anisotropy of hexagonal MoS(2) (a well-known lamellar compound) was theoretically investigated. A molecular dynamics method was adopted to study the dynamical friction of two-layered MoS(2) sheets at atomistic level. Rotational disorder was depicted by rotating one layer and was changed from 0° to 60°, in 5° intervals. The superimposed structures with misfit angle of 0° and 60° are commensurate, and others are incommensurate. Friction dynamics was simulated by applying an external pressure and a sliding speed to the model. During friction simulation, the incommensurate structures showed extremely low friction due to cancellation of the atomic force in the sliding direction, leading to smooth motion. On the other hand, in commensurate situations, all the atoms in the sliding part were overcoming the atoms in counterpart at the same time while the atomic forces were acted in the same direction, leading to 100 times larger friction than incommensurate situation. Thus, lubrication by MoS(2) strongly depended on its interlayer contacts in the atomic scale. According to part I of this paper [Onodera, T., et al. J. Phys. Chem. B 2009, 113, 16526-16536], interlayer sliding was source of friction reduction by MoS(2) and was originally derived by its material property (interlayer Coulombic interaction). In addition to this interlayer sliding, the rotational disorder was also important to achieve low friction state.

The effect of R249S carcinogenic and H168R-R249S suppressor mutations on p53-DNA interaction, a multi scale computational study.

In this study we have undertaken the theoretical analysis of the effect of R249S carcinogenic and H168R-R249S suppressor mutation at core domain of the tumor suppressor protein p53, on its natural interaction with DNA using a newly developed method. The results show that the carcinogenic mutation R249S affects the flexibility of L3 loop region in p53, inducing the loss of important hydrogen bonds observed at interaction in the wild-type with DNA, on the other hand the suppressor mutation H168R on the R249S assists in maintaining the wild-type like flexibility of the L3 region in p53 and thus recover the interaction terms lost in the carcinogenic mutation alone. The present study sets a new direction in the development of new drugs that may restore the interactions that lost as a consequence of the carcinogenic mutations in p53.

Quantum chemistry study on absorption spectra, electronic and electrical properties of organic dye on anatase(001).

As the most reactive surface, the stoichiometric O-bridge terminated anatase(001) surface attracted considerable attentions in many application fields. The interfacial electron transfer in dye-sensitized anatase(001) plays a principal role in a variety of photoinduced reactions. In the present work, the UV-vis absorption spectrum of TiO2 bulk and different surface models were calculated by means of tight-binding quantum chemical molecular dynamics program "Colors-excite" for the first time. The thickness dependence on electronic and electrical properties of anatase(001) surface was achieved. The anatase(001) surface with a thickness of 1.0 nm shows excellent electronic and electrical properties. Moreover, the most suitable binding mode (dissociative adsorption) and absorption spectra of perylene with acrylic acid (PAA) on the optimum anatase(001) were investigated. A significant red-shift was observed from the UV-vis absorption spectrum of PAA/anatase(001) system. The red-shift occurring when PAA adsorbed on anatase(001) surface suggests that PAA/anatase(001) may be potential candidate for dye-sensitized solar cell. This study also proposed an effective computational tool "Colors-excite" to study of the electronic excitation properties for both molecular and periodic systems.

Tribochemical reaction dynamics of molybdenum dithiocarbamate on nascent iron surface: a hybrid quantum chemical/classical molecular dynamics study.

Using a hybrid quantum chemical/classical molecular dynamics method, we have studied the tribochemical reaction dynamics of molybdenum dithiocarbamate (MoDTC), a commonly used friction modifier in automobile engine oils. MoDTC molecule adsorbed on rubbing nascent iron surface was situated. We firstly investigated the dynamic behavior of MoDTC molecule on the rubbing Fe(001) surface. During the friction simulation, the elongation of Mo-O bonds was observed, forming the Mo2S4 and thiocarbamic acid molecules. To unveil the detailed mechanism of this bond elongation, the electronic states of the MoDTC molecule and Fe(001) surface were computed, and the catalytic effects of Fe(001) surface to the molecule was found. We also found that extreme friction would influence the complete Mo-O bond dissociation. By using the hybrid quantum chemical/classical molecular dynamics method, we successfully simulated the tribochemical reaction dynamics of MoDTC as a friction modifier and obtained the influences of nascent iron surface and friction on its chemical reaction.

A computational chemistry study on friction of h-MoS(2). Part I. Mechanism of single sheet lubrication.

In this work, we theoretically investigated the friction mechanism of hexagonal MoS(2) (a well-known lamellar compound) using a computational chemistry method. First, we determined several parameters for molecular dynamics simulations via accurate quantum chemistry calculations and MoS(2) and MoS(2-x)O(x) structures were successfully reproduced. We also show that the simulated Raman spectrum and peak shift on X-ray diffraction patterns were in good agreement with those of experiment. The atomic interactions between MoS(2) sheets were studied by using a hybrid quantum chemical/classical molecular dynamics method. We found that the predominant interaction between two sulfur layers in different MoS(2) sheets was Coulombic repulsion, which directly affects the MoS(2) lubrication. MoS(2) sheets adsorbed on a nascent iron substrate reduced friction further due to much larger Coulombic repulsive interactions. Friction for the oxygen-containing MoS(2) sheets was influenced by not only the Coulomb repulsive interaction but also the atomic-scale roughness of the MoS(2)/MoS(2) sliding interface.

A graph theoretical approach for assessing bio-macromolecular complex structural stability.

Fast and proper assessment of bio macro-molecular complex structural rigidity as a measure of structural stability can be useful in systematic studies to predict molecular function, and can also enable the design of rapid scoring functions to rank automatically generated bio-molecular complexes. Based on the graph theoretical approach of Jacobs et al. [Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins: Struct Funct Genet 44:150-165] for expressing molecular flexibility, we propose a new scheme to analyze the structural stability of bio-molecular complexes. This analysis is performed in terms of the identification in interacting subunits of clusters of flappy amino acids (those constituting regions of potential internal motion) that undergo an increase in rigidity at complex formation. Gains in structural rigidity of the interacting subunits upon bio-molecular complex formation can be evaluated by expansion of the network of intra-molecular inter-atomic interactions to include inter-molecular inter-atomic interaction terms. We propose two indices for quantifying this change: one local, which can express localized (at the amino acid level) structural rigidity, the other global to express overall structural stability for the complex. The new system is validated with a series of protein complex structures reported in the protein data bank. Finally, the indices are used as scoring coefficients to rank automatically generated protein complex decoys.

Quantum chemical studies for oxidation of morpholine by Cytochrome P450.

Since morpholine oxidation has recently been shown to involve Cytochrome P450, the study on its mechanism at molecular level using quantum chemical calculations for the model of cytochrome active site is reported here. The reaction pathway is investigated for two electronic states, the doublet and the quartet, by means of density functional theory. The results show that morpholine hydroxylation occurs through hydrogen atom abstraction and rebound mechanism. However, in the low spin state, the reaction is concerted and hydrogen atom abstraction yields directly ferric-hydroxy morpholine complex without a distinct rebound step while in quartet state the reaction is stepwise. The presence of nitrogen in a morpholine heterocycle is postulated to greatly facilitate hydrogen abstraction. The hydroxylated product undergoes intramolecular hydrogen atom transfer from hydroxy group to nitrogen, leading to the cleavage of the C-N bond and the formation of 2-(2-aminoethoxy) acetaldehyde. The cleavage of the C-N bond is indicated as the rate-determining step for the studied reaction. The assistance of explicit water molecule is shown to lower the energy barrier for the C-N bond cleavage in enzymatic environment whereas solvent effects mimicked by COSMO solvent model have minor influence on relative energies along the pathway.

Parsing error correction of medical phrases for semantic annotation of clinical radiology reports.

The purpose of this study is to develop a module for correcting errors in the product of a natural language parser. When tested with 300 CT reports, a total of 604 patterns were generated. The recall and precision was improved to 90.7% and 74.1% after processed by the module from initial 80.5% and 42.8% respectively. This rule-based module will help health care personnel reduce the cost of manual tagging correction for corpus building.

Oxidation mechanism in the metabolism of (S)-N-[1-(3-morpholin-4-ylphenyl)ethyl]-3-phenylacrylamide on oxyferryl active site in CYP3A4 Cytochrome: DFT modeling.

The metabolism mechanism of (S)-N-[1-(3-morpholin-4ylphenyl)ethyl]-3-phenylacrylamide, mediated by CYP3A4 Cytochrome has been investigated by density functional QM calculations aided with molecular mechanics/molecular dynamics simulations. Two different orientations of phenyl ring for substrate approach toward oxyferryl center, imposing two subsequent rearrangement pathways have been investigated. Starting from sigma-complex in perpendicular orientation enzymatic mechanism involves consecutive proton shuttle intermediate, which further leads to the formation of alcohol and ketone. Parallel conformation leads solely to ketone product by 1,2 hydride shift. Although parallel and perpendicular sigma-complexes are energetically equivalent both for the gas phase or PCM solvent model, molecular dynamics studies in full CYP3A4 environment show that perpendicular conformation of the sigma-complex should be privileged, stabilized by hydrophobic interactions of phenylacrylamide chain. After assessing probability of the two conformations we postulate that the alcohol, accessible with the lowest energy barriers should be the major metabolite for studied substrate and CYP3A4 enzyme.

Combinatorial computational chemistry approach for materials design: applications in deNOx catalysis, Fischer-Tropsch synthesis, lanthanoid complex, and lithium ion secondary battery.

Computational chemistry can provide fundamental knowledge regarding various aspects of materials. While its impact in scientific research is greatly increasing, its contributions to industrially important issues are far from satisfactory. In order to realize industrial innovation by computational chemistry, a new concept "combinatorial computational chemistry" has been proposed by introducing the concept of combinatorial chemistry to computational chemistry. This combinatorial computational chemistry approach enables theoretical high-throughput screening for materials design. In this manuscript, we review the successful applications of combinatorial computational chemistry to deNO(x) catalysts, Fischer-Tropsch catalysts, lanthanoid complex catalysts, and cathodes of the lithium ion secondary battery.

Three-dimensional quantitative structure-activity relationship (3 D-QSAR) and docking studies on (benzothiazole-2-yl) acetonitrile derivatives as c-Jun N-terminal kinase-3 (JNK3) inhibitors.

Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were developed for 44 (benzothiazole-2-yl) acetonitrile derivatives, inhibiting c-Jun N-terminal kinase-3 (JNK3). It includes molecular field analysis (MFA) and receptor surface analysis (RSA). The QSAR model was developed using 34 compounds and its predictive ability was assessed using a test set of 10 compounds. The predictive 3D-QSAR models have conventional r2 values of 0.849 and 0.766 for MFA and RSA, respectively; while the cross-validated coefficient r(cv)2 values of 0.616 and 0.605 for MFA and RSA, respectively. The results of the QSAR model were further compared with a structure-based analysis using docking studies with crystal structure of JNK3. Ligands bind in the ATP pocket and the hydrogen bond with GLN155 was found to be crucial for selectivity among other kinases. The results of 3D-QSAR and docking studies validate each other and hence, the combination of both methodologies provides a powerful tool directed to the design of novel and selective JNK3 inhibitors.

Tribochemical reaction dynamics of phosphoric ester lubricant additive by using a hybrid tight-binding quantum chemical molecular dynamics method.

To study the atomistic behavior of the phosphoric ester molecule on the nascent Fe surface under boundary lubrication conditions, we adopted a hybrid tight-binding quantum chemical molecular dynamics method. First, we investigated chemical interactions between phosphoric ester and the nascent Fe surface. Phosphoric ester was shown to interact with the nascent Fe surface, forming both covalent and ionic bonds. Formation and dissociation dynamics of covalent bonds during tribochemical reaction was clearly observed during the simulation. The effect of friction condition on the tribochemical reaction dynamics was then studied, and it was indicated that friction would influence the formation and the dissociation of covalent bonds. By using a hybrid tight-binding quantum chemical molecular dynamics method, we obtained insights on initial tribochemical reaction processes for the formation of tribofilm from the phosphoric ester molecule on the nascent Fe surface.

First-principles study on proton dissociation properties of fluorocarbon- and hydrocarbon-based membranes in low humidity conditions.

We present a theoretical study on the proton dissociation properties of the membranes for polymer electrolyte fuel cells. A density functional theory method is used to study the influence of fluorocarbon and hydrocarbon backbones on proton dissociation, the interaction of water molecules with the sulfonic acid group, and the energy barriers for proton dissociation. Better proton dissociation properties of CH(3)SO(3)H compared to CF(3)SO(3)H are observed from statistical analyses of the optimized structures for both systems. However, the calculated energy barriers for proton dissociation are lower for CF(3)SO(3)H than for the CH(3)SO(3)H system. At the same time, the interaction of water molecules is stronger for CH(3)SO(3)H than for CF(3)SO(3)H. Also, the analysis of the hydrogen-bonding network in both systems shows that the number of hydrogen bonds formed around the sulfonic acid group in CH(3)SO(3)H is larger than that in CF(3)SO(3)H. Therefore, the decrease of the energy barrier with increasing number of coordinating water molecules, pronounced in the case of CH(3)SO(3)H, may lower the barrier, which enhances good proton conductivity of a hydrocarbon-based polymer in low humidity conditions. Thus the hydration ability of a sulfonic acid group is an important factor for realizing better proton dissociation in low humidity conditions.

Robotic path planning and protein complex modeling considering low frequency intra-molecular loop and domain motions.

A novel algorithm is introduced to deal with intra-molecular motions of loops and domains that undergo proteins at interaction with other proteins. The methodology is based on complex energy landscape sampling and robotic motion planning. Mapping high flexibility regions on the protein underlies the proposed algorithm. This is the first time this type of research has been reported. Application of the methodology to several protein complexes where remarkable backbone rearrangement is observed shows that the new algorithm is able to deal with the problem of change of backbone conformation at protein interaction. We have implemented the module within the system MIAX (Macromolecular interaction assessment computer system) and together with our already reported soft and flexible docking algorithms we have developed a powerful tool for protein function analysis as part of wide genome function evaluation.

Semantic distribution study of noun*noun compounds in the Japanese CT clinical reports.

The purpose of this study is to investigate the distribution of the semantic relationships between the two atomic medical terms of the noun-noun compounds extracted from the clinical documents in Japanese. Only 29.9% of the compounds had the UMLS semantic relation defined (mainly including "location_of" and "adjacent_to"). The results indicated that the semantic relations defined in the UMLS semantic network are not enough for describing the noun-noun medical compounds extracted from the Japanese clinical reports.

Density functional study of the insertion and ring-opening mechanism of MCP over Cp2LaH and Cp2LuH catalysts.

The insertion and ring opening of methylenecyclopropane (MCP) catalyzed by Cp2LnH (Ln = La and Lu) was investigated using DFT method. Geometries and energies of the reactants, minima, and transition states for this reaction were obtained. The present study indicates the formation of Cp2LaH-MCP complex followed by 1,2-insertion through a tetrahedral transition state with subsequent ring opening at the proximal bond via hydrogen transfer transition state resulting in the formation of the final product.