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  • 1
    Language: English
    In: Bioorganic Chemistry, Oct, 2013, Vol.50, p.11(6)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.bioorg.2013.07.002 Byline: E. Dushanov, Kh. Kholmurodov, K. Yasuoka Abstract: Display Omitted Article History: Received 14 February 2013
    ISSN: 0045-2068
    Source: Cengage Learning, Inc.
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  • 2
    Language: English
    In: Physics of Particles and Nuclei Letters, 2013, Vol.10(6), pp.597-605
    Description: In this work, molecular dynamics (MD) simulations were performed on a DNA photolyase protein with two cofactors, FAD (flavin adenine dinucleotide) and MTHF (methenyltetrahydrofolate), inside the enzyme pocket. A DNA photolyase is a highly efficient light-driven enzyme that repairs the UV-induced cyclobutane-pyrimidine dimer in damaged DNA. We were aimed to compare the conformational changes of the FAD cofactor and other constituent fragments of the molecular system under consideration. The conformational behavior of the FAD molecule is very important for understanding the functional and structural properties of the DNA repair protein photolyase. The photoactive FAD is an essential cofactor both for specificial binding to damaged DNA and for catalysis. The second chromophore (MTHF or 8-HDF) is not necessary for catalysis and has no effect on specific enzyme—substrate binding. The obtained results were discussed to gain insight into the light-driven mechanism of DNA repair by a DNA photolyase enzyme—based on the enzyme structure, the FAD mobility, and conformation shape.
    Keywords: Genetic Research ; Purines ; Enzymes ; Nuclear Physics ; Carbocyclic Compounds ; Dna;
    ISSN: 1547-4771
    E-ISSN: 1531-8567
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  • 3
    Language: English
    In: Biophysics, 2015, Vol.60(4), pp.529-537
    Description: The structures of three forms of the dimeric enzyme human inosine triphosphate pyrophosphatase (hITPA) are considered for identifying conformation changes that determine the inactivation effect of the P32T mutation. Nanosecond molecular dynamics were analyzed and the values of mean-square deviations of atoms for the wild-type and mutant homodimers, as well as the heterodimer, were calculated. Simulation of an interval of 3 ns demonstrates stronger atom displacements in mutant protomers. During the simulated time interval, the strongest changes are observed in the loop between α2 and β2 (residues 28–33, the area of the P32T mutation), the loop between β5 and β6, and the C-terminal end. The loop between α2 and β2 has two conformations characterized by different position of Phe31 side group. The distance between Cys33(C α ) and Phe31(C z ) for wild-type and mutant protomers is ~ 9.0 and 5.5 Å, respectively. These conformations are stably maintained.
    Keywords: molecular dynamics (MD) simulation ; inosine triphosphate pyrophosphatase ; mutant homoand heterodimeric P32T enzymes
    ISSN: 0006-3509
    E-ISSN: 1555-6654
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  • 4
    Language: English
    In: Russian Journal of Physical Chemistry A, June, 2014, Vol.88(6), p.951(8)
    Description: Byline: O. V. Artoshina (1,2), M. Yu. Vorob'eva (2), E. B. Dushanov (1), Kh. T. Kholmurodov (1,2) Keywords: molecular dynamics simulation; formamide molecule; hydrocyanic acid solution; formamide aqueous solution; catalytic surface; titanium dioxide Abstract: The behavior of water--formamide and hydrocyanic acid--formamide solutions on an anatase surface have been studied using molecular dynamics (MD) simulation method. The interaction activation energies have been estimated for the temperature range from 250 up to 400 K. The diffusion coefficients and structural radial distribution functions have been calculated for the formamide, water and hydrocyanic acid on an anatase surface. The calculated activation energies of the water--formamide--anatase and hydrocyanic acid--formamide--anatase systems were analyzed and compared. A comparative analysis of the systems under investigation was performed and a possible correlation between the obtained MD results and the molecular mechanism involving the formamide's interaction with dioxide titan adsorbing surface were discussed. Author Affiliation: (1) Joint Institute for Nuclear Research, Dubna, Moscow oblast, 141980, Russia (2) Dubna International University, Dubna, Moscow oblast, 141980, Russia Article History: Registration Date: 13/05/2014 Received Date: 10/08/2013 Online Date: 14/05/2014 Article note: Original Russian Text [c] O.V. Artoshina, M.Yu. Vorob'eva, E.B. Dushanov, Kh.T. Kholmurodov, 2014, published in Zhurnal Fizicheskoi Khimii, 2014, Vol. 88, No. 6, pp. 983--990. The article was translated by the authors.
    Keywords: Activation Energy -- Chemical Properties
    ISSN: 0036-0244
    E-ISSN: 1531863X
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  • 5
    Language: English
    In: The open biochemistry journal, 2013, Vol.7, pp.33-43
    Description: Formamide contains the four elements (C, H, O, and N) most required for life and it is attractive as a potential prebiotic starting material for nucleobase synthesis. In the presence of catalysts (for example, TiO2) and with moderate heating, formamide can pass surface energy barriers, yielding a complete set of nucleic bases and acyclonucleosides, and favoring both phosphorylations and transphosphorylations necessary for life. In the reaction mechanism, interaction with water seems to be an essential factor for the formamide molecule to function. In this paper, a formamide-water solution on a TiO$_2$ (anatase) surface is simulated using the molecular dynamics method, and activation energy calculations are performed for the temperature range of T = 250 K to T = 400 K. A correlation is established between the diffusion and density profiles for the formamide and water molecules on an anatase surface. Also, the calculated activation energies of the formamide-water-anatase and formamide-water-platinum systems are compared. A comparative analysis is performed of the behavior of formamide-water and ethanol-water interaction on the same (anatase and platinum) surfaces.
    Keywords: Formamide Molecule ; MD Simulations. ; Activation Energy ; Catalysts ; Surface ; Water
    ISSN: 1874-091X
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  • 6
    Language: Russian
    In: Biofizika, 2015, Vol.60(4), pp.646-55
    Description: The structure of three forms of a dimeric enzyme, human inosine triphosphate pyrophosphatase, is considered to identify the enzyme conformation changes causing the inactivation effect of a P32T mutation. Analysis of a nanosecond molecular dynamics is performed; the mean square deviations of the atoms between the wild-type and mutant homodimers, and also the heterodimer are calculated. A 3 ns modeling shows a greater displacement of atoms in mutant protomers. During molecular dynamics simulation, the strongest changes are observed in the loop between α2 and β2 (amino acid residues 28-33, an area of the P32T mutation), the loop between β5 and β6, and the C-terminal amino acid residues. The loop between (α2 and β2 has two conformations characterized by different positions of the Phe31 aromatic group. The distance between Cys33 (Cα) and Phe31 (C(z)) for wild-type and mutant protomers was -9 and 5.5 Å, respectively. These conformations were kept constant.
    Keywords: Molecular Dynamics Simulation ; Mutation ; Amino Acids -- Chemistry ; Inosine Triphosphate -- Chemistry ; Pyrophosphatases -- Chemistry
    ISSN: 0006-3029
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 7
    Language: English
    In: Materials transactions, 2015-09, Vol.56(9), pp.1390-1393
    Description: Material Type: 記事・論文
    Keywords: Nucleotide Chain (Nc) ; Gold Nanoparticles (Nps) ; Carbon Nanotube (Cnt) ; Van Der Waals (Vdw) Forces ; Molecular Dynamics (Md)
    ISSN: 13459678
    E-ISSN: 13475320
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  • 8
    Language: English
    In: Physics of Particles and Nuclei Letters, 2012, Vol.9(6), pp.541-551
    Description: The water-surface interaction is a research target of great importance for a broad spectrum of technological applications and fundamental scientific disciplines. In the present study, a comparative analysis is performed to clarify the structural and diffusion properties of water on a number of oxide surfaces. Based on the molecular dynamics (MD) simulation method, the water-surface interaction mechanism was investigated for the oxide materials TiO 2 (anatase), Al 2 O 3 (corundum), and Fe 2 O 3 (hematite). A comparison of the water-TiO 2 interaction with the water-Al 2 O 3 and water-Fe 2 O 3 systems demonstrates the specificity of the adsorption and layer formation on the atomic/molecular level scale. The obtained MD analysis data point to a considerable enhancement of water-TiO 2 surface adsorption and a relatively high density distribution profile near the surface. The novel data on water structure and diffusion on oxide surfaces are discussed from the point of view of possible material innovation and design.
    Keywords: Physics ; Particle and Nuclear Physics ; Physics;
    ISSN: 1547-4771
    E-ISSN: 1531-8567
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  • 9
    Language: English
    In: The open biochemistry journal, 2014, Vol.8, pp.35-43
    Description: An Anacystis nidulans photolyase enzyme containing two chromophore cofactors was simulated for a photoreaction DNA repairing process via molecular dynamics (MD) method. A novel approach has been introduced for the electron transfer between the FAD (flavin adenine dinucleotide; flavin) molecule and CPD (cyclobutane pyrimidine dimer). This approach involves four simulation stages with different charges for the FAD and CPD fragments and a role of a charged state of the active cofactor was qualified during the MD modeling. Observations show that flavin has actively participated in a charge transfer process, thereby involving the conformational changes of the DNA and CPD substrate fragment. The DNA conformation behavior has shown to correlate with the electron transfer from flavin to CPD. This is manifested on the similarities of the DNA repairing process by excision repair of the UV photoproducts.
    Keywords: Charge Transfer ; DNA Repair ; Chromophore Cofactors ; Cyclobutane Pyrimidine Dimer ; Flavin Adenine Dinucleotide ; Molecular Dynamics Modeling ; Photolyase Enzyme.
    ISSN: 1874-091X
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  • 10
    Language: English
    In: Bioorganic Chemistry, October 2013, Vol.50, pp.11-16
    Description: The photoreaction and adsorption properties on surfaces, thermal decomposition, chemical transformation, and other properties of the formamide molecule are widely used to understand the origins of the formation of biological molecules (nucleosides, amino acids, DNA, monolayers, etc.) needed for life. The titanium oxide (TiO ) surface can act both as a template on which the accumulation of adsorbed molecules like formamide occurs through the concentration effect, and as a catalytic material that lowers the activation energy needed for the formation of intermediate products. In this paper, a formamide–water solution interacting with TiO (anatase) surface is simulated using the molecular dynamics method. The structural, diffusion and density properties of formamide–water mixture on TiO are established for a wide temperature range from = 250 K up to = 400 K.
    Keywords: Formamide Molecule ; Water ; Surface ; Catalysts ; Molecular Structures ; Chemistry ; Anatomy & Physiology
    ISSN: 0045-2068
    E-ISSN: 1090-2120
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