11 |
Interakce kovových iontů v bioorganickém prostředí; kvantově-chemická a molekulově-mechanická výpočetní studie. / Interaction of Metal Cations in Bioorganic Environment. Computational Study Using Quantum Mechanics and Molecular MechanicsTools.Futera, Zdeněk January 2012 (has links)
Interactions of Metal Cations in Bioorganic Environment Computational Study Using Quantum Mechanics and Molecular Mechanics Tools Zdeněk Futera Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied by QM/MM computational technique. The whole re- action mechanism is divided into three phases - hydration of [RuII (η6 - benzene)(en)Cl]+ , consequent binding DNA and final intra-strand cross-link formation between two adjacent guanines. Free energy profiles of all reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex is described by DFT. For that purpose, special QM/MM software was developed to couple Gaussian and Amber programs. Calculated free energy barriers of Ru(II) hydration as well as DNA binding process are in good agreement with experimentally determined rate constants. Reaction pathway for cross-link formation was predicted that is feasible from both thermodynamical and kinetical point of view.
|
12 |
[pt] A RECONCILIAÇÃO ENTRE O COEFICIENTE DE PARTIÇÃO OCTANOL-ÁGUA EXPERIMENTAL E CALCULADO DO 1,2- DIPALMITOIL-SN-GLICERO-3-FOSFATIDILCOLINA USANDO DINÂMICA MOLECULAR ATOMÍSTICA: UMA QUESTÃO EM ABERTO / [en] THE RECONCILIATION BETWEEN THE EXPERIMENTAL AND CALCULATED OCTANOL-WATER PARTITION COEFFICIENT OF 1,2-DIPALMITOYL-SNGLYCERO-3-PHOSPHATIDYLCHOLINE USING ATOMISTIC MOLECULAR DYNAMICS: AN OPEN QUESTIONRAYLA KELLY MAGALHAES COSTA 18 May 2023 (has links)
[pt] O coeficiente de partição octanol-água do composto 1,2-dipalmitoilsn-glicero-3-fosfatidilcolina (DPPC) foi investigado utilizando os métodos
de integração termodinâmica e amostragem guarda-chuva através de
simulações de dinâmica molecular atomística. Os campos de força
AMBER/GAFF e CHARMM/CGenFF foram usados com seis modelos de
água (SPC, TIP3P, TIP4P, TIP5P, OPC3 e OPC4) amplamente utilizados
em simulações de dinâmica molecular. Dentre os modelos utilizados, o
modelo de água OPC4 com os dois campos de força em estudo forneceu
a melhor concordância com o coeficiente de partição experimental
octanol-água do DPPC. No entanto, ainda existe muito espaço para
melhorias nos modelos de água que estimam a tensão superficial de
forma apropriada. Usando o modelo de água OPC4, a energia livre de
Gibbs de transferência do DPPC do octanol para a fase aquosa foi
calculada em 19,8(mais ou menos)0,3 e 20,2(mais ou menos)0,3 kcal mol-1
, estimando um coeficiente de
partição octanol-água de 14,5(mais ou menos)0,4 e 14,8(mais ou menos)0,3 para os campos de força
AMBER/GAFF e CHARMM/CGenFF, respectivamente. A amostragem
guarda-chuva apresentou problemas de arrastes de moléculas de uma
fase para outra, gerando artefatos e consequentemente subestimando os
valores de energia livre e de coeficiente de partição octanol-água. Este
estudo mostra a importância do desenvolvimento de novos modelos de
água que reproduzam com precisão todas as suas características
experimentais. A conciliação entre medições experimentais e cálculos
teóricos do coeficiente de partição de moléculas anfifílicas poderia ser
resolvida através do ajuste dos parâmetros do modelo de água. Este
estudo possui grande importância na simulação de propriedades
moleculares de importância em muitas áreas de aplicações científicas e
industriais, tais como biofísica, surfactante, coloides, membranas,
medicina, nanotecnologia, e indústrias alimentícias e farmacêuticas. / [en] The octanol-water partition coefficient of the compost 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) molecule wasinvestigated using the methods of thermodynamic integration and umbrellasampling through atomistic molecular dynamics simulations. TheAMBER/GAFF and CHARMM/CGenFF force fields were used with sixwater models (SPC, TIP3P, TIP4P, TIP5P, OPC3, and OPC4) widely usedin molecular dynamics simulations. Among the models used, the OPC4water model with the two force fields provided the best agreement with theexperimental octanol-water partition coefficient of the DPPC. However,there is still much room for improvement in water models that correctlyestimate the surface tension. Using the OPC4 water model, the Gibbs freeenergy of transferring DPPC from octanol to the aqueous phase wascalculated to be 19.8(plus minus)0.3 and 20.2(plus minus)0.3 kcal mol-1, estimating an octanolwater partition coefficient of 14.5(plus minus)0.4 and 14.8(plus minus)0.3 for the AMBER/GAFFand CHARMM/CGenFF force fields, respectively. Umbrella samplingpresented issues of molecules being dragged between the two phases,generating artifacts, and consequently underestimating the values of freeenergy and octanol-water partition coefficient. This study shows theimportance of developing new models of water that accurately reproduceall its experimental characteristics. The reconciliation betweenexperimental measurements and theoretical calculations of partitioncoefficients of amphiphilic molecules. This study may have greatimportance in many areas of scientific and industrial applications, such asbiophysics, surfactant, colloids, membranes, medicine, nanotechnology,and food and pharmaceutical industries.
|
13 |
Study of Protein-protein Interactions using Molecular Dynamics SimulationMehrani, Ramin 16 September 2022 (has links)
No description available.
|
14 |
Selectivity, Regulation, and Inhibition of Aquaporin Channels. A Molecular Dynamics Study / Selektivität, Regulation und Inhibition von Aquaporinkanälen. Eine Untersuchung mittels MolekulardynamiksimulationenHub, Jochen Sebastian 28 January 2008 (has links)
No description available.
|
15 |
Příprava a charakterizace vazebných proteinů mimikujících epitopy protilátek neutralizujících virus HIV-1 / Preparation and Characterization of Protein Binders Mimicking Epitopes of HIV-1 Neutralizing AntibodiesŠulc, Josef January 2021 (has links)
For three decades, the ongoing HIV pandemic has taken the lives of tens of millions of people. Still, more tens of millions are fighting this incurable disease today. Current failures in combating this global problem are caused mainly by the virus's extreme ability of mutation, its very effective molecular shield which repels the immune system's attacks, and its immense variability. A breakthrough, achieved relatively recently, is the discovery of the so-called broadly neutralizing antibodies against HIV-1, which carry a very efficient and broad neutralizing response. So far, it's not known how to elucidate the production of these antibodies in the infected hosts to quell or altogether eliminate the virus. This work deals with experimental results, which led to both in vivo and in vitro proof-of-concept of the so-called protein mimetics, the ability to imitate viral surface epitopes, and therefore stimulate an efficient immune response carried by targeted broadly neutralizing antibodies. This effect is mediated by recombinant binding proteins, based on the Myomedin scaffold. This work describes the selection and characterization of these binding proteins mimicking the epitopes of one of the most effective broadly neutralizing antibodies, 10E8. It shows that the binding affinities of selected...
|
Page generated in 0.0193 seconds