Avaliação do valor prognóstico da detecção do status quimérico de pacientes após o transplante alogênico de células progenitoras hematopoéticas

Este trabalho teve por objetivo correlacionar o status quimérico de pacientes pós -TCPH alogênico com parâmetros clínicos, para avaliar o valor preditivo dos achados laboratorias de quimerismo. Amostras de sangue de 98 pacientes (67 em seguimento e 31 novos casos) foram submetidas à análise do status quimérico pós-TCPH. Os locianalisados por biologia molecular foram CS1PO, TPOX, F13A1, FESFPS, HUMTH01, VWA, SE33, HUMARA, HUMD21S11 e Amelogenina. Precocidade da evidência laboratorial de quimerismo misto (QM), em relação ao aparecimento dos sintomas clínicos de recaída, foi observada em 9 dos 12 pacientes nas LA, ou seja, nesses casos, a primeira manifestação de QM foi detectada pelo exame laboratorial antes de qualquer evidência citológica ou clínica de recaída. em todos eles, houve uma mudança terapêutica relacionada com esse momento do aparecimento do QM. em 100% dos pacientes com QM na LMC, a detecção do quimerismo pelo exame laboratorial foi anterior a qualquer evidência citológica ou clínica de recaída. de uma maneira geral, o exame laboratorial da avaliação do status quimérico pós-TCPH alogênico pela análise dos locihipervariáveis do genoma, mostrou ser um exame sensível, com detecção de até 1% de QM e precoce, visto que, muitas vezes, foi a primeira manifestação de doença residual antes de qualquer evidência citológica ou clínica da mesma. A associação da existência de QM e a recaída clínica e/ou óbito fica mais evidente nos casos de LA do que nos casos de LMC e AAS.

Vibrational analysis of boldine hydrochloride using QM/MM approach

A complete vibrational analysis was performed on the molecular structure of boldine hydrochloride using QM/MM method. The equilibrium geometry, harmonic vibrational frequencies and infrared intensities were calculated by QM/MM method with B3LYP/6-31G(d) and universal force field (UFF) combination using ONIOM code. We found the geometry obtained by the QM/MM method to be very accurate, and we can use this rapid method in place of time consuming ab initio methods for large molecules. A detailed interpretation of the infrared spectra of boldine hydrochloride is reported. The scaled theoretical wave numbers are in perfect agreement with the experimental values. The FT-IR spectra of boldine hydrochloride in the region 4000-500 cm(-1) were recorded in CsI (solid phase) and in chloroform with concentration 5 and 10 mg/ml.

Docking, molecular dynamics and QM/MM studies to delineate the mode of binding of CucurbitacinE to F-actin

CucurbitacinE (CurE) has been known to bind covalently to F-actin and inhibit depolymerization. However, the mode of binding of CurE to F-actin and the consequent changes in the F-actin dynamics have not been studied. Through quantum mechanical/molecular mechanical (QM/MM) and density function theory (DFT) simulations after the molecular dynamics (MD) simulations of the docked complex of F-actin and CurE, a detailed transition state (TS) model for the Michael reaction is proposed. The TS model shows nucleophilic attack of the sulphur of Cys257 at the beta-carbon of Michael Acceptor of CurE producing an enol intermediate that forms a covalent bond with CurE. The MD results show a clear difference between the structure of the F-actin in free form and F-actin complexed with CurE. CurE affects the conformation of the nucleotide binding pocket increasing the binding affinity between F-actin and ADP, which in turn could affect the nucleotide exchange. CurE binding also limits the correlated displacement of the relatively flexible domain 1 of F-actin causing the protein to retain a flat structure and to transform into a stable ``tense'' state. This structural transition could inhibit depolymerization of F-actin. In conclusion, CurE allosterically modulates ADP and stabilizes F-actin structure, thereby affecting nucleotide exchange and depolymerization of F-actin. (C) 2015 Elsevier Inc. All rights reserved.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by “GAMESS”, and the rest atoms are treated as MM part calculated by “TINKER”. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with theQMpart with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

Estudo sobre a PEC 10/1995, que institui o sistema distrital misto

Consultoria Legislativa - Área XIX - Ciência Política, Sociologia Política, História, Relações Internacionais.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by "GAMESS", and the rest atoms are treated as MM part calculated by "TINKER". The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(100) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the in-tidazole rings are attached to the substrate more tightly than other bases in this peptide.

Adoção do sistema eleitoral misto alemão nas eleições dos deputados federais brasileiros : a questão da fragmentação do sistema partidário

Analisa uma das principais teses recorrentemente suscitadas pelos defensores da implantação, no País, do referido sistema eleitoral alemão: a de que ele contribuiria para combater a fragmentação de nosso sistema partidário.

Hybrid Qm/Mm Simulation Of The Hydration Phenomena Of Dipalmitoylphosphatidylcholine Headgroup

The polar headgroup of dipalmitoylphosphatidylcholine (DPPC) molecule both in gas phase and aqueous Solution is investigated by the hybrid quantum mechanical/molecular mechanical (QM/MM) method, in which the polar head of DPPC molecule and the bound water molecules are treated with density functional theory (DFT), while the apolar hydrocarbon chain of DPPC molecule is treated with MM method. It is demonstrated that the hybrid QM/MM method is both accurate and efficient to describe the conformations of DPPC headgroup. Folded structures of headgroup are found in gas phase calculations. In this work, both monohydration and polyhydration phenomena are investigated. In monohydration, different water association sites are studied. Both the hydration energy and the quantum properties of DPPC and water molecules are calculated at the DFT level of theory after geometry optimization. The binding force of monohydration is estimated by using the scan method. In polyhydration, more extended conformations are found and hydration energies in different polyhydration styles are estimated. (C) 2008 Elsevier Inc. All rights reserved.

Evaluating boundary dependent errors in QM/MM simulations.

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful tool for studying chemical reactions, especially in complex biochemical systems. In most works to date, the quantum region is kept fixed throughout the simulation and is defined in an ad hoc way based on chemical intuition and available computational resources. The simulation errors associated with a given choice of the quantum region are, however, rarely assessed in a systematic manner. Here we study the dependence of two relevant quantities on the QM region size: the force error at the center of the QM region and the free energy of a proton transfer reaction. Taking lysozyme as our model system, we find that in an apolar region the average force error rapidly decreases with increasing QM region size. In contrast, the average force error at the polar active site is considerably higher, exhibits large oscillations and decreases more slowly, and may not fall below acceptable limits even for a quantum region radius of 9.0 A. Although computation of free energies could only be afforded until 6.0 A, results were found to change considerably within these limits. These errors demonstrate that the results of QM/MM calculations are heavily affected by the definition of the QM region (not only its size), and a convergence test is proposed to be a part of setting up QM/MM simulations.

Estudo da redução do NO pelo CO usando catalisadores de ródio suportado em óxido misto de cério e zircônio e óxido misto derivado de hidrotalcita

Esta tese teve como objetivo avaliar o desempenho de catalisadores de Rh suportados em cério-zircônio (CZ) e em óxido misto de magnésio e alumínio (HT) derivado de hidrotalcita na reação de redução do NO pelo CO em meio estequiométrico. Os suportes puros e impregnados com Rh foram nomeados CZ, RhCZ, HT e RhHT. Os suportes foram preparados por coprecipitação e o metal nobre foi adicionado no teor de 0,15% (m/m) por impregnação a seco. Foram realizados testes de caracterização como fisissorção de N2, DRX, TPR, espectroscopia Raman, DRIFTS, TGA-DTA e TPD-CO/NO. Para a avaliação catalítica, foi utilizada uma mistura de 1%NO + 1%CO em He e a atividade e seletividade foram expressas através das concentrações dos gases envolvidos ao longo de uma rampa de temperatura desde a temperatura ambiente até 500C. Os resultados de caracterização indicaram nítidas diferenças estruturais e físico-químicas entre os dois tipos de catalisadores nas isotermas de adsorção de N2, nos perfis de redução e nos difratogramas, já dando indícios de que os mecanismos de reação seriam diferentes. Pelas análises de DRIFTS identifica-se a presença de bandas características de espécies de CO adsorvidas no Rh somente para o catalisador RhCZ a baixa temperatura, ressaltando a interação Rh-CZ, também evidenciadas pelos resultados de Raman, mas que provavelmente não ocorrem com o óxido misto de Al e Mg. Observou-se que o suporte de CZ foi mais ativo a baixas temperaturas que o suporte de HT, porém o catalisador RhHT foi mais seletivo a N2 a 350C e emitiu menos N2O ao longo da faixa de temperatura avaliada do que o catalisador RhCZ. Resultados de TPD de NO e comparações de curvas experimentais e teóricas envolvendo as concentrações de CO, CO2 e NOx durante os testes catalíticos, acompanhados também pelas análises de DRIFTS nas mesmas condições, indicam que a redução do Rh e a afinidade do catalisador pelo NO são importantes para favorecer a maior seletividade da reação de redução do NO pelo CO a N2.

QM/MM simulation of liquid water with an adaptive quantum region.

The simulation of complex chemical systems often requires a multi-level description, in which a region of special interest is treated using a computationally expensive quantum mechanical (QM) model while its environment is described by a faster, simpler molecular mechanical (MM) model. Furthermore, studying dynamic effects in solvated systems or bio-molecules requires a variable definition of the two regions, so that atoms or molecules can be dynamically re-assigned between the QM and MM descriptions during the course of the simulation. Such reassignments pose a problem for traditional QM/MM schemes by exacerbating the errors that stem from switching the model at the boundary. Here we show that stable, long adaptive simulations can be carried out using density functional theory with the BLYP exchange-correlation functional for the QM model and a flexible TIP3P force field for the MM model without requiring adjustments of either. Using a primary benchmark system of pure water, we investigate the convergence of the liquid structure with the size of the QM region, and demonstrate that by using a sufficiently large QM region (with radius 6 Å) it is possible to obtain radial and angular distributions that, in the QM region, match the results of fully quantum mechanical calculations with periodic boundary conditions, and, after a smooth transition, also agree with fully MM calculations in the MM region. The key ingredient is the accurate evaluation of forces in the QM subsystem which we achieve by including an extended buffer region in the QM calculations. We also show that our buffered-force QM/MM scheme is transferable by simulating the solvated Cl(-) ion.

Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Elucidating solvent contributions to solution reactions with ab initio QM/MM methods.

Computer simulations of reaction processes in solution in general rely on the definition of a reaction coordinate and the determination of the thermodynamic changes of the system along the reaction coordinate. The reaction coordinate often is constituted of characteristic geometrical properties of the reactive solute species, while the contributions of solvent molecules are implicitly included in the thermodynamics of the solute degrees of freedoms. However, solvent dynamics can provide the driving force for the reaction process, and in such cases explicit description of the solvent contribution in the free energy of the reaction process becomes necessary. We report here a method that can be used to analyze the solvent contributions to the reaction activation free energies from the combined QM/MM minimum free-energy path simulations. The method was applied to the self-exchange S(N)2 reaction of CH(3)Cl + Cl(-), showing that the importance of solvent-solute interactions to the reaction process. The results were further discussed in the context of coupling between solvent and solute molecules in reaction processes.

The Role of Arg228 in the phosphorylation of galactokinase: The mechanism of GHMP kinases by QM/MM studies

GHMP kinases are a group of structurally-related small molecule kinases. They have been found in all kingdoms of life and are mostly responsible for catalysing the ATP-dependent phosphorylation of intermediary metabolites. Although the GHMP kinases are of clinical, pharmaceutical and biotechnological importance, the mechanism of GHMP-kinases is controversial. A catalytic base mechanism was suggested for mevalonate kinase that has a structural feature of the ?-phosphate of ATP close to an aspartate residue; however, for one GHMP member, homoserine kinase, where the residue acting as general base is absent, a direct phosphorylation mechanism was suggested. Furthermore, it has been proposed by some authors that all the GHMP kinases function via the direct phosphorylation mechanism. This controversy in mechanism has limited our ability to exploit these enzymes as drug targets and in biotechnology. Here the phosphorylation reaction mechanism of the human galactokinase, a member of GHMP kinase was investigated using molecular dynamics simulations and density functional theory-based QM/MM calculations (B3LYP-D/AMBER99). The reaction coordinates were localized by potential energy scan using adiabatic mapping method. Our results indicate that a highly conserved Glu174 captures Arg105 to the proximity of the a-phosphate of ATP forming a H-bond network, therefore the mobility of ATP in the large oxyanion hole is restricted. Arg228 functions to stabilize the negative charge developed at the ß,?-bridging oxygen of the ATP during bond cleavage. The reaction occurs via direct phosphorylation mechanism and the Asp186 in proximity of ATP does not directly participate in the reaction pathway. Since Arg228 is not conserved among GHMP kinases, reagents which form interactions with Arg228, and therefore can interrupt its function in phosphorylation may be developed into potential selective inhibitors for galactokinase.

Definição do modo de operação, descontínuo ou semi-descontínuo, para produção de bioetanol utilizando um novo substrato misto pela levedura Kluyveromyces sp.

Dissertação de mestrado, Engenharia Biológica, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015