Navegando por Palavras-chave "Molecular dynamics simulations"

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    P-I class metalloproteinase from Bothrops moojeni venom is a post-proline cleaving peptidase with kininogenase activity: Insights into substrate selectivity and kinetic behavior
    (Elsevier B.V., 2014-03-01) Okamoto, Debora Noma [UNIFESP]; Kondo, Marcia Yuri [UNIFESP]; Oliveira, Lilian Caroline Gonçalves de [UNIFESP]; Honorato, Rodrigo Vargas; Zanphorlin, Letícia Maria; Coronado, Monika Aparecida; Araujo, Mariana Silva [UNIFESP]; Motta, Guacyara da [UNIFESP]; Veronez, Camila Lopes [UNIFESP]; Andrade, Sheila Siqueira [UNIFESP]; Oliveira, Paulo Sergio Lopes de; Arni, Raghuvir Krishnaswamy; Cintra, Adélia Cristina Oliveira de; Sampaio, Suely Vilela; Juliano, Maria Aparecida [UNIFESP]; Juliano, Luiz [UNIFESP]; Murakami, Mario Tyago; Gouvea, Iuri Estrada [UNIFESP]; Universidade Federal de São Paulo (UNIFESP); Ctr Nacl Pesquisas Energia & Mat; Universidade Estadual de Campinas (UNICAMP); UNESP; Universidade de São Paulo (USP)
    Snake venom metalloproteinases (SVMPs) belonging to P-I class are able to hydrolyze extracellular matrix proteins and coagulation factors triggering local and systemic reactions by multiple molecular mechanisms that are not fully understood. BmooMP alpha-I, a P-I class SMVP from Bothrops moojeni venom, was active upon neuro- and vaso-active peptides including angiotensin I, bradykinin, neurotensin, oxytocin and substance P. Interestingly, BmooMPa-I showed a strong bias towards hydrolysis after proline residues, which is unusual for most of characterized peptidases. Moreover, the enzyme showed kininogenase activity similar to that observed in plasma and cells by kallikrein. FRET peptide assays indicated a relative promiscuity at its S-2-S '(2) subsites, with proline determining the scissile bond. This unusual post-proline cleaving activity was confirmed by the efficient hydrolysis of the synthetic combinatorial library MCA-GXXPXXQ-EDDnp, described as resistant for canonical peptidases, only after Pro residues. Structural analysis of the tripeptide LPL complexed with BmooMP alpha-I, generated by molecular dynamics simulations, assisted in defining the subsites and provided the structural basis for subsite preferences such as the restriction of basic residues at the S-2 subsite due to repulsive electrostatic effects and the steric impediment for large aliphatic or aromatic side chains at the Si subsite. These new functional and structural findings provided a further understanding of the molecular mechanisms governing the physiological effects of this important class of enzymes in envenomation process. (c) 2014 Elsevier B.V. All rights reserved.
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    Simulações computacionais de eletrólitos em interfaces
    (Universidade Federal de São Paulo, 2018-06-19) Cardoso, Pierluigi Fortunato [UNIFESP]; Siqueira, Leonardo José Amaral de [UNIFESP]; Universidade Federal de São Paulo (UNIFESP)
    In this work the molecular dynamics, which is a computational simulation method, is used for the study of electrical, structural and dynamics properties of electrolytes for lithium and / or supercapacitor batteries. The electrolytes formed by ionic liquid and polymer were simulated at the interface with a flat electrode model, ionic liquid (IL), P(EO)7,8-IL, P(EO)15,6-IL e P(EO)15,6-Li+-IL at different densities of charges, 0q/nm2, 0,25 q/nm2, 0,5q/nm2, 0,75 q/nm2 and 1,0 q/nm2. The potential drop were calculated and assisted the analysis of the differential capacitances, being possible to observe the effect of the polymer poly (ethylene oxide) that acted like solvent, causing the decrease of the overscreening in relation to the system composed only by ionic liquid [EMIm]-[TFSI]. In this way, it was possible to calculate the differential capacitances that were also calculated for the different systems, noting that the increase in the number of molecules of PEO influences the decrease of the differential capacitances for each of the systems, such as the P(EO)15,6-IL, which has the highest amount of polymer PEO, had the lowest differential capacitance (3.4 on the positive electrode and 2.9 on the negative electrode) in relation to the other systems studied. In the case of batteries, the values obtained for the lithium ion to adsorb on the surface of the negative electrode is between 3,66V ~ 5,74V.