Ligand recognition by chloroperoxidase using molecular interaction fields and quantum chemistry calculations

Correa-Basurto, José; Aburto, Jorge; Ferrara, José Trujillo; Torres, Eduardo

doi:10.1080/08927020701342041

Cited by 17 publications

(8 citation statements)

References 30 publications

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“…Thus, we consider that a relationship should exist between the formation of the T-shaped structure in asphaltene aggregates and the appearance of heteroatoms. A similar investigation had been made by J. Correa-Basurto’s work where they found a dihedral angle of 136.968° by ab initio calculations.…”

Section: Resultssupporting

confidence: 71%

Aggregate Structure in Heavy Crude Oil: Using a Dissipative Particle Dynamics Based Mesoscale Platform

et al. 2010

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Heavy crude oil consists of thousands of compounds and much of them have a fairly large relative molar mass and complex structure. It is hard to learn the dynamic behavior of this fluid system at all atom models. The present study aims at constructing a mesoscale platform to explore aggregate behavior of asphaltenes in heavy crude oil. The aggregate structure in heavy crude oils was investigated by introducing rigid body fragments, which represents the significant presence of structures of fused aromatic rings in fractions such as asphaltenes and resins into dissipative particle dynamics (DPD). Another pressing task about how to determine the structure of the average model molecules and conservative force parameters was discussed in detail. With some regularity concerning the number of rings, the distribution of side chains and heteroatoms in average model molecules are revealed. Finally, we integrated the modified DPD program, model molecules, and the parameters selected for the preliminarily simulation of the heavy crude oil and emulsion system. The interlayer distance and the number of layers of the well-ordered structure in heavy crude oil are similar to some molecular dynamics works and supported by X-ray and transmission electron microscopy (TEM) experimental data. The relationship between the stability and the mass ratio among components of heavy crude oil is explored, and the result of our simulations fits the regularity Shell once published. In the emulsion system, the surfactant-like feature of asphaltenes and resins are observed. The preliminary simulation results demonstrate the validity of the rotational algorithm and parameters employed and encourage us to extend this platform to study the rheological and colloidal characteristics of heavy crude oils in the future.

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Section: Resultssupporting

confidence: 71%

Aggregate Structure in Heavy Crude Oil: Using a Dissipative Particle Dynamics Based Mesoscale Platform

et al. 2010

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“…Thus, HSA movements are not sufficient to unfold the protein (see Figure 2), reproducing the environmental behavior of HSA. The results of this work suggest that HSA flexibility underlies the preferential affinity for several ligands by this protein, as has been observed for other known promiscuous proteins, such as CYP450 and chloroperoxidase 44, 45. These MD simulations support the idea that HSA displays conformational movements that modify several molecular properties and allow it to bind to several ligands at different times or even at the same time 46.…”

Section: Resultssupporting

confidence: 82%

The persistence of isolated tumor cells in bone marrow from patients with breast carcinoma predicts an increased risk for recurrence

Pitini

Arrigo

Righi

2005

Cancer

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We have carried out isotopic analysis (δ13C and δ15N) on five salt‐preserved bodies from the salt mine at Chehr Abad, Iran, dating from the 4th C. BC through to the 4th C. AD. In an attempt to identify the geographical origins of these people, we have analyzed over a hundred archeological bone samples from various archeological sites in Iran. From the faunal remains, we observe that the entire ecosystem appears to be enriched in 15N, which we suggest is due to the semi‐arid nature of the region. We have also observed a number of cattle remains from one site (Nargas Tepe) which have a significant C4 component to their diet from the 4th millennium BC. By combining our data with those published by [Bocherens et al.: Environ Archaeol 5 (2000) 1–19; Bocherens et al.: J Arch Sci 33 (2006) 253–264], we suggest that two of the “mummies” may have come from the Tehran/Qazvin Plain region (i.e., relatively local to the salt mine), and a further two appear on isotopic grounds to have come from the northeast of Iran or the Turkmenistan steppes. The fifth (no. 4), the best preserved, appears to have come from further afield. Collectively, these mummies and their contexts augment our knowledge of social mobility and technical innovation in Iran during the Achaemenid period. Am J Phys Anthropol 143:343‐354, 2010. © 2010 Wiley‐Liss, Inc.

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“…The molecular modeling has been used to study the binding of 4,6-dimethyl dibenzothiophene with CPO in order to obtain information about the ligand recognition and interactions mechanism. 38 The molecular dynamic calculations showed the existence of two substrate binding sites in CPO with similar affinities for the substrate. The results were extended to carbazole as substrate.…”

Section: Resultsmentioning

confidence: 96%

Stereoselective oxidation of R-(+)-limonene by chloroperoxidase from Caldariomyces fumago

Águila

Vázquez-Duhalt²,

Tinoco³

et al. 2008

Green Chem.

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The oxidation of R-(+)-limonene by chloroperoxidase (CPO) from Caldariomyces fumago is reported. The reaction was performed in 60 mM phosphate buffer at pH 3.0 and 6.0, and in the absence and in the presence of chloride ions. In the absence of chloride ions, at both pH values, the reaction was regio and stereoselective with a diasteromeric excess (de) >99% of (1S,2S)-4R-limonene-1,2-diol. On the other hand, when the reaction was carried out in the presence of chloride ions an enhancement in the reaction rate was observed, maintaining the regioselectivity, but not the stereoselectivity (de <5.4). The reaction products under these conditions were identified as (1S,2S)-4R-limonene-1,2-diol and (1R,2R)-4R-limonene-1,2-diol. It seems that in the absence of chloride ions the stereoselectivity is determined by stereospecific interaction of limonene with CPO active site, as supported by docking analysis, while in the presence of potassium chloride the limonene oxidation also occurs by the produced hypochlorite without stereoselectivity.

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Ligand recognition by chloroperoxidase using molecular interaction fields and quantum chemistry calculations

Cited by 17 publications

References 30 publications

Aggregate Structure in Heavy Crude Oil: Using a Dissipative Particle Dynamics Based Mesoscale Platform

Aggregate Structure in Heavy Crude Oil: Using a Dissipative Particle Dynamics Based Mesoscale Platform

The persistence of isolated tumor cells in bone marrow from patients with breast carcinoma predicts an increased risk for recurrence

Stereoselective oxidation of R-(+)-limonene by chloroperoxidase from Caldariomyces fumago

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