Relationship between global structural parameters and Enzyme Commission hierarchy: Implications for function prediction

In protein databases there is a substantial number of proteins structurally determined but without function annotation. Understanding the relationship between function and structure can be useful to predict function on a large scale. We have analyzed the similarities in global physicochemical parameters for a set of enzymes which were classified according to the four Enzyme Commission (EC) hierarchical levels. Using relevance theory we introduced a distance between proteins in the space of physicochemical characteristics. This was done by minimizing a cost function of the metric tensor built to reflect the EC classification system. Using an unsupervised clustering method on a set of 1025 enzymes, we obtained no relevant clustering formation compatible with EC classification. The distance distributions between enzymes from the same EC group and from different EC groups were compared by histograms. Such analysis was also performed using sequence alignment similarity as a distance. Our results suggest that global structure parameters are not sufficient to segregate enzymes according to EC hierarchy. This indicates that features essential for function are rather local than global. Consequently, methods for predicting function based on global attributes should not obtain high accuracy in main EC classes prediction without relying on similarities between enzymes from training and validation datasets. Furthermore, these results are consistent with a substantial number of studies suggesting that function evolves fundamentally by recruitment, i.e., a same protein motif or fold can be used to perform different enzymatic functions and a few specific amino acids (AAs) are actually responsible for enzyme activity. These essential amino acids should belong to active sites and an effective method for predicting function should be able to recognize them. (C) 2012 Elsevier Ltd. All rights reserved.

Host-guest interactions between xanthones and water: the role of O-H center dot center dot center dot O, C-H center dot center dot center dot O, and pi center dot center dot center dot pi contacts in the channel- and cage-type frameworks

In this article were studied two xanthone derivatives known as 1,5-dihydroxy-8-methoxyxanthone (I) and 1,3,7-trihydroxy-8-methoxyxanthone (II), which show one water molecule into their crystal structures. In xanthone I, there are water wires contributing to build up channel-like cavities along the c axis, whereas in xanthone II the water is surrounded by three xanthone molecules forming a cage-type structure. The geometries of I and II were optimized using the density functional theory method with B3LYP functional, and the results were compared with crystal structure. Both theoretical and experimental investigations reveal a concordance between structural parameters, with the xanthone core presenting an almost flat conformation and substituents adopting the more stable orientations. In the two compounds, the hydroxyl group linked at position 1 is involved in a resonance-assisted hydrogen bond with the carbonyl group. Besides, the supramolecular arrangement of the host/guest systems are stabilized mainly by classical intermolecular hydrogen bonds (O-H center dot center dot center dot O) involving xanthone-to-water and xanthone-to-xanthone. In addition, C-H center dot center dot center dot O weak hydrogen bonds, as well as pi-pi interactions play an important role to stabilize the crystal self-assembly of xanthones I and II. The results reported here underline the role of inclusion of water molecules and their different arrangement into the crystal structure of two xanthone host/guest systems.

Unveiling the relationship between complex networks metrics and word senses

The automatic disambiguation of word senses (i.e., the identification of which of the meanings is used in a given context for a word that has multiple meanings) is essential for such applications as machine translation and information retrieval, and represents a key step for developing the so-called Semantic Web. Humans disambiguate words in a straightforward fashion, but this does not apply to computers. In this paper we address the problem of Word Sense Disambiguation (WSD) by treating texts as complex networks, and show that word senses can be distinguished upon characterizing the local structure around ambiguous words. Our goal was not to obtain the best possible disambiguation system, but we nevertheless found that in half of the cases our approach outperforms traditional shallow methods. We show that the hierarchical connectivity and clustering of words are usually the most relevant features for WSD. The results reported here shed light on the relationship between semantic and structural parameters of complex networks. They also indicate that when combined with traditional techniques the complex network approach may be useful to enhance the discrimination of senses in large texts. Copyright (C) EPLA, 2012

The T-2 phase in the Nb-Si-B system studied by ab initio calculations and synchrotron X-ray diffraction

The solid solution based on Nb5Si3 (Cr5B3 structure type, D8(l), tl32, 14/mcm, No140, a=6.5767 angstrom, c=11.8967 angstrom) in the Nb-Si-B system was studied from the structural and thermodynamic point of view both experimentally and by ab initio calculations. Rietveld refinement of powder X-ray synchrotron data allowed to determine the boron to silicon substitution mechanism and the structural parameters. Ab initio calculations of different ordered compounds and selected disordered alloys allowed to obtain in addition to the enthalpy of formation of the solution, substitution mechanism and structural parameters which are in excellent agreement with the experimental data. The stability of the phase is discussed. (C) 2012 Elsevier Inc. All rights reserved.

Thiosaccharine disulfide: synthesis, crystal structure, spectroscopic characterization and theoretical study

The title compound, (thiosaccharine disulfide), bis[1,10dioxide-2,3-dihidro-1,2-benzoisothiazol]disulfide, (tsac)2 has been synthesized and fully characterized by UV–Visible, IR, Raman, 1H and 13C NMR spectroscopy elemental analysis and structural X-ray crystallography. A DFT theoretical study has been performed and good agreement between experimental and theoretical values of structural parameters and vibration frequencies have been achieved.

Structural and kinetic studies of Schistosoma mansoni adenylate kinases

The human parasite Schistosoma mansoni is totally dependent on the purine salvage pathway in order to supply large quantities of purine precursors for its energy and DNA biosynthetic needs. Adenylate kinase (ADK) is responsible for the conversion of AMP (produced by the adenosine kinase reaction) into ADP, which is subsequently converted into ATP by nucleoside diphosphate kinase (NDPK). ADK and NDPK are the most active enzymes of the pathway, probably reflecting an evolutionary adaptation due to the intense use of the branch in which they participate. However, notwithstanding their importance very little information has been accumulated found regarding these enzymes. In this work two adenylate kinases from S. mansoni were cloned and heterologously expressed in Escherichia coil. The purified products were utilized in activity assays, and displayed kinetic parameters similar to the corresponding human orthologous proteins. The cytosolic S. mansoni ADK was crystallized and its structure solved allowing us to detect a difference in the nucleotide binding site when compared with the human ortholog. (C) 2012 Elsevier B.V. All rights reserved.

Interaction between bradykinin potentiating nonapeptide (BPP9a) and beta-cyclodextrin: A structural and thermodynamic study

Herein, we demonstrate the physical and chemical characterizations of the supramolecular complex formed between beta-cyclodextrin (beta CD) and bradykinin potentiating nonapeptide (BPP9a), an endogenous toxin found in Bothrops jararaca. Circular dichroism results indicate a conformational change in the BPP9a secondary structure upon its complexation with beta CD. Nuclear magnetic resonance results, mainly from NOESY experiments, and theoretical calculations showed a favorable interaction between the tryptophan residue of BPP9a and the beta CD cavity. Thermodynamic inclusion parameters were investigated by isothermal titration calorimetry, demonstrating that beta CD/BPP9a complex formation is an exothermic process that results in a reduction in entropy. Additionally, in vitro degradation study of BPP9a against trypsin (37 degrees C, pH 7.2) showed higher stability of peptide in presence of beta CD. This beta CD/BPP9a complex, which presents new chemical properties arising from the peptide inclusion process, may be useful as an antihypertensive drug in oral pharmaceutical formulations. (C) 2011 Elsevier B.V. All rights reserved.

Effects of lithium on oxidative stress parameters in healthy subjects

Increased neuronal oxidative stress (OxS) induces deleterious effects on signal transduction, structural plasticity and cellular resilience, mainly by inducing lipid peroxidation in membranes, proteins and genes. Major markers of OxS levels include the thiobarbituric acid reactive substances (TBARS) and the enzymes superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase. Lithium has been shown to prevent and/or reverse DNA damage, free-radical formation and lipid peroxidation in diverse models. This study evaluates OxS parameters in healthy volunteers prior to and following lithium treatment. Healthy volunteers were treated with lithium in therapeutic doses for 2-4 weeks. Treatment with lithium in healthy volunteers selectively altered SOD levels in all subjects. Furthermore, a significant decrease in the SOD/CAT ratio was observed following lithium treatment, wich was associated with decreased OxS by lowering hydrogen peroxide levels. This reduction in the SOD/CAT ratio may lead to lower OxS, indicated primarily by a decrease in the concentration of cell hydrogen peroxide. Overall, the present findings indicate a potential role for the antioxidant effects of lithium in healthy subjects, supporting its neuroprotective profile in bipolar disorder (BD) and, possibly, in neurodegenerative processes.

A Robust Structural PGN Model for Control of Cell-Cycle Progression Stabilized by Negative Feedbacks

The cell division cycle comprises a sequence of phenomena controlled by a stable and robust genetic network. We applied a probabilistic genetic network (PGN) to construct a hypothetical model with a dynamical behavior displaying the degree of robustness typical of the biological cell cycle. The structure of our PGN model was inspired in well-established biological facts such as the existence of integrator subsystems, negative and positive feedback loops, and redundant signaling pathways. Our model represents genes interactions as stochastic processes and presents strong robustness in the presence of moderate noise and parameters fluctuations. A recently published deterministic yeast cell-cycle model does not perform as well as our PGN model, even upon moderate noise conditions. In addition, self stimulatory mechanisms can give our PGN model the possibility of having a pacemaker activity similar to the observed in the oscillatory embryonic cell cycle.

Structural and textural studies of NiO impregnation in mesoporous ZrO2-CeO2 for catalysis applications.

The synthesis of zirconia-based ordered mesoporous structures for catalytic applications is a research area under development. These systems are also potential candidates as anodes in intermediate temperature solid oxide fuel cells (it-SOFC) due to an enhancement on their surface area [1-4]. The structural features of mesoporous zirconia-ceria materials in combination with oxygen storage/release capacity (OSC) are crucial for various catalytic reactions. The direct use of hydrocarbons as fuel for the SOFC (instead of pure H2), without the necessity of reforming and purification reactors can improve global efficiency of these systems [4]. The X-ray diffraction data showed that ZrO2-x%CeO2 samples with x>50 are formed by a larger fraction of the cubic phase (spatial group Fm3m), while for x<50 the major crystalline structure is the tetragonal phase (spatial group P42/nmc). The crystallite size of the cubic phase increases with increase in ceria content. The tetragonal crystallite size decreases when ceria content increases. After impregnation, the Rietveld analysis showed a NiO content around 60wt.% for all samples. The lattice parameters for the ZrO2 tetragonal phase are lower for higher ZrO2 contents, while for all samples the cubic NiO and CeO2 parameters do not present changes. The calculated densities are higher for higher ceria content, as expected. The crystallite size of NiO are similar (~20nm) for all samples and 55nm for the NiO standard. Nitrogen adsorption experiments revealed a broader particle size distribution for higher CeO2 content. The superficial area values were around 35m2/g for all samples, the average pore diameter and pore volumes were higher when increasing ceria content. After NiO impregnation the particle size distribution was the same for all samples, with two pore sizes, the first around 3nm and a broader peak around 10nm. The superficial area increased to approximately 45m2/g for all samples, and the pore volume was also higher after impregnation and increased when ceria content increased. These results point up that the impregnation of NiO improves the textural characteristics of the pristine material. The complementary TEM/EDS images present a homogeneous coating of NiO particles over the ZrO2-x%CeO2 support, showing that these samples are excellent for catalysis applications. [1] D. Y. Zhao, J. Feng, Q. Huo, N. Melosh, G. H. Fredrickson, B. F. Chmelka, G. D. Stucky, Science 279, 548-552 (1998). [2] C. Yu, Y. Yu, D. Zhao, Chem. Comm. 575-576 (2000). [3] A. Trovarelli, M. Boaro, E. Rocchini, C. de Leitenburg, G. Dolcetti, J. Alloys Compd. 323-324 (2001) 584-591. [4] S. Larrondo, M. A. Vidal, B. Irigoyen, A. F. Craievich, D. G. Lamas, I. O. Fábregas, et al. Catal. Today 107–108 (2005) 53-59.