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31.
Timmers LF Ducati RG Sánchez-Quitian ZA Basso LA Santos DS de Azevedo WF 《Journal of molecular modeling》2012,18(2):467-479
Cytidine Deaminase (CD) is an evolutionarily conserved enzyme that participates in the pyrimidine salvage pathway recycling cytidine and deoxycytidine
into uridine and deoxyuridine, respectively. Here, our goal is to apply computational techniques in the pursuit of potential
inhibitors of Mycobacterium tuberculosis CD (MtCDA) enzyme activity. Molecular docking simulation was applied to find the possible hit compounds. Molecular dynamics simulations
were also carried out to investigate the physically relevant motions involved in the protein-ligand recognition process, aiming
at providing estimates for free energy of binding. The proposed approach was capable of identifying a potential inhibitor,
which was experimentally confirmed by IC50 evaluation. Our findings open up the possibility to extend this protocol to different databases in order to find new potential
inhibitors for promising targets based on a rational drug design process. 相似文献
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Carl R Harrington Sacha Lucchini Karyn P Ridgway Udo Wegmann Tracy J Eaton Jay CD Hinton Michael J Gasson Arjan Narbad 《BMC microbiology》2008,8(1):195
Background
The human gastrointestinal (GI) tract contains a diverse collection of bacteria, most of which are unculturable by conventional microbiological methods. Increasingly molecular profiling techniques are being employed to examine this complex microbial community. The purpose of this study was to develop a microarray technique based on 16S ribosomal gene sequences for rapidly monitoring the microbial population of the GI tract. 相似文献35.
Caceres RA Saraiva Timmers LF Dias R Basso LA Santos DS de Azevedo WF 《Bioorganic & medicinal chemistry》2008,16(9):4984-4993
This work describes for the first time a structural model of purine nucleoside phosphorylase from Streptococcus agalactiae (SaPNP). PNP catalyzes the cleavage of N-ribosidic bonds of the purine ribonucleosides and 2-deoxyribonucleosides in the presence of inorganic orthophosphate as a second substrate. This enzyme is a potential target for the development of antibacterial drugs. We modeled the complexes of SaPNP with 15 different ligands in order to determine the structural basis for the specificity of these ligands against SaPNP. The application of a novel empirical scoring function to estimate the affinity of a ligand for a protein was able to identify the ligands with high affinity for PNPs. The analysis of molecular dynamics trajectory for SaPNP indicates that the functionally important motifs have a very stable structure. This new structural model together with a novel empirical scoring function opens the possibility to explorer larger library of compounds in order to identify the new inhibitors for PNPs in virtual screening projects. 相似文献
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Nawel Selami Marie-Christine Auriac Olivier Catrice Delphine Capela Meriem Kaid-Harche Ton Timmers 《Plant and Soil》2014,374(1-2):109-119
Background and aims
In spite of the importance of Retama species for dune stabilization and re-vegetation and the contribution to the bio-fertilization of semi-arid and arid ecosystems, the symbiotic interaction of Retama species with rhizobia remains largely unstudied. In this paper, we aim to provide the first detailed study on nodule morphology and anatomy of Retama monosperma.Methods
We collected nodules from coastal areas nearby Oran (Algeria) and studied in detail their anatomy and ultrastructure by light and electron microscopy.Results
First, we confirmed the likely identity of the microsymbiont as B. retamae and found that nodules of R. monosperma belong to the genistoid type of indeterminate nodules. Infection threads, typical for most nodules of legumes, are absent in nodules of R. monosperma and bacterial spread is associated with plant cell division. The nitrogen fixation zone is homogenous with only invaded cells and a network of non-invaded cells found in many nodules, is absent. Moreover, endoreduplication does not take place in bacteroids in nodules of R. monosperma.Conclusions
The features observed in this study are compared to the morphology and anatomy of nodules of other legumes and the possible consequences for nodule functioning and the mode of infection during the establishment of the interaction are discussed. 相似文献37.
Sánchez-Quitian ZA Timmers LF Caceres RA Rehm JG Thompson CE Basso LA de Azevedo WF Santos DS 《Archives of biochemistry and biophysics》2011,(1):108-115
Cytidine deaminase (CDA) is a key enzyme in the pyrimidine salvage pathway. It is involved in the hydrolytic deamination of cytidine or 2′-deoxycytidine to uridine or 2′-deoxyuridine, respectively. Here we report the crystal structures of Mycobacterium tuberculosis CDA (MtCDA) in complex with uridine (2.4 Å resolution) and deoxyuridine (1.9 Å resolution). Molecular dynamics (MD) simulation was performed to analyze the physically relevant motions involved in the protein–ligand recognition process, showing that structural flexibility of some protein regions are important to product binding. In addition, MD simulations allowed the analysis of the stability of tetrameric MtCDA structure. These findings open-up the possibility to use MtCDA as a target in future studies aiming to the rational design of new inhibitor of MtCDA-catalyzed chemical reaction with potential anti-proliferative activity on cell growth of M. tuberculosis, the major causative agent of tuberculosis. 相似文献
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