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1.
Ribokinase (EC 2.1.7.15) from Leishmania major was cloned, sequenced and overexpressed in Escherichia coli. The gene expressed an active enzyme that had comparable activity to the same enzyme studied in E. coli. It specifically phosphorylated D-ribose. Under defined conditions, the Km for the substrates D-ribose and ATP were 0.3±0.04 mM and 0.2±0.02mM, respectively. The turnover numbers of the enzyme for the substrates were 10.8s~(-1) and 10.2 s~(-1), respectively. The enzyme product ribose 5-phosphate inhibited the phosphorylation of D-ribose with an apparent K_i of 0.4 mM, which is close to the K_m (0.3mM) of Dribose, suggesting that it might play a role in regulating flux through the enzyme. 相似文献
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Alanine racemase (AlaR) is a bacterial enzyme that catalyzes the interconversion of L- and D-alanine, which is an essential constituent of the peptidoglycan layer of the bacterial cell wall and requires pyridoxal 5'-phosphate (PLP) as a cofactor. The enzyme is universal to bacteria, including mycobacteria, making it an attractive target for drug design. To investigate the effects of flexibility on the binding modes of the substrate and an inhibitor and to analyze how the active site is affected by the presence of the substrate versus inhibitor, a molecular dynamics simulation on the full AlaR dimer from Bacillus stearothermophilus (pdb code: 1SFT) with a D-alanine molecule in one active site and the noncovalent inhibitor, propionate, in the second site has been carried out. Within the time scale of the simulation, we show that the active site becomes more stabilized in the presence of substrate versus inhibitor. The results of this simulation are in agreement with the proposed mechanism of alanine racemase reaction in which the substrate carboxyl group directly participates in the catalysis by acting cooperatively with Tyr 265' and Lys 39. A structural water molecule in contact with both substrate and inhibitor (i.e., in both active sites) and bridging residues in both active sites was identified. It shows a remarkably low mobility and does not exchange with bulk water. This water molecule can be taken into account for the design of specific AlaR inhibitors by either utilizing it as a bridging group or displacing it with an inhibitor atom. The results presented here provide insights into the dynamics of the alanine racemase in the presence of substrate/inhibitor, which will be used for the rational design of novel inhibitors. 相似文献
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L. Capece M. A. Marti A. Bidon‐Chanal A. Nadra F. J. Luque D. A. Estrin 《Proteins》2009,75(4):885-894
The influence of pressure on the equilibrium between five‐(5c) and six‐coordination (6c) forms in neuroglobin (Ngb) and myoglobin (Mb) has been examined by means of molecular dynamics (MD) simulations at normal and high pressure. The results show that the main effect of high pressure is to reduce the protein mobility without altering the structure in a significant manner. Moreover, our data suggest that the equilibrium between 5c and 6c states in globins is largely controlled by the structure and dynamics of the C‐D region. Finally, in agreement with the available experimental data, the free energy profiles obtained from steered MD for both proteins indicate that high pressure enhances hexacoordination. In Ngb, the shift in equilibrium is mainly related to an increase in the 6c→5c transition barrier, whereas in Mb such a shift is primarily due to a destabilization of the 5c state. Proteins 2009. © 2008 Wiley‐Liss, Inc. 相似文献
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B.L. de Groot D.M.F. van Aalten R.M. Scheek A. Amadei G. Vriend H.J.C. Berendsen 《Proteins》1997,29(2):240-251
A method is presented that generates random protein structures that fulfil a set of upper and lower interatomic distance limits. These limits depend on distances measured in experimental structures and the strength of the interatomic interaction. Structural differences between generated structures are similar to those obtained from experiment and from MD simulation. Although detailed aspects of dynamical mechanisms are not covered and the extent of variations are only estimated in a relative sense, applications to an IgG-binding domain, an SH3 binding domain, HPr, calmodulin, and lysozyme are presented which illustrate the use of the method as a fast and simple way to predict structural variability in proteins. The method may be used to support the design of mutants, when structural fluctuations for a large number of mutants are to be screened. The results suggest that motional freedom in proteins is ruled largely by a set of simple geometric constraints. Proteins 29:240–251, 1997. © 1997 Wiley-Liss, Inc. 相似文献
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Massimiliano Aschi Argante Bozzi Renato Di Bartolomeo Raffaele Petruzzelli 《Biopolymers》2010,93(10):917-926
The main purpose of this work is to analyse, by means of molecular dynamics (MD) simulations both structural and mechanical‐dynamical differences between Hepcidin‐20 and Hepcidin‐25 in both oxidized and reduced states in aqueous solution. Results indicate that the presence of disulfide bonds is essential, in both peptides, for maintaining their β‐hairpin motif. As a matter of fact, the lack of this intra‐peptide covalent interactions produces an almost immediate deviation from the oxidized, plausibly active, structure in both the systems. Interestingly, reduced Hepcidin‐25 turns out to be characterized by a highly fluctuating structure which is found to rapidly span a large number of configurations at equilibrium. On the other hand, loss of disulfide bonds in the shorter peptide, results in a more compact and relatively rigid double‐turn structure. Comparison of mechanical–dynamical properties and sidechains–sidechains interactions in oxidized Hepcidin‐20 and Hepcidin‐25 strongly suggest also the key role of N‐terminus in the aggregation tendency of Hepcidin‐25. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 917–926, 2010. 相似文献
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Isabella Daidone Massimiliano Aschi Maria Patamia Argante Bozzi Raffaele Petruzzelli 《Biopolymers》2013,99(1):47-54
Obtustatin and Lebestatin are lysine‐threonine‐serine (KTS)‐disintegrins, which are a family of low molecular weight polypeptides present in many viperidae venoms and are potent and specific inhibitors of collagen‐binding integrins. The integrin binding loop, harboring the 21KTS23 motif, and the C‐terminal tail are known to be responsible for the selective binding to the α1β1 integrin. Despite a very high sequence homology (only two mutations are present in Lebestatin relative to Obtustatin, namely R24L and S38L), Lebestatin exhibits a higher inhibitory effect than Obtustatin on cell adhesion and cell migration to collagens I and IV. Here we show, by means of molecular dynamics simulations of the two polypeptides in aqueous solution, that Lebestatin possesses a higher flexibility of the C‐terminal tail and a greater solvent accessibility of the integrin binding loop than Obtustatin. It may be hypothesized that these properties may contribute to the higher binding‐affinity of Lebestatin to its biological partner. © 2012 Wiley Periodicals, Inc. 相似文献
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M.E. Sarciron;R. Terreux;Y. Prieto;M. Cortes;M.A. Cuellar;R.A. Tapia;M. Domard;N. Walchshofer;A.F. Pétavy 《Parasite (Paris, France)》2017,12(3):251-258
33 polycyclic derivatives have been studied and tested on Leishmania donovani and L. major promastigotes. Their antileishmanial activity was assessed in vitro and an assay of their cytotoxicity was realized on human myelomonocytic cell line. The reference molecules used in the assays were amphotericin B and pentamidine. Among the compounds tested, 29 possess an antileishmanial activity; 25 of those were more active against L. donovani than amphotericin B, and nine were as effective as amphotericin B against L. major . Many synthesized derivatives were more active against L.donovani than against L. major . The cytotoxicity studies have shown that among the thirty-three derivatives tested, 12 molecules have an IC50 towards THP-1 cells about equal than that reference drugs, the 21 other derivatives are much less toxic. A 3D QSAR study was undertaken and has permitted to predict activity against L. donovani and L. major and to highlight critical area to optimize activity against the two species.https://doi.org/10.1051/parasite/2005123251 相似文献
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Bcl‐xl protein has a long unstructured loop attached to its structured region which joins two helices. The necessity to have this unstructured segment in Bcl‐xl is not yet well understood. To what extent the unstructured segment can influence the dynamics of the structured region of protein, with potential to influence the function, has been investigated in this work. Molecular dynamics simulation and principal component analysis show how the loop affects the internal motions of the protein, particularly its ligand binding pocket. Generally an unstructured region in the structure would promote flexibility resulting entropic stability but in contrary, here it narrows down the conformational space of the structured region of protein that could be hypothesized to impact the functional precision. Effects of the loop propagate to the binding pocket through structural rearrangements of polar side chains. The immediate suspicion of possible impact of phosphorylation to modulate the function of the protein is proven to be a fact, as the phosphorylated S49 and S62 located on the large unstructured region are seen to perturb the electrostatic network of the structure; an observation that validates and clarifies the role of loop as a modulator through biophysical and biochemical mechanisms. Proteins 2017; 85:1567–1579. © 2017 Wiley Periodicals, Inc. 相似文献
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Thouraya Boussoffara;Mohamed Samir Boubaker;Melika Ben Ahmed;Mourad Mokni;Ikram Guizani;Afif Ben Salah;Hechmi Louzir 《Parasite (Paris, France)》2019,26(1)
Lesion features in cutaneous leishmaniasis (CL) depend on the infecting Leishmania species as well as on host immune reponse. In this study,we evaluated the histological and immunological differences between two forms of CL described in Tunisia: zoonotic cutaneous leishmaniasis (ZCL) caused by L. major and sporadic cutaneous leishmaniasis (SCL) caused by L. infantum . Histological analysis showed a mild to moderate infiltrate within ZCL lesions. In contrast,massive infiltration of the dermis was observed within SCL lesions. Contrary to ZCL,infiltrates within SCL lesions were organized and showed granuloma composed of macrophages and lymphocytes. In addition,immunohistochemical analysis showed a predominance of CD4+T cells within both CL forms. Furthermore,expression of interferon-γ,interleukin (IL)-10,IL-8,IL-13 and monocyte chemotactic protein (MCP)-1 was evaluated using real-time quantitative polymerase chain reaction (RT-qPCR). MCP-1 and IL-10 were expressed at comparable levels in ZCL and SCL lesions. Interestingly,IL-8 mRNA levels were significantly higher in ZCL lesions compared to SCL lesions,but interferon-γ was significantly higher in SCL lesions than in ZCL lesions. 相似文献
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Savoia D Avanzini C Conti S Magliani V Frazzi R Polonelli L 《The Journal of eukaryotic microbiology》2002,49(4):319-323
The microbicidal effect of a monoclonal antiidiotypic antibody, mimicking the activity of a yeast killer toxin, characterized by a wide antimicrobial spectrum, has been evaluated in vitro against two relevant species of protozoan parasites, Leishmania major and Leishmania infantum. The antiidiotypic antibody exerted a significant and dose-dependent antileishmanial activity against parasite promastigotes in comparison to an irrelevant isotype-matched monoclonal antibody. This is the first demonstration that an antibody, which had been already shown to be fungicidal and bactericidal, may also exert a direct microbicidal activity against protozoa. 相似文献
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Artur T. Cordeiro Patricia R. Feliciano M. Cristina Nonato 《Acta Crystallographica. Section F, Structural Biology Communications》2006,62(10):1049-1051
Dihydroorotate dehydrogenases (DHODHs) are flavin‐containing enzymes that catalyze the oxidation of l ‐dihydroorotate to orotate, the fourth step in the de novo pyrimidine nucleotide synthesis pathway. In this study, DHODH from Leishmania major has been crystallized by the vapour‐diffusion technique using lithium sulfate as the precipitating agent. The crystals belong to space group P61, with unit‐cell parameters a = 143.7, c = 69.8 Å. X‐ray diffraction data were collected to 2.0 Å resolution using an in‐house rotating‐anode generator. Analysis of the solvent content and the self‐rotation function indicate the presence of two molecules in the asymmetric unit. The structure has been solved by the molecular‐replacement technique. 相似文献
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Haouas N Gorcii M Chargui N Aoun K Bouratbine A Messaadi Akrout F Masmoudi A Zili J Ben Said M Pratlong F Dedet JP Mezhoud H Azaiez R Babba H 《Parasite (Paris, France)》2007,14(3):239-246
The authors report the identification of Leishmania strains isolated from the Centre and the South of Tunisia. 266 strains were isolated between 1998 and 2006 from human (n=221 strains) and dogs (n=45 strains) hosts. The isoenzymatic identification exhibits the presence of in total five zymodemes belonging to three Leishmanio complexes: Leishmania infantum, L. major and L. killicki. All strains isolated from human and canine visceral leishmaniasis belonged to L. infantum. zymodeme MON-1 was the only one isolated from canine visceral leishmaniasis. However, it is predominant in human visceral leishmaniasis beside zymodeme MON-24 which was detected in two provinces of the Centre (Monastir and Kairouan) and zymodeme MON-80 isolated for the first time in Kairouan province. Three complexes are responsible for human cutaneous leishmaniasis: L. major MON-25 is the parasite the most frequently found in its classic foci in the Centre and the South of the country. L. infantum MON-24 was isolated for the first time in a small locality of Sfax (southern Tunisia) showing the appearance of a new focus of L. infantum. L. killicki was isolated in its original focus of Tataouine and in two new foci of the central part of the country (Sidi Bouzid and Kairouan). 相似文献
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Dunne Fong 《FEMS microbiology letters》1993,107(1):95-99
Abstract For the cis and trans stereoisomers of the synthetic anti-microtubule compound tubulozole, at micromolar concentrations, tubulozole-C is cytotoxic to mammalian cells whereas tubulozole-T is not. The effect of tubulozoles on the parasitic protozoan Leishmania was tested. For the promastigote stage of L. mexicana amazonensis , both isomers inhibited parasite growth. For the amastigote stage of L. mexicana amazonensis and L. major , within murine J774 macrophage line as host cells in vitro, tubulozole-T reduced the infective index. Despite the observation of macrophage cytotoxicity of tubulozole-T, this compound may be a potentially useful and novel anti-leishmanial drug. 相似文献
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Reza Esmaeeli Faramarz Mehrnejad Mohammad Mir-Derikvand Niloofar Gopalpoor 《Journal of cellular biochemistry》2019,120(2):2502-2514
The mycobacterial enzyme pyrazinamidase (PZase) is the target of key tuberculosis drug, pyrazinamide. Mutations in PZase cause drug resistance. Herein, three point mutations, W68G, L85P, and V155G, were investigated through over 8 µs of molecular dynamics simulations coupled with essential dynamics and binding pocket analysis at neutral (pH = 7) and acidic (pH = 4) ambient conditions. The 51-71 flap region exhibited drastic displacement leading to enlargement of binding cavity, especially at the lower pH. Accessibility of solvent to the active site of the mutant enzymes was also reduced. The protonation of key surface residues at low pH results in more contribution of these residues to structural stability and integrity of the enzyme and reduced interactions with solvent molecules, which acts as a cage, keeping the enzyme together. The observed results suggest a pattern of structural alterations due to point mutations in PZase, which is consistent with other experimental and theoretical investigations and, can be harnessed for drug design purposes. 相似文献
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Computer simulation of the conformations of short antigenic peptides (5-10 residues) either free or bound to their receptor, the major histocompatibility complex (MHC)-encoded glycoprotein H-2 Ld, was employed to explain experimentally determined differences in the antigenic activities within a set of related peptides. Starting for each sequence from the most probable conformations disclosed by a pattern-recognition technique, several energy-minimized structures were subjected to molecular dynamics simulations (MD) either in vacuo or solvated by water molecules. Notably, antigenic potencies were found to correlate to the peptides propensity to form and maintain an overall alpha-helical conformation through regular i,i + 4 hydrogen bonds. Accordingly, less active or inactive peptides showed a strong tendency to form i,i + 3 hydrogen bonds at their N-terminal end. Experimental data documented that the C-terminal residue is critical for interaction of the peptide with H-2 Ld. This finding could be satisfactorily explained by a 3-D Q.S.A.R. analysis postulating interactions between ligand and receptor by hydrophobic forces. A 3-D model is proposed for the complex between a high-affinity nonapeptide and the H-2 Ld receptor. First, the H-2 Ld molecule was built from X-ray coordinates of two homologous proteins: HLA-A2 and HLA-Aw68, energy-minimized and studied by MD simulations. With HLA-A2 as template, the only realistic simulation was achieved for a solvated model with minor deviations of the MD mean structure from the X-ray conformation. Water simulation of the H-2 Ld protein in complex with the antigenic nonapeptide was then achieved with the template-derived optimal parameters. The bound peptide retains mainly its alpha-helical conformation and binds to hydrophobic residues of H-2 Ld that correspond to highly polymorphic positions of MHC proteins. The orientation of the nonapeptide in the binding cleft is in accordance with the experimentally determined distribution of its MHC receptor-binding residues (agretope residues). Thus, computer simulation was successfully employed to explain functional data and predicts alpha-helical conformation for the bound peptide. 相似文献
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A comparison of a series of extended molecular dynamics (MD) simulations of bacteriophage T4 lysozyme in solvent with X-ray data is presented. Essential dynamics analyses were used to derive collective fluctuations from both the simulated trajectories and a distribution of crystallographic conformations. In both cases the main collective fluctuations describe domain motions. The protein consists of an N- and C-terminal domain connected by a long helix. The analysis of the distribution of crystallographic conformations reveals that the N-terminal helix rotates together with either of these two domains. The main domain fluctuation describes a closure mode of the two domains in which the N-terminal helix rotates concertedly with the C-terminal domain, while the domain fluctuation with second largest amplitude corresponds to a twisting mode of the two domains, with the N-terminal helix rotating concertedly with the N-terminal domain. For the closure mode, the difference in hinge-bending angle between the most open and most closed X-ray structure along this mode is 49 degrees. In the MD simulation that shows the largest fluctuation along this mode, a rotation of 45 degrees was observed. Although the twisting mode has much less freedom than the closure mode in the distribution of crystallographic conformations, experimental results suggest that it might be functionally important. Interestingly, the twisting mode is sampled more extensively in all MD simulations than it is in the distribution of X-ray conformations. Proteins 31:116–127, 1998. © 1998 Wiley-Liss, Inc. 相似文献