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The dynamic evolution of the PrP(C) from its NMR-derived conformation to a beta-sheet-rich, aggregation-prone conformation is studied through all-atom, explicit solvent molecular dynamics in different temperature and pH conditions. The trajectories are analyzed by means of a recently introduced energy decomposition approach aimed at identifying the key residues for the stabilization and folding of the protein. It is shown that under native conditions the stabilization energy is concentrated in regions of the helices H1 and H3, whereas under misfolding conditions (low pH, high temperature, or mutations in selected sites) it is spread out over helix H2. Misfolding appears to be a rearrangement of the chain that disrupts most of the native secondary structure of the protein, producing some beta-rich conformations with an energy distribution similar to that of the native state. 相似文献
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Overcoming phylogenetic and geographic uncertainties to test for correlates of range size evolution in gymnophthalmid lizards 下载免费PDF全文
Agustín Camacho Renato Recoder Mauro Teixeira Jr Tiana Kohlsdorf Miguel Trefaut Rodrigues Michael S. Y. Lee 《Ecography》2017,40(6):764-773
Patterns of range size evolution are important for developing an evolutionary biogeographical theory and supporting conservation actions. Determining those patterns is however hampered by multiple factors acting on range size and by our uncertainty with regard to species' phylogenetic relationships and geographic distribution. In addition, given the diversity of analytic approaches existing in the literature, there are concerns regarding whether different methods might lead to different patterns. Here, we addressed these uncertainties in order to test for correlations between the evolution of morphology (body size and shape) and range size. We studied lizards of the family Gymnophthalmidae, representing changes of an order of magnitude in body size and also two independent lineages with limb‐reduced (snake‐like) morphs. We used phylogenetic multivariate methods (pPCA) to control for allometric effects of body size over shape. Then, we performed multiple regressions under three approaches: ‘naive’ least squares, Bayesian comparative methods that accounted for uncertainties in trait optimization, tree topology and branch length, and a novel permutative procedure based on phylogenetic generalized least squares (pGLS) to assess the robustness of our relationships to uncertainties in the range sizes of the species studied. All approaches led to the same answer: only body size was related to range size. While bigger gymnophthalmids tend to have relatively large ranges, small species can have either small or large ones. Our results’ robustness to strong uncertainties in both phylogenetic relationships and range sizes shows there are opportunities for overcoming those problems and produce reliable patterns of range size evolution. However, interpretation of the processes driving patterns of range size evolution will still require advances in phylogenetic and taxonomic knowledge. We discuss the application of morphology–range size relationships to conservation planning in the light of existing uncertainties in the geographic knowledge of our studied species group and workarounds for data availability. 相似文献
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While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the detailed, biological active, three-dimensional structure of a protein whose sequence is known. Using insight obtained from lattice model simulations of the folding of small proteins (fewer than 100 residues), in particular of the fact that this phenomenon is essentially controlled by conserved contacts (Mirny et al., Proc Natl Acad Sci USA 1995;92:1282) among (few) strongly interacting ("hot") amino acids (Tiana et al., J Chem Phys 1998;108:757-761), which also stabilize local elementary structures formed early in the folding process and leading to the (postcritical) folding core when they assemble together (Broglia et al., Proc Natl Acad Sci USA 1998;95:12930, Broglia & Tiana, J Chem Phys 2001;114:7267), we have worked out a successful strategy for reading the three-dimensional structure of lattice model-designed proteins from the knowledge of only their amino acid sequence and of the contact energies among the amino acids. 相似文献
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Alterations of Antioxidant Enzymes and Oxidative Damage to Macromolecules in Different Organs of Rats During Aging 总被引:12,自引:0,他引:12
Oxygen free radicals have been hypothesized to play an important role in the aging process. To investigate the correlation between the oxidative stress and aging, we have determined the levels of oxidative protein damage and lipid peroxidation in the brain and liver, and activities of antioxidant enzymes in the brain, liver, heart, kidney, and serum from the Fisher 344 rats at ages of 1, 6, 12, 18, and 24 months. The results showed that the level of oxidative protein damage (measured as carbonyl content) in the brain and liver was significantly higher in older animals than in young animals. No statistical difference was observed in the lipid peroxidation of the liver and brain between young and old animals. The activities of antioxidant enzymes in most tissues displayed an age-dependent decline. Superoxide dismutases in the heart, kidney, and serum, glutathione peroxidase activities in the serum and kidney, and catalase activities in the brain, liver, and kidney, significantly decreased during aging. Cytochrome c oxidase, an enzyme involved in electron transport in mitochondria, initially increased, but subsequently decreased in the aged brain, whereas no significant alteration was observed in the liver mitochondrial antioxidant enzymes. The present studies suggest that the accumulation of oxidized proteins during aging is most likely to be linked with an age-related decline of antioxidant enzyme activities, whereas lipid peroxidation is less sensitive to predict the aging process. 相似文献
5.
Venturelli Diego P. Lofeu Leandro Kohlsdorf Tiana Klein Wilfried 《Hydrobiologia》2022,849(7):1613-1624
Hydrobiologia - In species with complex life cycles, such as anuran amphibians, several traits are influenced by ecological factors during ontogeny. The anuran Physalaemus nattereri shows an... 相似文献
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Heike I. Rsner Martina Caldarini Gregory Potel Daniel Malmodin Maria A. Vanoni Alessandro Aliverti Ricardo A. Broglia Birthe B. Kragelund Guido Tiana 《Proteins》2022,90(1):96-109
The denatured state of several proteins has been shown to display transient structures that are relevant for folding, stability, and aggregation. To detect them by nuclear magnetic resonance (NMR) spectroscopy, the denatured state must be stabilized by chemical agents or changes in temperature. This makes the environment different from that experienced in biologically relevant processes. Using high-resolution heteronuclear NMR spectroscopy, we have characterized several denatured states of a monomeric variant of HIV-1 protease, which is natively structured in water, induced by different concentrations of urea, guanidinium chloride, and acetic acid. We have extrapolated the chemical shifts and the relaxation parameters to the denaturant-free denatured state at native conditions, showing that they converge to the same values. Subsequently, we characterized the conformational properties of this biologically relevant denatured state under native conditions by advanced molecular dynamics simulations and validated the results by comparison to experimental data. We show that the denatured state of HIV-1 protease under native conditions displays rich patterns of transient native and non-native structures, which could be of relevance to its guidance through a complex folding process. 相似文献
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Ricardo Luría-Manzano Paulo D. P. Pinheiro Tiana Kohlsdorf Célio F. B. Haddad Marcio Martins 《Journal of evolutionary biology》2023,36(8):1090-1101
Given the diverse nature of traits involved in territorial defence, they may respond to different selective pressures and then exhibit distinct patterns of evolution. These selective pressures also may cause territorial behaviour to be associated with environmental and morphological variables. Such associations, however, have mostly been studied at the intraspecific level, being phylogenetic analyses of territoriality in a broad taxonomic framework rare in the literature. We used the anuran subfamily Hylinae to test (1) whether two territorial-behaviour traits with different levels of aggression—territorial call and physical combat—are evolutionarily more labile than a morphological trait used in physical combat—the spine-shaped prepollex; (2) whether reproduction in lentic waters and phytotelmata, as well as resource scarcity, might favour the occurrence of territoriality; (3) if physical combat is more important than territorial call for the evolution of body size and sexual size dimorphism and (4) the relationships between territorial-behaviour traits and lineage diversification. We mainly used the literature to build two datasets with different levels of certainty. Territorial-behaviour traits exhibited intermediate levels of phylogenetic signal in Hylinae, whereas the phylogenetic signal for the presence of the spine-shaped prepollex was strong. We found support for the hypothesis that reproduction in lentic water favours the occurrence of territorial behaviour, because the expression of territorial-behaviour traits was more associated with reproduction in lentic than in lotic waters. Territorial-behaviour traits were not correlated with annual precipitation nor with habitat complexity. Body size and sexual size dimorphism were not correlated with the presence of territorial call nor with physical combat. We identified negative correlations between diversification rates and physical combat. Relationships of territorial call and physical combat with diversification rates suggest that these territorial behaviours influence evolutionary processes in different ways. 相似文献
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Borges FP de Brum Vieira P Wiltuschnig RC Tasca T De Carli GA Bonan CD 《FEMS microbiology letters》2008,283(2):189-195
Here we described an nucleoside triphosphate diphosphohydrolase (NTPDase) activity in living trophozoites of Trichomonas gallinae. The enzyme hydrolyzes a variety of purine and pyrimidine nucleoside di- and triphosphates in an optimum pH range of 6.0-8.0. This enzyme activity was activated by high concentrations of divalent cations, such as calcium and magnesium. Contaminant activities were ruled out because the enzyme was not inhibited by classical inhibitors of ATPases (ouabain, 5.0 mM sodium azide, oligomycin) and alkaline phosphatases (levamisole). A significant inhibition of ATP hydrolysis (38%) was observed in the presence of 20 mM sodium azide. Sodium orthovanadate inhibited ATP and ADP hydrolysis (24% and 78%), respectively. The apparent K(M) (Michaelis constant) values were 667.62+/-13 microM for ATP and 125+/-5.3 microM for ADP. V(max) (maximum velocity) values were 0.44+/-0.007 nmol Pi min(-1) per 10(6) trichomonads and 0.91+/-0.12 nmol Pi min(-1) per 10(6) trichomonads for ATP and ADP, respectively. Moreover, we showed a marked decrease in ATP, ADP and AMP hydrolysis when the parasites were grown in the presence of penicillin and streptomycin. The existence of an NTPDase activity in T. gallinae may be involved in pathogenicity, protecting the parasite from the cytolytic effects of the extracellular nucleotides. 相似文献
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Metadynamics is a powerful computational tool to obtain the free-energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus to gain an ever-increasing understanding on the general principles underlying the mechanism of protein folding. We show that it is possible to couple metadynamics and Monte Carlo algorithms to obtain the free energy of model proteins in a way which is computationally very economical. 相似文献