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Echave J.,National University of San Martin of Argentina
Pure and Applied Chemistry | Year: 2012

Proteins fluctuate, and such fluctuations are functionally important. As with any functionally relevant trait, it is interesting to study how fluctuations change during evolution. In contrast with sequence and structure, the study of the evolution of protein motions is much more recent. Yet, it has been shown that the overall fluctuation pattern is evolutionarily conserved. Moreover, the lowest-energy normal modes have been found to be the most conserved. The reasons behind such a differential conservation have not been explicitly studied. There are two limiting explanations. A "biological"explanation is that because such modes are functional, there is natural selection pressure against their variation. An alternative "physical" explanation is that the lowest-energy normal modes may be more conserved because they are just more robust with respect to random mutations. To investigate this issue, I studied a set of globin-like proteins using a perturbed elastic network model (ENM) of the effect of random mutations on normal modes. I show that the conservation predicted by the model is in excellent agreement with observations. These results support the physical explanation: the lowest normal modes are more conserved because they are more robust. © 2012 IUPAC. Source

Fuglebakk E.,University of Bergen | Echave J.,National University of San Martin of Argentina | Reuter N.,University of Bergen
Bioinformatics | Year: 2012

Motivation: The function of a protein depends not only on its structure but also on its dynamics. This is at the basis of a large body of experimental and theoretical work on protein dynamics. Further insight into the dynamics-function relationship can be gained by studying the evolutionary divergence of protein motions. To investigate this, we need appropriate comparative dynamics methods. The most used dynamical similarity score is the correlation between the root mean square fluctuations (RMSF) of aligned residues. Despite its usefulness, RMSF is in general less evolutionarily conserved than the native structure. A fundamental issue is whether RMSF is not as conserved as structure because dynamics is less conserved or because RMSF is not the best property to use to study its conservation.Results: We performed a systematic assessment of several scores that quantify the (dis)similarity between protein fluctuation patterns. We show that the best scores perform as well as or better than structural dissimilarity, as assessed by their consistency with the SCOP classification. We conclude that to uncover the full extent of the evolutionary conservation of protein fluctuation patterns, it is important to measure the directions of fluctuations and their correlations between sites. © The Author 2012. Published by Oxford University Press on behalf of The Society for Financial Studies. All rights reserved. Source

Roncaroli F.,Comision Nacional de la Energia Atomica | Blesa M.A.,National University of San Martin of Argentina
Physical Chemistry Chemical Physics | Year: 2010

A FTIR-ATR kinetic study on the adsorption of carboxylic acids (oxalic, citric, malonic, succinic, gallic, EDTA and TTHA acids, where EDTA = ethylenediaminetetraacetate and TTHA = triethylenetetramine-N,N,N′, N′′,N′′′,N′′′-hexaacetate, in the concentration range 6 × 10-7 M-2 × 10-5 M on TiO2 (Degussa P25) by ATR-FT-IR is reported. The influence of carboxylic acid concentration, pH, ionic strength, TiO2 load in the film is presented. The adsorption processes follows pseudo-first-order kinetics at constant ligand concentration, even though several adsorption modes have been reported in the literature. Plots of the pseudo first order constant k obsvs. carboxylic acid concentration are linear for all the studied ligands. The slopes of these plots (a) are not very sensitive to the nature of the ligands; a decrease in a is observed as the size increases. The intercept (b) is inversely related to the stability of the surface complexes. We propose that both the rate of adsorption, and the desorption rate are controlled by the diffusion through the pores of the film, although in the case of (b), the desorption rate is modulated by the stability of the surface complex. These results are relevant for oxide dissolution, remediation of water, pollutants removal, sensors design and heterogeneous photocatalysis. © 2010 the Owner Societies. Source

Flannery A.R.,University of Maryland University College | Flannery A.R.,Yale University | Czibener C.,National University of San Martin of Argentina | Andrews N.W.,University of Maryland University College | Andrews N.W.,Yale University
Journal of Cell Biology | Year: 2010

Syt VII is a Ca2+ sensor that regulates lysosome exocytosis and plasma membrane repair. Because it lacks motifs that mediate lysosomal targeting, it is unclear how Syt VII traffics to these organelles. In this paper, we show that mutations or inhibitors that abolish palmitoylation disrupt Syt VII targeting to lysosomes, causing its retention in the Golgi complex. In macrophages, Syt VII is translocated simultaneously with the lysosomal tetraspanin CD63 from tubular lysosomes to nascent phagosomes in a Ca 2+-dependent process that facilitates particle uptake. Mutations in Syt VII palmitoylation sites block trafficking of Syt VII, but not CD63, to lysosomes and phagosomes, whereas tyrosine replacement in the lysosomal targeting motif of CD63 causes both proteins to accumulate on the plasma membrane. Complexes of CD63 and Syt VII are detected only when Syt VII palmitoylation sites are intact. These findings identify palmitoylation- dependent association with the tetraspanin CD63 as the mechanism by which Syt VII is targeted to lysosomes. © 2010 Flannery et al. Source

Montagna G.N.,Max Planck Institute for Infection Biology | Matuschewski K.,Max Planck Institute for Infection Biology | Buscaglia C.A.,National University of San Martin of Argentina
Frontiers in Bioscience | Year: 2012

Plasmodium, the causative agent of malaria, employs its own actin/myosin-based motor for forward locomotion, penetration of molecular and cellular barriers, and invasion of target cells. The sporozoite is unique amongst the extracellular Plasmodium developmental forms in that it has to cross considerable distances and different tissues inside the mosquito and vertebrate hosts to ultimately reach a parenchymal liver cell, the proper target cell where to transform and replicate. Throughout this dangerous journey, the parasite alternates between being passively transported by the body fluids and using its own active cellular motility to seamlessly glide through extracellular matrix and cell barriers. But irrespective of the chosen path, the sporozoite is compelled to keep on moving at a fairly fast pace to escape destruction by host defense mechanisms. Here, we highlight and discuss recent findings collected in Plasmodium sporozoites and related parasites that shed new light on the biological significance of apicomplexan motility and on the structure and regulation of the underlying motor machinery. Source

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