Statistical properties of contact vectors

We study the statistical properties of contact vectors, a construct to characterize a protein's structure. The contact vector of an N-residue protein is a list of N integers n_i, representing the number of residues in contact with residue i. We study analytically (at mean-field level) and numerically the amount of structural information contained in a contact vector. Analytical calculations reveal that a large variance in the contact numbers reduces the degeneracy of the mapping between contact vectors and structures. Exact enumeration for lengths up to N=16 on the three dimensional cubic lattice indicates that the growth rate of number of contact vectors as a function of N is only 3% less than that for contact maps. In particular, for compact structures we present numerical evidence that, practically, each contact vector corresponds to only a handful of structures. We discuss how this information can be used for better structure prediction.Comment: 20 pages, 6 figure

Produtividade e características agronômicas de Brachiaria brizantha cv. Paiaguás submetida a doses de nitrogênio sob cortes

Objetivou-se descrever a resposta da Brachiaria brizantha cv. Paiaguás em doses de adubação nitrogenada no segundo ano de produção. O experimento foi conduzido na área experimental da Universidade do Estado de Mato Grosso, localizada no município de Tangará da Serra, em blocos casualizados, com seis tratamentos (doses de 0, 50, 100, 150, 200 e 250 kg/ha de N) e quatro repetições, em parcelas de 9 m2 cada. As doses foram parceladas em quatro vezes, aplicadas após cada corte. Observou-se efeito significativo (P ≤ 0,05) para as variáveis alturas de plantas, número de perfilhos/m2, porcentagem de matéria seca, massa verde/ha, massa seca/ha, massa seca de folhas e massa seca de colmos/ha. Os resultados mostram que em doses de 250 kg/ha de N, com condições climáticas favoráveis ao crescimento da forragem há efeito positivo do N sobre o número de perfilhos/m2, a massa seca/ha, a massa seca de folhas e a massa seca de colmos/ha de Brachiaria brizantha cv. Paiaguás

On the form of growing strings

Patterns and forms adopted by Nature, such as the shape of living cells, the geometry of shells and the branched structure of plants, are often the result of simple dynamical paradigms. Here we show that a growing self-interacting string attached to a tracking origin, modeled to resemble nascent polypeptides in vivo, develops helical structures which are more pronounced at the growing end. We also show that the dynamic growth ensemble shares several features of an equilibrium ensemble in which the growing end of the polymer is under an effective stretching force. A statistical analysis of native states of proteins shows that the signature of this non-equilibrium phenomenon has been fixed by evolution at the C-terminus, the growing end of a nascent protein. These findings suggest that a generic non-equilibrium growth process might have provided an additional evolutionary advantage for nascent proteins by favoring the preferential selection of helical structures.Comment: 4 pages, 3 figures. Accepted for publication in Phys. Rev. Let

Proteome-wide observation of the phenomenon of life on the edge of solubility

To function effectively proteins must avoid aberrant aggregation, and hence they are expected to be expressed at concentrations safely below their solubility limits. By analyzing proteome-wide mass spectrometry data of Caenorhabditis elegans, however, we show that the levels of about three-quarters of the nearly 4, 000 proteins analyzed in adult animals are close to their intrinsic solubility limits, indeed exceeding them by about 10% on average. We next asked how aging and functional self-assembly influence these solubility limits. We found that despite the fact that the total quantity of proteins within the cellular environment remains approximately constant during aging, protein aggregation sharply increases between days 6 and 12 of adulthood, after the worms have reproduced, as individual proteins lose their stoichiometric balances and the cellular machinery that maintains solubility undergoes functional decline. These findings reveal that these proteins are highly prone to undergoing concentration-dependent phase separation, which on aging is rationalized in a decrease of their effective solubilities, in particular for proteins associated with translation, growth, reproduction, and the chaperone system

Dynamical chaos and power spectra in toy models of heteropolymers and proteins

The dynamical chaos in Lennard-Jones toy models of heteropolymers is studied by molecular dynamics simulations. It is shown that two nearby trajectories quickly diverge from each other if the heteropolymer corresponds to a random sequence. For good folders, on the other hand, two nearby trajectories may initially move apart but eventually they come together. Thus good folders are intrinsically non-chaotic. A choice of a distance of the initial conformation from the native state affects the way in which a separation between the twin trajectories behaves in time. This observation allows one to determine the size of a folding funnel in good folders. We study the energy landscapes of the toy models by determining the power spectra and fractal characteristics of the dependence of the potential energy on time. For good folders, folding and unfolding trajectories have distinctly different correlated behaviors at low frequencies.Comment: 8 pages, 9 EPS figures, Phys. Rev. E (in press

Critical exponents of the anisotropic Bak-Sneppen model

We analyze the behavior of spatially anisotropic Bak-Sneppen model. We demonstrate that a nontrivial relation between critical exponents tau and mu=d/D, recently derived for the isotropic Bak-Sneppen model, holds for its anisotropic version as well. For one-dimensional anisotropic Bak-Sneppen model we derive a novel exact equation for the distribution of avalanche spatial sizes, and extract the value gamma=2 for one of the critical exponents of the model. Other critical exponents are then determined from previously known exponent relations. Our results are in excellent agreement with Monte Carlo simulations of the model as well as with direct numerical integration of the new equation.Comment: 8 pages, three figures included with psfig, some rewriting, + extra figure and table of exponent

Critical Casimir effect in films for generic non-symmetry-breaking boundary conditions

Systems described by an O(n) symmetrical $\phi^4$ Hamiltonian are considered in a $d$-dimensional film geometry at their bulk critical points. A detailed renormalization-group (RG) study of the critical Casimir forces induced between the film's boundary planes by thermal fluctuations is presented for the case where the O(n) symmetry remains unbroken by the surfaces. The boundary planes are assumed to cause short-ranged disturbances of the interactions that can be modelled by standard surface contributions $\propto \bm{\phi}^2$ corresponding to subcritical or critical enhancement of the surface interactions. This translates into mesoscopic boundary conditions of the generic symmetry-preserving Robin type $\partial_n\bm{\phi}=\mathring{c}_j\bm{\phi}$. RG-improved perturbation theory and Abel-Plana techniques are used to compute the $L$-dependent part $f_{\mathrm{res}}$ of the reduced excess free energy per film area $A\to\infty$ to two-loop order. When $d<4$, it takes the scaling form $f_{\mathrm{res}}\approx D(c_1L^{\Phi/\nu},c_2L^{\Phi/\nu})/L^{d-1}$ as $L\to\infty$, where $c_i$ are scaling fields associated with the surface-enhancement variables $\mathring{c}_i$, while $\Phi$ is a standard surface crossover exponent. The scaling function $D(\mathsf{c}_1,\mathsf{c}_2)$ and its analogue $\mathcal{D}(\mathsf{c}_1,\mathsf{c}_2)$ for the Casimir force are determined via expansion in $\epsilon=4-d$ and extrapolated to $d=3$ dimensions. In the special case $\mathsf{c}_1=\mathsf{c}_2=0$, the expansion becomes fractional. Consistency with the known fractional expansions of D(0,0) and $\mathcal{D}(0,0)$ to order $\epsilon^{3/2}$ is achieved by appropriate reorganisation of RG-improved perturbation theory. For appropriate choices of $c_1$ and $c_2$, the Casimir forces can have either sign. Furthermore, crossovers from attraction to repulsion and vice versa may occur as $L$ increases.Comment: Latex source file, 40 pages, 9 figure

Infestação por ictio em surubim híbrido durante a fase inicial de criação.

bitstream/item/42263/1/COT-165-2011.pd

Intrinsic determinants of neurotoxic aggregate formation by the amyloid β peptide

The extent to which proteins aggregate into distinct structures ranging from prefibrillar oligomers to amyloid fibrils is key to the pathogenesis of many age-related degenerative diseases. We describe here for the Alzheimer's disease-related amyloid β peptide (Aβ) an investigation of the sequence-based determinants of the balance between the formation of prefibrillar aggregates and amyloid fibrils. We show that by introducing single-point mutations, it is possible to convert the normally harmless Aβ40 peptide into a pathogenic species by increasing its relative propensity to form prefibrillar but not fibrillar aggregates, and, conversely, to abolish the pathogenicity of the highly neurotoxic E22G Aβ42 peptide by reducing its relative propensity to form prefibrillar species rather than mature fibrillar ones. This observation can be rationalized by the demonstration that whereas regions of the sequence of high aggregation propensity dominate the overall tendency to aggregate, regions with low intrinsic aggregation propensities exert significant control over the balance of the prefibrillar and fibrillar species formed, and therefore play a major role in determining the neurotoxicity of the Aβ peptide. © 2010 by the Biophysical Society

A metastable subproteome underlies inclusion formation in muscle proteinopathies

Protein aggregation is a pathological feature of neurodegenerative disorders. We previously demonstrated that protein inclusions in the brain are composed of supersaturated proteins, which are abundant and aggregation-prone, and form a metastable subproteome. It is not yet clear, however, whether this phenomenon is also associated with non-neuronal protein conformational disorders. To respond to this question, we analyzed proteomic datasets from biopsies of patients with genetic and acquired protein aggregate myopathy (PAM) by quantifying the changes in composition, concentration and aggregation propensity of proteins in the fibers containing inclusions and those surrounding them. We found that a metastable subproteome is present in skeletal muscle from healthy patients. The expression of this subproteome escalate as proteomic samples are taken more proximal to the pathologic inclusion, eventually exceeding its solubility limits and aggregating. While most supersaturated proteins decrease or maintain steady abundance across healthy fibers and inclusion-containing fibers, proteins within the metastable subproteome rise in abundance, suggesting that they escape regulation. Taken together, our results show in the context of a human conformational disorder that the supersaturation of a metastable subproteome underlies widespread aggregation and correlates with the histopathological state of the tissue