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

Sobrevivência de mudas clonais de erva-mate submetidas a adubação mineral.

Até o momento, poucos foram os avanços na área de nutrição na cultura da erva-mate, o que justifica que o atual sistema de produção seja baseado no extrativismo. O trabalho objetivou avaliar a sobrevivência de clones de erva-mate submetidos a doses de N, P, K, S e micronutrientes (B, Cu e Zn). Nos cinco experimentos, instalados em setembro de 2013 em Três Barras-SC, avaliaram-se quatro clones (F1, F2, F3 e M1) e doses de: 0, 125, 250, 375 e 500 mg dm-3 de N; 0, 75, 150, 225 e 300 mg dm-3 de P2O5; 0, 40, 80, 120 e 160 mg dm-3 de K2O; 0, 20, 40, e 60 mg dm-3 de S; e um Mix de micronutrientes de 0, 0,5 e 1,0 mg dm-3 de B e Cu, e 0, 1,0 e 2,0 mg dm-3 de Zn. Utilizou-se o delineamento blocos casualizados com quatro repetições em esquema fatorial com parcelas subdivididas. As mudas foram propagadas por miniestaquia de matrizes selecionadas, plantadas a campo com altura média de 12 cm. A sobrevivência foi avaliada mensalmente até aos 120 dias. Após os dados submetidos à análise estatística, verificou-se que a época influenciou negativamente a sobrevivência de mudas de erva-mate. A ausência da significância do fator dose na sobrevivência das mudas, possivelmente esteja relacionada a boa fertilidade do solo local. Conclui-se que a adubação não atua na sobrevivência de mudas de erva-mate. Mudas de erva-mate dos clones F1 e F2 são as mais indicadas para plantio na região de Três Barras

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 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

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

Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric aggregates

The presence of oligomeric aggregates, which is often observed during the process of amyloid formation, has recently attracted much attention since it has been associated with neurodegenerative conditions such as Alzheimer's and Parkinson's diseases. We provide a description of a sequence-indepedent mechanism by which polypeptide chains aggregate by forming metastable oligomeric intermediate states prior to converting into fibrillar structures. Our results illustrate how the formation of ordered arrays of hydrogen bonds drives the formation of beta-sheets within the disordered oligomeric aggregates that form early under the effect of hydrophobic forces. Initially individual beta-sheets form with random orientations, which subsequently tend to align into protofilaments as their lengths increases. Our results suggest that amyloid aggregation represents an example of the Ostwald step rule of first order phase transitions by showing that ordered cross-beta structures emerge preferentially from disordered compact dynamical intermediate assemblies.Comment: 14 pages, 4 figure

A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation

Nanoparticles introduced in living cells are capable of strongly promoting the aggregation of peptides and proteins. We use here molecular dynamics simulations to characterise in detail the process by which nanoparticle surfaces catalyse the self- assembly of peptides into fibrillar structures. The simulation of a system of hundreds of peptides over the millisecond timescale enables us to show that the mechanism of aggregation involves a first phase in which small structurally disordered oligomers assemble onto the nanoparticle and a second phase in which they evolve into highly ordered beta-sheets as their size increases

Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as geometric statistical potentials. We also describe a geometric model for developing both linear and non-linear potential functions by optimization. Applications of knowledge-based potential functions in protein-decoy discrimination, in protein-protein interactions, and in protein design are then described. Several issues of knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe