303 research outputs found
Processamento de batata (Solanum tuberosum L.) : fritura
bitstream/item/32408/1/documento-104.pd
Comportamento de cultivares chilenas de batata na zona Sul do Rio Grande do Sul.
bitstream/item/30995/1/comunicado-104.pd
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
Protein folding using contact maps
We present the development of the idea to use dynamics in the space of
contact maps as a computational approach to the protein folding problem. We
first introduce two important technical ingredients, the reconstruction of a
three dimensional conformation from a contact map and the Monte Carlo dynamics
in contact map space. We then discuss two approximations to the free energy of
the contact maps and a method to derive energy parameters based on perceptron
learning. Finally we present results, first for predictions based on threading
and then for energy minimization of crambin and of a set of 6 immunoglobulins.
The main result is that we proved that the two simple approximations we studied
for the free energy are not suitable for protein folding. Perspectives are
discussed in the last section.Comment: 29 pages, 10 figure
Statistical Properties of Contact Maps
A contact map is a simple representation of the structure of proteins and
other chain-like macromolecules. This representation is quite amenable to
numerical studies of folding. We show that the number of contact maps
corresponding to the possible configurations of a polypeptide chain of N amino
acids, represented by (N-1)-step self avoiding walks on a lattice, grows
exponentially with N for all dimensions D>1. We carry out exact enumerations in
D=2 on the square and triangular lattices for walks of up to 20 steps and
investigate various statistical properties of contact maps corresponding to
such walks. We also study the exact statistics of contact maps generated by
walks on a ladder.Comment: Latex file, 15 pages, 12 eps figures. To appear on Phys. Rev.
Information Loss in Coarse Graining of Polymer Configurations via Contact Matrices
Contact matrices provide a coarse grained description of the configuration
omega of a linear chain (polymer or random walk) on Z^n: C_{ij}(omega)=1 when
the distance between the position of the i-th and j-th step are less than or
equal to some distance "a" and C_{ij}(omega)=0 otherwise. We consider models in
which polymers of length N have weights corresponding to simple and
self-avoiding random walks, SRW and SAW, with "a" the minimal permissible
distance. We prove that to leading order in N, the number of matrices equals
the number of walks for SRW, but not for SAW. The coarse grained Shannon
entropies for SRW agree with the fine grained ones for n <= 2, but differs for
n >= 3.Comment: 18 pages, 2 figures, latex2e Main change: the introduction is
rewritten in a less formal way with the main results explained in simple
term
Metastability of native proteins and the phenomenon of amyloid formation
An experimental determination of the thermodynamic stabilities of a series of amyloid fibrils reveals that this structural form is likely to be the most stable one that protein molecules can adopt even under physiological conditions. This result challenges the conventional assumption that functional forms of proteins correspond to the global minima in their free energy surfaces and suggests that living systems are conformationally as well as chemically metastable. © 2011 American Chemical Society
Nanobodies raised against monomeric alpha-synuclein inhibit fibril formation and destabilize toxic oligomeric species
BACKGROUND:
The aggregation of the protein ɑ-synuclein (ɑS) underlies a range of increasingly common neurodegenerative disorders including Parkinson’s disease. One widely explored therapeutic strategy for these conditions is the use of antibodies to target aggregated ɑS, although a detailed molecular-level mechanism of the action of such species remains elusive. Here, we characterize ɑS aggregation in vitro in the presence of two ɑS-specific single-domain antibodies (nanobodies), NbSyn2 and NbSyn87, which bind to the highly accessible C-terminal region of ɑS.
RESULTS:
We show that both nanobodies inhibit the formation of ɑS fibrils. Furthermore, using single-molecule fluorescence techniques, we demonstrate that nanobody binding promotes a rapid conformational conversion from more stable oligomers to less stable oligomers of ɑS, leading to a dramatic reduction in oligomer-induced cellular toxicity.
CONCLUSIONS:
The results indicate a novel mechanism by which diseases associated with protein aggregation can be inhibited, and suggest that NbSyn2 and NbSyn87 could have significant therapeutic potential
Rational design of a conformation-specific antibody for the quantification of A beta oligomers
The accurate quantification of the amounts of small oligomeric assemblies formed by the amyloid β (Aβ) peptide represents a major challenge in the Alzheimer’s field. There is therefore great interest in the development of methods to specifically detect these oligomers by distinguishing them from larger aggregates. The availability of these methods will enable the development of effective diagnostic and therapeutic interventions for this and other diseases related to protein misfolding and aggregation. We describe here a single-domain antibody able to selectively quantify oligomers of the Aβ peptide in isolation and in complex protein mixtures from animal models of disease
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