Research Article

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12/19/2012
DNA extraction; Leguminosae; RAPD; SRAP; SSR

Current DNA extraction protocols, which require liquid nitrogen, lyophilization and considerable infrastructure in terms of instrumentation, often impede the application of biotechnological tools in less researched crops in laboratories in developing countries. We modified and optimized the existing CTAB method for plant genomic DNA extraction by avoiding liquid nitrogen usage and ... more

I.O. Agbagwa; S. Datta; P.G. Patil; P. Singh; N. Nadarajan
09/03/2013
MC1R; Molecular evolution; Positive selection; Rodentia

Adaptive variation in the melanocortin 1-receptor gene (MC1R), a key locus in melanogenesis, has been identified in some species of rodents. However, in others, MC1R has no causative role in pigmentation phenotypes despite their coat color variation. In this study, we characterized the rates and patterns of MC1R nucleotide and amino acid sequence evolution and ... more

G.L. Gonçalves; V.R. Paixão-Côrtes; T.R.O. Freitas
02/08/2013
Innate immunity; Molecular evolution; PGLYRP1 gene; Positive selection; Primate; Purifying selection

Short-type peptidoglycan (PGN)-recognition protein 1 (PGLYRP1), an innate immunity protein that directly breaks down the structure of microbial cell wall PGNs, plays an important role both in antibacterial defenses and several inflammatory diseases. To explore the adaptive evolution of the PGLYRP1 gene in primates and provide insight into the function of this antibacterial ... more

W. Liu; Y.F. Yao; L. Zhou; Q.Y. Ni; H.L. Xu
10/04/2007
Complex networks; Myoglobins; Protein structure

The construction of a realistic theoretical model of proteins is determinant for improving the computational simulations of their structural and functional aspects. Modeling proteins as a network of non-covalent connections between the atoms of amino acid residues has shown valuable insights into these macromolecules. The energy-related properties of protein structures are known to ... more

C.J.M. Veloso; C.H. Silveira; R.C. Melo; C. Ribeiro; J.C.D. Lopes; M.M. Santoro; W. Meira
06/30/2007
Amphipathy scale; Hydrophobic protein regions; Membrane protein; Primary structures; Protein structure; α-Helix transmembrane segments

We recently developed an amphipathy scale, elaborated from molecular dynamics data that can be used for the identification of hydrophobic or hydrophilic regions in proteins. This amphipathy scale reflects side chain/water molecule interaction energies. We have now used this amphipathy scale to find candidates for transmembrane segments, by examining a large sample of membrane proteins with α- ... more

F.M. Mazzé; C.A. Fuzo; P. Ciancaglini; L. Degrève
05/15/2006
Contact maps; Content-based image retrieval; Image registration; Image-matching; Protein structure

We modeled the problem of identifying how close two proteins are structurally by measuring the dissimilarity of their contact maps. These contact maps are colored images, in which the chromatic information encodes the chemical nature of the contacts. We studied two conceptually distinct image-processing algorithms to measure the dissimilarity between these contact maps; one was a ... more

R.C. de Melo; C.Eduardo R. Lopes; F.A. Fernandes; C.Henrique da Silveira; M.M. Santoro; R.L. Carceroni; W. Meira; Ade A. Araújo
03/31/2006
Bayesian classifier; Data classification; Enzyme classification number; Naive Bayes; Protein function prediction; Protein structure

Predicting enzyme class from protein structure parameters is a challenging problem in protein analysis. We developed a method to predict enzyme class that combines the strengths of statistical and data-mining methods. This method has a strong mathematical foundation and is simple to implement, achieving an accuracy of 45%. A comparison with the methods found in the literature designed ... more

L.C. Borro; S.R.M. Oliveira; M.E.B. Yamagishi; A.L. Mancini; J.G. Jardine; I. Mazoni; R.H. Higa; P.R. Kuser; G. Neshich; E.H. dos Santos
09/23/2008
binding site prediction; binding sites; interaction site prediction; interaction sites; Protein structure

Computational methods for predicting protein-protein interaction sites based on structural data are characterized by an accuracy between 70 and 80%. Some experimental studies indicate that only a fraction of the residues, forming clusters in the center of the interaction site, are energetically important for binding. In addition, the analysis of amino acid composition has shown that residues ... more

R.H. Higa; C.L. Tozzi
08/06/2012
Gene expression; HSP104; Protein structure; Trypanosoma cruzi

Heat shock protein (HSP) 104 is a highly conserved molecular chaperone that catalyzes protein unfolding, disaggregation and degradation under stress conditions. We characterized HSP104 gene structure and expression in Trypanosoma cruzi, a protozoan parasite that causes Chagas’ disease. The T. cruzi HSP104 is an 869 amino-acid protein encoded by a single-copy ... more

R.A. Campos; M.L. da Silva; G.V. da Costa; P.M. Bisch; J.M. Peralta; R. Silva; E. Rondinelli; T.P. Ürményi
11/28/2014
Bioinformatics; Morquio syndrome; Protein structure

The goals were to analyze and characterize the secondary structure, regions of intrinsic disorder and physicochemical characteristics of three classes of mutations described in the enzyme N-acetylgalactosamine-6-sulfatase that cause mucopolysaccharidosis IVA: missense mutations, insertions and deletions. All mutations were compared to wild-type enzyme, and the results showed that with 25 ... more

E.R. Tamarozzi; E. Torrieri; E.P. Semighini; S. Giuliatti

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