Revealing highly conserved regions in the E6 protein among distinct human papillomavirus types using comparative analysis of multiple sequence alignments

Gabriel, Jane Eyre; Figueiredo, D D L G de; Farias, R P de

doi:10.1590/s1519-69842013000200030

Cited by 3 publications

(3 citation statements)

References 9 publications

(15 reference statements)

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“…The biological fields have progressed tremendously in the ability to process and interpret large volumes of biological data using computational biology analyses, advancing molecular and structural characterization of bioactive molecules of interest (Schatz et al, 2010;Gabriel et al, 2013). The purpose of the present study was to comparatively assess multiple sequences of the leptin protein in distinct animal species to establish new insights into the conservation degree of biological sequences and evolutionary biology among mammals using computational biology tools.…”

Section: Introductionmentioning

confidence: 99%

Short Communication Molecular conservation of the mammalian leptin protein

Gabriel

Lidani

2015

Genet. Mol. Res.

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ABSTRACT. In this study, we comparatively assessed multiple sequences of the leptin protein from different animal species to establish new insights into conservation degree of biological sequences and evolutionary biology among mammals using computational biology tools. First, amino acid sequences of the leptin protein from Homo sapiens (human, P41159), Sus scrofa (wild pig, Q29406), Felis catus (domestic cat, Q29406), Rattus norvegicus (rat, P50596), and Mus musculus (mouse, P41160) were randomly searched in the high-quality annotated and non-redundant protein sequence database UniProtKB/Swiss-Prot. A dendogram showing the evolutionary relationships among specimens was constructed from the sequences of interest using the Mega 6.0 software with the neighbor-joining method. The resulting tree presenting the evolutionary relationships among specimens inferred from amino acid sequences of the leptin protein in mammals demonstrated 2 main branches: 1 cluster including the rat and mouse species (0.02) and a second cluster containing both (2015) J.E. Gabriel and K.C.F. Lidani wild pig and domestic cat species grouped in a sub-branch (0.04 and 0.06, respectively), linking them to the human sequence (0.08). These findings were reinforced by comparing estimates of evolutionary divergence among leptin sequences analyzed. Based on comparative analyses of multiple sequence alignments in the present study, there was a stronger conservation degree of the leptin protein in evolutionarily close species and several conservative changes along the sequences of interest, revealing information regarding the evolutionary biology among mammals.

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Section: Introductionmentioning

confidence: 99%

Short Communication Molecular conservation of the mammalian leptin protein

Gabriel

Lidani

2015

Genet. Mol. Res.

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“…In the last decades, bioinformatics has contributed to the development of computational biology tools and their application for several research fields in biology, furthering the understanding of living systems at all scales through the application of computational methods (Schatz, Delcher, Salzberg, 2010;Gabriel, 2012;Gabriel, de Figueiredo, de Farias, 2013). One of these applications is to improve the performance of L. braziliensis, L. major and L. donovani) and other animal species, such as rhesus monkey Macaca mulatta in the chromosomes 2 and 10, respectively (Table 1).…”

Section: Introductionmentioning

confidence: 99%

Evaluating the specificity of primers employed for PCR-based diagnostics of Leishmaniases using multiple alignment analysis

Gabriel¹

2013

Estud Biol.

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The purpose of this study was to assess the specificity of distinct primers used in the molecular diagnosis for Leishmania detection by using biological sequence search and alignment tools. Four primer pairs routinely employed in the PCR-based diagnostics for Leishmaniasis detection were evaluated through the software Primer-BLAST, which compares nucleotide sequences against user-selected database to avoid primer pairs cause non-specific amplifications. The LU5A-LB3C primer pair showed good specificity among all primers analyzed, generating alignments exclusively against distinct sequences of Leishmania species and no matches were found with other parasite species. Whereas the primer pairs designated MP3H--MP1L, B1-B2 and 13A-13B demonstrated matches against distinct sequences of Leishmania strains and other species, such as Rhesus monkey (Macaca mulatta) and starlet sea anemone (Nematostella vectensis). These findings emphasize the importance of selecting suitable primers for diagnosis of molecular diseases by conducting previous screenings in order to infer their specificity and identity against target templates within biological sequence annotation database.O objetivo deste estudo foi avaliar o grau de especificidade de oligonucleotídeos iniciadores empregados rotineiramente no diagnóstico molecular de Leishmania a partir de ferramentas de bioinformática. Quatro pares de oligonucleotídeos iniciadores foram analisados pelo programa Primer-BLAST, o qual permite comparar a especificidade dos iniciadores a partir de um banco de dados de sequências de DNA e, assim, evitar a possível presença de fragmentos não específicos nas reações de amplificação. O par de iniciadores LU5A-LB3C demonstrou boa especificidade em comparação aos demais iniciadores analisados, gerando alinhamentos que reconheceram exclusivamente fragmentos genômicos de Leishmania. Por outro lado, os pares de iniciadores MP3H-MP1L, B1-B2 e 13A-13B apresentaram alinhamentos compatíveis a fragmentos genômicos de distintas linhagens de Leishmania, além de reconhecer fragmentos genômicos não específicos, tais como de macaco Rhesus (Macaca mulatta) e uma espécie de anêmona (Nematostella vectensis). Esses resultados enfatizam a importância de efetuar análises prévias da especificidade de oligonucleotídeos iniciadores a fim de promover melhor desempenho e sensibilidade acurada nos métodos de diagnóstico molecular de doenças.Palavras-chave: Biologia computacional. Diagnóstico molecular. Identidade de oligonucleotídeos.

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“…Thus, efforts should be focused on development of comparative protein structure modelling algorithms usable to minimize typical limitations associated with remarkable complexity and variability of transmembrane proteins, such as the number of torsion angles in disallowed regions and exposed hydrophobic residues, hydrogen bonds and exposed polar or charged residues (Zhu et al, 2001). Members of a same family of proteins containing non-synonymous replacements of amino acids have frequently predicted structural and functional differences by computational biology analyses (Gabriel et al, 2013). Substitutions, deletions or insertions of amino acid residues are extensively typical in the outer surface of the proteins, particularly in the loops, structurally variable regions most exposed to the protein.…”

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confidence: 99%

Characterizing the polymorphism K232A of the diacylglycerol-acyltransferase-1 lipogenic enzyme of bovine Bos taurus using in silico comparative protein prediction analyses

et al. 2017

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(With 1 figure) The diacylglycerol-acyltransferase-1 lipogenic enzyme (DGAT1) is a multi-pass transmembrane protein that catalyzes the conversion of diacylglycerol and fatty acyl CoA to triacylglycerol or retinol (LIU et al., 2012). The lysine to alanine polymorphism in the DGAT1 (K232A) is directly associated with 50% of the genetic variation in milk-fat percentage and exerts a strong effect on milk fatty acid composition (Schennink et al., 2008). Within this perspective, this study aimed to predict potential structural and functional effects of the polymorphism K232A on DGAT1 protein sequences of bovine Bos taurus using in silico comparative modelling prediction analyses.Two sequences of the DGAT1 protein of bovine Bos taurus were analyzed in this study: the non-polymorphic DGAT1 sequence (ID:Q8MK44) searched and selected from a non-redundant protein sequence database UniProtKB/ Swiss-Prot, and polymorphic DGAT1 sequence harboring the mutation K232A. Functional predictions of these proteins were evaluated using SIFT and PolyPhen-2 tools that infer the effect of an amino acid substitution on the structure and function of a protein using sequence homology (Kumar et al., 2009;Adzhubei et al., 2010). The prediction of differences in the protein stability due to mutation was also estimated from Gibbs free energy change (DDG) using I-Mutant version 2.0 (Capriotti et al., 2005). In silico comparative modelling prediction analyses of the tertiary and quaternary structures of the non-polymorphic and polymorphic DGAT-1 proteins were predicted using Phyre2 (Kelley et al., 2015) and Swiss-Model (Biasini et al., 2014) servers that build 3D theoretical models for protein fold recognition based on evolutionary related proteins and homology modelling. All computational biology tools selected in current study have been largely described in the literature as sufficient and reliable evaluative tools for in silico characterization of multiple target proteins.The SIFT and PolyPhen-2 results demonstrated that the mutation K232A was predicted to be tolerated with a score of 0.19 and benign with a score to 0.001, 0.99 sensitivity and 0.15 specificity. Furthermore, DDG value resulting of the polymorphism K232A was 0.78, indicating an increase in the structural stability of the polymorphic DGAT1. In Phyre2 analyses the modelling prediction for the non-polymorphic DGAT1 sequence targeted directly to Chain A of the membrane channel protein WSK3, a watersoluble analogue of the potassium channel KcsA, modelling 96 residues (20% of the sequence) with 23.9% confidence ( Figure 1A). Values of the global modelling quality estimation (GMQE and QMEAN) of the target-template alignment were 0.06 and -3.57, respectively. Notably, the modelling prediction for the polymorphic DGAT1 sequence matched to Chain A of a stromal interaction molecule 2, modelling 21 residues (4% of the sequence) with 23.0% confidence ( Figure 1B), and 0.04 GMQE and -6.27 QMEAN values. According to Kelley et al. (2015), 3D structure protein modellings may be very useful as ...

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Revealing highly conserved regions in the E6 protein among distinct human papillomavirus types using comparative analysis of multiple sequence alignments

Cited by 3 publications

References 9 publications

Short Communication Molecular conservation of the mammalian leptin protein

Short Communication Molecular conservation of the mammalian leptin protein

Evaluating the specificity of primers employed for PCR-based diagnostics of Leishmaniases using multiple alignment analysis

Characterizing the polymorphism K232A of the diacylglycerol-acyltransferase-1 lipogenic enzyme of bovine Bos taurus using in silico comparative protein prediction analyses

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