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1
A toy model of prebiotic peptide evolution: the possible role of relative amino acid abundances
100%
Polanco C. , Buhse T. , Samaniego J. L. , Castanon-Gonzalez J. A.
Acta Biochimica Polonica
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2013
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tom 60
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nr 2
EN
 This paper presents a mathematical-computational toy model based on the assumed dynamic principles of prebiotic peptide evolution. Starting from a pool of amino acid monomers, the model describes in a generalized manner the generation of peptides and their sequential information. The model integrates the intrinsic and dynamic key elements of the initiation of biopolymerization, such as the relative amino acid abundances and polarities, as well as the oligomer reversibility, i.e. fragmentation and recombination, and peptide self-replication. Our modeling results suggest that the relative amino acid abundances, as indicated by Miller-Urey type electric discharge experiments, played a principal role in the early sequential information of peptide profiles. Moreover, the computed profiles display an astonishing similarity to peptide profiles observed in so-called biological common ancestors found in the following three microorganisms; E. coli, M. jannaschii, and S. cereviasiae. The prebiotic peptide fingerprint was obtained by the so-called polarity index method that was earlier reported as a tool for the identification of cationic amphipathic antibacterial short peptides.
2
Detection of selective antibacterial peptides by the polarity profile method
100%
Polanco C. , Buhse T. , Samaniego J. L. , Castanon-Gonzalez J. A.
Acta Biochimica Polonica
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2013
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tom 60
|
nr 2
EN
 Antimicrobial peptides occupy a prominent place in the production of pharmaceuticals, because of their effective contribution to the protection of the immune system against almost all types of pathogens. These peptides are thoroughly studied by computational methods designed to shed light on their main functions. In this paper, we propose a computational approach, named the Polarity Profile method that represents an improvement to the former Polarity Index method. The Polarity Profile method is very effective in detecting the subgroup of antibacterial peptides called selective cationic amphipathic antibacterial peptides (SCAAP) that show high toxicity towards bacterial membranes and exhibit almost zero toxicity towards mammalian cells. Our study was restricted to the peptides listed in the antimicrobial peptides database (APD2) of December 19, 2012. Performance of the Polarity Profile method is demonstrated through a comparison to the former Polarity Index method by using the same sets of peptides. The efficiency of the Polarity Profile method exceeds 85% taking into account the false positive and/or false negative peptides.
3
Possible computational filter to detect proteins associated to influenza A subtype H1N1
100%
Polanco C. , Buhse T. , Castanon-Gonzalez J. A. , Samaniego J. L.
Acta Biochimica Polonica
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2014
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tom 61
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nr 4
4
Characterization of a possible uptake mechanism of selective antibacterial peptides
88%
Polanco C. , Samaniego J. L. , Castanon-Gonzalez J. A. , Buhse T. , Sordo M. L.
Acta Biochimica Polonica
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2013
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tom 60
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nr 4
EN
Selective antibacterial peptides containing less than 30 amino acid residues, cationic, with amphipathic properties, have been the subject of several studies due to their active participation and beneficial effects in strengthening the immune system of all living organisms. This manuscript reports the results of a comparison between the group of selective antibacterial peptides and another group called "cell penetrating peptides". An important number of the selective antibacterial peptides are cell penetrating peptides, suggesting that their toxicity is related to their uptake mechanism. The verification of this observation also includes the adaptation of a method previously published, called Polarity index, which reproduces and confirms the action of this new set of peptides. The efficiency of this method was verified based on four different databases, yielding a high score. The verification was based exclusively on the peptides already reported in the databases which have been experimentally verified.
5
Classifying lipoproteins based on their polar profilesp.
88%
Polanco C. , Castanon-Gonzalez J. A. , Buhse T. , Uversky V. N. , Amkie R. Z.
Acta Biochimica Polonica
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2016
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tom 63
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nr 2
6
Electronegativity and intrinsic disorder of preeclampsia-related proteins
75%
Polanco C. , Castanon-Gonzalez J. A. , Uversky V. N. , Buhse T. , Samaniego Mendoza J. L. , Calva J. J.
Acta Biochimica Polonica
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2017
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tom 64
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nr 1
7
Identification of proteins associated with Mycobacterium tuberculosis virulence pathway by their polar profile
75%
Palanco C. , Castanon-Gonzalez J. A. , Mancilla R. , Buhse T. , Samaniego J. L. , Gimbel A.
Acta Biochimica Polonica
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2015
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tom 62
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nr 2
8
Identification of proteins associated with amyloidosis by polarity index method
51%
Polanco C. , Samaniego J. L. , Uversky V. N. , Castanon-Gonzalez J. A. , Buhse T. , Leopold-Sordo M. , Madero-Arteage A. , Morales-Reyes A. , Tavera-Sierra L. , Gonzales-Bernal J. A. , Arias-Estrada M.
Acta Biochimica Polonica
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2015
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tom 62
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nr 1
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