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Tytuł:
Electronegativity and intrinsic disorder of preeclampsia-related proteins
Autorzy:
Polanco, Carlos
Castañón-González, Jorge
Uversky, Vladimir
Buhse, Thomas
Samaniego Mendoza, José
Calva, Juan
Powiązania:
https://bibliotekanauki.pl/articles/1038693.pdf
Data publikacji:
2017
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
preeclampsia
intrinsically disordered proteins
structural proteomics
bioinformatics
antimicrobial peptides
polarity index method
lipoproteins
angiogenesis proteins
Opis:
Preeclampsia, hemorrhage, and infection are the leading causes of maternal death in underdeveloped countries. Since several proteins associated with preeclampsia are known, we conducted a computational study which evaluated the commonness and potential functionality of intrinsic disorder of these proteins and also made an attempt to characterize their origin. The origin of the preeclampsia-related proteins was assessed with a supervised technique, a Polarity Index Method (PIM), which evaluates the electronegativity of proteins based solely on their sequence. The commonness of intrinsic disorder was evaluated using several disorder predictors from the PONDR family, the charge-hydropathy plot (CH-plot) and cumulative distribution function (CDF) analyses, and using the MobiDB web-based tool, whereas potential functionality of intrinsic disorder was studied with the D2P2 resource and ANCHOR predictor of disorder-based binding sites, and the STRING tool was used to build the interactivity networks of the preeclampsia-related proteins. Peculiarities of the PIM-derived polar profile of the group of preeclampsia-related proteins were then compared with profiles of a group of lipoproteins, antimicrobial peptides, angiogenesis-related proteins, and the intrinsically disordered proteins. Our results showed a high graphical correlation between preeclampsia proteins, lipoproteins, and the angiogenesis proteins. We also showed that many preeclampsia-related proteins contain numerous functional disordered regions. Therefore, these bioinformatics results led us to assume that the preeclampsia proteins are highly associated with the lipoproteins group, and that some preeclampsia-related proteins contain significant amounts of functional disorders.
Źródło:
Acta Biochimica Polonica; 2017, 64, 1; 99-111
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Non-racemic mixture model: a computational approach
Autorzy:
Polanco, Carlos
Buhse, Thomas
Powiązania:
https://bibliotekanauki.pl/articles/1038677.pdf
Data publikacji:
2017
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
origin of homochirality
prebiotic peptide formation
chiral asymmetry
amino acids
Opis:
The behavior of a slight chiral bias in favor of l-amino acids over d-amino acids was studied in an evolutionary mathematical model generating mixed chiral peptide hexamers. The simulations aimed to reproduce a very generalized prebiotic scenario involving a specified couple of amino acid enantiomers and a possible asymmetric amplification through autocatalytic peptide self-replication while forming small multimers of a defined length. Our simplified model allowed the observation of a small ascending but not conclusive tendency in the l-amino acid over the d-amino acid profile for the resulting mixed chiral hexamers in computer simulations of 100 peptide generations. This simulation was carried out by changing the chiral bias from 1% to 3%, in three stages of 15, 50 and 100 generations to observe any alteration that could mean a drastic change in behavior. So far, our simulations lead to the assumption that under the exposure of very slight non-racemic conditions, a significant bias between l- and d-amino acids, as present in our biosphere, was unlikely generated under prebiotic conditions if autocatalytic peptide self-replication was the main or the only driving force of chiral auto-amplification.
Źródło:
Acta Biochimica Polonica; 2017, 64, 1; 17-19
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The polar profile of ancient proteins: a computational extrapolation from prebiotics to paleobiochemistry
Autorzy:
Polanco, Carlos
Buhse, Thomas
Vizcaíno, Gloria
Picciotto, Jacobo
Powiązania:
https://bibliotekanauki.pl/articles/1038695.pdf
Data publikacji:
2017
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
origins of life
prebiotic protein formation
abiogenesis
Opis:
This paper addresses the polar profile of ancient proteins using a comparative study of amino acids found in 25 000 000-year-old shells described in Abelson's work. We simulated the polar profile with a computer platform that represented an evolutionary computational toy model that mimicked the generation of small proteins starting from a pool of monomeric amino acids and that included several dynamic properties, such as self-replication and fragmentation-recombination of the proteins. The simulations were taken up to 15 generations and produced a considerable number of proteins of 25 amino acids in length. The computational model included the amino acids found in the ancient shells, the thermal degradation factor, and the relative abundance of the amino acids observed in the Miller-Urey experimental simulation of the prebiotic amino acid formation. We found that the amino acid polar profiles of the ancient shells and those simulated and extrapolated from the Miller-Urey abundances are coincident.
Źródło:
Acta Biochimica Polonica; 2017, 64, 1; 117-122
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Classifying lipoproteins based on their polar profiles
Autorzy:
Polanco, Carlos
Castañón-González, Jorge
Buhse, Thomas
Uversky, Vladimir
Amkie, Rafael
Powiązania:
https://bibliotekanauki.pl/articles/1038801.pdf
Data publikacji:
2016
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
potential of association
lipoproteins
polar balance
polarity index method
unfolded proteins
folded proteins
partially folded proteins
intrinsically disordered proteins
atherosclerosis
Opis:
The lipoproteins are an important group of cargo proteins known for their unique capability to transport lipids. By applying the Polarity index algorithm, which has a metric that only considers the polar profile of the linear sequences of the lipoprotein group, we obtained an analytical and structural differentiation of all the lipoproteins found in UniProt Database. Also, the functional groups of lipoproteins, and particularly of the set of lipoproteins relevant to atherosclerosis, were analyzed with the same method to reveal their structural preference, and the results of Polarity index analysis were verified by an alternate test, the Cumulative Distribution Function algorithm, applied to the same groups of lipoproteins.
Źródło:
Acta Biochimica Polonica; 2016, 63, 2; 235-241
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Identification of antimicrobial peptides by using eigenvectors
Autorzy:
Polanco, Carlos
Powiązania:
https://bibliotekanauki.pl/articles/1038767.pdf
Data publikacji:
2016
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
antimicrobial peptides
supervised methods
structural bioinformatics
Opis:
Antibacterial peptides are subject to broad research due to their potential application and the benefit they can provide for a wide range of diseases. In this work, a mathematical-computational method, called the Polarity Vector Method, is introduced that has a high discriminative level (>70%) to identify peptides associated with Gram (-) bacteria, Gram (+) bacteria, cancer cells, fungi, insects, mammalian cells, parasites, and viruses, taken from the Antimicrobial Peptides Database. This supervised method uses only eigenvectors from the incident polar matrix of the group studied. It was verified with a comparative study with another extensively verified method developed previously by our team, the Polarity Index Method. The number of positive hits of both methods was up to 98% in all the tests conducted.
Źródło:
Acta Biochimica Polonica; 2016, 63, 3; 483-491
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Structure and function relationships of proteins based on polar profile: a review
Autorzy:
Polanco, Carlos
Buhse, Thomas
Uversky, Vladimir
Powiązania:
https://bibliotekanauki.pl/articles/1038800.pdf
Data publikacji:
2016
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
amino acids
polarity profile
pattern recognition
dynamical systems theory
atherosclerosis
selective antibacterial peptides
intrinsically disordered proteins
Opis:
Proteins in the post-genome era impose diverse research challenges, the main are the understanding of their structure-function mechanism, and the growing need for new pharmaceutical drugs, particularly antibiotics that help clinicians treat the ever- increasing number of Multidrug-Resistant Organisms (MDROs). Although, there is a wide range of mathematical-computational algorithms to satisfy the demand, among them the Quantitative Structure-Activity Relationship algorithms that have shown better performance using a characteristic training data of the property searched; their performance has stagnated regardless of the number of metrics they evaluate and their complexity. This article reviews the characteristics of these metrics, and the need to reconsider the mathematical structure that expresses them, directing their design to a more comprehensive algebraic structure. It also shows how the main function of a protein can be determined by measuring the polarity of its linear sequence, with a high level of accuracy, and how such exhaustive metric stands as a "fingerprint" that can be applied to scan the protein regions to obtain new pharmaceutical drugs, and thus to establish how the singularities led to the specialization of the protein groups known today.
Źródło:
Acta Biochimica Polonica; 2016, 63, 2; 229-233
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Identification of proteins associated with amyloidosis by polarity index method
Autorzy:
Polanco, Carlos
Samaniego, José
Uversky, Vladimir
Castañón-González, Jorge
Buhse, Thomas
Leopold-Sordo, Marili
Madero-Arteaga, Alejandro
Morales-Reyes, Alicia
Tavera-Sierra, Lourdes
González-Bernal, Jesus
Arias-Estrada, Miguel
Powiązania:
https://bibliotekanauki.pl/articles/1039130.pdf
Data publikacji:
2015
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
Polarity index method
natively unfolded proteins
intrinsically disordered proteins
natively folded proteins
neurons
amyloidosis
amyloid
amyloidogenic protein
Opis:
There is a natural protein form, insoluble and resistant to proteolysis, adopted by many proteins independently of their amino acid sequences via specific misfolding-aggregation process. This dynamic process occurs in parallel with or as an alternative to physiologic folding, generating toxic protein aggregates that are deposited and accumulated in various organs and tissues. These proteinaceous deposits typically represent bundles of β-sheet-enriched fibrillar species known as the amyloid fibrils that are responsible for serious pathological conditions, including but not limited to neurodegenerative diseases, grouped under the term amyloidoses. The proteins that might adopt this fibrillar conformation are some globular proteins and natively unfolded (or intrinsically disordered) proteins. Our work shows that intrinsically disordered and intrinsically ordered proteins can be reliably identified, discriminated, and differentiated by analyzing their polarity profiles generated using a computational tool known as the polarity index method (Polanco & Samaniego, 2009; Polanco et al., 2012; 2013; 2013a; 2014; 2014a; 2014b; 2014c; 2014d). We also show that proteins expressed in neurons can be differentiated from proteins in these two groups based on their polarity profiles, and also that this computational tool can be used to identify proteins associated with amyloidoses. The efficiency of the proposed method is high (i.e. 70%) as evidenced by the analysis of peptides and proteins in the APD2 database (2012), AVPpred database (2013), and CPPsite database (2013), the set of selective antibacterial peptides from del Rio et al. (2001), the sets of natively unfolded and natively folded proteins from Oldfield et al. (2005), the set of human revised proteins expressed in neurons, and non-human revised proteins expressed in neurons, from the Uniprot database (2014), and also the set of amyloidogenic proteins from the AmyPDB database (2014).
Źródło:
Acta Biochimica Polonica; 2015, 62, 1; 41-55
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Identification of proteins associated with Mycobacterium tuberculosis virulence pathway by their polar profile
Autorzy:
Polanco, Carlos
Castañón-González, Jorge
Mancilla, Raul
Buhse, Thomas
Samaniego, José
Gimbel, Arturo
Powiązania:
https://bibliotekanauki.pl/articles/1039087.pdf
Data publikacji:
2015
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
Mycobacterium tuberculosis bacteria virulence pathway
Polarity Index Method
Opis:
With almost one third of the world population infected, tuberculosis is one of the most devastating diseases worldwide and it is a major threat to any healthcare system. With the mathematical-computational method named "Polarity Index Method", already published by this group, we identified, with high accuracy (70%), proteins related to Mycobacterium tuberculosis bacteria virulence pathway from the Tuberculist Database. The test considered the totality of proteins cataloged in the main domains: fungi, bacteria, and viruses from three databases: Antimicrobial Peptide Database (APD2), Tuberculist Database, Uniprot Database, and four antigens of Mycobacterium tuberculosis: PstS-1, 38-kDa, 19-kDa, and H37Rv ORF. The method described was calibrated with each database to achieve the same performance, showing a high percentage of coincidence in the identification of proteins associated with Mycobacterium tuberculosis bacteria virulence pathway located in the Tuberculist Database, and identifying a polar pattern regardless of the group studied. This method has already been used in the identification of diverse groups of proteins and peptides, showing that it is an effective discriminant. Its metric considers only one physico-chemical property, i.e. polarity.
Źródło:
Acta Biochimica Polonica; 2015, 62, 2; 191-196
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Computational model of abiogenic amino acid condensation to obtain a polar amino acid profile
Autorzy:
Polanco, Carlos
Buhse, Thomas
Samaniego, José
Castañón González, Jorge
Estrada, Miguel
Powiązania:
https://bibliotekanauki.pl/articles/1039283.pdf
Data publikacji:
2014
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
amino acids
proteinoids
origins of life
polarity
computer simulations
Opis:
In accordance with the second law of thermodynamics, the Universe as a whole tends to higher entropy. However, the sequence of far-from-equilibrium events that led to the emergence of life on Earth could have imposed order and complexity during the course of chemical reactions in the so-called primordial soup of life. Hence, we may expect to find characteristic profiles or biases in the prebiotic product mixtures, as for instance among the first amino acids. Seeking to shed light on this hypothesis, we have designed a high performance computer program that simulates the spontaneous formation of the amino acid monomers in closed environments. The program was designed in reference to a prebiotic scenario proposed by Sydney W. Fox. The amino acid abundances and their polarities as the two principal biases were also taken into consideration. We regarded the computational model as exhaustive since 200 000 amino acid dimers were formed by simulation, subsequently expressed in a vector and compared with the corresponding amino acid dimers that were experimentally obtained by Fox. We found a very high similarity between the experimental results and our simulations.
Źródło:
Acta Biochimica Polonica; 2014, 61, 2; 253-258
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Discrete dynamic system oriented on the formation of prebiotic dipeptides from Rodes experiment
Autorzy:
Polanco, Carlos
Samaniego, José
Buhse, Thomas
Castañón González, Jorge
Powiązania:
https://bibliotekanauki.pl/articles/1039201.pdf
Data publikacji:
2014
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
origins of life
biogenesis
dipeptides
salt-induced peptide formation
Opis:
This work attempts to rationalize the possible prebiotic profile of the first dipeptides of about 4 billion years ago based on a computational discrete dynamic system that uses the final yields of the dipeptides obtained in Rode's experiments of salt-induced peptide formation (Rode et al., 1999, Peptides 20: 773-786). The system built a prebiotic scenario that allowed us to observe that (i) the primordial peptide generation was strongly affected by the abundances of the amino acid monomers, (ii) small variations in the concentration of the monomers have almost no effect on the final distribution pattern of the dipeptides and (iii) the most plausible chemical reaction of prebiotic peptide bond formation can be linked to Rode's hypothesis of a salt-induced scenario. The results of our computational simulations were related to former simulations of the Miller, and Fox & Harada experiments on amino acid monomer and oligomer generation, respectively, offering additional information to our approach.
Źródło:
Acta Biochimica Polonica; 2014, 61, 4; 717-726
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Possible computational filter to detect proteins associated to influenza A subtype H1N1
Autorzy:
Polanco, Carlos
Buhse, Thomas
Castañón-González, Jorge
Samaniego, José
Powiązania:
https://bibliotekanauki.pl/articles/1039197.pdf
Data publikacji:
2014
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
Polarity Index Method
influenza A virus subtype H1N1
drug design
QSAR method
Opis:
The design of drugs with bioinformatics methods to identify proteins and peptides with a specific toxic action is increasingly recurrent. Here, we identify toxic proteins towards the influenza A virus subtype H1N1 located at the UniProt database. Our quantitative structure-activity relationship (QSAR) approach is based on the analysis of the linear peptide sequence with the so-called Polarity Index Method that shows an efficiency of 90% for proteins from the Uniprot Database. This method was exhaustively verified with the APD2, CPPsite, Uniprot, and AmyPDB databases as well as with the set of antibacterial peptides studied by del Rio et al. and Oldfield et al.
Źródło:
Acta Biochimica Polonica; 2014, 61, 4; 693-698
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A toy model of prebiotic peptide evolution: the possible role of relative amino acid abundances
Autorzy:
Polanco, Carlos
Buhse, Thomas
Samaniego, José
Castañón González, Jorge
Powiązania:
https://bibliotekanauki.pl/articles/1039570.pdf
Data publikacji:
2013
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
polarity index method.
computer simulation
prebiotic polymerization
toy model
peptides
amino acids
Opis:
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.
Źródło:
Acta Biochimica Polonica; 2013, 60, 2; 175-182
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Characterization of a possible uptake mechanism of selective antibacterial peptides
Autorzy:
Polanco, Carlos
Samaniego, José
Castañón-González, Jorge
Buhse, Thomas
Sordo, Marili
Powiązania:
https://bibliotekanauki.pl/articles/1039457.pdf
Data publikacji:
2013
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
Polarity index method
cell penetrating peptides
selective antibacterial peptides
Opis:
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.
Źródło:
Acta Biochimica Polonica; 2013, 60, 4; 629-633
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Detection of selective antibacterial peptides by the Polarity Profile method
Autorzy:
Polanco, Carlos
Buhse, Thomas
Samaniego, José
Castañón-González, Jorge
Powiązania:
https://bibliotekanauki.pl/articles/1039571.pdf
Data publikacji:
2013
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
selective cationic amphipathic antibacterial peptides
Polarity Profile method
Polarity Index method
Opis:
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.
Źródło:
Acta Biochimica Polonica; 2013, 60, 2; 183-189
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Biased versus unbiased randomness in homo-polymers and copolymers of amino acids in the prebiotic world
Autorzy:
Mosqueira, Fernando
Negron, Alicia
Ramos, Sergio
Polanco, Carlos
Powiązania:
https://bibliotekanauki.pl/articles/1039646.pdf
Data publikacji:
2012
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
polarity of amino acids
homo-peptides
prebiotic co-polypeptides
lysine
Markov chain
prebiotic homo polymerization of amino acids
Opis:
The polymerization of amino acids under anhydrous prebiotic conditions was first studied several decades ago. Here we use a stochastic model stressing the relevant role of the polarity of amino acids in the formation of oligopeptides in a prebiotic milieu. Our goal is to outline the predominance of co-polypeptides over homo-polypeptides, resulting not only from the randomness, but also from polarity properties of amino acids. Our results conclude that there was a higher probability of the formation of co-polypeptides than of homo-polymers. Besides, we may hypothesize that the former would have a more ample spectrum of possible chemical functions than homo-polypeptides.
Źródło:
Acta Biochimica Polonica; 2012, 59, 4; 543-547
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
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