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Wyszukujesz frazę "Thomas." wg kryterium: Autor


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:
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:
Size, shape and secondary structure of calponin.
Autorzy:
Czuryło, Edward
Eimer, Wolfgang
Kulikova, Natalia
Hellweg, Thomas
Powiązania:
https://bibliotekanauki.pl/articles/1044328.pdf
Data publikacji:
2000
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
dynamic light scattering
secondary structure prediction
calponin
circular dichroism
secondary structure estimation
Opis:
The overall size and shape of the chicken gizzard calponin (CaP) h1 molecule was investigated by dynamic light scattering (DLS) measurements. From the DLS experiments, a z-averaged translational diffusion coefficient is derived (5.75 ± 0.3) × 10-7cm2s-1, which corresponds to a hydrodynamic radius of 3.72 nm for calponin. The frictional ratio (1.8 for the unhydrated molecule and 1.5 for the hydrated one) suggests a pronounced anisotropic structure for the molecule. An ellipsoidal model in length 19.4 nm and with a diameter of 2.6 nm used for hydrodynamic calculations was found to reproduce the DLS experimental data. The evaluation of the secondary structure of CaP h1 from the CD spectra by two independent methods has revealed that it contains, on average, 23% helix, 19% β-strand, 18% β-turns and loops, and 40% of remainder structures. These values are in good agreement with those predicted from the amino-acid sequence. Predictions used for CaP h1 were applied to other isoforms of known sequences and revealed that all calponins share a common secondary structure. Moreover, the predicted structure of the calponin CH domain is identical to that found by X-ray studies of the spectrin, fimbrin and utrophin CH domains.
Źródło:
Acta Biochimica Polonica; 2000, 47, 3; 791-806
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:
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:
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:
Comparative biochemical analysis of lectin and nuclease from Chelidonium majus L.
Autorzy:
Fik, Ewa
Dalgalarrondo, Michele
Haertlé, Thomas
Goździcka-Józefiak, Anna
Powiązania:
https://bibliotekanauki.pl/articles/1044368.pdf
Data publikacji:
2000
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
glycoproteins
glycosylation
plant lectins
Chelidonium majus
Opis:
It has been recently recognized that lectins exhibit other activities besides hemagglutination. Previously we have found that purified lectin from Chelidonium majus showed DNase activity (Fik, Goździcka-Józefiak & Kędzia, 1995, Herba Polon. 41, 84-95). Comparison of lectin and DNase from the sap from leaves and roots of Chelidonium majus proved that both these compounds are composed of 24 kDa monomer subunits which have an identical N-terminal sequence but differ in amino-acid composition and degree of glycosylation. Possible interrelationship between lectin and DNase is discussed.
Źródło:
Acta Biochimica Polonica; 2000, 47, 2; 413-420
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:
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:
How the RNA isolation method can affect microRNA microarray results
Autorzy:
Podolska, Agnieszka
Kaczkowski, Bogumil
Litman, Thomas
Fredholm, Merete
Cirera, Susanna
Powiązania:
https://bibliotekanauki.pl/articles/1039846.pdf
Data publikacji:
2011
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
microarray
microRNA isolation method
microRNA
small RNA fraction
pig
Opis:
The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform microRNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.
Źródło:
Acta Biochimica Polonica; 2011, 58, 4; 535-540
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Mutations in DNA polymerase gamma cause error prone DNA synthesis in human mitochondrial disorders
Autorzy:
Copeland, William
Ponamarev, Mikhail
Nguyen, Dinh
Kunkel, Thomas
Longley, Matthew
Powiązania:
https://bibliotekanauki.pl/articles/1043659.pdf
Data publikacji:
2003
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
aging
DNA replication
mitochondria
DNA repair
DNA polymerase
Opis:
This paper summarizes recent advances in understanding the links between the cell's ability to maintain integrity of its mitochondrial genome and mitochondrial genetic diseases. Human mitochondrial DNA is replicated by the two-subunit DNA polymerase γ (pol γ). We investigated the fidelity of DNA replication by pol γ with and without exonucleolytic proofreading and its p55 accessory subunit. Pol γ has high base substitution fidelity due to efficient base selection and exonucleolytic proofreading, but low frameshift fidelity when copying homopolymeric sequences longer than four nucleotides. Progressive external ophthalmoplegia (PEO) is a rare disease characterized by the accumulation of large deletions in mitochondrial DNA. Recently, several mutations in the polymerase and exonuclease domains of the human pol γ have been shown to be associated with PEO. We are analyzing the effect of these mutations on the human pol γ enzyme. In particular, three autosomal dominant mutations alter amino acids located within polymerase motif B of pol γ. These residues are highly conserved among family A DNA polymerases, which include T7 DNA polymerase and E. coli pol I. These PEO mutations have been generated in pol γ to analyze their effects on overall polymerase function as well as the effects on the fidelity of DNA synthesis. One mutation in particular, Y955C, was found in several families throughout Europe, including one Belgian family and five unrelated Italian families. The Y955C mutant pol γ retains a wild-type catalytic rate but suffers a 45-fold decrease in apparent binding affinity for the incoming dNTP. The Y955C derivative is also much less accurate than is wild-type pol γ, with error rates for certain mismatches elevated by 10- to 100-fold. The error prone DNA synthesis observed for the Y955C pol γ is consistent with the accumulation of mtDNA mutations in patients with PEO. The effects of other pol γ mutations associated with PEO are discussed.
Źródło:
Acta Biochimica Polonica; 2003, 50, 1; 155-167
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The decisive role of the water structure in changes of conformation of nucleic acids
Autorzy:
Barciszewski, Jan
Jurczak, Janusz
Porowski, Sylwester
Specht, Thomas
Erdmann, Volker
Powiązania:
https://bibliotekanauki.pl/articles/1044550.pdf
Data publikacji:
1999
Wydawca:
Polskie Towarzystwo Biochemiczne
Źródło:
Acta Biochimica Polonica; 1999, 46, 1; 133-144
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł

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