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Contribution to the prediction of the fold code : application to immunoglobulin and flavodoxin cases

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Contribution to the prediction of the fold code : application to immunoglobulin and flavodoxin cases

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dc.contributor.author Banach, Mateusz [SAP20011078] pl
dc.contributor.author Prudhomme, Nicolas pl
dc.contributor.author Carpentier, Mathilde pl
dc.contributor.author Duprat, Elodie pl
dc.contributor.author Papandreou, Nikolaos pl
dc.contributor.author Kalinowska, Barbara [USOS61115] pl
dc.contributor.author Chomilier, Jacques pl
dc.contributor.author Roterman-Konieczna, Irena [SAP20000474] pl
dc.date.accessioned 2015-07-17T13:18:47Z
dc.date.available 2015-07-17T13:18:47Z
dc.date.issued 2015 pl
dc.identifier.uri http://ruj.uj.edu.pl/xmlui/handle/item/13248
dc.language eng pl
dc.rights Udzielam licencji. Uznanie autorstwa 4.0 Międzynarodowa *
dc.rights.uri http://creativecommons.org/licenses/by/4.0/pl/legalcode *
dc.title Contribution to the prediction of the fold code : application to immunoglobulin and flavodoxin cases pl
dc.type JournalArticle pl
dc.abstract.en Background. Folding nucleus of globular proteins formation starts by the mutual interaction of a group of hydrophobic amino acids whose close contacts allow subsequent formation and stability of the 3D structure. These early steps can be predicted by simulation of the folding process through a Monte Carlo (MC) coarse grain model in a discrete space. We previously defined MIRs (Most Interacting Residues), as the set of residues presenting a large number of non-covalent neighbour interactions during such simulation. MIRs are good candidates to define the minimal number of residues giving rise to a given fold instead of another one, although their proportion is rather high, typically [15-20]% of the sequences. Having in mind experiments with two sequences of very high levels of sequence identity (up to 90%) but different folds, we combined the MIR method, which takes sequence as single input, with the "fuzzy oil drop" (FOD) model that requires a 3D structure, in order to estimate the residues coding for the fold. FOD assumes that a globular protein follows an idealised 3D Gaussian distribution of hydrophobicity density, with the maximum in the centre and minima at the surface of the "drop". If the actual local density of hydrophobicity around a given amino acid is as high as the ideal one, then this amino acid is assigned to the core of the globular protein, and it is assumed to follow the FOD model. Therefore one obtains a distribution of the amino acids of a protein according to their agreement or rejection with the FOD model. Results. We compared and combined MIR and FOD methods to define the minimal nucleus, or keystone, of two populated folds: immunoglobulin-like (Ig) and flavodoxins (Flav). The combination of these two approaches defines some positions both predicted as a MIR and assigned as accordant with the FOD model. It is shown here that for these two folds, the intersection of the predicted sets of residues significantly differs from random selection. It reduces the number of selected residues by each individual method and allows a reasonable agreement with experimentally determined key residues coding for the particular fold. In addition, the intersection of the two methods significantly increases the specificity of the prediction, providing a robust set of residues that constitute the folding nucleus. pl
dc.description.volume 10 pl
dc.description.number 4 pl
dc.description.publication 1,5 pl
dc.identifier.doi 10.1371/journal.pone.0125098 pl
dc.identifier.eissn 1932-6203 pl
dc.title.journal PLoS ONE pl
dc.language.container eng pl
dc.affiliation Wydział Lekarski : Zakład Bioinformatyki i Telemedycyny pl
dc.subtype Article pl
dc.identifier.articleid e0125098 pl
dc.rights.original CC-BY; otwarte czasopismo; ostateczna wersja wydawcy; w momencie opublikowania; 0; pl
dc.identifier.project ROD UJ / OP pl
.pointsMNiSW [2015 A]: 40


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Udzielam licencji. Uznanie autorstwa 4.0 Międzynarodowa Except where otherwise noted, this item's license is described as Udzielam licencji. Uznanie autorstwa 4.0 Międzynarodowa