Downhill, ultrafast and fast folding proteins revised

2020
journal article
article
23
dc.abstract.enResearch on the protein folding problem differentiates the protein folding process with respect to the duration of this process. The current structure encoded in sequence dogma seems to be clearly justified, especially in the case of proteins referred to as fast-folding, ultra-fast-folding or downhill. In the present work, an attempt to determine the characteristics of this group of proteins using fuzzy oil drop model is undertaken. According to the fuzzy oil drop model, a protein is a specific micelle composed of bi-polar molecules such as amino acids. Protein folding is regarded as a spherical micelle formation process. The presence of covalent peptide bonds between amino acids eliminates the possibility of free mutual arrangement of neighbors. An example would be the construction of co-micelles composed of more than one type of bipolar molecules. In the case of fast folding proteins, the amino acid sequence represents the optimal bipolarity system to generate a spherical micelle. In order to achieve the native form, it is enough to have an external force field provided by the water environment which directs the folding process towards the generation of a centric hydrophobic core. The influence of the external field can be expressed using the 3D Gaussian function which is a mathematical model of the folding process orientation towards the concentration of hydrophobic residues in the center with polar residues exposed on the surface. The set of proteins under study reveals a hydrophobicity distribution compatible with a 3D Gaussian distribution, taken as representing an idealized micelle-like distribution. The structure of the present hydrophobic core is also discussed in relation to the distribution of hydrophobic residues in a partially unfolded form.pl
dc.affiliationWydział Lekarski : Zakład Bioinformatyki i Telemedycynypl
dc.cm.date2021-02-15
dc.cm.id101787
dc.contributor.authorBanach, Mateusz - 103003 pl
dc.contributor.authorStąpor, Katarzyna - 337899 pl
dc.contributor.authorKonieczny, Leszekpl
dc.contributor.authorFabian, Piotrpl
dc.contributor.authorRoterman-Konieczna, Irena - 133298 pl
dc.date.accessioned2021-02-15T01:24:34Z
dc.date.available2021-02-15T01:24:34Z
dc.date.issued2020pl
dc.date.openaccess0
dc.description.accesstimew momencie opublikowania
dc.description.number20pl
dc.description.points140
dc.description.versionostateczna wersja wydawcy
dc.description.volume21pl
dc.identifier.articleid7632pl
dc.identifier.doi10.3390/ijms21207632pl
dc.identifier.eissn1422-0067pl
dc.identifier.projectROD UJ / OPpl
dc.identifier.urihttps://ruj.uj.edu.pl/xmlui/handle/item/264498
dc.languageengpl
dc.language.containerengpl
dc.rightsUdzielam licencji. Uznanie autorstwa 4.0 Międzynarodowa*
dc.rights.licenceCC-BY
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/legalcode.pl*
dc.share.typeotwarte czasopismo
dc.subject.enultrafast foldingpl
dc.subject.endownhill foldingpl
dc.subject.enhydrophobic corepl
dc.subtypeArticlepl
dc.titleDownhill, ultrafast and fast folding proteins revisedpl
dc.title.journalInternational Journal of Molecular Sciencespl
dc.typeJournalArticlepl
dspace.entity.typePublication
dc.abstract.enpl
Research on the protein folding problem differentiates the protein folding process with respect to the duration of this process. The current structure encoded in sequence dogma seems to be clearly justified, especially in the case of proteins referred to as fast-folding, ultra-fast-folding or downhill. In the present work, an attempt to determine the characteristics of this group of proteins using fuzzy oil drop model is undertaken. According to the fuzzy oil drop model, a protein is a specific micelle composed of bi-polar molecules such as amino acids. Protein folding is regarded as a spherical micelle formation process. The presence of covalent peptide bonds between amino acids eliminates the possibility of free mutual arrangement of neighbors. An example would be the construction of co-micelles composed of more than one type of bipolar molecules. In the case of fast folding proteins, the amino acid sequence represents the optimal bipolarity system to generate a spherical micelle. In order to achieve the native form, it is enough to have an external force field provided by the water environment which directs the folding process towards the generation of a centric hydrophobic core. The influence of the external field can be expressed using the 3D Gaussian function which is a mathematical model of the folding process orientation towards the concentration of hydrophobic residues in the center with polar residues exposed on the surface. The set of proteins under study reveals a hydrophobicity distribution compatible with a 3D Gaussian distribution, taken as representing an idealized micelle-like distribution. The structure of the present hydrophobic core is also discussed in relation to the distribution of hydrophobic residues in a partially unfolded form.
dc.affiliationpl
Wydział Lekarski : Zakład Bioinformatyki i Telemedycyny
dc.cm.date
2021-02-15
dc.cm.id
101787
dc.contributor.authorpl
Banach, Mateusz - 103003
dc.contributor.authorpl
Stąpor, Katarzyna - 337899
dc.contributor.authorpl
Konieczny, Leszek
dc.contributor.authorpl
Fabian, Piotr
dc.contributor.authorpl
Roterman-Konieczna, Irena - 133298
dc.date.accessioned
2021-02-15T01:24:34Z
dc.date.available
2021-02-15T01:24:34Z
dc.date.issuedpl
2020
dc.date.openaccess
0
dc.description.accesstime
w momencie opublikowania
dc.description.numberpl
20
dc.description.points
140
dc.description.version
ostateczna wersja wydawcy
dc.description.volumepl
21
dc.identifier.articleidpl
7632
dc.identifier.doipl
10.3390/ijms21207632
dc.identifier.eissnpl
1422-0067
dc.identifier.projectpl
ROD UJ / OP
dc.identifier.uri
https://ruj.uj.edu.pl/xmlui/handle/item/264498
dc.languagepl
eng
dc.language.containerpl
eng
dc.rights*
Udzielam licencji. Uznanie autorstwa 4.0 Międzynarodowa
dc.rights.licence
CC-BY
dc.rights.uri*
http://creativecommons.org/licenses/by/4.0/legalcode.pl
dc.share.type
otwarte czasopismo
dc.subject.enpl
ultrafast folding
dc.subject.enpl
downhill folding
dc.subject.enpl
hydrophobic core
dc.subtypepl
Article
dc.titlepl
Downhill, ultrafast and fast folding proteins revised
dc.title.journalpl
International Journal of Molecular Sciences
dc.typepl
JournalArticle
dspace.entity.type
Publication
Affiliations

* The migration of download and view statistics prior to the date of April 8, 2024 is in progress.