Model of Early Stage Intermediate in Respect to Its Final Structure.
early stage
hydrophobicity
protein folding
structural codes
Journal
Biomolecules
ISSN: 2218-273X
Titre abrégé: Biomolecules
Pays: Switzerland
ID NLM: 101596414
Informations de publication
Date de publication:
12 12 2019
12 12 2019
Historique:
received:
05
11
2019
revised:
06
12
2019
accepted:
10
12
2019
entrez:
18
12
2019
pubmed:
18
12
2019
medline:
17
9
2020
Statut:
epublish
Résumé
The model, describing a method of determining the structure of an early intermediate in the process of protein folding to analyze nonredundant PDB protein bases, allows determining the relationship between the sequence of tetrapeptides and their structural forms expressed by structural codes. The contingency table expressing such a relationship can be used to predict the structure of polypeptides by proposing a structural form with a precision limited to the structural code. However, by analyzing structural forms in native forms of proteins based on the fuzzy oil drop model, one can also determine the status of polypeptide chain fragments with respect to the assumptions of this model. Whether the probability distributions for both compliant and noncompliant forms were similar or whether the tetrapeptide sequences showed some differences at a level of a set of structural codes was investigated. The analysis presented here indicated that some sequences in both forms revealed differences in probability distributions expressed as a negative statistically significant correlation coefficient. This meant that the identified sections (tetrapeptides) took different forms against the fuzzy oil drop model. It may suggest that the information of the final status with respect to hydrophobic core formation is already carried by the structure of the early-stage intermediate.
Identifiants
pubmed: 31842350
pii: biom9120866
doi: 10.3390/biom9120866
pmc: PMC6995543
pii:
doi:
Substances chimiques
Oligopeptides
0
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Références
Pac Symp Biocomput. 2002;:601-12
pubmed: 11928512
Trends Biochem Sci. 1997 Jan;22(1):6-10
pubmed: 9020583
Curr Opin Struct Biol. 1996 Apr;6(2):227-31
pubmed: 8728656
J Theor Biol. 1995 Dec 7;177(3):283-8
pubmed: 8746328
Phys Chem Chem Phys. 2011 Oct 14;13(38):16890-901
pubmed: 21643583
Nature. 1990 Apr 19;344(6268):715-6
pubmed: 1691821
Nucleic Acids Res. 2018 Jul 2;46(W1):W304-W309
pubmed: 29718313
Nucleic Acids Res. 2017 Jan 4;45(D1):D289-D295
pubmed: 27899584
Proteins. 2014 Feb;82 Suppl 2:1-6
pubmed: 24344053
Proteins. 2018 Mar;86 Suppl 1:113-121
pubmed: 28940798
FASEB J. 1996 Jan;10(1):110-8
pubmed: 8566531
J Mol Biol. 1979 Apr 15;129(3):411-31
pubmed: 458851
Proteins. 1994 Apr;18(4):338-52
pubmed: 8208726
Curr Biol. 1991 Feb;1(1):8-10
pubmed: 15336191
Genome Biol. 2004;5(2):R7
pubmed: 14759257
Curr Biol. 1992 Jul;2(7):347-9
pubmed: 15335922
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W526-31
pubmed: 15215442
Proteins. 2010 Jul;78(9):2041-8
pubmed: 20455261
Biochem J. 1990 Aug 15;270(1):1-16
pubmed: 2204340
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
pubmed: 10592235
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2362-7
pubmed: 15677316
Curr Protoc Bioinformatics. 2015 Dec 17;52:5.8.1-5.8.15
pubmed: 26678386
Bioinformation. 2015 Oct 31;11(10):486-8
pubmed: 26664034
Int J Mol Sci. 2018 Sep 25;19(10):
pubmed: 30257460
Proteins. 2003;53 Suppl 6:524-33
pubmed: 14579342
Nature. 1989 May 4;339(6219):14-5
pubmed: 2716825
Biochimie. 1995;77(3):204-16
pubmed: 7647113