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Open AccessArticle

Downhill, Ultrafast and Fast Folding Proteins Revised

1
Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Lazarza 16, 31-533 Krakow, Poland
2
Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
3
Chair of Medical Biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(20), 7632; https://doi.org/10.3390/ijms21207632
Received: 30 August 2020 / Revised: 6 October 2020 / Accepted: 11 October 2020 / Published: 15 October 2020
(This article belongs to the Special Issue Protein Folding and Misfolding ---- Structure and Functions)
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. View Full-Text
Keywords: ultrafast folding; downhill folding; hydrophobic core ultrafast folding; downhill folding; hydrophobic core
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MDPI and ACS Style

Banach, M.; Stapor, K.; Konieczny, L.; Fabian, P.; Roterman, I. Downhill, Ultrafast and Fast Folding Proteins Revised. Int. J. Mol. Sci. 2020, 21, 7632. https://doi.org/10.3390/ijms21207632

AMA Style

Banach M, Stapor K, Konieczny L, Fabian P, Roterman I. Downhill, Ultrafast and Fast Folding Proteins Revised. International Journal of Molecular Sciences. 2020; 21(20):7632. https://doi.org/10.3390/ijms21207632

Chicago/Turabian Style

Banach, Mateusz; Stapor, Katarzyna; Konieczny, Leszek; Fabian, Piotr; Roterman, Irena. 2020. "Downhill, Ultrafast and Fast Folding Proteins Revised" Int. J. Mol. Sci. 21, no. 20: 7632. https://doi.org/10.3390/ijms21207632

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