Comparative Hydrophobicity Analysis of Human β-Tubulin and Bacterial FtsZ Using the Fuzzy Oil Drop Model: Potential Implications for Chaperone-Assisted Folding
4 affiliations
- 1Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, 30-688 Kraków, Poland .
- 2Faculty of Automatic, Electronics and Computer Science, Department of Applied Informatics, Silesian University of Technology, 44-100 Gliwice, Poland .
- 3ASSA ABLOY Opening Solutions, Leszno, Poland .
- 4Chair of Medical Biochemistry, Jagiellonian University—Medical College, 31-034 Kraków, Poland .
Abstract
The issue of protein folding in vivo remains an unsolved problem despite important progress achieved by artificial intelligence (AlphaFold). Experimental studies have shown that there are several mechanisms involved in this process. The main distinction concerns the involvement of chaperone proteins in this process as opposed to spontaneous folding. Evolutionary analysis shows that tubulin in eukaryotic organisms requires engagement of the ATP-dependent ring-shaped chaperonin TRiC/CCT, while the homologous protein in prokaryotic organisms obtains its functional structure without the support from other proteins. This study—limited to 2 examples: one human tubulin β chain and one structure of homologous bacterial FtsZ protein—presents hypothetical interpretation of these differences based on the external conditions for folding process. The differences of the distribution of hydrophobicity in the compared proteins are taken as the criteria for comparison. The fuzzy oil drop model (FOD-M) assumes the folding of prokaryotic proteins as a spontaneous process aided only by the presence of the water environment that directs the folding toward the generation of a centrally located hydrophobic core with a polar surface. Eukaryotic protein—tubulin—exhibits a distribution of hydrophobicity that lacks this type of order as it is interpreted based on the FOD-M assumptions. The difference seems to be the result of the involvement of different external force fields in the folding process. These 2 proteins are an example that suggest the need to include the active influence of the local environment. The hypothesis for in silico methods of folding process simulation is assumed to use a multiple-object optimization technique that takes into account the optimization of the energy state of protein E as a function dependent on 2 functions: EINT (internal force field) and EEXT (external force field).
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BibTeX
@article{roterman2026comparative,
title = {{Comparative Hydrophobicity Analysis of Human β-Tubulin and Bacterial FtsZ Using the Fuzzy Oil Drop Model: Potential Implications for Chaperone-Assisted Folding}},
author = {Irena Roterman and Katarzyna Stapor and Dawid Dulak and Leszek Konieczny},
journal = {Computational and structural biotechnology journal},
year = {2026},
month = oct,
doi = {10.34133/csbj.0250},
url = {https://europepmc.org/article/PMC/PMC13720138},
note = {CC BY},
}
RIS
TY - JOUR
TI - Comparative Hydrophobicity Analysis of Human β-Tubulin and Bacterial FtsZ Using the Fuzzy Oil Drop Model: Potential Implications for Chaperone-Assisted Folding
AU - Irena Roterman
AU - Katarzyna Stapor
AU - Dawid Dulak
AU - Leszek Konieczny
PY - 2026
DA - 2026/10/30
JO - Computational and structural biotechnology journal
DO - 10.34133/csbj.0250
UR - https://europepmc.org/article/PMC/PMC13720138
AB - The issue of protein folding in vivo remains an unsolved problem despite important progress achieved by artificial intelligence (AlphaFold). Experimental studies have shown that there are several mechanisms involved in this process. The main distinction concerns the involvement of chaperone proteins in this process as opposed to spontaneous folding. Evolutionary analysis shows that tubulin in eukaryotic organisms requires engagement of the ATP-dependent ring-shaped chaperonin TRiC/CCT, while the homologous protein in prokaryotic organisms obtains its functional structure without the support from other proteins. This study—limited to 2 examples: one human tubulin β chain and one structure of homologous bacterial FtsZ protein—presents hypothetical interpretation of these differences based on the external conditions for folding process. The differences of the distribution of hydrophobicity in the compared proteins are taken as the criteria for comparison. The fuzzy oil drop model (FOD-M) assumes the folding of prokaryotic proteins as a spontaneous process aided only by the presence of the water environment that directs the folding toward the generation of a centrally located hydrophobic core with a polar surface. Eukaryotic protein—tubulin—exhibits a distribution of hydrophobicity that lacks this type of order as it is interpreted based on the FOD-M assumptions. The difference seems to be the result of the involvement of different external force fields in the folding process. These 2 proteins are an example that suggest the need to include the active influence of the local environment. The hypothesis for in silico methods of folding process simulation is assumed to use a multiple-object optimization technique that takes into account the optimization of the energy state of protein E as a function dependent on 2 functions: EINT (internal force field) and EEXT (external force field).
SN - 2001-0370
ER -