On the Dependence of Prion and Amyloid Structure on the Folding Environment
Abstract
:1. Introduction
2. Results
2.1. Description of the Model Used—The Fuzzy Oil Drop Model
2.2. Prions
2.3. Partially Unfolded Prion Proteins
2.4. Prion Protein in Form of Dimers
2.5. Prion-like Proteins
2.6. Prion Proteins in Form of Complexes with Fab Fragments of IgG
2.6.1. Amyloids
2.6.2. Super-Fibrillary Amyloids
3. Discussion
4. Materials and Methods
4.1. Programs Used
- The program allowing calculation of RD is accessible upon request on CodeOcean platform: [66] https://codeocean.com/capsule/3084411/tree. Please contact the corresponding author to obtain access to your private program instance.
- In order to ensure reproducibility of results and provide easy access to the computations discussed in this paper, the authors have also implemented an online tool where the FOD computations can be performed on arbitrary protein structures, including the structures discussed in this paper. The application—implemented in collaboration with the Sano Centre for Computational Medicine (https://sano.science, accessed on November 2021) and running on resources contributed by ACC Cyfronet AGH (https://www.cyfronet.pl, accessed on November 2021) in the framework of the PL-Grid Infrastructure (https://plgrid.pl, accessed on December 2021)—provides a web wrapper for the abovementioned computational component, and it is freely available at [67] https://hphob.sano.science—the dialog window shown in Figure 21.
4.2. Data
5. Conclusions
- Fundamental change in the strategy of creating large-molecular structures by amyloids in relation to protein complexes;
- Participation of the environment in the discussed process, resulting in the conclusion that the modification of the environment may result in amyloid transformation of almost any protein [56].
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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PDB-ID | Chain | Fragment Limited by SS-Bond | ||
---|---|---|---|---|
RD | K | RD | K | |
1HJN | 0.232 | 0.0 | 0.255 | 0.1 |
1HJM | 0.373 | 0.2 | 0.376 | 0.1 |
6FNV | 0.385 | 0.0 | 0.469 | 0.0 |
1E1W | 0.388 | 0.2 | 0.352 | 0.1 |
1DX0 | 0.412 | 0.2 | 0.393 | 0.0 |
6DU9 | 0.425 | 0.3 | 0.413 | 0.2 |
1QM3 | 0.441 | 0.3 | 0.413 | 0.2 |
1FKC | 0.448 | 0.3 | 0.470 | 0.3 |
1DX1 | 0.452 | 0.3 | 0.396 | 0.1 |
1AG2 | 0.454 | 0.3 | 0.455 | 0.3 |
1DWZ | 0.457 | 0.3 | 0.394 | 0.1 |
1QLZ | 0.471 | 0.3 | 0.472 | 0.2 |
Protein | Chain | Fragment Limited by SS-Bond | ||
---|---|---|---|---|
RD | K | RD | K | |
5YJ5 | 0.539 | 0.5 | 0.466 | 0.0 |
90–145 | 0.751 | 2.3 | ||
145–231 | 0.513 | 0.4 | 0.524 | 0.3 |
6FNV | 0.583 | 0.5 | 0.536 | 0.3 |
90–145 | 0.765 | 3.2 | ||
145–233 | 0.491 | 0.4 | 0.506 | 0.3 |
5L6R | 0.622 | 0.5 | 0.456 | 0.0 |
90–130 | 0.776 | 2.1 | ||
130–234 | 0.512 | 0.3 | 0.547 | 0.3 |
5YJ4 | 0.639 | 0.5 | 0.372 | 0.4 |
90–140 | 0.712 | 2.1 | ||
140–231 | 0.416 | 0.2 | 0.352 | 0.1 |
PDB-ID | Dimer/Monomer | Status as Part of Complex | Fragment Limited by SS-Bond | |||
---|---|---|---|---|---|---|
RD | K | RD | K | RD | K | |
4HLS—AB | 0.547 | 0.4 | ||||
A | 0.413 | 0.3 | 0.536 | 0.5 | 0.445 | 0.2 |
B | 0.440 | 0.3 | 0.555 | 0.4 | 0.361 | 0.1 |
4HMM—AB | 0.544 | 0.4 | ||||
A | 0.418 | 0.3 | 0.543 | 0.5 | 0.449 | 0.25 |
B | 0.428 | 0.3 | 0.543 | 0.4 | 0.357 | 0.1 |
4HMR—AB | 0.530 | 0.4 | ||||
A | 0.434 | 0.3 | 0.520 | 0.4 | 0.451 | 0.2 |
B | 0.429 | 0.3 | 0.539 | 0.4 | 0.360 | 0.1 |
PDB-ID | Chain | Fragment Limited by SS-Bond | ||
---|---|---|---|---|
RD | K | RD | K | |
1LG4 | 0.484 | 0.4 | 0.494 | 0.3 |
1I17 | 0.427 | 0.2 | 0.373 | 0.1 |
PDB-ID | Complex/Monomer | Status as Part of Complex | Fragment Limited by SS-Bond | |||
---|---|---|---|---|---|---|
RD | K | RD | K | RD | K | |
6AQ7 | 0.717 | |||||
6AQ7-P | 0.466 | 0.3 | 0.655 | 1.5 | 0.438 | 0.2 |
4YXL | 0.752 | |||||
4YXL-P | 0.500 | 0.4 | 0.761 | 2.7 | 0.438 | 0.2 |
4MA7 | 0.759 | |||||
4MA7-P | 0.481 | 0.4 | 0.766 | 2.4 | 0.434 | 0.2 |
4MA8 | 0.779 | |||||
4MA8-P | 0.525 | 0.5 | 0.812 | 4.0 | 0.447 | 0.2 |
PDB-ID | Super-Fibril | Proto-Fibril | One Level | Chain—Individual | ||||
---|---|---|---|---|---|---|---|---|
RD | K | RD | K | RD | K | RD | K | |
2KJ3 | 0.418 | 0.2 | 0.618 | 0.6 | ||||
2RNM | 0.446 | 0.3 | 0.644 | 0.8 | ||||
2MUS | 0.596 | 0.6 | 0.636 | 0.6 | ||||
2LBU | 0.604 | 0.6 | 0.652 | 0.8 | ||||
7LNA | 0.612 | 0.6 | 0.568 | 0.5 | ||||
5W3N | 0.641 | 0.6 | 0.749 | 0.7 | ||||
6EKA | 0.666 | 0.9 | 0.660 | 0.7 | ||||
6UUR | 0.668 | 0.7 | 0.745 | 1.0 | 0.659 | 0.6 | 0.730 | 0.8 |
6ZCF (2) | 0.716 | 1.5 | 0.620 | 0.8 | 0.756 | 1.6 | 0.695 | 1.0 |
6ZCG (4) | 0.778 | 2.0 | 0.623 | 0.9 | 0.828 | 2.1 | 0.673 | 0.9 |
6LNI (2) | 0.794 | 2.3 | 0.624 | 0.8 | 0.810 | 2.2 | 0.663 | 0.8 |
6VPS (3) | 0.814 | 1.6 | 0.790 | 1.3 | 0.827 | 1.1 | 0.806 | 1.1 |
7BX7 (2) | 0.823 | 2.7 | 0.790 | 2.7 | 0.831 | 2.7 | 0.789 | 1.5 |
1PGZ | 0.582 | 0.6 | ||||||
D1 (8–95) | 0.319 | 0.1 | ||||||
D2 (96–190) | 0.454 | 0.3 |
PDB-ID | Fibril Superfibril | Proto-Fibril | Chain—Individual | |||
---|---|---|---|---|---|---|
RD | K | RD | K | RD | K | |
7LNA | 0.718 | 1.0 | 0.706 | 1 | ||
6LNI (2) | 0.717 | 2.2 | 0.650 | 0.7 | 0.708 | 0.7 |
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Roterman, I.; Stapor, K.; Gądek, K.; Gubała, T.; Nowakowski, P.; Fabian, P.; Konieczny, L. On the Dependence of Prion and Amyloid Structure on the Folding Environment. Int. J. Mol. Sci. 2021, 22, 13494. https://doi.org/10.3390/ijms222413494
Roterman I, Stapor K, Gądek K, Gubała T, Nowakowski P, Fabian P, Konieczny L. On the Dependence of Prion and Amyloid Structure on the Folding Environment. International Journal of Molecular Sciences. 2021; 22(24):13494. https://doi.org/10.3390/ijms222413494
Chicago/Turabian StyleRoterman, Irena, Katarzyna Stapor, Krzysztof Gądek, Tomasz Gubała, Piotr Nowakowski, Piotr Fabian, and Leszek Konieczny. 2021. "On the Dependence of Prion and Amyloid Structure on the Folding Environment" International Journal of Molecular Sciences 22, no. 24: 13494. https://doi.org/10.3390/ijms222413494