| Autor: |
Murilo N. Sanches, R. Gonzalo Parra, Rafael G. Viegas, Antonio B. Oliveira, Peter G. Wolynes, Diego U. Ferreiro, Vitor B.P. Leite |
| Jazyk: |
angličtina |
| Rok vydání: |
2022 |
| Předmět: |
|
| Zdroj: |
QRB Discovery, Vol 3 (2022) |
| Druh dokumentu: |
article |
| ISSN: |
2633-2892 |
| DOI: |
10.1017/qrd.2022.4 |
| Popis: |
Ankyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein–protein interactions in a diversity of biological systems. These proteins have an elongated non-globular shape and often display complex folding mechanisms. This work investigates the energy landscape of representative proteins of this class made up of 3, 4 and 6 ANK repeats using the energy-landscape visualisation method (ELViM). By combining biased and unbiased coarse-grained molecular dynamics AWSEM simulations that sample conformations along the folding trajectories with the ELViM structure-based phase space, one finds a three-dimensional representation of the globally funnelled energy surface. In this representation, it is possible to delineate distinct folding pathways. We show that ELViMs can project, in a natural way, the intricacies of the highly dimensional energy landscapes encoded by the highly symmetric ankyrin repeat proteins into useful low-dimensional representations. These projections can discriminate between multiplicities of specific parallel folding mechanisms that otherwise can be hidden in oversimplified depictions. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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