Abstract
Understanding how polypeptides can efficiently and reproducibly attain a self-entangled conformation is a compelling biophysical challenge, which might shed new light on our general knowledge of protein folding. Complex Lassos, namely self-entangled protein structures characterized by a covalent loop sealed by a cysteine bridge, represent an ideal test system in the framework of entangled folding. Indeed, as cysteine bridges form in oxidizing conditions, they can be used as on/off switches of the structure topology, to investigate the role played by the backbone entanglement in the process.
In the present work we have used molecular dynamics to simulate the folding of a complex lasso glycoprotein, Granulocyte-macrophage colony-stimulating factor, modeling both reducing and oxidizing conditions. Together with a well-established Gō-like description, we have employed the elastic folder model, a Coarse-Grained, minimalistic representation of the polypeptide chain, driven by a structure-based angular potential. The purpose of this study is to assess the kinetically optimal pathways, in relation to the formation of the native topology. To this end we have implemented an evolutionary strategy that tunes the elastic folder model potentials to maximize the folding probability within the early stages of the dynamics. The resulting protein model is capable of folding with high success rate, avoiding the kinetic traps that hamper the efficient folding in the other tested models. Employing specifically designed topological descriptors, we could observe that the selected folding routes avoid the topological bottleneck by locking the cysteine bridge after the topology is formed.
These results provide valuable insights on the selection of mechanisms in self-entangled protein folding while, at the same time, the proposed methodology can complement the usage of established minimalistic models, and draw useful guidelines for more detailed simulations.
Author summary We have investigated, by means of numerical methods, the folding mechanism of Granulocyte-macrophage colony-stimulating factor, a glycoprotein that handles a variety of functions in the human body. Our interest in this protein focuses on the self-entangled native state, which is classified as a so-called complex lasso. Complex lasso structures contain a backbone loop, closed by a cysteine bridge, which is pierced one or more times by the protein chain, resulting in an entangled conformation. Understanding how a polypeptide can encode into its sequence the capability of tying itself into such kind of structures would represent a major advancement in the comprehension of a crucial biological process such as protein folding.
To study this folding mechanism we have employed molecular dynamics simulations, adopting both a well-known minimalistic model of the protein, and an alternative model, that was specifically proposed for unveiling the preferential pathways of entangled folding. Our calculations show how the protein can avoid the kinetic traps related to self-entanglement, managing to fold in a reproducible and efficient way.
Footnotes
↵* perego{at}mpip-mainz.mpg.de