Energy-dependent protein folding: modeling how a protein folding machine may work

Abstract

Background: Proteins fold robustly and reproducibly in vivo, but many cannot fold in vitro in isolation from cellular components. Despite the remarkable progress that has been achieved by the artificial intelligence approaches in predicting the protein native conformations, the pathways that lead to such conformations, either in vitro or in vivo, remain largely unknown. The slow progress in recapitulating protein folding pathways in silico may be an indication of the fundamental deficiencies in our understanding of folding as it occurs in nature. Here we consider the possibility that protein folding in living cells may not be driven solely by the decrease in Gibbs free energy and propose that protein folding in vivo should be modeled as an active energy-dependent process. The mechanism of action of such a protein folding machine might include direct manipulation of the peptide backbone. Methods: To show the feasibility of a protein folding machine, we conducted molecular dynamics simulations that were augmented by the application of mechanical force to rotate the C-terminal amino acid while simultaneously limiting the N-terminal amino acid movements. Results: Remarkably, the addition of this simple manipulation of peptide backbones to the standard molecular dynamics simulation indeed facilitated the formation of native structures in five diverse alpha-helical peptides. Steric clashes that arise in the peptides due to the forced directional rotation resulted in the behavior of the peptide backbone no longer resembling a freely jointed chain. Conclusions: These simulations show the feasibility of a protein folding machine operating under the conditions when the movements of the polypeptide backbone are restricted by applying external forces and constraints. Further investigation is needed to see whether such an effect may play a role during co-translational protein folding in vivo and how it can be utilized to facilitate folding of proteins in artificial environments.

Keywords: Protein folding; chaperone; co-translational protein folding; computer modeling; energy-dependent protein folding; molecular dynamics; nascent peptide rotation; peptide backbone manipulation; protein folding machine; ribosome function.

Figure 1.. Schematic representation of the energy-dependent peptide folding protocol employed in this study.

The force vectors applied to the C- and N-termini of a peptide in the simulation box are shown by black arrows. All force values are in kJ/mol*nm ². The purple curled arrow indicates the direction of the clockwise rotation of the peptides that resulted in the accelerated productive folding of all peptides to their helical conformations. The restrained groups are shown by green outline.

Figure 2.. Folding of peptides in the force field with and without an augmentation by the application of external rotation forces to the polypeptide backbone.

Each horizontal pane represents molecular dynamics simulations for one peptide, numbered P1 through P5 ( Table 1). On the left side, top three curves (dark blue, orange, and yellow) indicate three independent runs for one peptide in the standard force field without externally applied backbone rotation, and the bottom three curves (purple, green, and light blue) indicate three runs in the presence of the clockwise rotational force. On the right side, the bottom three curves are the same as in the corresponding left pane (three runs in the presence of the clockwise rotational force), and the top three curves (dark blue, orange, and yellow) indicate three runs for the same peptide in the presence of the counterclockwise rotational force.