The Computational Studies of Co-Translational Protein Folding

Abstract

Protein synthesis in all kingdoms of life occurs on the ribosome, a macromolecular machine of >2.5 MDa. Most of the current knowledge about the crucial process of protein folding is based on in vitro investigation of isolated polypeptide chains, which typically consider the refolding of full length proteins previously denaturated by various chemical or thermal conditions. However, in vitro folding is likely to differ from in vivo, as in the latter proteins start to fold while they are still gradually emerging through the ribosomal exit tunnel. The available conformational space to the nascent polypeptide chain is therefore different from that of the full-length protein.Excellent system to study impact of protein vectorial synthesis on protein structure and dynamics are protein C-terminal truncations. Specifically, carried in our group NMR and computational investigations of C-terminal truncations (delta4 and delta6) of an immunoglobulin fold - ddFLN, the F-actin cross-linking gelation factor from Dictyostelium discoideum - are allowing us to present, the energy landscape that emerges from these co-translational folding mimetics In my work I provide atomistic details to this energy landscape by carrying out bias exchange metadynamics simulations with chemical shifts used as structural restrains. Using this approach I overcome, in large part, the two main limitations of molecular dynamics simulations in structural studies of proteins, firstly the inaccuracies in the use of force field alone and secondly the limitations inherent in sampling of conformational space.My study presents a structural and dynamical characterization of the free energy landscape of this C-terminal truncation as well as changes in the landscape, while a protein is folding in the vectorial manner. Hence, it is providing insights into a better understanding of co-translational folding, which still represents a major open problem in molecular biology.