Proteins that fail to fold correctly may populate misfolded conformations with disparate structure and function. Misfolding is the focus of intense research interest due to its putative and confirmed role in various diseases, including neurodegenerative diseases such as Parkinson’s and Alzheimer’s Diseases as well as cystic fibrosis (PMID: 16689923).
Many open questions about protein misfolding remain to be answered. For example, how do misfolded proteins evade cellular quality control mechanisms like chaperones to remain soluble but non-functional for long timescales? How long do misfolded states persist on average? How widespread is misfolding? Experiments indicate that misfolding can even be caused by synonymous mutations that alter the speed of protein translation but not the sequence of the protein produced (PMID: 23417067), introducing the additional puzzle of how the protein maintains a “memory” of its translation kinetics after synthesis is complete.
A series of four recent preprints (Preprints 1, 2, 3, and 4, see below) suggests that these questions can be answered by the partitioning of proteins into long-lived self-entangled conformations that are structurally similar to the native state but with perturbed function. Simulation of the synthesis, termination, and post-translational dynamics of a large dataset of E. coli proteins suggests that misfolding and entanglement are widespread, with two thirds of proteins misfolding some of the time (Preprint 1). Many misfolded conformations may bypass proteostasis machinery to remain soluble but non-functional due to their structural similarity to the native state. Critically, entanglement is associated with particularly long-lived misfolded states based on simulated folding kinetics.
Coarse-grain and all-atom simulation results indicate that these misfolded conformations interact with chaperones like GroEL and HtpG to a similar extent as does the native state (Preprint 2). These results suggest an explanation for why some protein always fails to refold while remaining soluble, even in the presence of multiple folding chaperones – it remains trapped in entangled conformations that resemble the native state and thus fail to recruit chaperones.
Finally, simulations indicate that changes to the translation kinetics of oligoribonuclease introduced by synonymous mutations cause a large change in its probability of entanglement at the dimerization interface (Preprint 3). These entanglements localized at the interface alter its ability to dimerize even after synthesis is complete. These simulations provide a structural explanation for how translation kinetics can have a long-timescale influence on protein behavior.
Together, these preprints suggest that misfolding into entangled conformations is a widespread phenomenon that may provide a consistent explanation for many unanswered question in molecular biology. It should be noted that entanglement is not exclusive to other types of misfolding, such as domain swapping, that may contribute to misfolding in cells. Experimental validation of the existence of entangled conformations is a critical aspect of testing this hypothesis; for comparisons between simulation and experiment, see Preprint 4.
Preprint 1: https://www.biorxiv.org/content/10.1101/2021.08.18.456613v1
Preprint 2: https://www.biorxiv.org/content/10.1101/2021.08.18.456736v1
Preprint 3: https://www.biorxiv.org/content/10.1101/2021.10.26.465867v1
Preprint 4: https://www.biorxiv.org/content/10.1101/2021.08.18.456802v1
