Publications

2025

1. 

   Noncovalent Lasso Entanglements are Common in Experimentally Derived Intrinsically Disordered Protein Ensembles and Strongly Influenced by Protein Length and Charge

   Quyen V. Vu, Ian Sitarik, Mai Suan Li, and 1 more author

   The Journal of Physical Chemistry B, May 2025

   DOI

2. 

   Non-native entanglement protein misfolding observed in all-atom simulations and supported by experimental structural ensembles

   Quyen V. Vu, Ian Sitarik, Yang Jiang, and 7 more authors

   Science Advances, Aug 2025

   Abs DOI

   Several mechanisms are known to cause monomeric protein misfolding. Coarse-grained simulations have predicted an additional mechanism exists involving off-pathway, noncovalent lasso entanglements, which are long-lived kinetic traps and structurally resemble the native state. Here, we examine whether such misfolded states occur in long-timescale, all-atom folding simulations of ubiquitin and λ-repressor. We find that these entangled misfolded states are populated in higher-resolution models. However, because of the small size of ubiquitin and λ-repressor, these states are short-lived. In contrast, coarse-grained simulations of a larger protein, IspE, predict that it populates long-lived misfolded states. Using an Arrhenius extrapolation applied to all-atom simulations, we estimate that these IspE misfolded states have lifetimes similar to the native state while remaining soluble. We further show that these misfolded states are consistent with the structural changes inferred from limited proteolysis and cross-linking mass spectrometry experiments. Our results indicate that misfolded states composed of non-native entanglements can persist for long timescales in both all-atom simulations and experiments.

3. 

   A widespread protein misfolding mechanism is differentially rescued in vitro by chaperones based on gene essentiality

   Ian Sitarik, Quyen V. Vu, Justin Petucci, and 3 more authors

   Nature Communications, Dec 2025

   DOI

2024

1. 

   Synonymous Mutations Can Alter Protein Dimerization Through Localized Interface Misfolding Involving Self-entanglements

   Pham Dang Lan, Daniel Allen Nissley, Ian Sitarik, and 7 more authors

   Journal of Molecular Biology, 2024

   Abs DOI

   Synonymous mutations in messenger RNAs (mRNAs) can reduce protein–protein binding substantially without changing the protein’s amino acid sequence. Here, we use coarse-grain simulations of protein synthesis, post-translational dynamics, and dimerization to understand how synonymous mutations can influence the dimerization of two E. coli homodimers, oligoribonuclease and ribonuclease T. We synthesize each protein from its wildtype, fastest- and slowest-translating synonymous mRNAs in silico and calculate the ensemble-averaged interaction energy between the resulting dimers. We find synonymous mutations alter oligoribonuclease’s dimer properties. Relative to wildtype, the dimer interaction energy becomes 4% and 10% stronger, respectively, when translated from its fastest- and slowest-translating mRNAs. Ribonuclease T dimerization, however, is insensitive to synonymous mutations. The structural and kinetic origin of these changes are misfolded states containing non-covalent lasso-entanglements, many of which structurally perturb the dimer interface, and whose probability of occurrence depends on translation speed. These entangled states are kinetic traps that persist for long time scales. Entanglements cause altered dimerization energies for oligoribonuclease, as there is a large association (odds ratio: 52) between the co-occurrence of non-native self-entanglements and weak-binding dimer conformations. Simulated at all-atom resolution, these entangled structures persist for long timescales, indicating the conclusions are independent of model resolution. Finally, we show that regions of the protein we predict to have changes in entanglement are also structurally perturbed during refolding, as detected by limited-proteolysis mass spectrometry. Thus, non-native changes in entanglement at dimer interfaces is a mechanism through which oligomer structure and stability can be altered.

2023

1. 

   Is Posttranslational Folding More Efficient Than Refolding from a Denatured State: A Computational Study

   Quyen V. Vu, Daniel A Nissley, Yang Jiang, and 2 more authors

   The Journal of Physical Chemistry B, Jun 2023

   DOI
2. How soluble misfolded proteins bypass chaperones at the molecular level

   Ritaban Halder, Daniel A Nissley, Ian Sitarik, and 6 more authors

   Nature Communications, Jun 2023

   Abs DOI

   Subpopulations of soluble, misfolded proteins can bypass chaperones within cells. The extent of this phenomenon and how it happens at the molecular level are unknown. Through a meta-analysis of the experimental literature we find that in all quantitative protein refolding studies there is always a subpopulation of soluble but misfolded protein that does not fold in the presence of one or more chaperones, and can take days or longer to do so. Thus, some misfolded subpopulations commonly bypass chaperones. Using multi-scale simulation models we observe that the misfolded structures that bypass various chaperones can do so because their structures are highly native like, leading to a situation where chaperones do not distinguish between the folded and near-native-misfolded states. More broadly, these results provide a mechanism by which long-time scale changes in protein structure and function can persist in cells because some misfolded states can bypass components of the proteostasis machinery.

2021

1. 

   The driving force for co-translational protein folding is weaker in the ribosome vestibule due to greater water ordering

   Quyen V. Vu, Yang Jiang, Mai Suan Li, and 1 more author

   Chemical Science, 2021

   Abs DOI

   In the ribosome vestibule, the contact minimum between two methane molecules is half as stable as compared to in bulk solution, demonstrating that the hydrophobic effect is weakened in the vestibule of ribosome exit tunnel.Interactions between the ribosome and nascent chain can destabilize folded domains in the ribosome exit tunnel’s vestibule, the last 3 nm of the exit tunnel where tertiary folding can occur. Here, we test if a contribution to this destabilization is a weakening of hydrophobic association, the driving force for protein folding. Using all-atom molecular dynamics simulations, we calculate the potential-of-mean force between two methane molecules along the center line of the ribosome exit tunnel and in bulk solution. Associated methanes, we find, are half as stable in the ribosome’s vestibule as compared to bulk solution, demonstrating that the hydrophobic effect is weakened by the presence of the ribosome. This decreased stability arises from a decrease in the amount of water entropy gained upon the association of the methanes. And this decreased entropy gain originates from water molecules being more ordered in the vestibule as compared to bulk solution. Therefore, the hydrophobic effect is weaker in the vestibule because waters released from the first solvation shell of methanes upon association do not gain as much entropy in the vestibule as they do upon release in bulk solution. These findings mean that nascent proteins pass through a ribosome vestibule environment that can destabilize folded structures, which has the potential to influence co-translational protein folding pathways, energetics, and kinetics.

2. 

   Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force

   Sarah E. Leininger, Judith Rodriguez, Quyen V. Vu, and 4 more authors

   Biochemistry, Nov 2021

   Abs DOI

   The speed of protein synthesis can dramatically change when consecutively charged residues are incorporated into an elongating nascent protein by the ribosome. The molecular origins of this class o...

2020

1. 

   Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling

   Daniel A. Nissley, Quyen V. Vu, Fabio Trovato, and 4 more authors

   Journal of the American Chemical Society, 2020

   Abs DOI

   The ejection of nascent proteins out of the ribosome exit tunnel, after their covalent bond to transfer-RNA has been broken, has not been experimentally studied due to challenges in sample preparation. Here, we investigate this process using a combination of multiscale modeling, ribosome profiling, and gene ontology analyses. Simulating the ejection of a representative set of 122 E. coli proteins we find a greater than 1000-fold variation in ejection times. Nascent proteins enriched in negatively charged residues near their C-terminus eject the fastest, while nascent chains enriched in positively charged residues tend to eject much more slowly. More work is required to pull slowly ejecting proteins out of the exit tunnel than quickly ejecting proteins, according to all-atom simulations. An energetic decomposition reveals, for slowly ejecting proteins, that this is due to the strong attractive electrostatic interactions between the nascent chain and the negatively charged ribosomal-RNA lining the exit tunnel, and for quickly ejecting proteins, it is due to their repulsive electrostatic interactions with the exit tunnel. Ribosome profiling data from E. coli reveals that the presence of slowly ejecting sequences correlates with ribosomes spending more time at stop codons, indicating that the ejection process might delay ribosome recycling. Proteins that have the highest positive charge density at their C-terminus are overwhelmingly ribosomal proteins, suggesting the possibility that this sequence feature may aid in the cotranslational assembly of ribosomes by delaying the release of nascent ribosomal proteins into the cytosol. Thus, nascent chain ejection times from the ribosome can vary greatly between proteins due to differential electrostatic interactions, can influence ribosome recycling, and could be particularly relevant to the synthesis and cotranslational behavior of some proteins.