Biophysics Seminar- “Determinants for the morphologies of biomolecular condensates” with Yi Zhang and “Measurements of DNA dynamics and deformability with implications for DNA mismatch repair” with Viktoriya Zvoda
Biophysics Seminar
April 12, 2024
2:00 PM - 3:00 PM
Location
SES 2214
Calendar
Download iCal FileDeterminants for the morphologies of biomolecular condensates
Yi Zhang, Zhou Lab, UIC Department of Chemistry
Condensates formed by intrinsically disordered proteins mediate a myriad of cellular processes and are linked to pathological conditions including neurodegeneration. Condensate morphologies ranging from liquid droplets to gels have been observed and have direct functional consequences, but what determines the morphologies is poorly understood. We observed four different morphologies on condensates formed by tetrapeptides of the form XXssXX, where X is an amino acid and ss represents a disulfide bond along the backbone. Depending on concentration and pH, liquid droplets (X = F, L, M, P, V, A), amorphous dense liquids (X = L, M, P, V, A), amorphous aggregates (X = W), and gels (X = I, V, A) were formed. Side-chain interaction strength appears to be a determinant of morphology but other factors are certainly at play, as illustrated by the fact AAssAA can form three types of condensates. To engineer condensate morphologies and uncover additional determinants, we expanded into heterotetrapeptides (XYssYX) as well as tetrapeptide mixtures. We were able to make droplets by mixing AAssAA and AIssIA, which alone would form amorphous dense liquids and gels, respectively. Interestingly, AIssIA formed gels whereas IAssAI formed amorphous dense liquids, leading to the hypothesis that the inner residue plays a dominant role in determining condensate morphology. All-atom molecular dynamics simulations revealed that the inner peptide plane has a strong propensity in forming backbone hydrogen bonds. Current NMR experiments are testing this hydrogen bonding propensity. Together with other ongoing studies, we are reaching a comprehensive understanding of how amino acids, sequence position, and external conditions including pH, temperature, and salt tune the morphologies of biomolecular condensates.
Measurements of DNA dynamics and deformability with implications for DNA mismatch repair
Viktoriya Zvoda, Ansari Lab, UIC Department of Physics
Post-replication DNA mismatch repair is initiated by MutS protein, which recognizes single mismatches/insertiondeletion errors. However, all mismatches are not recognized or repaired equally efficiently, and sequence context is often important. While many studies suggest that MutS senses mismatch-induced alterations in DNA flexibility, characterizing this flexibility in different sequence contexts remains a challenge. In this study, we used 6-MI placed adjacent to the mismatch as a probe of local DNA flexibility. We used fluorescence lifetime studies to obtain equilibrium conformational distributions and laser T-jump to measure µs-resolved conformational dynamics of 61-bp DNA with T-bulge & G.T (robustly repaired mismatches regardless of the context), and with T.T & T.C (mismatches whose repair efficiencies are strongly context-dependent). We uncovered that T-bulge DNA toggled between two distinct conformations, stacked and unstacked/kinked, and that these conformations interconverted on <10-µs timescales, similar to 1D diffusion times of MutS translocating on DNA. G.T DNA exhibited a distorted (partially unstacked) conformation compared with the matched counterpart but appeared to be less dynamic than T-bulge. Surprisingly, T.T and T.C were indistinguishable from the matched counterpart, both in their conformational distributions and their dynamics, even though they are efficiently repaired. We conclude that robustly repaired mismatches induce severe disruptions in base stacking at the mismatch site, resulting in rapid kinking fluctuations (as in T-bulge) and/or shape distortions (as in G.T) that are sensed by our probe; these distortions/dynamics could stall a diffusing protein to facilitate recognition. What features of DNA distinguish efficiently versus inefficiently repaired substrates where sequence context is paramount remains unclear.
Date posted
Jan 18, 2024
Date updated
Apr 24, 2024