Biophysics Seminar- “Base-Pair Disruption Facilitates DNA binding of an Arginine-Rich Disordered Protein” with Anshika Dhiman and “Determinants of tetrapeptide condensates morphology” with Yi Zhang
Biophysics Seminar
October 4, 2024
10:30 AM - 11:30 AM
Location
SELE 2101
Calendar
Download iCal FileDeterminants of tetrapeptide condensates morphology
Yi Zhang
Zhou Lab, Department of Chemistry
Yi Zhang
Zhou Lab, Department of Chemistry
Condensate morphologies ranging from liquid droplets to gels have direct functional consequences. Tetrapeptide condensates were previously found to have four morphologies: amorphous dense liquids, liquid droplets, amorphous aggregates, and gels, depending on concentration and pH1. Side-chain interaction strength appears to be the main determinant for the first three morphologies, but additional factors are at play for gels, as illustrated by the fact LLssLL formed droplets but IIssII and VVssVV formed gels. All-atom molecular dynamics simulations suggested that backbone hydrogen bonding may contribute to gel formation, as LLssLL had a lower hydrogen-bonding propensity than IIssII and VVssVV. The addition of urea, which may disrupt backbone hydrogen bonding, dissolved IIssII gels and converted VVssVV gels into dense liquids, therefore supporting the hydrogen bonding hypothesis. The present study aimed to put this hypothesis to a strict test. Our first result was initially puzzling: IAssIA formed droplets but AIssIA formed gels. The molecular dynamics simulations provided an explanation: the inner amides (between Y and s in XYssYX) have a greater ability to form hydrogen bonds than the outer amides (between X and Y). We then reasoned that the level of hydrogen bonding would be reduced if we mixed AIssIA with AAssAA, which had a low hydrogen-bonding propensity and only formed dense liquids at most concentrations and pHs. Indeed, mixing in AAssAA turned AIssIA gels into droplets. Lastly, we used N-methylation to eliminate backbone hydrogen bonding. N-methylation of either the inner amides or the outer amides turned AIssIA gels into dense liquids or droplets. Together, these results provide a comprehensive understanding of how amino acids, sequence position, and external conditions including pH, temperature, and salt tune the morphologies of biomolecular condensates.
1. Zhang et al. (2024). Cell Rep Phys Sci 5, 102218.
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Base-Pair Disruption Facilitates DNA binding of an Arginine-Rich Disordered Protein
Anshika Dhiman
Zhou Lab, Department of Chemistry
Anshika Dhiman
Zhou Lab, Department of Chemistry
Protamine, an arginine-rich disordered protein, replaces histones to compact DNA in sperm cells, achieving a high level of DNA condensation1. However, an atomic-level understanding of
protamine-mediated DNA compaction is lacking. Here, we use all-atom molecular dynamics simulations to investigate protamine binding to both intact and partially melted DNA. The arginine residues of protamine form salt bridges with the phosphate backbone but also hydrogen bonds with nucleobases. For intact DNA, each arginine sidechain tends to hydrogen bond with multiple bases, in the form of a wedge between the two DNA strands or a clamp between two or three adjacent bases on the same strand. Such strong interactions enable protamine to compact DNA into super-stable structures known as tangles in single-molecule pulling2. Notably, arginine wedges are frequently found at base-pairs that are transiently disrupted, indicating that the DNA molecule sacrifices internal stability to strengthen its interactions with protamine. Corroborating the latter observation, arginine wedges are often formed at the boundaries between melted and intact regions of partially melted DNA. These computational results are supported by the experimental observation that strand separation nucleates tangle formation. In melted regions of partially melted DNA, the exposed nucleobases have an elevated probability of interacting with arginines, but the interactions are much weaker than in wedges and clamps. The latter result explains why protamine:double-stranded DNA mixtures form aggregates but protamine:single-stranded DNA mixtures form liquid droplets. Protamine can therefore take advantage of structural disruptions of DNA to form various condensates for a multitude of functions.
protamine-mediated DNA compaction is lacking. Here, we use all-atom molecular dynamics simulations to investigate protamine binding to both intact and partially melted DNA. The arginine residues of protamine form salt bridges with the phosphate backbone but also hydrogen bonds with nucleobases. For intact DNA, each arginine sidechain tends to hydrogen bond with multiple bases, in the form of a wedge between the two DNA strands or a clamp between two or three adjacent bases on the same strand. Such strong interactions enable protamine to compact DNA into super-stable structures known as tangles in single-molecule pulling2. Notably, arginine wedges are frequently found at base-pairs that are transiently disrupted, indicating that the DNA molecule sacrifices internal stability to strengthen its interactions with protamine. Corroborating the latter observation, arginine wedges are often formed at the boundaries between melted and intact regions of partially melted DNA. These computational results are supported by the experimental observation that strand separation nucleates tangle formation. In melted regions of partially melted DNA, the exposed nucleobases have an elevated probability of interacting with arginines, but the interactions are much weaker than in wedges and clamps. The latter result explains why protamine:double-stranded DNA mixtures form aggregates but protamine:single-stranded DNA mixtures form liquid droplets. Protamine can therefore take advantage of structural disruptions of DNA to form various condensates for a multitude of functions.
1. Ward, W. S.; Coffey, D. S. DNA packaging and organization in mammalian spermatozoa: Comparison with somatic cells. Biol Reprod 1991, 44, 569-574.
2. Ahlawat V., Dhiman A., Mudiyanselage H.E., Zhou H.-X., Protamine-mediated Tangles Produce Extreme DNA Compaction, BioRxiv (2024).
2. Ahlawat V., Dhiman A., Mudiyanselage H.E., Zhou H.-X., Protamine-mediated Tangles Produce Extreme DNA Compaction, BioRxiv (2024).
Date posted
Sep 25, 2024
Date updated
Oct 2, 2024