Biophysics Seminar- “NaCl Mediates the Phase Separation of the hnRNPA1 Low-Complexity Domain by Neutralizing Charges and Bridging Intermolecular Interaction Networks” with Matt Macainsh and “Spin-coupled electron densities of iron-sulfur cluster imaged by in situ serial Laue diffraction” with Zhong Ren
November 3, 2023
2:00 PM - 3:00 PM
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Title: “NaCl Mediates the Phase Separation of the hnRNPA1 Low-Complexity Domain by Neutralizing Charges and Bridging Intermolecular Interaction Networks”
Presenter: Matt Macainsh, Zhou Lab, UIC Department of Chemistry
Abstract: The low-complexity domain of hnRNPA1 (A1-LCD) phase separates in a salt dependent manner. Unlike many intrinsically disordered proteins (IDPs) that phase separate at both low ( 1500 mM) salts, A1-LCD does not phase separate at low salt but does so at > 300 mM NaCl. To investigate the atypical salt effects on A1-LCD phase separation, we carried out all-atom molecular dynamics simulations of multiple A1-LCD chains at NaCl concentrations from 50 to 1000 mM NaCl. The ions both form first-shell coordination and bind loosely to the IDP chains, with Arg sidechains and backbone carbonyls the favored partners of Cl– and Na+, respectively. They play two direct roles in helping drive A1-LCD phase separation. The first is to neutralize the high net charge of the protein (+9) by an excess of bound Cl– over Na+; the second is to bridge between different A1-LCD chains by both Cl–and Na+, thereby fortifying the intermolecular interaction networks in the dense phase. At high concentrations, NaCl also strengthens cation-pi and pi-pi interactions, which dominate the intermolecular interactions. Based on these observations, we conclude that, at low salt, A1-LCD is prevented from phase separation by the repulsion of net charges; at medium concentrations, NaCl neutralizes enough of the net charge while also bridging IDP chains to drive phase separation. This drive becomes stronger as the salt concentration is further increased. These mechanistic insights broaden our understanding of the drive for phase separation in general and the dependence of salt effects on IDP sequences in particular.
Title: “Spin-coupled electron densities of iron-sulfur cluster imaged by in situ serial Laue diffraction”
Presenter: Zhong Ren, UIC Department of Chemistry
Abstract: Iron-sulfur clusters are inorganic cofactors found in many proteins involved in fundamental biological processes including DNA processing. The prokaryotic DNA repair enzyme PhrB, a member of the protein family of cryptochromes and photolyases, carries a four-iron-four-sulfur cluster ([4Fe4S]) in addition to the catalytic flavin and a second ribolumazine cofactors. Two interdependent photoreductions of the flavin and ribolumazine cofactors are mediated by the [4Fe4S] cluster functioning as an electron cache to hold a fine balance of electrons. We apply the more traditional temperature-scan cryo-trapping technique in protein crystallography and the newly developed technology of in situ serial Laue diffraction at room temperature. These diffraction methods in dynamic crystallography enable us to capture strong signals of electron density changes in the [4Fe4S] cluster that depict quantized electronic movements. The mixed valence layers of the [4Fe4S] cluster due to spin coupling and their dynamic responses to light illumination are observed directly in our difference maps between its redox states. These direct observations of the quantum effects in a protein bound iron-sulfur cluster have thus opened a window into the mechanistic understanding of metal clusters in biological systems.
Oct 31, 2023
Oct 31, 2023