The serine/threonine protein phosphatase 1 (PP1) dephosphorylates hundreds of key biological targets by associating with nearly 200 regulatory proteins to form highly specific holoenzymes. However, how these proteins direct PP1 specificity and the ability to predict how these PP1 interacting proteins bind PP1 from sequence alone is still missing. PP1 nuclear targeting subunit (PNUTS) is a PP1 targeting protein that, with PP1, plays a central role in the nucleus, where it regulates chromatin decondensation, RNA processing, and the phosphorylation state of fundamental cell cycle proteins, including the retinoblastoma protein (Rb), p53, and MDM2. The molecular function of PNUTS in these processes is completely unknown. Here, we show that PNUTS, which is intrinsically disordered in its free form, interacts strongly with PP1 in a highly extended manner. Unexpectedly, PNUTS blocks one of PP1's substrate binding grooves while leaving the active site accessible. This interaction site, which we have named the arginine site, allowed us to define unique PP1 binding motifs, which advances our ability to predict how more than a quarter of the known PP1 regulators bind PP1. Additionally, the structure shows how PNUTS inhibits the PP1-mediated dephosphorylation of critical substrates, especially Rb, by blocking their binding sites on PP1, insights that are providing strategies for selectively enhancing Rb activity.nuclear phosphatases | enzyme regulation | enzyme specificity | X-ray crystal structure | nuclear magnetic resonance P rotein phosphatase 1 (PP1; ∼38.5 kDa), a single-domain protein, is the most widely expressed and abundant serine/threonine phosphatase (1). By dephosphorylating a variety of protein substrates, PP1 regulates diverse biological processes, including protein synthesis, muscle contraction, carbohydrate metabolism, neuronal signaling and, of specific interest for this work, cell-cycle progression. Although the intrinsic substrate specificity of PP1 is very low, by interacting with regulatory proteins (∼200 biochemically confirmed PP1 interactors), PP1 achieves high specificity (2-5). The majority of PP1 regulators and some substrates bind PP1 via a primary PP1-binding motif, the RVxF motif, which binds to a hydrophobic groove on PP1 ∼20 Å distal from its catalytic center (6). Outside of the RVxF motif, PP1 regulatory proteins mostly lack any apparent sequence similarity. Thus, additional interaction sites, such as the SILK (7), the MyPhoNE (8), and the recently identified ΦΦ motif (9) can only be identified by structural analysis, a major challenge for a comprehensive understanding of PP1 regulation. Only when the primary sequences of PP1 regulators are correlated with specific PP1 binding modes and activities will the PP1 interactome, and the biological processes it regulates, become a viable drug target for the multitude of PP1-associated diseases, such as multiple cancers.One of the key PP1 regulatory targeting proteins in the nucleus, in addition to nuclear inhibitor of PP1 (NIPP1) and Repoman, is the...

Scaling of quantum capacitances and valence electron detachment energies is studied for icosahedral and nonicosahedral fullerenes. Scaling trends are considered from zero to infinite average radius, where a fullerene's local surface properties are similar to those of graphene. Detailed density functional theory calculations are performed to determine the geometries and detachment energies of icosahedral fullerenes, while values of these quantities are obtained for nonicosahedral species from previously published experimental results. Strongly linear, quasiclassical scaling versus average radii rn is seen for the quantum capacitances, but on two di↵erent scaling lines for icosahedral and nonicosahedral species, respectively. By contrast, nonclassical, nonlinear scaling versus 1/rn is seen for the electron detachment energies-i.e., the valence ionization potentials and electron a nities. This nonlinearity is not accounted for by classical theories that are used to explain trends in electronic properties of fullerenes and usually give accurate quantitative estimates. Instead, simple quantum equations are derived to account for nonlinearities in the metal-particle-like electron detachment energy scaling and to show that these are responsible for nonclassical, nonzero intercepts in the capacitance scaling lines of the fullerenes. Last, it is found that points representing the carbon atom and the graphene limit lie on scaling lines for icosahedral fullerenes, so their quantum capacitances and their detachment energies scale smoothly from one C atom, to C 60, to graphene.

Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary timescales. Building on our previous work (Mavor et al., 2016), we used deep mutational scanning to determine how twelve new chemicals (3-Amino-1,2,4-triazole, 5-fluorocytosine, Amphotericin B, CaCl2, Cerulenin, Cobalt Acetate, Menadione, Nickel Chloride, p-Fluorophenylalanine, Rapamycin, Tamoxifen, and Tunicamycin) reveal novel mutational sensitivities of ubiquitin residues. Collectively, our experiments have identified eight new sensitizing conditions for Lys63 and uncovered a sensitizing condition for every position in Ub except Ser57 and Gln62. By determining the ubiquitin fitness landscape under different chemical constraints, our work helps to resolve the inconsistencies between deep mutational scanning experiments and sequence conservation over evolutionary timescales.

Scaling of quantum capacitances and valence electron detachment energies is studied for icosahedral and nonicosahedral fullerenes. Scaling trends are considered from zero to infinite average radius, where a fullerene's local surface properties are similar to those of graphene. Detailed density functional theory calculations are performed to determine the geometries and detachment energies of icosahedral fullerenes, while values of these quantities are obtained for nonicosahedral species from previously published experimental results. Strongly linear, quasiclassical scaling versus average radii rn is seen for the quantum capacitances, but on two di↵erent scaling lines for icosahedral and nonicosahedral species, respectively. By contrast, nonclassical, nonlinear scaling versus 1/rn is seen for the electron detachment energies-i.e., the valence ionization potentials and electron a nities. This nonlinearity is not accounted for by classical theories that are used to explain trends in electronic properties of fullerenes and usually give accurate quantitative estimates. Instead, simple quantum equations are derived to account for nonlinearities in the metal-particle-like electron detachment energy scaling and to show that these are responsible for nonclassical, nonzero intercepts in the capacitance scaling lines of the fullerenes. Lastly, it is found that points representing the carbon atom and the graphene limit lie on scaling lines for icosahedral fullerenes, so their quantum capacitances and their detachment energies scale smoothly from one C atom, through C 60, to graphene.

We use computational modeling to study within-host viral infection and evolution. In our model, viruses exhibit variable binding to cells, with better infection and replication countered by a stronger immune response and a high rate of mutation. By varying host conditions (permissivity to viral entry T and immune clearance intensity A) for large numbers of cells and viruses, we study the dynamics of how viral populations evolve from initial infection to steady state and obtain a phase diagram of the range of cell and viral responses. We find three distinct replicative strategies corresponding to three physiological classes of viral infections: acute, chronic, and opportunistic. We show similarities between our findings and the behavior of real viral infections such as common flu, hepatitis, and SARS-CoV-2019. The phases associated with the three strategies are separated by a phase transition of primarily first order, in addition to a crossover region. Our simulations also reveal a wide range of physical phenomena, including metastable states, periodicity, and glassy dynamics. Lastly, our results suggest that the resolution of acute viral disease in patients whose immunity cannot be boosted can only be achieved by significant inhibition of viral infection and replication.