Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores.

Hydrophobic cores are often viewed as tightly packed and rigid, but they do show some plasticity and could thus be attractive targets for protein design. Here we explored the role of different functional pressures on the core packing and ligand recognition of the SH3 domain from human Fyn tyrosine kinase. We randomized the hydrophobic core and used phage display to select variants that bound to each of three distinct ligands. The three evolved groups showed remarkable differences in core composition, illustrating the effect of different selective pressures on the core. Changes in the core did not significantly alter protein stability, but were linked closely to changes in binding affinity and specificity. Structural analysis and molecular dynamics simulations revealed the structural basis for altered specificity. The evolved domains had significantly reduced core volumes, which in turn induced increased backbone flexibility. These motions were propagated from the core to the binding surface and induced significant conformational changes. These results show that alternative core packing and consequent allosteric modulation of binding interfaces could be used to engineer proteins with novel functions

Massively parallel de novo protein design for targeted therapeutics

De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing

Suppression of non-prompt J/psi, prompt J/psi, and Upsilon(1S) in PbPb collisions at root s(NN)=2.76 TeV

Yields of prompt and non-prompt J/ψ, as well as Y(1S) mesons, are measured by the CMS experiment via their μ +μ - decays in PbPb and pp collisions at √/s NN = 2.76 TeV for quarkonium rapidity |y| < 2.4. Differential cross sections and nuclear modification factors are reported as functions of y and transverse momentum pT, as well as collision centrality. For prompt J/ψ with relatively high pT (6.5 < pT < 30 GeV/c), a strong, centrality-dependent suppression is observed in PbPb collisions, compared to the yield in pp collisions scaled by the number of inelastic nucleon-nucleon collisions. In the same kinematic range, a suppression of non-prompt J/ψ, which is sensitive to the in-medium b-quark energy loss, is measured for the first time. Also the low-pT Y(1S) mesons are suppressed in PbPb collisions. © CERN