An LIR motif in the Rift Valley fever virus NSs protein is critical for the interaction with LC3 family members and inhibition of autophagy.

Rift Valley fever virus (RVFV) is a viral zoonosis that causes severe disease in ruminants and humans. The nonstructural small (NSs) protein is the primary virulence factor of RVFV that suppresses the host's antiviral innate immune response. Bioinformatic analysis and AlphaFold structural modeling identified four putative LC3-interacting regions (LIR) motifs (NSs 1-4) in the RVFV NSs protein, which suggest that NSs interacts with the host LC3-family proteins. Using, isothermal titration calorimetry, X-ray crystallography, co-immunoprecipitation, and co-localization experiments, the C-terminal LIR motif (NSs4) was confirmed to interact with all six human LC3 proteins. Phenylalanine at position 261 (F261) within NSs4 was found to be critical for the interaction of NSs with LC3, retention of LC3 in the nucleus, as well as the inhibition of autophagy in RVFV infected cells. These results provide mechanistic insights into the ability of RVFV to overcome antiviral autophagy through the interaction of NSs with LC3 proteins.

Resources to Discover and Use Short Linear Motifs in Viral Proteins.

Viral proteins evade host immune function by molecular mimicry, often achieved by short linear motifs (SLiMs) of three to ten consecutive amino acids (AAs). Motif mimicry tolerates mutations, evolves quickly to modify interactions with the host, and enables modular interactions with protein complexes. Host cells cannot easily coordinate changes to conserved motif recognition and binding interfaces under selective pressure to maintain critical signaling pathways. SLiMs offer potential for use in synthetic biology, such as better immunogens and therapies, but may also present biosecurity challenges. We survey viral uses of SLiMs to mimic host proteins, and information resources available for motif discovery. As the number of examples continues to grow, knowledge management tools are essential to help organize and compare new findings.

Quantum control of the hyperfine spin of a Cs atom ensemble.

We demonstrate quantum control of a large spin angular momentum associated with the F=3 hyperfine ground state of 133Cs. Time-dependent magnetic fields and a static tensor light shift are used to implement near-optimal controls and map a fiducial state to a broad range of target states, with yields in the range 0.8-0.9. Squeezed states are produced also by an adiabatic scheme that is more robust against errors. Universal control facilitates the encoding and manipulation of qubits and qudits in atomic ground states and may lead to the improvement of some precision measurements.

Efficient quantum-state estimation by continuous weak measurement and dynamical control.

We demonstrate a fast, robust, and nondestructive protocol for quantum-state estimation based on continuous weak measurement in the presence of a controlled dynamical evolution. Our experiment uses optically probed atomic spins as a test bed and successfully reconstructs a range of trial states with fidelities of approximately 90%. The procedure holds promise as a practical diagnostic tool for the study of complex quantum dynamics, the testing of quantum hardware, and as a starting point for new types of quantum feedback control.

Quantum state reconstruction via continuous measurement.

We present a new procedure for quantum state reconstruction based on weak continuous measurement of an ensemble average. By applying controlled evolution to the initial state, new information is continually mapped onto the measured observable. A Bayesian filter is then used to update the state estimate in accordance with the measurement record. This generalizes the standard paradigm for quantum tomography based on strong, destructive measurements on separate ensembles. This approach to state estimation induces minimal perturbation of the measured system, giving information about observables whose evolution cannot be described classically in real time and opening the door to new types of quantum feedback control.

Generalized pseudopotentials for higher partial wave scattering.

We derive a generalized zero-range pseudopotential applicable to all partial wave solutions to the Schrödinger equation based on a delta-shell potential in the limit that the shell radius approaches zero. This properly models all higher order multipole moments not accounted for with a monopolar delta function at the origin, as used in the familiar Fermi pseudopotential for s-wave scattering. By making the strength of the potential energy dependent, we derive self-consistent solutions for the entire energy spectrum of the realistic potential. We apply this to study two particles in an isotropic harmonic trap, interacting through a central potential, and derive analytic expressions for the energy eigenstates and eigenvalues.

Continuous weak measurement and nonlinear dynamics in a cold spin ensemble.

A weak continuous quantum measurement of an atomic spin ensemble can be implemented via Faraday rotation of an off-resonance probe beam, and may be used to create and probe nonclassical spin states and dynamics. We show that the probe light shift leads to nonlinearity in the spin dynamics and limits the useful Faraday measurement window. Removing the nonlinearity allows a nonperturbing measurement on the much longer time scale set by decoherence. The nonlinear spin Hamiltonian is of interest for studies of quantum chaos and real-time quantum state estimation.