SCF E3 Ligase Substrates Switch from CAN-D to Can-ubiquitylate

Liu et al. (2018) report a mathematical model predicting how the cellular repertoire of SCF E3 ligases is assembled by “adaptive exchange on demand,” with the limited pool of CUL1 scanning the vast sea of F-box proteins for those with substrates demanding ubiquitylation

Ratcheting up energy by means of measurement

The destruction of quantum coherence can pump energy into a system. For our examples this is paradoxical since the destroyed correlations are ordinarily considered negligible. Mathematically the explanation is straightforward and physically one can identify the degrees of freedom supplying this energy. Nevertheless, the energy input can be calculated without specific reference to those degrees of freedom.Comment: To appear in Phys. Rev. Let

Multiple phases in stochastic dynamics: geometry and probabilities

Stochastic dynamics is generated by a matrix of transition probabilities. Certain eigenvectors of this matrix provide observables, and when these are plotted in the appropriate multi-dimensional space the phases (in the sense of phase transitions) of the underlying system become manifest as extremal points. This geometrical construction, which we call an \textit{observable-representation of state space}, can allow hierarchical structure to be observed. It also provides a method for the calculation of the probability that an initial points ends in one or another asymptotic state

Imaging geometry through dynamics: the observable representation

For many stochastic processes there is an underlying coordinate space, $V$, with the process moving from point to point in $V$ or on variables (such as spin configurations) defined with respect to $V$. There is a matrix of transition probabilities (whether between points in $V$ or between variables defined on $V$) and we focus on its ``slow'' eigenvectors, those with eigenvalues closest to that of the stationary eigenvector. These eigenvectors are the ``observables,'' and they can be used to recover geometrical features of $V$

Violation of the zeroth law of thermodynamics for a non-ergodic interaction

The phenomenon described by our title should surprise no one. What may be surprising though is how easy it is to produce a quantum system with this feature; moreover, that system is one that is often used for the purpose of showing how systems equilibrate. The violation can be variously manifested. In our detailed example, bringing a detuned 2-level system into contact with a monochromatic reservoir does not cause it to relax to the reservoir temperature; rather, the system acquires the reservoir's level-occupation-ratio

Path integral in a magnetic field using the Trotter product formula

The derivation of the Feynman path integral based on the Trotter product formula is extended to the case where the system is in a magnetic field.Comment: To appear in the American Journal of Physics, 200

Relative momentum for identical particles

Possible definitions for the relative momentum of identical particles are considered

A switch element in the autophagy E2 Atg3 mediates allosteric regulation across the lipidation cascade

Autophagy depends on the E2 enzyme, Atg3, functioning in a conserved E1-E2-E3 trienzyme cascade that catalyzes lipidation of Atg8-family ubiquitin-like proteins (UBLs). Molecular mechanisms underlying Atg8 lipidation remain poorly understood despite association of Atg3, the E1 Atg7, and the composite E3 Atg12-Atg5-Atg16 with pathologies including cancers, infections and neurodegeneration. Here, studying yeast enzymes, we report that an Atg3 element we term E123IR (E1, E2, and E3-interacting region) is an allosteric switch. NMR, biochemical, crystallographic and genetic data collectively indicate that in the absence of the enzymatic cascade, the Atg3(E123IR) makes intramolecular interactions restraining Atg3's catalytic loop, while E1 and E3 enzymes directly remove this brace to conformationally activate Atg3 and elicit Atg8 lipidation in vitro and in vivo. We propose that Atg3's E123IR protects the E2 similar to UBL thioester bond from wayward reactivity toward errant nucleophiles, while Atg8 lipidation cascade enzymes induce E2 active site remodeling through an unprecedented mechanism to drive autophagy