2,453 research outputs found
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 âadaptive exchange on demand,â with the limited pool of CUL1 scanning the vast sea of F-box proteins for those with substrates demanding ubiquitylation
Imaging geometry through dynamics: the observable representation
For many stochastic processes there is an underlying coordinate space, ,
with the process moving from point to point in or on variables (such as
spin configurations) defined with respect to . There is a matrix of
transition probabilities (whether between points in or between variables
defined on ) 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
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
NEDD8 and ubiquitin ligation by cullin-RING E3 ligases
RING E3s comprise the largest family of ubiquitin (UB) and ubiquitin-like protein (UBL) ligases. RING E3s typically promote UB or UBL transfer from the active site of an associated E2 enzyme to a distally-recruited substrate. Many RING E3s â including the cullin-RING ligase family â are multifunctional, interacting with various E2s (or other E3s) to target distinct proteins, transfer different UBLs, or to initially modify substrates with UB or subsequently elongate UB chains. Here we consider recent structures of cullin-RING ligases, and their partner E2 enzymes, representing ligation reactions. The studies collectively reveal multimodal mechanisms â interactions between ancillary E2 or E3 domains, post-translational modifications, or auxiliary binding partners â directing cullin-RING E3-E2 enzyme active sites to modify their specific targets
Spectral properties of zero temperature dynamics in a model of a compacting granular column
The compacting of a column of grains has been studied using a one-dimensional
Ising model with long range directed interactions in which down and up spins
represent orientations of the grain having or not having an associated void.
When the column is not shaken (zero 'temperature') the motion becomes highly
constrained and under most circumstances we find that the generator of the
stochastic dynamics assumes an unusual form: many eigenvalues become
degenerate, but the associated multi-dimensional invariant spaces have but a
single eigenvector. There is no spectral expansion and a Jordan form must be
used. Many properties of the dynamics are established here analytically; some
are not. General issues associated with the Jordan form are also taken up.Comment: 34 pages, 4 figures, 3 table
Sharing Polarization within Quantum Subspaces
Given an ensemble of n spins, at least some of which are partially polarized,
we investigate the sharing of this polarization within a subspace of k spins.
We assume that the sharing results in a pseudopure state, characterized by a
single purity parameter which we call the bias. As a concrete example we
consider ensembles of spin-1/2 nuclei in liquid-state nuclear magnetic
resonance (NMR) systems. The shared bias levels are compared with some current
entanglement bounds to determine whether the reduced subspaces can give rise to
entangled states.Comment: 7 pages, 3 figure
Analysis of a three-component model phase diagram by Catastrophe Theory
We analyze the thermodynamical potential of a lattice gas model with three
components and five parameters using the methods of Catastrophe Theory. We find
the highest singularity, which has codimension five, and establish its
transversality. Hence the corresponding seven-degree Landau potential, the
canonical form Wigwam or , constitutes the adequate starting point to
study the overall phase diagram of this model.Comment: 16 pages, Latex file, submitted to Phys. Rev.
The Power of Duples (in Self-Assembly): It's Not So Hip To Be Square
In this paper we define the Dupled abstract Tile Assembly Model (DaTAM),
which is a slight extension to the abstract Tile Assembly Model (aTAM) that
allows for not only the standard square tiles, but also "duple" tiles which are
rectangles pre-formed by the joining of two square tiles. We show that the
addition of duples allows for powerful behaviors of self-assembling systems at
temperature 1, meaning systems which exclude the requirement of cooperative
binding by tiles (i.e., the requirement that a tile must be able to bind to at
least 2 tiles in an existing assembly if it is to attach). Cooperative binding
is conjectured to be required in the standard aTAM for Turing universal
computation and the efficient self-assembly of shapes, but we show that in the
DaTAM these behaviors can in fact be exhibited at temperature 1. We then show
that the DaTAM doesn't provide asymptotic improvements over the aTAM in its
ability to efficiently build thin rectangles. Finally, we present a series of
results which prove that the temperature-2 aTAM and temperature-1 DaTAM have
mutually exclusive powers. That is, each is able to self-assemble shapes that
the other can't, and each has systems which cannot be simulated by the other.
Beyond being of purely theoretical interest, these results have practical
motivation as duples have already proven to be useful in laboratory
implementations of DNA-based tiles
Reflections on Tiles (in Self-Assembly)
We define the Reflexive Tile Assembly Model (RTAM), which is obtained from
the abstract Tile Assembly Model (aTAM) by allowing tiles to reflect across
their horizontal and/or vertical axes. We show that the class of directed
temperature-1 RTAM systems is not computationally universal, which is
conjectured but unproven for the aTAM, and like the aTAM, the RTAM is
computationally universal at temperature 2. We then show that at temperature 1,
when starting from a single tile seed, the RTAM is capable of assembling n x n
squares for n odd using only n tile types, but incapable of assembling n x n
squares for n even. Moreover, we show that n is a lower bound on the number of
tile types needed to assemble n x n squares for n odd in the temperature-1
RTAM. The conjectured lower bound for temperature-1 aTAM systems is 2n-1.
Finally, we give preliminary results toward the classification of which finite
connected shapes in Z^2 can be assembled (strictly or weakly) by a singly
seeded (i.e. seed of size 1) RTAM system, including a complete classification
of which finite connected shapes be strictly assembled by a "mismatch-free"
singly seeded RTAM system.Comment: New results which classify the types of shapes which can
self-assemble in the RTAM have been adde
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