51 research outputs found
On Vague Computers
Vagueness is something everyone is familiar with. In fact, most people think
that vagueness is closely related to language and exists only there. However,
vagueness is a property of the physical world. Quantum computers harness
superposition and entanglement to perform their computational tasks. Both
superposition and entanglement are vague processes. Thus quantum computers,
which process exact data without "exploiting" vagueness, are actually vague
computers
Roy-Steiner equations for pion-nucleon scattering
Starting from hyperbolic dispersion relations, we derive a closed system of
Roy-Steiner equations for pion-nucleon scattering that respects analyticity,
unitarity, and crossing symmetry. We work out analytically all kernel functions
and unitarity relations required for the lowest partial waves. In order to
suppress the dependence on the high-energy regime we also consider once- and
twice-subtracted versions of the equations, where we identify the subtraction
constants with subthreshold parameters. Assuming Mandelstam analyticity we
determine the maximal range of validity of these equations. As a first step
towards the solution of the full system we cast the equations for the
partial waves into the form of a Muskhelishvili-Omn\`es
problem with finite matching point, which we solve numerically in the
single-channel approximation. We investigate in detail the role of individual
contributions to our solutions and discuss some consequences for the spectral
functions of the nucleon electromagnetic form factors.Comment: 106 pages, 18 figures; version published in JHE
Detailed Regulatory Mechanism of the Interaction between ZO-1 PDZ2 and Connexin43 Revealed by MD Simulations
The gap junction protein connexin43 (Cx43) binds to the second PDZ domain of Zonula occludens-1 (ZO-1) through its C-terminal tail, mediating the regulation of gap junction plaque size and dynamics. Biochemical study demonstrated that the very C-terminal 12 residues of Cx43 are necessary and sufficient for ZO-1 PDZ2 binding and phosphorylation at residues Ser (-9) and Ser (-10) of the peptide can disrupt the association. However, only a crystal structure of ZO-1 PDZ2 in complex with a shorter 9 aa peptide of connexin43 was solved experimentally. Here, the interactions between ZO-1 PDZ2 and the short, long and phosphorylated Cx43 peptides were studied using molecular dynamics (MD) simulations and free energy calculation. The short peptide bound to PDZ2 exhibits large structural variations, while the extension of three upstream residues stabilizes the peptide conformation and enhanced the interaction. Phosphorylation at Ser(-9) significantly weakens the binding and results in conformational flexibility of the peptide. Glu210 of ZO-1 PDZ2 was found to be a key regulatory point in Cx43 binding and phosphorylation induced dissociation
PDZ domains and their binding partners: structure, specificity, and modification
PDZ domains are abundant protein interaction modules that often recognize short amino acid motifs at the C-termini of target proteins. They regulate multiple biological processes such as transport, ion channel signaling, and other signal transduction systems. This review discusses the structural characterization of PDZ domains and the use of recently emerging technologies such as proteomic arrays and peptide libraries to study the binding properties of PDZ-mediated interactions. Regulatory mechanisms responsible for PDZ-mediated interactions, such as phosphorylation in the PDZ ligands or PDZ domains, are also discussed. A better understanding of PDZ protein-protein interaction networks and regulatory mechanisms will improve our knowledge of many cellular and biological processes
The nature of dietary fatty acids affects the glycemic and insulinemic responses to carbohydrates in healthy subjects
International audienc
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