Arabidopsis bZIP11 is a transcription factor that modulates amino acid metabolism under high-sucrose conditions. Expression of bZIP11 is downregulated in a sucrose-dependent manner during translation. Previous in vivo studies have identified the second upstream open reading frame (uORF2) as an essential regulatory element for the sucrose-dependent translational repression of bZIP11. However, it remains unclear how uORF2 represses bZIP11 expression under high-sucrose conditions. Through biochemical experiments using cell-free translation systems, we report on sucrose-mediated ribosome stalling at the stop codon of uORF2. The C-terminal 10 amino acids (29-SFSVxFLxxLYYV-41) of uORF2 are important for ribosome stalling. Our results demonstrate that uORF2 encodes a regulatory nascent peptide that functions to sense intracellular sucrose abundance. This is the first biochemical identification of the intracellular sucrose sensor.

A method for the computation of nuclear magnetic resonance (NMR) shieldings with second-order Møller–Plesset perturbation theory (MP2) is presented which allows to efficiently compute the entire set of shieldings for a given molecular structure. The equations are derived using Laplace-transformed atomic orbital second-order Møller–Plesset perturbation theory as a starting point. The Z-vector approach is employed for minimizing the number of coupled-perturbed self-consistent-field equations that need to be solved. In addition, the method uses the resolution-of-the-identity approximation with an attenuated Coulomb metric and Cholesky decomposition of pseudo-density matrices. The sparsity in the three-center integrals is exploited with sparse linear algebra approaches, leading to reduced computational cost and memory demands. Test calculations show that the deviations from NMR shifts obtained with canonical MP2 are small if appropriate thresholds are used. The performance of the method is illustrated in calculations on DNA strands and on glycine chains with up to 283 atoms and 2864 basis functions.

We employ various reduced scaling techniques to accelerate the recently developed least-squares tensor hypercontraction (LS-THC) approximation [ParrishR. M.HohensteinE. G.MartínezT. J.SherrillC. D. Parrish, R. M. Hohenstein, E. G. Martínez, T. J. Sherrill, C. D. J. Chem. Phys.2012137224106] for electron repulsion integrals (ERIs) and apply it to second-order Møller–Plesset perturbation theory (MP2). The grid-projected ERI tensors are efficiently constructed using a localized Cholesky molecular orbital basis from density-fitted integrals with an attenuated Coulomb metric. Additionally, rigorous integral screening and the natural blocking matrix format are applied to reduce the complexity of this step. By recasting the equations to form the quantized representation of the 1/r operator Z into the form of a system of linear equations, the bottleneck of inverting the grid metric via pseudoinversion is removed. This leads to a reduced scaling THC algorithm and application to MP2 yields the (sub-)­quadratically scaling THC-ω-RI-CDD-SOS-MP2 method. The efficiency of this method is assessed for various systems including DNA fragments with over 8000 basis functions and the subquadratic scaling is illustrated.

We present a benchmark study on the gauge-origin dependence of the electronic g-tensor using data from unrestricted density functional theory calculations with the spin-orbit mean field ansatz. Our data suggest in accordance with previous studies that g-tensor calculations employing a common gauge-origin are sufficiently accurate for small molecules; however, for extended molecules, the introduced errors can become relevant and significantly exceed the basis set error. Using calculations with the spin-orbit mean field ansatz and gauge-including atomic orbitals as a reference, we furthermore show that the accuracy and reliability of common gauge-origin approaches in larger molecules depends strongly on the locality of the spin density distribution. We propose a new pragmatic ansatz for choosing the gauge-origin which takes the spin density distribution into account and gives reasonably accurate values for molecules with a single localized spin center. For more general cases like molecules with several spatially distant spin centers, common gauge-origin approaches are shown to be insufficient for consistently achieving high accuracy. Therefore the computation of g-tensors using distributed gauge-origin methods like gauge-including atomic orbitals is considered as the ideal approach and is recommended for larger molecular systems.