No abstract

Alignment of molecules through electric fields minimizes the averaging over orientations, e. g., in single-particleimaging experiments. The response of molecules to external ac electric fields is governed by their polarizability tensor, which is usually calculated using quantum-chemistry methods. These methods are not feasible for large molecules. Here, we calculate the polarizability tensor of proteins using a regression model that correlates the polarizabilities of the 20 amino acids with perfect conductors of the same shape. The dielectric constant of the molecules could be estimated from the slope of the regression line based on Clausius-Mossotti equation. We benchmark our predictions against the quantum-chemistry results for the Trp cage mini protein and the measured dielectric constants of larger proteins. Our method has applications in computing laser-alignment of macromolecules, for instance, benefiting single particle imaging, as well as for the estimation of the optical and electrostatic characteristics of proteins and other macromolecules. TOC GRAPHICPolarizability of Perfect Conductor αc Polarizability of Molecule αm

No abstract

The human let-7 miRNA family consists of thirteen members that play critical roles in many biological processes, including development timing and tumor suppression, and their levels are disrupted in several diseases. Dicer is the endoribonuclease responsible for processing the precursor miRNA (pre-miRNA) to yield the mature miRNA, and thereby plays a crucial role in controlling the cellular levels of let-7 miRNAs. It is well established that the sequence and structural features of pre-miRNA hairpins such as the 5'-phosphate, the apical loop, and the 2-nt 3'-overhang are important for the processing activity of Dicer. Exceptionally, nine precursors of the let-7 family (pre-let-7) contain a 1-nt 3'-overhang and get mono-uridylated in vivo, presumably to allow efficient processing by Dicer. Pre-let-7 are also oligo-uridylated in vivo to promote their degradation and likely prevent their efficient processing by Dicer. In this study, we systematically investigated the impact of sequence and structural features of all human let-7 pre-miRNAs, including their 3'-end modifications, on Dicer binding and processing. Through the combination of SHAPE structural probing, in vitro binding and kinetic studies using purified human Dicer, we show that despite structural discrepancies among pre-let-7 RNAs, Dicer exhibits remarkable promiscuity in binding and cleaving these substrates. Moreover, the 1- or 2-nt 3'-overhang, 3'mono-uridylation and 3'-oligo-uridylation of pre-let-7 substrates appear to have little effect on Dicer binding and cleavage rate. Thus, this study extends current knowledge regarding the broad specificity of Dicer and provides novel insight regarding the effect of 3'-modifications on binding and cleavage by Dicer.