Prefrontal deep projection neurons enable cognitive flexibility via persistent feedback monitoring.

Cognitive flexibility, the ability to alter strategy according to changing stimulus-response-reward relationships, is critical for updating learned behavior. Attentional set-shifting, a test of cognitive flexibility, depends on the activity of prefrontal cortex (PFC). It remains unclear, however, what role PFC neurons play to support set-shifting. Using optogenetics and two-photon calcium imaging, we demonstrate that medial PFC activity does not bias sensorimotor responses during set-shifting, but rather enables set-shifting by encoding trial feedback information, a role it has been known to play in other contexts. Unexpectedly, the functional properties of PFC cells did not vary with their efferent projection targets. Instead, representations of trial feedback formed a topological gradient, with cells more strongly selective for feedback information located further from the pial surface, where afferent input from the anterior cingulate cortex was denser. These findings identify a critical role for deep PFC projection neurons in enabling set-shifting through behavioral feedback monitoring.

PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser.

Molecular dynamics (MD) simulations reveal molecular motions at atomic resolution. Recent advances in high-performance computing now enable microsecond-long simulations capable of sampling a wide range of biologically relevant events. But the disk space required to store an MD trajectory increases with simulation length and system size, complicating collaborative sharing and visualization. To overcome these limitations, we created PCAViz, an open-source toolkit for sharing and visualizing MD trajectories via the web browser. PCAViz includes two components: the PCAViz Compressor, which compresses and saves simulation data; and the PCAViz Interpreter, which decompresses the data in users' browsers and feeds it to any of several browser-based molecular-visualization libraries (e.g., 3Dmol.js, NGL Viewer, etc.). An easy-to-install WordPress plugin enables "plug-and-play" trajectory visualization. PCAViz will appeal to a broad audience of researchers and educators. The source code is available at http://durrantlab.com/pcaviz/ , and the WordPress plugin is available via the official WordPress Plugin Directory.

Regulation of social interaction in mice by a frontostriatal circuit modulated by established hierarchical relationships.

Social hierarchies exert a powerful influence on behavior, but the neurobiological mechanisms that detect and regulate hierarchical interactions are not well understood, especially at the level of neural circuits. Here, we use fiber photometry and chemogenetic tools to record and manipulate the activity of nucleus accumbens-projecting cells in the ventromedial prefrontal cortex (vmPFC-NAcSh) during tube test social competitions. We show that vmPFC-NAcSh projections signal learned hierarchical relationships, and are selectively recruited by subordinate mice when they initiate effortful social dominance behavior during encounters with a dominant competitor from an established hierarchy. After repeated bouts of social defeat stress, this circuit is preferentially activated during social interactions initiated by stress resilient individuals, and plays a necessary role in supporting social approach behavior in subordinated mice. These results define a necessary role for vmPFC-NAcSh cells in the adaptive regulation of social interaction behavior based on prior hierarchical interactions.

Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules.

Small-molecule protonation can promote or discourage protein binding by altering hydrogen-bond, electrostatic, and van-der-Waals interactions. To improve virtual-screen pose and affinity predictions, researchers must account for all major small-molecule ionization states. But existing programs for calculating these states have notable limitations such as high cost, restrictive licenses, slow execution times, and poor modularity. Here, we present dimorphite-DL 1.0, a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states. Dimorphite-DL uses a straightforward empirical algorithm that leverages substructure searching and draws on a database of experimentally characterized ionizable molecules. We have tested dimorphite-DL using several versions of Python and RDKit on all major operating systems. We release it under the terms of the Apache License, Version 2.0. A copy is available free of charge from http://durrantlab.com/dimorphite-dl/ .

Capturing the Mechanism Underlying TOP mRNA Binding to LARP1.

The RNA-binding protein La-related protein 1 (LARP1) plays a central role in ribosome biosynthesis. Its C-terminal DM15 region binds the 7-methylguanosine (m7G) cap and 5' terminal oligopyrimidine (TOP) motif characteristic of transcripts encoding ribosomal proteins and translation factors. Under the control of mammalian target of rapamycin complex 1 (mTORC1), LARP1 regulates translation of these transcripts. Characterizing the dynamics of DM15-TOP recognition is essential to understanding this fundamental biological process. We use molecular dynamics simulations, biophysical assays, and X-ray crystallography to reveal the mechanism of DM15 binding to TOP transcripts. Residues C-terminal to the m7G-binding site play important roles in cap recognition. Furthermore, we show that the unusually static pocket that recognizes the +1 cytosine characteristic of TOP transcripts drives binding specificity. Finally, we demonstrate that the DM15 pockets involved in TOP-specific m7GpppC-motif recognition are likely druggable. Collectively, these studies suggest unique opportunities for further pharmacological development.