Author: Anton Thynell

Related Articles Identification of simple reaction coordinates from complex dynamics. J Chem Phys. 2017 01 28;146(4):044109 Authors: McGibbon RT, Husic BE, Pande VS Abstract Reaction coordinates are widely used throughout…

Na+/K+-ATPase transports Na+ and K+ ions across the cell membrane via an ion-binding site becoming alternatively accessible to the intra- and extracellular milieu by conformational transitions that confer marked changes in ion-binding stoichiometry and selectivity. To probe the mechanism of these changes, we used molecular simulation and free-energy perturbation approaches to identify probable protonation states of Na+- and K+-coordinating residues in E1P and E2P conformations of Na+/K+-ATPase…

Discovery of novel brain permeable and G protein-biased beta-1 adrenergic receptor partial agonists for the treatment of neurocognitive disorders. PLoS One. 2017;12(7):e0180319 Authors: Yi B, Jahangir A, Evans AK, Briggs…

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Comput Biol. 2017 Jul 26;13(7):e1005659 Authors: Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA,…

Molecular simulation has been used to model the detailed folding properties of peptides, yet prospective computational peptide design by such approaches remains challenging and nontrivial. To test the accuracy of simulation-based hairpin design, we characterized the folding properties of a series of so-called β-cap hairpin peptides designed to mimic a conserved hairpin of LapD, a bacterial intracellular signaling protein, both experimentally by NMR spectroscopy and computationally by implicit-…

Is Multitask Deep Learning Practical for Pharma? J Chem Inf Model. 2017 Jul 10;: Authors: Ramsundar B, Liu B, Wu Z, Verras A, Tudor M, Sheridan RP, Pande VS Abstract…

The energy flow during natural photosynthesis is controlled by maintaining the spatial arrangement of pigments, employing helices as scaffolds. In this study, we have developed porphyrin-peptoid (pigment-helix) conjugates (PPCs) that can modulate the donor-acceptor energy transfer efficiency with exceptional precision by controlling the relative distance and orientation of the two pigments. Five donor-acceptor molecular dyads were constructed using zinc porphyrin and free base porphyrin (Zn(i …

Related Articles MSMBuilder: Statistical Models for Biomolecular Dynamics. Biophys J. 2017 Jan 10;112(1):10-15 Authors: Harrigan MP, Sultan MM, Hernández CX, Husic BE, Eastman P, Schwantes CR, Beauchamp KA, McGibbon RT,…

The oral microbiome is a dynamic environment inhabited by both commensals and pathogens. Among these is Streptococcus mutans, the causative agent of dental caries, the most prevalent childhood disease. Carolacton has remarkably specific activity against S. mutans, causing acid-mediated cell death during biofilm formation; however, its complex structure limits its utility. Herein, we report the diverted total synthesis and biological evaluation of a rationally designed library of simplified ana…