Related Articles Note: MSM lag time cannot be used for variational model selection. J Chem Phys. 2017 Nov 07;147(17):176101 Authors: Husic BE, Pande VS Abstract The variational principle for conformational…
Read moreRelated Articles Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes. Nat Commun. 2017 02 23;8(1):6 Authors: Ryckbosch SM, Wender PA, Pande VS Abstract Bryostatin is…
Read moreThe retinoid X receptor α (RXRA) has been implicated in diverse hematological processes. To identify natural ligands of RXRA that are present in hematopoietic cells, we adapted an upstream activation sequence-green fluorescent protein (UAS-GFP) reporter mouse to detect natural RXRA ligands in vivo. We observed reporter activity in diverse types of hematopoietic cells in vivo. Reporter activity increased during granulocyte colony-stimulating factor (G-CSF)-induced granulopoiesis and after pheny…
Read moreRelated Articles Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor-Acceptor Polymer Single Chains. J Phys Chem Lett. 2017 Oct 25;: Authors: Lee FL, Barati Farimani A, Gu KL, Yan H,…
Read moreSimulated Dynamics of Glycans on Ligand-Binding Domain of NMDA Receptors Reveals Strong Dynamic Coupling between Glycans and Protein Core. J Chem Theory Comput. 2017 Oct 11;: Authors: Sinitskiy AV, Pande…
Read moreTransfer Learning from Markov Models Leads to Efficient Sampling of Related Systems. J Phys Chem B. 2017 Sep 22;: Authors: Sultan MM, Pande VS Abstract We recently showed that the…
Read moreRelated Articles Modeling the mechanism of CLN025 beta-hairpin formation. J Chem Phys. 2017 Sep 14;147(10):104107 Authors: McKiernan KA, Husic BE, Pande VS Abstract Beta-hairpins are substructures found in proteins that…
Read moreUnder normal cellular conditions, the tumor suppressor protein p53 is kept at low levels in part due to ubiquitination by MDM2, a process initiated by binding of MDM2 to the intrinsically disordered transactivation domain (TAD) of p53. Many experimental and simulation studies suggest that disordered domains such as p53 TAD bind their targets nonspecifically before folding to a tightly associated conformation, but the microscopic details are unclear. Toward a detailed prediction of binding mech…
Read moreRelated 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…
Read moreNa+/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…
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