A minimum variance clustering approach produces robust and interpretable coarse-grained models. J Chem Theory Comput. 2017 Dec 18;: Authors: Husic BE, McKiernan KA, Wayment-Steele HK, Sultan MM, Pande VS Abstract…
Read moreAllosteric drugs, which bind to proteins in regions other than their main ligand-binding or active sites, make it possible to target proteins considered “undruggable” and to develop new therapies that circumvent existing resistance. Despite growing interest in allosteric drug discovery, rational design is limited by a lack of sufficient structural information about alternative binding sites in proteins. Previously, we used Markov State Models (MSMs) to identify such “cryptic pockets,” and here…
Read moreNature utilizes optimally organized pigments in light-harvesting complexes. To mimic the natural photosynthetic proteins, effective control over inter-pigment interactions is necessary to attain the desired photophysical properties. Previously, we developed porphyrin-peptoid conjugates (PPCamide) and displayed two porphyrins at defined positions on an α-helical peptoid using a flexible n-butyl linker. Herein, we synthesized new porphyrin-peptoid conjugates (PPCC-C), where porphyrins are conjug…
Read moreRXRA regulates transcription as part of a heterodimer with 14 other nuclear receptors, including the peroxisome proliferator-activated receptors (PPARs). Analysis from TCGA raised the possibility that hyperactive PPAR signaling, either due to PPAR gamma gene amplification or RXRA hot-spot mutation (S427F/Y) drives 20-25% of human bladder cancers. Here, we characterize mutant RXRA, demonstrating it induces enhancer/promoter activity in the context of RXRA/PPAR heterodimers in human bladder canc…
Read moreMillisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain. Sci Rep. 2017 Nov 15;7(1):15604 Authors: Sultan MM, Denny RA, Unwalla R, Lovering F, Pande VS Abstract…
Read moreRelated 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…
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