News

Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models.

by

Protein stabilization is fundamental to enzyme function and evolution, yet understanding the determinants of a protein’s stability remains a challenge. This is largely due to a shortage of atomically detailed models for the ensemble of relevant protein conformations and their relative populations. For example, the M182T substitution in TEM β-lactamase, an enzyme that confers antibiotic resistance to bacteria, is stabilizing but the precise mechanism remains unclear. Here, we employ Markov stat…

Read more

Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators.

by

Allosteric 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 more

Control of porphyrin interactions via structural changes of a peptoid scaffold.

by

Nature 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 more

Bladder-cancer-associated mutations in RXRA activate peroxisome proliferator-activated receptors to drive urothelial proliferation.

by

RXRA 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 more

Endogenous retinoid X receptor ligands in mouse hematopoietic cells.

by

The 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 more