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Journal article

Deubiquitinase-Targeting Chimeras for Targeted Protein Stabilization

Authors : Henning, Nathaniel J. (2021)

Targeted protein degradation is a powerful therapeutic modality that uses heterobifunctional small-molecules to induce proximity between E3 ubiquitin ligases and target proteins to ubiquitinate and degrade specific proteins of interest. However, many proteins are ubiquitinated and degraded to drive disease pathology; in these cases targeted protein stabilization (TPS), rather than degradation, of the actively degraded target using a smallmolecule would be ther...

Journal article

Exchangeable HaloTag Ligands (xHTLs) for multi-modal super-resolution fluorescence microscopy

Authors : Bruins, orick (2023)

We introduce exchangeable ligands for fluorescence labeling of HaloTag7 as an alternative to covalently bound probes. The exchangeable ligands open up new possibilities in imaging for a widely used labeling approach, including applications in points accumulation for imaging in nanoscale topography (PAINT), MINFLUX and live-cell, multi-frame stimulated emission depletion (STED) microscopy. We furthermore introduce orthogonal pairs of exchangeable ligands and HaloTag...

Journal Article

Identifying Selectivity Filters in Protein Biosensor for Ligand Screening

Authors : Sahil, Mohammad (2023)

Bacterial transcription initiation mainly occurs via two diverse RNA polymerases, namely 70 and 54. While 70 polymerase transcribes housekeeping genes and does not require any external activation to form transcriptionally competent open complex, the alternate polymerase 54 require regulatory proteins, typically AAA+ ATPases, that aid in converting the closed RNA polymerase complex to an active open state.1,2 External stimuli and enviro...

Journal article

Ligand-induced shifts in conformational ensembles that predict transcriptional activation

Authors : Khan, Sabab Hasan (2023)

Nuclear receptors function as ligand-regulated transcription factors whose ability to regulate diverse physiological processes is closely linked with conformational changes induced upon ligand binding. Understanding how conformational populations of nuclear receptors are shifted by various ligands could illuminate strategies for the design of synthetic modulators to regulate specific transcriptional programs. Here, we investigate ligand-induced conformational changes using a ...

Journal Article

Selective inhibition of hsp90 paralogs: Structure and binding studies uncover the role of helix 1 in Grp94-selective ligand binding

Authors : Que, Nanette L.S. (2023)

Grp94 is the endoplasmic reticulum paralog of the hsp90 family of chaperones, which have been targeted for therapeutic intervention via their highly conserved ATP binding sites. The design of paralog-selective inhibitors relies on understanding the structural elements that mediate each paralog’s response to inhibitor binding. Here, we determined the structures of Grp94 and Hsp90 in complex with the Grp94-selective inhibitor PU-H36, and of Grp94 ...

Journal Article

Synergistic computational and experimental studies of a phosphoglycosyl transferase membrane/ligand ensemble

Authors : Majumder, Ayan (2023)

Complex glycans serve important functions in all living systems. Many of these intricate and byzantine biomolecules are assembled employing biosynthetic pathways wherein the constituent enzymes are membrane associated. A signature feature of the stepwise assembly processes is the essentiality of unusual linear long-chain polyprenol phosphate-linked substrates, such as un-decaprenol phosphate in bacteria. In this study we focus on a small enzyme, PglC from Campylobacter,...

Journal article

Tannic Acid Inhibits α-Synuclein Amyloid Fibril Formation via Binding to the Monomer N-terminal Domain

Authors : Stoeber, Jonathan (2021)

α-Synuclein (αS) is an intrinsically disordered protein (IDP) that aggregates into amyloid fibrils during the progression of Parkinson’s Disease and other synucleinopathies. The N-terminal domain (residues 1-60) is now understood to play a critical role in the initial nucleation of aggregation, as well as a pivotal role in the monomer-fibril interaction underlying amyloid seeding. Here we report on the interaction between αS and&#x...

Ebooks (Sách điện tử)

The impact of molecular variants, crystallization conditions and space group on structure-ligand complexes: A case study on Bacterial Phosphotriesterase Variants and complexes

Authors : Dym, Orly (2023)

While attempting to study the 3D structure of proteins with bound ligands, one often encounters considerable difficulties. We illustrate, as an example, the bacterial enzyme phosphotriesterase and specifically examine the effects of multiple factors such as the molecular constructs, ligands used during protein expression and purification, crystallization precipitance, and space group on the visualization of molecular complexes of organophosphate ligands bound to the enzyme....

Journal article

The P1 and P2 helices of the Guanidinium-II riboswitch interact in a ligand-dependent manner

Authors : Fuks, Christin (2021)

Riboswitch RNAs regulate gene expression by conformational changes induced by environmental conditions and specific ligand binding. The guanidine-II riboswitch is proposed to bind the small molecule guanidinium and to subsequently form a kissing loop interaction between the P1 and P2 hairpins. While an interaction was shown for isolated hairpins in crystallization and EPR experiments, an intrastrand kissing loop formation has not been demonstrated. Here, we report...

Journal Article

ThermoBRET: a ligand-engagement nanoscale thermostability assay applied to GPCRs

Authors : Hoare, Bradley L. (2023)

Measurements of membrane protein thermostability allows indirect detection of ligand 3 binding. Current thermostability assays require protein purification or rely on pre4 existing radiolabelled or fluorescent ligands, limiting their application to established 5 target proteins. Alternative methods detect protein aggregation which requires 6 sufficiently high level of protein expression. 7 Here, we present a ThermoBRET method to quantify the relative thermost...