More Like this

1. Inhibiting the Keap1/Nrf2 Protein‐Protein Interaction with Protein‐Like Polymers

   https://doi.org/10.1002/adma.202311467  

   Carrow, Kendal_P; Hamilton, Haylee_L; Hopps, Madeline_P; Li, Yang; Qiao, Baofu; Payne, N_Connor; Thompson, Matthew_P; Zhang, Xiaoyu; Magassa, Assa; Fattah, Mara; et al (February 2024, Advanced Materials)

   Abstract Successful and selective inhibition of the cytosolic protein‐protein interaction (PPI) between nuclear factor erythroid 2‐related factor 2 (Nrf2) and Kelch‐like ECH‐associating protein 1 (Keap1) can enhance the antioxidant response, with the potential for a therapeutic effect in a range of settings including in neurodegenerative disease (ND). Small molecule inhibitors have been developed, yet many have off‐target effects, or are otherwise limited by poor cellular permeability. Peptide‐based strategies have also been attempted to enhance specificity, yet face challenges due to susceptibility to degradation and lack of cellular penetration. Herein, these barriers are overcome utilizing a polymer‐based proteomimetics. The protein‐like polymer (PLP) consists of a synthetic, lipophilic polymer backbone displaying water soluble Keap1‐binding peptides on each monomer unit forming a brush polymer architecture. The PLPs are capable of engaging Keap1 and displacing the cellular protective transcription factor Nrf2, which then translocates to the nucleus, activating the antioxidant response element (ARE). PLPs exhibit increased Keap1 binding affinity by several orders of magnitude compared to free peptides, maintain serum stability, are cell‐penetrant, and selectively activate the ARE pathway in cells, including in primary cortical neuronal cultures. Keap1/Nrf2‐inhibitory PLPs have the potential to impact the treatment of disease states associated with dysregulation of oxidative stress, such as NDs. 

   more » « less
2. The Transcriptional Coregulatory Protein YAP1 Interacts with RNA Binding Protein NPM1

   Dwead, Abdulrahman; Al-Mathkour, Marwah; Cinar, Bekir (April 2022, Experimental Biology 2022 Annual Meeting)

   RNA binding proteins (RBPs) regulate all aspects of RNA biogenesis from transcription, splicing, and translation to degradation, and they have a critical role in cellular homeostasis and functional diversity. Recent studies have indicated that altered expressions of RBPs are associated with many human diseases ranging from neurologic disorders to cancer. The transcriptional coregulator yes-associated protein 1 (YAP1), a critical nuclear effector of the mammalian Hippo pathway, regulates cell fate, cell contact, metabolism, and developmental processes. This study demonstrates a link between YAP1 and nucleophosmin1 (NPM1) protein. NPM1 is an RNA-binding protein that regulates many cellular activities, including ribosome biogenesis, RNA processing, chromatin remodeling, DNA repair, and genomic stability. We identified NPM1 from YAP1 protein complexes of androgen-responsive human cancer cells using proteomics approaches. Our proximity ligation assay demonstrated that YAP1 and NPM1 physically interacted with each other. The interaction between YAP1 and NPM1 occurred in cell nuclei and was regulated by androgen hormone signaling. In addition, our GST-pulldown assay demonstrated that NPM1 formed a protein complex with the proline-rich domain of YAP1. Furthermore, our enhanced RNA interactome capture (eRIC) assay showed that androgen also regulated the interaction of RBPs to polyA+ mRNA within the cell. Consistent with this observation, our eRIC assay combined with the mass spectrometry method enabled us to identify distinct RBP patterns in human cancer cells that are genetically related but phenotypically different. These observations indicate that global alterations of RBPs under changing environmental conditions may have essential roles in cellular physiology and disease biology. 

   more » « less
3. Measuring Novel Protein-Protein Binding with Surface Plasmon Resonance in the Physical Chemistry Lab

   McFarland, BJ (July 2018, ACS Symposium Series)

   In the laboratory for Survey of Physical Chemistry, students proceeded through a five-week project in which they measured protein-protein binding. This project engaged the students in learning physical chemistry and laboratory teachniques as they took ownership of a particular, novel protein-protein interaction. First students purified new proteins by size-exclusion chromatography and learned about separation and diffusion. Then students measured the binding strength of new protein-protein combinations using surface plasmon resonance (SPR) as they learned about SPR physics, experimental design, equilibrium binding, and data fitting using integrated rate laws. The web-based platform GENI provided protocols to the students and collected data, organizing projects spanning multiple classes. In the space of an academic year, students asked a question, then found the answer in the lab. Together, by expressing new proteins and measuring binding thermodynamics and kinetics, we found that the NKG2D immunoreceptor and its MIC ligand proteins show remarkable cross-reactivity among human, rabbit, and gorilla orthologs. 

   more » « less
4. Redefining Protein Interfaces within Protein Single Crystals with DNA

   https://doi.org/10.1021/jacs.1c04191  

   Partridge, Benjamin E.; Winegar, Peter H.; Han, Zhenyu; Mirkin, Chad A. (June 2021, Journal of the American Chemical Society)
5. Accurate protein structure prediction with hydroxyl radical protein footprinting data

   https://doi.org/10.1038/s41467-020-20549-7  

   Biehn, Sarah E.; Lindert, Steffen (January 2021, Nature Communications)

   Abstract Hydroxyl radical protein footprinting (HRPF) in combination with mass spectrometry reveals the relative solvent exposure of labeled residues within a protein, thereby providing insight into protein tertiary structure. HRPF labels nineteen residues with varying degrees of reliability and reactivity. Here, we are presenting a dynamics-driven HRPF-guided algorithm for protein structure prediction. In a benchmark test of our algorithm, usage of the dynamics data in a score term resulted in notable improvement of the root-mean-square deviations of the lowest-scoring ab initio models and improved the funnel-like metric P_nearfor all benchmark proteins. We identified models with accurate atomic detail for three of the four benchmark proteins. This work suggests that HRPF data along with side chain dynamics sampled by a Rosetta mover ensemble can be used to accurately predict protein structure. 

   more » « less