@article{mantooth_hancock_thompson_varghese_meritet_vrabel_hu_zaharoff_2024, title={Characterization of an Injectable Chitosan Hydrogel for the Tunable, Localized Delivery of Immunotherapeutics}, volume={10}, ISSN={["2373-9878"]}, url={https://doi.org/10.1021/acsbiomaterials.3c01580}, DOI={10.1021/acsbiomaterials.3c01580}, abstractNote={Localized delivery of immunotherapeutics within a tumor has the potential to reduce systemic toxicities and improve treatment outcomes in cancer patients. Unfortunately, local retention of therapeutics following intratumoral injection is problematic and is insufficiently considered. Dense tumor architectures and high interstitial pressures rapidly exclude injections of saline and other low-viscosity solutions. Hydrogel-based delivery systems, on the other hand, can resist shear forces that cause tumor leakage and thus stand to improve the local retention of coformulated therapeutics. The goal of the present work was to construct a novel, injectable hydrogel that could be tuned for localized immunotherapy delivery. A chitosan-based hydrogel, called XCSgel, was developed and subsequently characterized. Nuclear magnetic resonance studies were performed to describe the chemical properties of the new entity, while cryo-scanning electron microscopy allowed for visualization of the hydrogel's cross-linked network. Rheology experiments demonstrated that XCSgel was shear-thinning and self-healing. Biocompatibility studies, both in vitro and in vivo, showed that XCSgel was nontoxic and induced transient mild-to-moderate inflammation. Release studies revealed that coformulated immunotherapeutics were released over days to weeks in a charge-dependent manner. Overall, XCSgel displayed several clinically important features, including injectability, biocompatibility, and imageability. Furthermore, the properties of XCSgel could also be controlled to tune the release of coformulated immunotherapeutics.}, number={2}, journal={ACS BIOMATERIALS SCIENCE & ENGINEERING}, author={Mantooth, Siena M. and Hancock, Asher M. and Thompson, Peter M. and Varghese, P. J. George and Meritet, Danielle M. and Vrabel, Maura R. and Hu, Jingjie and Zaharoff, David A.}, year={2024}, month={Jan}, pages={905–920} }
 @article{gonzalez-delgado_thompson_andralojc_gdaniec_ghiladi_franzen_2024, title={Comparison of the Backbone Dynamics of Dehaloperoxidase-Hemoglobin Isoenzymes}, volume={4}, ISSN={["1520-5207"]}, DOI={10.1021/acs.jpcb.3c07176}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Gonzalez-Delgado, Jessica M. and Thompson, Peter M. and Andralojc, Witold and Gdaniec, Zofia and Ghiladi, Reza A. and Franzen, Stefan}, year={2024}, month={Apr} }
 @article{lodge_scheidemantle_adams_cottam_richard_breuer_thompson_shrestha_liu_kennedy_2024, title={Fructose regulates the pentose phosphate pathway and induces an inflammatory and resolution phenotype in Kupffer cells}, volume={14}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-024-54272-w}, abstractNote={Abstract Over-consumption of fructose in adults and children has been linked to increased risk of non-alcoholic fatty liver disease (NAFLD). Recent studies have highlighted the effect of fructose on liver inflammation, fibrosis, and immune cell activation. However, little work summarizes the direct impact of fructose on macrophage infiltration, phenotype, and function within the liver. We demonstrate that chronic fructose diet decreased Kupffer cell populations while increasing transitioning monocytes. In addition, fructose increased fibrotic gene expression of collagen 1 alpha 1 ( Col1a1) and tissue metallopeptidase inhibitor 1 ( Timp1) as well as inflammatory gene expression of tumor necrosis factor alpha ( Tnfa) and expression of transmembrane glycoprotein NMB ( Gpnmb) in liver tissue compared to glucose and control diets. Single cell RNA sequencing (scRNAseq) revealed fructose elevated expression of matrix metallopeptidase 12 ( Mmp12) , interleukin 1 receptor antagonist (Il1rn), and radical S-adenosyl methionine domain ( Rsad2) in liver and hepatic macrophages. In vitro studies using IMKC and J774.1 cells demonstrated decreased viability when exposed to fructose. Additionally, fructose increased Gpnmb , Tnfa , Mmp12 , Il1rn , and Rsad2 in unpolarized IMKC. By mass spectrometry, C13 fructose tracing detected fructose metabolites in glycolysis and the pentose phosphate pathway (PPP). Inhibition of the PPP further increased fructose induced Il6, Gpnmb , Mmp12 , Il1rn , and Rsad2 in nonpolarized IMKC. Taken together, fructose decreases cell viability while upregulating resolution and anti-inflammatory associated genes in Kupffer cells.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Lodge, Mareca and Scheidemantle, Grace and Adams, Victoria R. and Cottam, Matthew A. and Richard, Daniel and Breuer, Denitra and Thompson, Peter and Shrestha, Kritika and Liu, Xiaojing and Kennedy, Arion}, year={2024}, month={Feb} }
 @article{phan_manley_skirboll_cha_hilovsky_chang_thompson_liu_makris_2023, title={Excision of a Protein-Derived Amine for <i>p</i>-Aminobenzoate Assembly by the Self-Sacrificial Heterobimetallic Protein CADD}, volume={62}, ISSN={["1520-4995"]}, url={https://doi.org/10.1021/acs.biochem.3c00406}, DOI={10.1021/acs.biochem.3c00406}, abstractNote={Chlamydia protein associating with death domains (CADD), the founding member of a recently discovered class of nonheme dimetal enzymes termed hemeoxygenase-like dimetaloxidases (HDOs), plays an indispensable role in pathogen survival. CADD orchestrates the biosynthesis of p-aminobenzoic acid (pABA) for integration into folate via the self-sacrificial excision of a protein-derived tyrosine (Tyr27) and several additional processing steps, the nature and timing of which have yet to be fully clarified. Nuclear magnetic resonance (NMR) and proteomics approaches reveal the source and probable timing of amine installation by a neighboring lysine (Lys152). Turnover studies using limiting O2 have identified a para-aminobenzaldehyde (pABCHO) metabolic intermediate that is formed on the path to pABA formation. The use of pABCHO and other probe substrates shows that the heterobimetallic Fe/Mn form of the enzyme is capable of oxygen insertion to generate the pABA-carboxylate.}, number={22}, journal={BIOCHEMISTRY}, author={Phan, Han N. and Manley, Olivia M. and Skirboll, Sydney S. and Cha, Lide and Hilovsky, Dalton and Chang, Wei-chen and Thompson, Peter M. and Liu, Xiaojing and Makris, Thomas M.}, year={2023}, month={Nov}, pages={3276–3282} }
 @article{barnes_rodriguez-zapata_juarez-nunez_gates_janzen_kur_wang_jensen_estevez-palmas_crow_et al._2022, title={An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time}, volume={119}, ISSN={["1091-6490"]}, url={http://dx.doi.org/10.1073/pnas.2100036119}, DOI={10.1073/pnas.2100036119}, abstractNote={Native Americans domesticated maize ( Zea mays ssp. mays ) from lowland teosinte parviglumis ( Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 ( HPC1 ), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.}, number={27}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Barnes, Allison C. and Rodriguez-Zapata, Fausto and Juarez-Nunez, Karla A. and Gates, Daniel J. and Janzen, Garrett M. and Kur, Andi and Wang, Li and Jensen, Sarah E. and Estevez-Palmas, Juan M. and Crow, Taylor M. and et al.}, year={2022}, month={Jul} }
 @article{foo_thompson_chen_jadi_lupo_derose_arora_placentra_premkumar_perera_et al._2021, title={The mosquito protein AEG12 displays both cytolytic and antiviral properties via a common lipid transfer mechanism.}, volume={118}, url={https://doi.org/10.1073/pnas.2019251118}, DOI={10.1073/pnas.2019251118}, abstractNote={Significance Lipid-enveloped viruses such as flaviviruses and coronaviruses underlie numerous human illnesses. Strategies which target this shared membrane feature may be useful as broad-spectrum antiviral agents. The mosquito protein AEG12 disrupts lipid membranes via delivery of a fatty acid in exchange for diacylphospholipids. This mechanism allows the mosquito to digest red blood cells after a meal and disrupts lipid coat viruses as part of the mosquito immune response to infection. It may be possible to engineer this strategy for human therapeutics. The mosquito protein AEG12 is up-regulated in response to blood meals and flavivirus infection though its function remained elusive. Here, we determine the three-dimensional structure of AEG12 and describe the binding specificity of acyl-chain ligands within its large central hydrophobic cavity. We show that AEG12 displays hemolytic and cytolytic activity by selectively delivering unsaturated fatty acid cargoes into phosphatidylcholine-rich lipid bilayers. This property of AEG12 also enables it to inhibit replication of enveloped viruses such as Dengue and Zika viruses at low micromolar concentrations. Weaker inhibition was observed against more distantly related coronaviruses and lentivirus, while no inhibition was observed against the nonenveloped virus adeno-associated virus. Together, our results uncover the mechanistic understanding of AEG12 function and provide the necessary implications for its use as a broad-spectrum therapeutic against cellular and viral targets.}, number={11}, journal={Proceedings of the National Academy of Sciences of the United States of America}, publisher={Proceedings of the National Academy of Sciences}, author={Foo, Alexander C. Y. and Thompson, Peter M. and Chen, Shih-Heng and Jadi, Ramesh and Lupo, Brianna and DeRose, Eugene F. and Arora, Simrat and Placentra, Victoria C. and Premkumar, Lakshmanane and Perera, Lalith and et al.}, year={2021}, month={Mar} }
 @article{klimczak_eschenbach_thompson_buters_mueller_2020, title={Mixture analyses of air-sampled pollen extracts can accurately differentiate pollen taxa}, volume={243}, ISSN={["1873-2844"]}, DOI={10.1016/j.atmosenv.2020.117746}, abstractNote={The daily pollen forecast provides crucial information for allergic patients to avoid exposure to specific pollen. Pollen counts are typically measured with air samplers and analyzed with microscopy by trained experts. In contrast, this study evaluated the effectiveness of identifying the component pollens using the metabolites extracted from an air-sampled pollen mixture. Ambient air-sampled pollen from Munich in 2016 and 2017 was visually identified from reference pollens and extracts were prepared. The extracts were lyophilized, rehydrated in optimal NMR buffers, and filtered to remove large proteins. NMR spectra were analyzed for pollen associated metabolites. Regression and decision-tree based algorithms using the concentration of metabolites, calculated from the NMR spectra outperformed algorithms using the NMR spectra themselves as input data for pollen identification. Categorical prediction algorithms trained for low, medium, high, and very high pollen count groups had accuracies of 74% for the tree, 82% for the grass, and 93% for the weed pollen count. Deep learning models using convolutional neural networks performed better than regression models using NMR spectral input, and were the overall best method in terms of relative error and classification accuracy (86% for tree, 89% for grass, and 93% for weed pollen count). This study demonstrates that NMR spectra of air-sampled pollen extracts can be used in an automated fashion to provide taxa and type-specific measures of the daily pollen count.}, journal={ATMOSPHERIC ENVIRONMENT}, author={Klimczak, Leszek J. and Eschenbach, Cordula Ebner and Thompson, Peter M. and Buters, Jeroen T. M. and Mueller, Geoffrey A.}, year={2020}, month={Dec} }
 @article{foo_thompson_perera_arora_derose_williams_mueller_2019, title={Hydrophobic ligands influence the structure, stability, and processing of the major cockroach allergen Bla g 1}, volume={9}, DOI={10.1038/s41598-019-54689-8}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Foo, Alexander C. Y. and Thompson, Peter M. and Perera, Lalith and Arora, Simrat and DeRose, Eugene F. and Williams, Jason and Mueller, Geoffrey A.}, year={2019} }
 @inproceedings{influence of hydrophobic cargo binding on the structure, stability, and allergenicity of the cockroach allergen bla g 1_2019, url={http://dx.doi.org/10.1016/j.jaci.2018.12.649}, DOI={10.1016/j.jaci.2018.12.649}, abstractNote={The rate of endosomal processing of allergens by antigen presenting cells has been suggested to influence sensitization. In addition, allergens often occur in the presence of lipids and other hydrophobic ligands, which also influence allergenicity. Due to its ability to bind a variety of hydrophobic cargoes, the cockroach allergen Bla g 1 was used as a model system to probe for a potential connection between antigen processing and lipid delivery, and the molecular mechanisms underlying this interaction. The effect of various fatty-acid, phospholipid, and lipotechchoic acid (LTA) cargoes on Bla g 1 structure and thermostability was assessed using circular dichroism coupled with solution-NMR, and molecular modeling, while proteolytic assays were used to probe for changes in its susceptibility to cleavage by the endosomal protease cathepsin S, a key player in the antigen processing pathway. Binding of fatty-acids enhanced the stability of Bla g 1. This effect was dependent on alkyl chain length, with longer-chain cargoes providing up to a ∼20oC increase in melting temperature while simultaneously eliminating cathepsin cleavage. Phospholipid and LTA’s provided similar enhancements to thermostability. However, the former yielded only a modest (0-2 fold) reduction in cathepsin proteolysis while the latter showed a strong dependence on the source organism, with more pathogenic species exerting a strongest (>2-fold) protective effect. Binding of lipid cargoes can enhance the stability and proteolytic resistance of Bla g 1. We hypothesize that this hinders endosomal processing and antigen presentation, skewing the TH1/TH2 response to favor allergy.}, booktitle={Journal of Allergy and Clinical Immunology}, year={2019}, month={Feb} }
 @article{multiple roles of bet v 1 ligands in allergen stabilization and modulation of endosomal protease activity._2019, url={https://europepmc.org/articles/PMC6910946}, DOI={10.1111/all.13948}, abstractNote={Over 100 million people worldwide suffer from birch pollen allergy. Bet v 1 has been identified as the major birch pollen allergen. However, the molecular mechanisms of birch allergic sensitization, including the roles of Bet v 1 and other components of the birch pollen extract, remain incompletely understood. Here, we examined how known birch pollen–derived molecules influence the endolysosomal processing of Bet v 1, thereby shaping its allergenicity.}, journal={Allergy}, year={2019}, month={Oct} }
 @article{a structural model for vinculin insertion into pip<sub>2</sub>-containing membranes and the effect of insertion on vinculin activation and localization._2017, url={https://europepmc.org/articles/PMC5299030}, DOI={10.1016/j.str.2016.12.002}, abstractNote={Vinculin, a scaffolding protein that localizes to focal adhesions (FAs) and adherens junctions, links the actin cytoskeleton to the adhesive super-structure. While vinculin binds to a number of cytoskeletal proteins, it can also associate with phosphatidylinositol 4,5-bisphosphate (PIP2) to drive membrane association. To generate a structural model for PIP2-dependent interaction of vinculin with the lipid bilayer, we conducted lipid-association, nuclear magnetic resonance, and computational modeling experiments. We find that two basic patches on the vinculin tail drive membrane association: the basic collar specifically recognizes PIP2, while the basic ladder drives association with the lipid bilayer. Vinculin mutants with defects in PIP2-dependent liposome association were then expressed in vinculin knockout murine embryonic fibroblasts. Results from these analyses indicate that PIP2 binding is not required for localization of vinculin to FAs or FA strengthening, but is required for vinculin activation and turnover at FAs to promote its association with the force transduction FA nanodomain.}, journal={Structure (London, England : 1993)}, year={2017}, month={Jan} }
 @inproceedings{role of pip2-dependent membrane interactions in vinculin activation, motility and force transmission_2017, url={http://dx.doi.org/10.1016/j.bpj.2016.11.2594}, DOI={10.1016/j.bpj.2016.11.2594}, abstractNote={Vinculin is a highly conserved scaffolding protein that localizes to focal adhesions (FA) and adherens junctions, where it binds actin and links the actin cytoskeleton to the adhesive structure. Vinculin also binds to phosphatidylinositol 4,5-bisphosphate (PIP2). However, despite recent structural studies, it is unclear how vinculin associates with PIP2 in the context of a lipid bilayer and how binding to PIP2 regulates vinculin localization, activation, turnover at FAs and cell motility. Herein, we incorporate lipid-association data, nuclear magnetic resonance (NMR), and computational modeling to generate an experimentally-driven structural model for PIP2-dependent interaction of vinculin with the lipid bilayer. According to our model, two basic patches on the vinculin tail drive membrane association: the basic collar specifically recognizes the PIP2 head group, while the basic ladder drives association with the lipid bilayer. As mutations within the basic collar impair vinculin-mediated actin crosslinking, basic ladder mutations that disrupt PIP2-dependent liposome association were made to evaluate the cellular consequences of vinculin binding to PIP2. Results obtained from cellular expression of the PIP2 deficient vinculin mutants suggest that PIP2-binding is not required for localization of vinculin to FAs or FA strengthening. Rather. PIP2-binding is specifically required for vinculin activation and turnover at FAs to promote its association with the force-transduction FA nanodomain.}, booktitle={Biophysical Journal}, year={2017}, month={Feb} }
 @article{a metabolomic, geographic, and seasonal analysis of the contribution of pollen-derived adenosine to allergic sensitization_2016, url={http://dx.doi.org/10.1007/s11306-016-1130-6}, DOI={10.1007/s11306-016-1130-6}, abstractNote={Studies on ragweed and birch pollen extracts suggested that the adenosine content is an important factor in allergic sensitization. However, exposure levels from other pollens and considerations of geographic and seasonal factors have not been evaluated. This study compared the metabolite profile of pollen species important for allergic disease, specifically measured the adenosine content, and evaluated exposure to pollen-derived adenosine. An NMR metabolomics approach was used to measure metabolite concentrations in 26 pollen extracts. Pollen count data was analyzed from five cities to model exposure. A principal component analysis of the various metabolites identified by NMR showed that pollen extracts could be differentiated primarily by sugar content: glucose, fructose, sucrose, and myo-inositol. In extracts of 10 mg of pollen/ml, the adenosine was highest for grasses (45 µM) followed by trees (23 µM) and weeds (19 µM). Pollen count data showed that tree pollen was typically 5–10 times the amount of other pollens. At the daily peaks of tree, grass, and weed season the pollen-derived adenosine exposure per day is likely to be only 1.1, 0.11, and 0.12 µg, respectively. Seasonal models of pollen exposure and respiration suggest that it would be a rare event limited to tree pollen season for concentrations of pollen-derived adenosine to approach physiological levels. Sugar content and other metabolites may be useful in classifying pollens. Unless other factors create localized exposures that are very different from these models, pollen-derived adenosine is unlikely to be a major factor in allergic sensitization.}, journal={Metabolomics}, year={2016}, month={Dec} }
 @article{campbell_thompson_tolbert_case_ramachandran_pershad_dokholyan_burridge_waterman_2016, title={Role of PIP2-Dependent Membrane Interactions in Vinculin Activation, Motility and Force Transmission}, volume={110}, DOI={10.1016/j.bpj.2015.11.3075}, abstractNote={Vinculin is an essential and abundant cytoskeletal protein localized to focal adhesions and cell-cell contacts, where it participates in the linkage of transmembrane receptors to the actin cytoskeleton to control cell survival and migration. Loss of vinculin results in increased cell migration, apoptotic resistance, and the acquisition of tumorigenic properties. Mutations in vinculin and its splice variant, metavinculin, are associated with cardiac disease. Vinculin consists of a head domain (Vh) and a tail domain (Vt) that form autoinhibitory interactions in its inactive state, but release upon activation, exposing phosphorylation, protein and phosphoinositol 4,5-bisphosphate (PIP2) binding sites. The interaction of vinculin with PIP2 is believed critical for its function, however, it is currently unclear how vinculin specifically recognizes PIP2 and regulates vinculin. Vt forms an antiparallel five-helix bundle with amino-terminal (NT) and carboxyl terminal (CT) extensions. While a crystal structure of an oligomerized Vt mutant complexed to a short chain PIP2 has recently been published (Chinthalapudi et al. (JCB, 2014)), the structure is incompatible with membrane insertion. We propose an alternative model using experimental data, molecular docking and dynamics simulations and provide validation of the model through biophysical and biochemical analyses. In our model, the PIP2 head group binds to the Vt basic collar, and promotes release of Vt's strap and CT to facilitate membrane insertion. The role of vinculin/PIP2 interaction in mediating vinculin activation, localization, cell migration, force sensing and transmission has also been characterized using cell microscopy, including super-resolution microscopy approaches, by examining WT and PIP2-deficient full length vinculin in knockout cells. Information derived from these analyses will result in an unprecedented understanding of vinculin function from the molecular to the cellular level and will enable us to build more comprehensive models of vinculin membrane interactions.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Campbell, Sharon L. and Thompson, Peter M. and Tolbert, Caitlin E. and Case, Lindsay and Ramachandran, Srinivas and Pershad, Mihir and Dokholyan, Nikolay and Burridge, Keith and Waterman, Clare}, year={2016}, month={Feb}, pages={575a} }
 @article{kim_thompson_lee_pershad_campbell_alushin_2016, title={The Structural Basis of Actin Organization by Vinculin and Metavinculin}, volume={428}, DOI={10.1016/j.jmb.2015.09.031}, abstractNote={Vinculin is an essential adhesion protein that links membrane-bound integrin and cadherin receptors through their intracellular binding partners to filamentous actin, facilitating mechanotransduction. Here we present an 8.5-Å-resolution cryo-electron microscopy reconstruction and pseudo-atomic model of the vinculin tail (Vt) domain bound to F-actin. Upon actin engagement, the N-terminal “strap” and helix 1 are displaced from the Vt helical bundle to mediate actin bundling. We find that an analogous conformational change also occurs in the H1′ helix of the tail domain of metavinculin (MVt) upon actin binding, a muscle-specific splice isoform that suppresses actin bundling by Vt. These data support a model in which metavinculin tunes the actin bundling activity of vinculin in a tissue-specific manner, providing a mechanistic framework for understanding metavinculin mutations associated with hereditary cardiomyopathies.}, number={1}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Kim, Laura Y. and Thompson, Peter M. and Lee, Hyunna T. and Pershad, Mihir and Campbell, Sharon L. and Alushin, Gregory M.}, year={2016}, month={Jan}, pages={10–25} }
 @article{kim_thompson_lee_pershad_campbell_alushin_2015, title={MDFF model of the vinculin tail domain bound to F-actin}, DOI={10.2210/pdb3jbi/pdb}, publisher={Protein Data Bank, Rutgers University}, author={Kim, L.Y. and Thompson, P.M. and Lee, H.T. and Pershad, M. and Campbell, S.L. and Alushin, G.M.}, year={2015}, month={Nov} }
 @article{thompson_lee_kim_ramachandran_tandon_mendez-giraldez_alushin_dokholyan_campbell_2015, title={New Models for Regulation of Vinculin by Actin and Phospholipids}, volume={108}, url={http://dx.doi.org/10.1016/j.bpj.2014.11.2784}, DOI={10.1016/j.bpj.2014.11.2784}, abstractNote={Vinculin is an essential cytoskeletal protein that is a prominent component of focal adhesions and adherens junctions. It exists in an autoinhibited conformation that masks interactions of ligands with the head (Vh) and tail (Vt) domain. Upon activation, vinculin functions as a scaffold to regulate cellular events resulting in cell migration, cell survival and embryogenesis. Vinculin null cells display tumorigenic properties and mutation or loss of vinculin is associated with cardiac disease. The interaction between vinculin and actin plays a pivotal role in linking transmembrane receptors to the cytoskeleton, which, in turn, is important for controlling cellular cell morphology, force transmission and motility. Binding of F-actin to Vt causes a conformational change that induces formation of a cryptic dimer necessary for actin filament bundling, however, the conformational change that occurs and dimer that is formed is unknown. It is also unclear how vinculin recognizes PIP2, inserts into membranes and is regulated by this interaction. We have now obtained a sub-nanometer resolution reconstruction of the Vt/actin complex which sheds light on actin-induced conformational changes necessary for vinculin dimerization and actin filament bundling, and have integrated computational and experimental approaches to generate and test models for the actin-induced vinculin dimer and vinculin/PIP2 membrane interaction and assess their significance in vinculin function both in vitro and in cells.}, number={2}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Thompson, Peter M. and Lee, Hyunna T. and Kim, Laura and Ramachandran, Srinivas and Tandon, Arpit and Mendez-Giraldez, Raul and Alushin, Gregory M. and Dokholyan, Nikolay V. and Campbell, Sharon L.}, year={2015}, month={Jan}, pages={508a–509a} }
 @article{thompson_beck_campbell_2015, title={Protein-Protein Interaction Analysis by Nuclear Magnetic Resonance Spectroscopy}, DOI={10.1007/978-1-4939-2425-7_16}, abstractNote={AbstractNuclear magnetic resonance (NMR) has continued to evolve as a powerful method, with an increase in the number of pulse sequences and techniques available to study protein-protein interactions. In this chapter, a straightforward method to map a protein–protein interface and design a structural model is described, using chemical shift perturbation, paramagnetic relaxation enhancement, and data-driven docking.Key wordsNuclear magnetic resonance (NMR)Protein-protein interactionChemical-shift perturbation (CSP)Paramagnetic relaxation enhancement (PRE)Docking}, journal={Protein-Protein Interactions}, publisher={Springer Science \mathplus Business Media}, author={Thompson, Peter M. and Beck, Moriah R. and Campbell, Sharon L.}, year={2015}, pages={267–279} }
 @article{tolbert_thompson_superfine_burridge_campbell_2014, title={Correction to Phosphorylation at Y1065 in Vinculin Mediates Actin Bundling, Cell Spreading, and Mechanical Responses to Force}, volume={53}, DOI={10.1021/bi501135k}, abstractNote={This work was supported by National Institutes of Health Grants {"type":"entrez-nucleotide","attrs":{"text":"GM029860","term_id":"218106509","term_text":"GM029860"}}GM029860 (K.B.), {"type":"entrez-nucleotide","attrs":{"text":"GM081764","term_id":"222004111","term_text":"GM081764"}}GM081764 (S.L.C.), and {"type":"entrez-nucleotide","attrs":{"text":"GM080568","term_id":"221620998","term_text":"GM080568"}}GM080568 (S.L.C.) and NIH/NIBIB 5P41EB002025 (R.S.).}, number={39}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={Tolbert, Caitlin E. and Thompson, Peter M. and Superfine, Richard and Burridge, Keith and Campbell, Sharon L.}, year={2014}, month={Oct}, pages={6286–6286} }
 @article{thompson_tolbert_shen_kota_palmer_plevock_orlova_galkin_burridge_egelman_et al._2014, title={Identification of an Actin Binding Surface on Vinculin that Mediates Mechanical Cell and Focal Adhesion Properties}, volume={22}, DOI={10.1016/j.str.2014.03.002}, abstractNote={Vinculin, a cytoskeletal scaffold protein essential for embryogenesis and cardiovascular function, localizes to focal adhesions and adherens junctions, connecting cell surface receptors to the actin cytoskeleton. While vinculin interacts with many adhesion proteins, its interaction with filamentous actin regulates cell morphology, motility, and mechanotransduction. Disruption of this interaction lowers cell traction forces and enhances actin flow rates. Although a model for the vinculin:actin complex exists, we recently identified actin-binding deficient mutants of vinculin outside sites predicted to bind actin and developed an alternative model to better define this actin-binding surface, using negative-stain electron microscopy (EM), discrete molecular dynamics, and mutagenesis. Actin-binding deficient vinculin variants expressed in vinculin knockout fibroblasts fail to rescue cell-spreading defects and reduce cellular response to external force. These findings highlight the importance of this actin-binding surface and provide the molecular basis for elucidating additional roles of this interaction, including actin-induced conformational changes that promote actin bundling.}, number={5}, journal={Structure}, publisher={Elsevier BV}, author={Thompson, Peter M. and Tolbert, Caitlin E. and Shen, Kai and Kota, Pradeep and Palmer, Sean M. and Plevock, Karen M. and Orlova, Albina and Galkin, Vitold E. and Burridge, Keith and Egelman, Edward H. and et al.}, year={2014}, month={May}, pages={697–706} }
 @article{tolbert_thompson_superfine_burridge_campbell_2014, title={Phosphorylation at Y1065 in Vinculin Mediates Actin Bundling, Cell Spreading, and Mechanical Responses to Force}, volume={53}, DOI={10.1021/bi500678x}, abstractNote={Vinculin is an essential structural adaptor protein that localizes to sites of adhesion and is involved in a number of cell processes including adhesion, spreading, motility, force transduction, and cell survival. The C-terminal vinculin tail domain (Vt) contains the necessary structural components to bind and cross-link actin filaments. Actin binding to Vt induces a conformational change that promotes dimerization through the C-terminal hairpin of Vt and enables actin filament cross-linking. Here we show that Src phosphorylation of Y1065 within the C-terminal hairpin regulates Vt-mediated actin bundling and provide a detailed characterization of Y1065 mutations. Furthermore, we show that phosphorylation at Y1065 plays a role in cell spreading and the response to the application of mechanical force.}, number={34}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={Tolbert, Caitlin E. and Thompson, Peter M. and Superfine, Richard and Burridge, Keith and Campbell, Sharon L.}, year={2014}, month={Sep}, pages={5526–5536} }
 @article{waldon_thompson_hahn_taylor_2014, title={SketchBio: a scientist’s 3D interface for molecular modeling and animation}, volume={15}, ISSN={1471-2105}, url={http://dx.doi.org/10.1186/1471-2105-15-334}, DOI={10.1186/1471-2105-15-334}, abstractNote={Because of the difficulties involved in learning and using 3D modeling and rendering software, many scientists hire programmers or animators to create models and animations. This both slows the discovery process and provides opportunities for miscommunication. Working with multiple collaborators, a tool was developed (based on a set of design goals) to enable them to directly construct models and animations.SketchBio is presented, a tool that incorporates state-of-the-art bimanual interaction and drop shadows to enable rapid construction of molecular structures and animations. It includes three novel features: crystal-by-example, pose-mode physics, and spring-based layout that accelerate operations common in the formation of molecular models. Design decisions and their consequences are presented, including cases where iterative design was required to produce effective approaches.The design decisions, novel features, and inclusion of state-of-the-art techniques enabled SketchBio to meet all of its design goals. These features and decisions can be incorporated into existing and new tools to improve their effectiveness.}, number={1}, journal={BMC Bioinformatics}, publisher={Springer Science and Business Media LLC}, author={Waldon, Shawn M and Thompson, Peter M and Hahn, Patrick J and Taylor, Russell M}, year={2014}, month={Oct} }
 @article{der_jha_lewis_thompson_guntas_kuhlman_2013, title={Combined computational design of a zinc-binding site and a protein-protein interaction: One open zinc coordination site was not a robust hotspot for de novo ubiquitin binding}, volume={81}, DOI={10.1002/prot.24379}, abstractNote={Originally published in PROTEINS: Structure, Function, and Bioinformatics 2013;81(7):1245–1255 (DOI: 10.1002/prot.24280) Due to a print error in the originally published version of this article, the author's name is incorrect as published. The correct spelling is Ramesh K. Jha.}, number={9}, journal={Proteins}, publisher={Wiley-Blackwell}, author={Der, Bryan S. and Jha, Raamesh K. and Lewis, Steven M. and Thompson, Peter M. and Guntas, Gurkan and Kuhlman, Brian}, year={2013}, month={Aug}, pages={1678–1679} }
 @article{der_jha_lewis_thompson_guntas_kuhlman_2013, title={Combined computational design of a zinc-binding site and a protein-protein interaction: One open zinc coordination site was not a robust hotspot for de novo ubiquitin binding}, volume={81}, ISSN={0887-3585}, url={http://dx.doi.org/10.1002/prot.24280}, DOI={10.1002/prot.24280}, abstractNote={ABSTRACT}, number={7}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Der, Bryan S. and Jha, Raamesh K. and Lewis, Steven M. and Thompson, Peter M. and Guntas, Gurkan and Kuhlman, Brian}, year={2013}, month={Apr}, pages={1245–1255} }
 @article{thompson_tolbert_campbell_2013, title={Vinculin and metavinculin: Oligomerization and interactions with F-actin}, volume={587}, DOI={10.1016/j.febslet.2013.02.042}, abstractNote={Vinculin, and its splice variant metavinculin, are scaffolding proteins that localize to cellular adhesions. Vinculin is a key player in mediating cell adhesion, motility, and cellular response to force. In the past decade, a number of new studies have evaluated the importance of vinculin oligomers, especially in their role of bundling F‐actin. Emerging evidence also suggests that vinculin oligomerization is important for vinculin's scaffolding function. Here we describe the latest findings on vinculin's interaction with F‐actin and we clarify the different known vinculin oligomers. Differences in these functions between vinculin and metavinculin provide key insights to the structure and function of these oligomers, and should guide further studies.}, number={8}, journal={FEBS Letters}, publisher={Wiley-Blackwell}, author={Thompson, Peter M. and Tolbert, Caitlin E. and Campbell, Sharon L.}, year={2013}, month={Mar}, pages={1220–1229} }
 @article{thievessen_thompson_berlemont_plevock_plotnikov_zemljic-harpf_ross_davidson_danuser_campbell_et al._2013, title={Vinculin–actin interaction couples actin retrograde flow to focal adhesions, but is dispensable for focal adhesion growth}, volume={202}, DOI={10.1083/jcb.201303129}, abstractNote={In migrating cells, integrin-based focal adhesions (FAs) assemble in protruding lamellipodia in association with rapid filamentous actin (F-actin) assembly and retrograde flow. How dynamic F-actin is coupled to FA is not known. We analyzed the role of vinculin in integrating F-actin and FA dynamics by vinculin gene disruption in primary fibroblasts. Vinculin slowed F-actin flow in maturing FA to establish a lamellipodium–lamellum border and generate high extracellular matrix (ECM) traction forces. In addition, vinculin promoted nascent FA formation and turnover in lamellipodia and inhibited the frequency and rate of FA maturation. Characterization of a vinculin point mutant that specifically disrupts F-actin binding showed that vinculin–F-actin interaction is critical for these functions. However, FA growth rate correlated with F-actin flow speed independently of vinculin. Thus, vinculin functions as a molecular clutch, organizing leading edge F-actin, generating ECM traction, and promoting FA formation and turnover, but vinculin is dispensible for FA growth.}, number={1}, journal={J Cell Biol}, publisher={Rockefeller University Press}, author={Thievessen, Ingo and Thompson, Peter M. and Berlemont, Sylvain and Plevock, Karen M. and Plotnikov, Sergey V. and Zemljic-Harpf, Alice and Ross, Robert S. and Davidson, Michael W. and Danuser, Gaudenz and Campbell, Sharon L. and et al.}, year={2013}, month={Jul}, pages={163–177} }
 @article{cooper_cho_thompson_wallace_2008, title={Phthalate induction of CYP3A4 is dependent on glucocorticoid regulation of PXR expression}, volume={103}, ISSN={["1096-0929"]}, DOI={10.1093/toxsci/kfn047}, abstractNote={Cytochrome P450 3A4 (CYP3A4) is responsible for oxidative metabolism of more than 60% of all pharmaceuticals. CYP3A4 is inducible by xenobiotics that activate pregnane X receptor (PXR), and enhanced CYP3A4 activity has been implicated in adverse drug interactions. Recent evidence suggest that the widely used plasticizer, di-2-ethylhexyl phthalate (DEHP), and its primary metabolite mono-2-ethylhexyl phthalate (MEHP) may act as agonists for PXR. Hospital patients are uniquely exposed to high levels of DEHP as well as being administered glucocorticoids. Glucocorticoids positively regulate PXR expression in a glucocorticoid receptor (GR)-mediated mechanism. We suggest that the magnitude of CYP3A4 induction by phthalates is dependent on the expression of PXR and may be significantly higher in the presence of glucocorticoids. DEHP and MEHP induced PXR-mediated transcription of the CYP3A4 promoter in a dose-dependent fashion. Coexposure to phthalates and dexamethasone (Dex) resulted in enhanced CYP3A4 promoter activity; furthermore, this induction was abrogated by both the GR antagonist RU486 and GR small interfering ribonucleic acid. Dex induced PXR protein expression in human hepatocytes and a liver-derived rat cell line. CYP3A4 protein was highly induced by Dex and DEHP coadministration in human hepatocyte cultures. Finally, enhanced 6beta-hydroxytestosterone formation in Dex and phthalate cotreated human hepatocytes confirmed CYP3A4 enzyme induction. Concomitant exposure to glucocorticoids and phthalates resulting in enhanced metabolic activity of CYP3A4 may play a role in altered efficacy of pharmaceutical agents. Understanding the role of glucocorticoid regulation of PXR as a key determinant in the magnitude of CYP3A4 induction by xenobiotics may provide insight into adverse drug effects in a sensitive population.}, number={2}, journal={TOXICOLOGICAL SCIENCES}, publisher={Oxford University Press (OUP)}, author={Cooper, Beth W. and Cho, Taehyeon M. and Thompson, Peter M. and Wallace, Andrew D.}, year={2008}, month={Jun}, pages={268–277} }