@article{pmid32698016,

title = {The Chemical Biology of Reversible Lysine Post-translational Modifications},

author = {Z. A. Wang and P. A. Cole},

year  = {2020},

date = {2020-07-01},

urldate = {2020-07-01},

journal = {Cell Chem. Biol.},

abstract = {Lysine (Lys) residues in proteins undergo a wide range of reversible post-translational modifications (PTMs), which can regulate enzyme activities, chromatin structure, protein-protein interactions, protein stability, and cellular localization. Here we discuss the "writers," ërasers," and "readers" of some of the common protein Lys PTMs and summarize examples of their major biological impacts. We also review chemical biology approaches, from small-molecule probes to protein chemistry technologies, that have helped to delineate Lys PTM functions and show promise for a diverse set of biomedical applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32371576,

title = {Combined Targeting of the BRD4-NUT-p300 Axis in NUT Midline Carcinoma by Dual Selective Bromodomain Inhibitor, NEO2734},

author = {C. D. Morrison-Smith and T. M. Knox and I. Filic and K. M. Soroko and B. K. Eschle and M. K. Wilkens and P. C. Gokhale and F. Giles and A. Griffin and B. Brown and G. I. Shapiro and B. E. Zucconi and P. A. Cole and M. E. Lemieux and C. A. French},

year  = {2020},

date = {2020-07-01},

journal = {Mol. Cancer Ther.},

volume = {19},

number = {7},

pages = {1406–1414},

abstract = {NUT midline carcinoma (NMC) is a rare, aggressive subtype of squamous carcinoma that is driven by the BRD4-NUT fusion oncoprotein. BRD4, a BET protein, binds to chromatin through its two bromodomains, and NUT recruits the p300 histone acetyltransferse (HAT) to activate transcription of oncogenic target genes. BET-selective bromodomain inhibitors have demonstrated on-target activity in patients with NMC, but with limited efficacy. P300, like BRD4, contains a bromodomain. We show that combining selective p300/CBP and BET bromodomain inhibitors, GNE-781 and OTX015, respectively, induces cooperative depletion of MYC and synergistic inhibition of NMC growth. Treatment of NMC cells with the novel dual p300/CBP and BET bromodomain-selective inhibitor, NEO2734, potently inhibits growth and induces differentiation of NMC cells in vitro; findings that correspond with potentiated transcriptional effects from combined BET and p300 bromodomain inhibition. In three disseminated NMC xenograft models, NEO2734 provided greater growth inhibition, with tumor regression and significant survival benefit seen in two of three models, compared with a lead clinical BET inhibitor or "standard" chemotherapy. Our findings provide a strong rationale for clinical study of NEO2734 in patients with NMC. Moreover, the synergistic inhibition of NMC growth by CBP/p300 and BET bromodomain inhibition lays the groundwork for greater mechanistic understanding of the interplay between p300 and BRD4-NUT that drives this cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32501215,

title = {Diverse nucleosome Site-Selectivity among histone deacetylase complexes},

author = {Z. A. Wang and C. J. Millard and C. L. Lin and J. E. Gurnett and M. Wu and K. Lee and L. Fairall and J. W. Schwabe and P. A. Cole},

year  = {2020},

date = {2020-06-01},

journal = {Elife},

volume = {9},

abstract = {Histone acetylation regulates chromatin structure and gene expression and is removed by histone deacetylases (HDACs). HDACs are commonly found in various protein complexes to confer distinct cellular functions, but how the multi-subunit complexes influence deacetylase activities and site-selectivities in chromatin is poorly understood. Previously we reported the results of studies on the HDAC1 containing CoREST complex and acetylated nucleosome substrates which revealed a notable preference for deacetylation of histone H3 acetyl-Lys9 vs. acetyl-Lys14 (Wu et al, 2018). Here we analyze the enzymatic properties of five class I HDAC complexes: CoREST, NuRD, Sin3B, MiDAC and SMRT with site-specific acetylated nucleosome substrates. Our results demonstrate that these HDAC complexes show a wide variety of deacetylase rates in a site-selective manner. A Gly13 in the histone H3 tail is responsible for a sharp reduction in deacetylase activity of the CoREST complex for H3K14ac. These studies provide a framework for connecting enzymatic and biological functions of specific HDAC complexes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1573452,

title = {Paul Talalay 1923-2019 A Biographical Memoir},

author = {P. A. Cole and T. Shapiro},

url = {http://www.nasonline.org/publications/biographical-memoirs/memoir-pdfs/talalay-paul.pdf},

year  = {2020},

date = {2020-01-01},

journal = {National Academy of Sciences},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32475408,

title = {Selective protein N-terminal labeling with N-hydroxysuccinimide esters},

author = {H. Jiang and G. D. D’Agostino and P. A. Cole and D. R. Dempsey},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Methods Enzymol.},

volume = {639},

pages = {333–353},

abstract = {In order to gain detailed insight into the biochemical behavior of proteins, researchers have developed chemical tools to incorporate new functionality into proteins beyond the canonical 20 amino acids. Important considerations regarding effective chemical modification of proteins include chemoselectivity, near stoichiometric labeling, and reaction conditions that maintain protein stability. Taking these factors into account, we discuss an N-terminal labeling strategy that employs a simple two-step öne-pot" method using N-hydroxysuccinimide (NHS) esters. The first step converts a R-NHS ester into a more chemoselective R-thioester. The second step reacts the in situ generated R-thioester with a protein that harbors an N-terminal cysteine to generate a new amide bond. This labeling reaction is selective for the N-terminus with high stoichiometry. Herein, we provide a detailed description of this method and further highlight its utility with a large protein (>100kDa) and labeling with a commonly used cyanine dye.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1523679,

title = {Editorial Overview: Biological catalysis at the cross-roads of signaling and metabolism},

author = {A. Mattevi and P. A. Cole},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Curr. Opin. Struct. Biol.},

volume = {59},

pages = {iii-iv},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1523678,

title = {Essential Role of the CoREST Complex in Foxp3+ T-Regulatory Cell Functions},

author = {Y. Xiong and L. Wang and E. D. Giorgio and T. Akimova and U. H. Beier and R. Han and M. Trevisanut and J. H. Kalin and P. A. Cole and W. W. Hancock},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {J. Clin. Invest.},

volume = {130},

pages = {1830-1842},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1523677,

title = {Mechanism of Crosstalk between the LSD1 Demethylase and HDAC1 Deacetylase in the CoREST Complex},

author = {Y. Song and L. Dagil and L. Fairall and N. Robertson and M. Wu and T. J. Ragan and C. G. Savva and A. Saleh and N. Morone and M. B. A. Kunze and A. G. Jamieson and P. A. Cole and D. F. Hansen and J. W. R. Schwabe},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Cell Rep.},

volume = {30},

pages = {2699-2711},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31704733,

title = {Lysine-Specific Demethylase 1 Mediates AKT Activity and Promotes Epithelial-to-Mesenchymal Transition in PIK3CA-Mutant Colorectal Cancer},

author = {S. A. Miller and R. A. Policastro and S. S. Savant and S. Sriramkumar and N. Ding and X. Lu and H. P. Mohammad and S. Cao and J. H. Kalin and P. A. Cole and G. E. Zentner and H. M. O’Hagan},

year  = {2020},

date = {2020-01-01},

journal = {Mol. Cancer Res.},

volume = {18},

number = {2},

pages = {264–277},

abstract = {Activation of the epithelial-to-mesenchymal transition (EMT) program is a critical mechanism for initiating cancer progression and migration. Colorectal cancers contain many genetic and epigenetic alterations that can contribute to EMT. Mutations activating the PI3K/AKT signaling pathway are observed in >40% of patients with colorectal cancer contributing to increased invasion and metastasis. Little is known about how oncogenic signaling pathways such as PI3K/AKT synergize with chromatin modifiers to activate the EMT program. Lysine-specific demethylase 1 (LSD1) is a chromatin-modifying enzyme that is overexpressed in colorectal cancer and enhances cell migration. In this study, we determine that LSD1 expression is significantly elevated in patients with colorectal cancer with mutation of the catalytic subunit of PI3K, PIK3CA, compared with patients with colorectal cancer with WT PIK3CA. LSD1 enhances activation of the AKT kinase in colorectal cancer cells through a noncatalytic mechanism, acting as a scaffolding protein for the transcription-repressing CoREST complex. In addition, growth of PIK3CA-mutant colorectal cancer cells is uniquely dependent on LSD1. Knockdown or CRISPR knockout of LSD1 blocks AKT-mediated stabilization of the EMT-promoting transcription factor Snail and effectively blocks AKT-mediated EMT and migration. Overall, we uniquely demonstrate that LSD1 mediates AKT activation in response to growth factors and oxidative stress, and LSD1-regulated AKT activity promotes EMT-like characteristics in a subset of PIK3CA-mutant cells. IMPLICATIONS: Our data support the hypothesis that inhibitors targeting the CoREST complex may be clinically effective in patients with colorectal cancer harboring PIK3CA mutations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32144660,

title = {Methods and Applications of Expressed Protein Ligation},

author = {Z. A. Wang and P. A. Cole},

year  = {2020},

date = {2020-01-01},

journal = {Methods Mol. Biol.},

volume = {2133},

pages = {1–13},

abstract = {Expressed protein ligation is a method of protein semisynthesis and typically involves the reaction of recombinant protein C-terminal thioesters with N-cysteine containing synthetic peptides in a chemoselective ligation. The recombinant protein C-terminal thioesters are produced by exploiting the action of nature’s inteins which are protein modules that catalyze protein splicing. This chapter discusses the basic principles of expressed protein ligation and recent advances and applications in this protein semisynthesis field. Comparative strengths and weaknesses of the method and future challenges are highlighted.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1470476,

title = {Comparative analysis of the catalytic regulation of NEDD4-1 and WWP2 ubiquitin ligases},

author = {H. Jiang and S. N. Thomas and Z. Chen and C. Y. Chiang and P. A. Cole},

doi = {10.1074/jbc.RA119.009211},

issn = {1083-351X},

year  = {2019},

date = {2019-10-01},

urldate = {2019-10-01},

journal = {J. Biol. Chem.},

abstract = {NEDD4-1 E3 ubiquitin protein ligase (NEDD4-1) and WW domain-containing E3 ubiquitin ligase (WWP2) are HECT family ubiquitin E3 ligases. They catalyze Lys ubiquitination of themselves and other proteins and are important in cell growth and differentiation. Regulation of NEDD4-1 and WWP2 catalytic activities are important for controlling cellular protein homeostasis and their dysregulation may lead to cancer and other diseases. Previous work has implicated non-catalytic regions, including the C2 domain and/or WW domain linkers in NEDD4-1 and WWP2, in contributing to autoinhibition of the catalytic HECT domains by intramolecular interactions. Here, we explored the molecular mechanisms of these NEDD4-1 and WWP2 regulatory regions and their interplay with allosteric binding proteins such as Nedd4 family interacting protein (NDFIP1), engineered ubiquitin variants, and linker phosphomimics. We found that in addition to influencing catalytic activities, the WW domain linker regions in NEDD4-1 and WWP2 can impact product distribution, including the degree of polyubiquitination and Lys-48 versus Lys-63 linkages. We show that allosteric activation by NDFIP1 or engineered ubiquitin variants is largely mediated by relief of WW domain linker autoinhibition. WWP2-mediated ubiquitination of WW domain-binding protein 2 (WBP2), phosphatase and tensin homolog (PTEN), and p62 proteins by WWP2 suggests that substrate ubiquitination can also be influenced by WW linker autoinhibition, although to differing extents. Overall, our results provide a deeper understanding of the intricate and multifaceted set of regulatory mechanisms in the control of NEDD4-1 related ubiquitin ligases.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1457468,

title = {CREB Promotes Beta Cell Gene Expression by Targeting Its Coactivators to Tissue-Specific Enhancers},

author = {S. V. de Velde and E. Wiater and M. Tran and Y. Hwang and P. A Cole and M. Montminy},

doi = {10.1128/MCB.00200-19},

issn = {1098-5549},

year  = {2019},

date = {2019-09-01},

urldate = {2019-09-01},

journal = {Mol. Cell Biol.},

volume = {39},

number = {17},

abstract = {CREB mediates effects of cyclic AMP on cellular gene expression. Ubiquitous CREB target genes are induced following recruitment of CREB and its coactivators to promoter proximal binding sites. We found that CREB stimulates the expression of pancreatic beta cell-specific genes by targeting CBP/p300 to promoter-distal enhancer regions. Subsequent increases in histone acetylation facilitate recruitment of the coactivators CRTC2 and BRD4, leading to release of RNA polymerase II over the target gene body. Indeed, CREB-induced hyperacetylation of chromatin over superenhancers promoted beta cell-restricted gene expression, which is sensitive to inhibitors of CBP/p300 and BRD4 activity. Neurod1 appears critical in establishing nucleosome-free regions for recruitment of CREB to beta cell-specific enhancers. Deletion of a CREB-Neurod1-bound enhancer within the superenhancer disrupted the expression of both genes and decreased beta cell function. Our results demonstrate how cross talk between signal-dependent and lineage-determining factors promotes the expression of cell-type-specific gene programs in response to extracellular cues.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1457469,

title = {Analysis of Site-specific Phosphorylation of PTEN using Enzyme-Catalyzed Expressed Protein Ligation},

author = {S. Henager and S. Henriquez and D. R. Dempsey and P. A. Cole},

doi = {10.1002/cbic.201900316},

issn = {1439-7633},

year  = {2019},

date = {2019-06-01},

urldate = {2019-06-01},

journal = {ChemBioChem},

abstract = {The activity and localization of PTEN, a tumor suppressor lipid phosphatase that converts the phospholipid PIP3 to PIP2, is governed in part by phosphorylation on a cluster of four Ser and Thr residues near the C-terminus. Prior enzymatic characterization of the four mono-phosphorylated (1p) PTENs using classical expressed protein ligation (EPL) was complicated by the inclusion of a non-native Cys at the ligation junction (aa379), which may alter the properties of the semisynthetic protein. Here we apply subtiligase-mediated EPL to create wt 1p-PTENs. These PTENs are more autoinhibited than previously appreciated, consistent with Tyr379’s role in driving autoinhibition. Alkaline phosphatase sensitivity analysis revealed that these autoinhibited 1p conformations are kinetically labile. In contrast to the Cys mutant 1p-PTENs, which are poorly recognized by an anti-phospho-PTEN Ab, three of the four wt 1p-PTENs are recognized by a commonly used anti-phospho-PTEN Ab.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1457443,

title = {MITF Expression Predicts Therapeutic Vulnerability to p300 Inhibition in Human Melanoma},

author = {E. Kim and B. E. Zucconi and M. Wu and S. E. Nocco and D. J. Meyers and J. S. McGee and S. Venkatesh and D. L. Cohen and E. C. Gonzalez and B. Ryu and P. A. Cole and R. M. Alani},

doi = {10.1158/0008-5472.CAN-18-2331},

issn = {1538-7445},

year  = {2019},

date = {2019-05-01},

urldate = {2019-05-01},

journal = {Cancer Res.},

volume = {79},

number = {10},

pages = {2649-2661},

abstract = {Histone modifications, largely regulated by histone acetyltransferases (HAT) and histone deacetylases, have been recognized as major regulatory mechanisms governing human diseases, including cancer. Despite significant effort and recent advances, the mechanism by which the HAT and transcriptional coactivator p300 mediates tumorigenesis remains unclear. Here, we use a genetic and chemical approach to identify the microphthalmia-associated transcription factor (MITF) as a critical downstream target of p300 driving human melanoma growth. Direct transcriptional control of MITF by p300-dependent histone acetylation within proximal gene regulatory regions was coupled to cellular proliferation, suggesting a significant growth regulatory axis. Further analysis revealed forkhead box M1 (FOXM1) as a key effector of the p300-MITF axis driving cell growth that is selectively activated in human melanomas. Targeted chemical inhibition of p300 acetyltransferase activity using a potent and selective catalytic p300/CBP inhibitor demonstrated significant growth inhibitory effects in melanoma cells expressing high levels of MITF. Collectively, these data confirm the critical role of the p300-MITF-FOXM1 axis in melanoma and support p300 as a promising novel epigenetic therapeutic target in human melanoma. SIGNIFICANCE: These results show that MITF is a major downstream target of p300 in human melanoma whose expression is predictive of melanoma response to small-molecule inhibition of p300 HAT activity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1457466,

title = {Combination Targeting of the Bromodomain and Acetyltransferase Active Site of p300/CBP},

author = {B. E. Zucconi and J. L. Makofske and D. J. Meyers and Y. Hwang and M. Wu and M. I. Kuroda and P. A. Cole},

doi = {10.1021/acs.biochem.9b00160},

issn = {1520-4995},

year  = {2019},

date = {2019-04-01},

urldate = {2019-04-01},

journal = {Biochemistry},

volume = {58},

number = {16},

pages = {2133-2143},

abstract = {p300 and CBP are highly related histone acetyltransferase (HAT) enzymes that regulate gene expression, and their dysregulation has been linked to cancer and other diseases. p300/CBP is composed of a number of domains including a HAT domain, which is inhibited by the small molecule A-485, and an acetyl-lysine binding bromodomain, which was recently found to be selectively antagonized by the small molecule I-CBP112. Here we show that the combination of I-CBP112 and A-485 can synergize to inhibit prostate cancer cell proliferation. We find that the combination confers a dramatic reduction in p300 chromatin occupancy compared to the individual effects of blocking either domain alone. Accompanying this loss of p300 on chromatin, combination treatment leads to the reduction of specific mRNAs including androgen-dependent and pro-oncogenic prostate genes such as KLK3 (PSA) and c-Myc. Consistent with p300 directly affecting gene expression, mRNAs that are significantly reduced by combination treatment also exhibit a strong reduction in p300 chromatin occupancy at their gene promoters. The relatively few mRNAs that are up-regulated upon combination treatment show no correlation with p300 occupancy. These studies provide support for the pharmacologic advantage of concurrent targeting of two domains within one key epigenetic modification enzyme.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1457467,

title = {Complementary Roles of GCN5 and PCAF in Foxp3+ T-Regulatory Cells},

author = {Yujie Liu and Chunrong Bao and Liqing Wang and Rongxiang Han and Ulf H Beier and Tatiana Akimova and Philip A Cole and Sharon Y R Dent and Wayne W Hancock},

doi = {10.3390/cancers11040554},

issn = {2072-6694},

year  = {2019},

date = {2019-04-01},

journal = {Cancers (Basel)},

volume = {11},

number = {4},

abstract = {Functions of the GCN5-related N-acetyltransferase (GNAT) family of histone/protein acetyltransferases (HATs) in Foxp3+ T-regulatory (Treg) cells are unexplored, despite the general importance of these enzymes in cell biology. We now show that two prototypical GNAT family members, GCN5 (general control nonrepressed-protein 5, lysine acetyltransferase (KAT)2a) and p300/CBP-associated factor (p300/CBP-associated factor (PCAF), Kat2b) contribute to Treg functions through partially distinct and partially overlapping mechanisms. Deletion of Gcn5 or PCAF did not affect Treg development or suppressive function in vitro, but did affect inducible Treg (iTreg) development, and in vivo, abrogated Treg-dependent allograft survival. Contrasting effects were seen upon targeting of each HAT in all T cells; mice lacking GCN5 showed prolonged allograft survival, suggesting this HAT might be a target for epigenetic therapy in allograft recipients, whereas transplants in mice lacking PCAF underwent acute allograft rejection. PCAF deletion also enhanced anti-tumor immunity in immunocompetent mice. Dual deletion of GCN5 and PCAF led to decreased Treg stability and numbers in peripheral lymphoid tissues, and mice succumbed to severe autoimmunity by 3-4 weeks of life. These data indicate that HATs of the GNAT family have contributions to Treg function that cannot be replaced by the functions of previously characterized Treg HATs (CBP, p300, and Tip60), and may be useful targets in immuno-oncology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1457441,

title = {AKTivation mechanisms},

author = {Philip A Cole and Nam Chu and Antonieta L Salguero and Hwan Bae},

doi = {10.1016/j.sbi.2019.02.004},

issn = {1879-033X},

year  = {2019},

date = {2019-03-01},

journal = {Curr Opin Struct Biol},

volume = {59},

pages = {47-53},

abstract = {Akt1-3 (Akt) are a subset of the AGC protein Ser/Thr kinase family and play important roles in cell growth, metabolic regulation, cancer, and other diseases. We describe some of the roles of Akt in cell signaling and the biochemical and structural mechanisms of the regulation of Akt catalysis by the phospholipid PIP3 and by phosphorylation. Recent findings highlight a diverse set of strategies to control Akt catalytic activity to ensure its normal biological functions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1470510,

title = {Re-programing Chromatin with a Bifunctional LSD1/HDAC Inhibitor Induces Therapeutic Differentiation in DIP},

author = {Jamie N Anastas and Barry M Zee and Jay H Kalin and Mirhee Kim and Robyn Guo and Sanda Alexandrescu and Mario Andres Blanco and Stefanie Giera and Shawn M Gillespie and Jayanta Das and Muzhou Wu and Sarah Nocco and Dennis M Bonal and Quang-De Nguyen and Mario L Suva and Bradley E Bernstein and Rhoda Alani and Todd R Golub and Philip A Cole and Mariella G Filbin and Yang Shi},

url = {https://www.sciencedirect.com/science/article/abs/pii/S1535610819304258?via%3Dihub},

year  = {2019},

date = {2019-01-01},

journal = {Cancer Cell},

abstract = {H3K27M mutations resulting in epigenetic dysfunction are frequently observed in diffuse intrinsic pontine glioma (DIPGs), an incurable pediatric cancer. We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts. Mechanistically, Corin increases H3K27me3 levels suppressed by H3K27M histones, and simultaneously increases HDAC-targeted H3K27ac and LSD1-targeted H3K4me1 at differentiation-associated genes. Corin treatment induces cell death, cell-cycle arrest, and a cellular differentiation phenotype and drives transcriptional changes correlating with increased survival time in DIPG patients. These data suggest a strategy for treating DIPG by simultaneously inhibiting LSD1 and HDACs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1470509,

title = {Comparative analysis of the catalytic regulation of NEDD4-1 and WWP2 ubiquitin ligases.},

author = {Hanjie Jiang and Stefani N. Thomas and Zan Chen and Claire Y. Chiang and Philip A. Cole},

url = {https://www.ncbi.nlm.nih.gov/pubmed/?term=31578285},

year  = {2019},

date = {2019-01-01},

journal = {J Biol Chem},

abstract = {NEDD4-1 E3 ubiquitin protein ligase (NEDD4-1) and WW domain-containing E3 ubiquitin ligase (WWP2) are HECT family ubiquitin E3 ligases. They catalyze Lys ubiquitination of themselves and other proteins and are important in cell growth and differentiation. Regulation of NEDD4-1 and WWP2 catalytic activities are important for controlling cellular protein homeostasis and their dysregulation may lead to cancer and other diseases. Previous work has implicated non-catalytic regions, including the C2 domain and/or WW domain linkers in NEDD4-1 and WWP2, in contributing to autoinhibition of the catalytic HECT domains by intramolecular interactions. Here, we explored the molecular mechanisms of these NEDD4-1 and WWP2 regulatory regions and their interplay with allosteric binding proteins such as Nedd4 family interacting protein (NDFIP1), engineered ubiquitin variants, and linker phosphomimics. We found that in addition to influencing catalytic activities, the WW domain linker regions in NEDD4-1 and WWP2 can impact product distribution, including the degree of polyubiquitination and Lys-48 versus Lys-63 linkages. We show that allosteric activation by NDFIP1 or engineered ubiquitin variants is largely mediated by relief of WW domain linker autoinhibition. WWP2-mediated ubiquitination of WW domain-binding protein 2 (WBP2), phosphatase and tensin homolog (PTEN), and p62 proteins by WWP2 suggests that substrate ubiquitination can also be influenced by WW linker autoinhibition, although to differing extents. Overall, our results provide a deeper understanding of the intricate and multifaceted set of regulatory mechanisms in the control of NEDD4-1 related ubiquitin ligases.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31653360,

title = {Editorial overview: Biological catalysis at the cross-roads of signaling and metabolism},

author = {P. A. Cole and A. Mattevi},

year  = {2019},

date = {2019-01-01},

journal = {Curr. Opin. Struct. Biol.},

volume = {59},

pages = {iii-v},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1457440,

title = {Getting the Most Out of Your Crystals: Data Collection at the New High-Flux, Microfocus MX Beamlines at NSLS-II},

author = {Michelle S Miller and Sweta Maheshwari and Wuxian Shi and Yuan Gao and Nam Chu and Alexei S Soares and Philip A Cole and L Mario Amzel and Martin R Fuchs and Jean Jakoncic and Sandra B Gabelli},

doi = {10.3390/molecules24030496},

issn = {1420-3049},

year  = {2019},

date = {2019-01-01},

journal = {Molecules},

volume = {24},

number = {3},

abstract = {Advances in synchrotron technology are changing the landscape of macromolecular crystallography. The two recently opened beamlines at NSLS-II-AMX and FMX-deliver high-flux microfocus beams that open new possibilities for crystallographic data collection. They are equipped with state-of-the-art experimental stations and automation to allow data collection on previously intractable crystals. Optimized data collection strategies allow users to tailor crystal positioning to optimally distribute the X-ray dose over its volume. Vector data collection allows the user to define a linear trajectory along a well diffracting volume of the crystal and perform rotational data collection while moving along the vector. This is particularly well suited to long, thin crystals. We describe vector data collection of three proteins-Akt1, PI3Kα, and CDP-Chase-to demonstrate its application and utility. For smaller crystals, we describe two methods for multicrystal data collection in a single loop, either manually selecting multiple centers (using H108A-PHM as an example), or "raster-collect", a more automated approach for a larger number of crystals (using CDP-Chase as an example).},

keywords = {Crystallography, Models, Molecular, Phosphatidylinositol 3-Kinases, Protein Conformation, Proteins, Pyrophosphatases, X-Ray},

pubstate = {published},

tppubtype = {article}

}

@article{1457465,

title = {Investigation into the Use of Histone Deacetylase Inhibitor MS-275 as a Topical Agent for the Prevention and Treatment of Cutaneous Squamous Cell Carcinoma in an SKH-1 Hairless Mouse Model},

author = {J. H Kalin and A. Eroglu and H. Liu and W. D. Holtzclaw and I. Leigh and C. M. Proby and J. W. Fahey and P. A. Cole and A. T Dinkova-Kostova},

doi = {10.1371/journal.pone.0213095},

issn = {1932-6203},

year  = {2019},

date = {2019-00-00},

urldate = {2019-00-00},

journal = {PLoS One},

volume = {14},

number = {3},

pages = {e0213095},

abstract = {Cutaneous squamous cell carcinomas are a common form of highly mutated keratinocyte skin cancers that are of particular concern in immunocompromised patients. Here we report on the efficacy of topically applied MS-275, a clinically used histone deacetylase inhibitor, for the treatment and management of this disease. At 2 mg/kg, MS-275 significantly decreased tumor burden in an SKH-1 hairless mouse model of UVB radiation-induced skin carcinogenesis. MS-275 was cell permeable as a topical formulation and induced histone acetylation changes in mouse tumor tissue. MS-275 was also effective at inhibiting the proliferation of patient derived cutaneous squamous cell carcinoma lines and was particularly potent toward cells isolated from a regional metastasis on an immunocompromised individual. Our findings support the use of alternative routes of administration for histone deacetylase inhibitors in the treatment of high-risk squamous cell carcinoma which may ultimately lead to more precise delivery and reduced systemic toxicity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1332026,

title = {Hydrazide Mimics for Protein Lysine Acylation To Assess Nucleosome Dynamics and Deubiquitinase Action},

author = {Shridhar Bhat and Yousang Hwang and Matthew D Gibson and Michael T Morgan and Sean D Taverna and Yingming Zhao and Cynthia Wolberger and Michael G Poirier and Philip A Cole},

doi = {10.1021/jacs.8b03572},

issn = {1520-5126},

year  = {2018},

date = {2018-08-01},

journal = {J Am Chem Soc},

volume = {140},

number = {30},

pages = {9478-9485},

abstract = {A range of acyl-lysine (acyl-Lys) modifications on histones and other proteins have been mapped over the past decade but for most, their functional and structural significance remains poorly characterized. One limitation in the study of acyl-Lys containing proteins is the challenge of producing them or their mimics in site-specifically modified forms. We describe a cysteine alkylation-based method to install hydrazide mimics of acyl-Lys post-translational modifications (PTMs) on proteins. We have applied this method to install mimics of acetyl-Lys, 2-hydroxyisobutyryl-Lys, and ubiquityl-Lys that could be recognized selectively by relevant acyl-Lys modification antibodies. The acyl-Lys modified histone H3 proteins were reconstituted into nucleosomes to study nucleosome dynamics and stability as a function of modification type and site. We also installed a ubiquityl-Lys mimic in histone H2B and generated a diubiquitin analog, both of which could be cleaved by deubiquitinating enzymes. Nucleosomes containing the H2B ubiquityl-Lys mimic were used to study the SAGA deubiquitinating module’s molecular recognition. These results suggest that acyl-Lys mimics offer a relatively simple and promising strategy to study the role of acyl-Lys modifications in the function, structure, and regulation of proteins and protein complexes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1332028,

title = {Author Correction: Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours},

author = {Loren M Lasko and Clarissa G Jakob and Rohinton P Edalji and Wei Qiu and Debra Montgomery and Enrico L Digiammarino and T Matt Hansen and Roberto M Risi and Robin Frey and Vlasios Manaves and Bailin Shaw and Mikkel Algire and Paul Hessler and Lloyd T Lam and Tamar Uziel and Emily Faivre and Debra Ferguson and Fritz G Buchanan and Ruth L Martin and Maricel Torrent and Gary G Chiang and Kannan Karukurichi and J William Langston and Brian T Weinert and Chunaram Choudhary and Peter Vries and Arthur F Kluge and Michael A Patane and John H Van Drie and Ce Wang and David McElligott and Edward A Kesicki and Ronen Marmorstein and Chaohong Sun and Philip A Cole and Saul H Rosenberg and Michael R Michaelides and Albert Lai and Kenneth D Bromberg},

doi = {10.1038/s41586-018-0111-5},

issn = {1476-4687},

year  = {2018},

date = {2018-06-01},

journal = {Nature},

volume = {558},

number = {7710},

pages = {E1},

abstract = {In the originally published version of this Letter, the authors Arthur F. Kluge, Michael A. Patane and Ce Wang were inadvertently omitted from the author list. Their affiliations are: I-to-D, Inc., PO Box 6177, Lincoln, Massachusetts 01773, USA (A.F.K.); Mitobridge, Inc. 1030 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA (M.A.P.); and China Novartis Institutes for BioMedical Research, No. 4218 Jinke Road, Zhangjiang Hi-Tech Park, Pudong District, Shanghai 201203, China (C.W.). These authors contributed to the interpretation of results and design of compounds. In addition, author ’Edward A. Kesicki’ was misspelled as ’Ed Kesicki’. These errors have been corrected online.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1332029,

title = {Lysine-14 acetylation of histone H3 in chromatin confers resistance to the deacetylase and demethylase activities of an epigenetic silencing complex},

author = {Mingxuan Wu and Dawn Hayward and Jay H Kalin and Yun Song and John W R Schwabe and Philip A Cole},

doi = {10.7554/eLife.37231},

issn = {2050-084X},

year  = {2018},

date = {2018-06-01},

journal = {Elife},

volume = {7},

abstract = {The core CoREST complex (LHC) contains histone deacetylase HDAC1 and histone demethylase LSD1 held together by the scaffold protein CoREST. Here, we analyze the purified LHC with modified peptide and reconstituted semisynthetic mononucleosome substrates. LHC demethylase activity toward methyl-Lys4 in histone H3 is strongly inhibited by H3 Lys14 acetylation, and this appears to be an intrinsic property of the LSD1 subunit. Moreover, the deacetylase selectivity of LHC unexpectedly shows a marked preference for H3 acetyl-Lys9 versus acetyl-Lys14 in nucleosome substrates but this selectivity is lost with isolated acetyl-Lys H3 protein. This diminished activity of LHC to Lys-14 deacetylation in nucleosomes is not merely due to steric accessibility based on the pattern of sensitivity of the LHC enzymatic complex to hydroxamic acid-mediated inhibition. Overall, these studies have revealed how a single Lys modification can confer a composite of resistance in chromatin to a key epigenetic enzyme complex involved in gene silencing.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1299782,

title = {Analysis of Cellular Tyrosine Phosphorylation via Chemical Rescue of Conditionally Active Abl Kinase},

author = {Zhihong Wang and Min-Sik Kim and Isabel Martinez-Ferrando and Anthony J Koleske and Akhilesh Pandey and Philip A Cole},

doi = {10.1021/acs.biochem.7b01158},

issn = {1520-4995},

year  = {2018},

date = {2018-02-01},

journal = {Biochemistry},

abstract = {Identifying direct substrates targeted by protein kinases is important in understanding cellular physiology and intracellular signal transduction. Mass spectrometry-based quantitative proteomics provides a powerful tool for comprehensively characterizing the downstream substrates of protein kinases. This approach is efficiently applied to receptor kinases that can be precisely, directly, and rapidly activated by some agent, such as a growth factor. However, nonreceptor tyrosine kinase Abl lacks the experimental advantage of extracellular growth factors as immediate and direct stimuli. To circumvent this limitation, we combine a chemical rescue approach with quantitative phosphoproteomics to identify targets of Abl and their phosphorylation sites with enhanced temporal resolution. Both known and novel putative substrates are identified, presenting opportunities for studying unanticipated functions of Abl under physiological and pathological conditions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1299932,

title = {Discovery of Spiro Oxazolidinediones as Selective, Orally Bioavailable Inhibitors of p300/CBP Histone Acetyltransferases},

author = {Michael R Michaelides and Arthur Kluge and Michael Patane and John H Van Drie and Ce Wang and T Matthew Hansen and Roberto M Risi and Robert Mantei and Carmen Hertel and Kannan Karukurichi and Alexandre Nesterov and David McElligott and Peter Vries and J William Langston and Philip A Cole and Ronen Marmorstein and Hong Liu and Loren Lasko and Kenneth D Bromberg and Albert Lai and Edward A Kesicki},

doi = {10.1021/acsmedchemlett.7b00395},

issn = {1948-5875},

year  = {2018},

date = {2018-01-01},

journal = {ACS Med Chem Lett},

volume = {9},

number = {1},

pages = {28-33},

abstract = {p300 and its paralog CBP can acetylate histones and other proteins and have been implicated in a number of diseases characterized by aberrant gene activation, such as cancer. A novel, highly selective, orally bioavailable histone acetyltransferase (HAT) domain inhibitor has been identified through virtual ligand screening and subsequent optimization of a unique hydantoin screening hit. Conformational restraint in the form of a spirocyclization followed by substitution with a urea led to a significant improvement in potency. Replacement of the hydantoin moiety with an oxazolidinedione followed by fluoro substitution led to A-485, which exhibits potent cell activity, low clearance, and high oral bioavailability.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1299936,

title = {Measurement of nanoscale DNA translocation by uracil DNA glycosylase in human cells},

author = {Alexandre Esadze and Gaddiel Rodriguez and Brian P Weiser and Philip A Cole and James T Stivers},

doi = {10.1093/nar/gkx848},

issn = {1362-4962},

year  = {2017},

date = {2017-12-01},

journal = {Nucleic Acids Res},

volume = {45},

number = {21},

pages = {12413-12424},

abstract = {DNA ’sliding’ by human repair enzymes is considered to be important for DNA damage detection. Here, we transfected uracil-containing DNA duplexes into human cells and measured the probability that nuclear human uracil DNA glycosylase (hUNG2) excised two uracil lesions spaced 10-80 bp apart in a single encounter without escaping the micro-volume containing the target sites. The two-site transfer probabilities were 100% and 54% at a 10 and 40 bp spacing, but dropped to only 10% at 80 bp. Enzyme trapping experiments suggested that site transfers over 40 bp followed a DNA ’hopping’ pathway in human cells, indicating that authentic sliding does not occur even over this short distance. The transfer probabilities were much greater than observed in aqueous buffers, but similar to in vitro measurements in the presence of polymer crowding agents. The findings reveal a new role for the crowded nuclear environment in facilitating DNA damage detection.},

keywords = {Cell Line, DNA, DNA Glycosylases, Humans, Uracil},

pubstate = {published},

tppubtype = {article}

}

@article{1299940,

title = {Investigation of N-Terminal Phospho-Regulation of~Uracil DNA Glycosylase Using Protein Semisynthesis},

author = {Brian P Weiser and James T Stivers and Philip A Cole},

doi = {10.1016/j.bpj.2017.06.016},

issn = {1542-0086},

year  = {2017},

date = {2017-07-01},

journal = {Biophys J},

volume = {113},

number = {2},

pages = {393-401},

abstract = {Uracil DNA Glycosylase (UNG2) is the primary enzyme in humans that prevents the stable incorporation of deoxyuridine monophosphate into DNA in the form of U/A basepairs. During S-phase, UNG2 remains associated with the replication fork through its interactions with two proteins, Proliferating Cell Nuclear Antigen (PCNA) and Replication Protein A (RPA), which are critical for DNA replication and repair. In this work, we used protein semisynthesis and fluorescence anisotropy assays to explore the interactions of UNG2 with PCNA and RPA and to determine the effects of two UNG2 phosphorylation sites (Thr6 and Tyr8) located within its PCNA-interacting motif (PIP-box). In binding assays, we found that phosphorylation of Thr6 or Tyr8 on UNG2 can impede PCNA binding without affecting UNG2 catalytic activity or its RPA interaction. Our data also suggests that unmodified UNG2, PCNA, and RPA can form a ternary protein complex. We propose that the UNG2 N-terminus may serve as a flexible scaffold to tether PCNA and RPA at the replication fork, and that post-translational modifications on the UNG2 N-terminus disrupt formation of the PCNA-UNG2-RPA protein complex.},

keywords = {Catalysis, DNA Glycosylases, Electrospray Ionization, Escherichia coli, Humans, Mass, Mutation, Phosphorylation, Proliferating Cell Nuclear Antigen, Protein Binding, Protein Domains, Protein Stability, Replication Protein A, Spectrometry},

pubstate = {published},

tppubtype = {article}

}

@article{1299944,

title = {A Tunable Brake for HECT Ubiquitin Ligases},

author = {Zan Chen and Hanjie Jiang and Wei Xu and Xiaoguang Li and Daniel R Dempsey and Xiangbin Zhang and Peter Devreotes and Cynthia Wolberger and L Mario Amzel and Sandra B Gabelli and Philip A Cole},

doi = {10.1016/j.molcel.2017.03.020},

issn = {1097-4164},

year  = {2017},

date = {2017-05-01},

journal = {Mol Cell},

volume = {66},

number = {3},

pages = {345-357.e6},

abstract = {The HECT E3 ligases ubiquitinate numerous transcription factors and signaling molecules, and their activity must be tightly controlled to prevent cancer, immune disorders, and other diseases. In this study, we have found unexpectedly that peptide linkers tethering WW domains in several HECT family members are key regulatory elements of their catalytic activities. Biochemical, structural, and cellular analyses have revealed that the linkers can lock the HECT domain in an inactive conformation and block the proposed allosteric ubiquitin binding site. Such linker-mediated autoinhibition of the HECT domain can be relieved by linker post-translational modifications, but complete removal of the brake can induce hyperactive autoubiquitination and E3 self destruction. These results clarify the mechanisms of several HECT protein cancer associated mutations and provide a new framework for understanding how HECT ubiquitin ligases must be finely tuned to ensure normal cellular behavior.},

keywords = {Allosteric Regulation, Endosomal Sorting Complexes Required for Transport, Enzyme Activation, Enzyme Stability, HeLa Cells, Humans, Models, Molecular, Mutation, Nedd4 Ubiquitin Protein Ligases, Phosphorylation, Post-Translational, Protein Domains, Protein Processing, Proteolysis, Repressor Proteins, Structure-Activity Relationship, Transfection, Ubiquitin-Protein Ligases},

pubstate = {published},

tppubtype = {article}

}

@article{1299945,

title = {Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution},

author = {Gary C H Mo and Brian Ross and Fabian Hertel and Premashis Manna and Xinxing Yang and Eric Greenwald and Chris Booth and Ashlee M Plummer and Brian Tenner and Zan Chen and Yuxiao Wang and Eileen J Kennedy and Philip A Cole and Karen G Fleming and Amy Palmer and Ralph Jimenez and Jie Xiao and Peter Dedecker and Jin Zhang},

doi = {10.1038/nmeth.4221},

issn = {1548-7105},

year  = {2017},

date = {2017-04-01},

journal = {Nat Methods},

volume = {14},

number = {4},

pages = {427-434},

abstract = {Compartmentalized biochemical activities are essential to all cellular processes, but there is no generalizable method to visualize dynamic protein activities in living cells at a resolution commensurate with cellular compartmentalization. Here, we introduce a new class of fluorescent biosensors that detect biochemical activities in living cells at a resolution up to threefold better than the diffraction limit. These ’FLINC’ biosensors use binding-induced changes in protein fluorescence dynamics to translate kinase activities or protein-protein interactions into changes in fluorescence fluctuations, which are quantifiable through stochastic optical fluctuation imaging. A protein kinase A (PKA) biosensor allowed us to resolve minute PKA activity microdomains on the plasma membranes of living cells and to uncover the role of clustered anchoring proteins in organizing these activity microdomains. Together, these findings suggest that biochemical activities of the cell are spatially organized into an activity architecture whose structural and functional characteristics can be revealed by these new biosensors.},

keywords = {Biosensing Techniques, Cell Membrane, Cyclic AMP-Dependent Protein Kinases, Escherichia coli, Fluorescence Resonance Energy Transfer, Fluorescent Dyes, Green Fluorescent Proteins, HeLa Cells, Humans, Microscopy, Molecular Imaging, Mutagenesis, Protein Interaction Mapping, Site-Directed, Stochastic Processes},

pubstate = {published},

tppubtype = {article}

}

@article{1299948,

title = {Interaction with the DNA Repair Protein Thymine DNA Glycosylase Regulates Histone Acetylation by p300},

author = {Ryan A Henry and Pietro Mancuso and Yin-Ming Kuo and Rossella Tricarico and Marc Tini and Philip A Cole and Alfonso Bellacosa and Andrew J Andrews},

doi = {10.1021/acs.biochem.6b00841},

issn = {1520-4995},

year  = {2016},

date = {2016-12-01},

journal = {Biochemistry},

volume = {55},

number = {49},

pages = {6766-6775},

abstract = {How protein-protein interactions regulate and alter histone modifications is a major unanswered question in epigenetics. The histone acetyltransferase p300 binds thymine DNA glycosylase (TDG); utilizing mass spectrometry to measure site-specific changes in histone acetylation, we found that the absence of TDG in mouse embryonic fibroblasts leads to a reduction in the rate of histone acetylation. We demonstrate that TDG interacts with the CH3 domain of p300 to allosterically promote p300 activity to specific lysines on histone H3 (K18 and K23). However, when TDG concentrations approach those of histones, TDG acts as a competitive inhibitor of p300 histone acetylation. These results suggest a mechanism for how histone acetylation is fine-tuned via interaction with other proteins, while also highlighting a connection between regulators of two important biological processes: histone acetylation and DNA repair/demethylation.},

keywords = {Acetylation, Animals, Cell Line, Cells, Cultured, DNA Repair, E1A-Associated p300 Protein, Histones, Knockout, Mice, Thymine DNA Glycosylase},

pubstate = {published},

tppubtype = {article}

}

@article{1299949,

title = {Enzyme-catalyzed expressed protein ligation},

author = {Samuel H Henager and Nam Chu and Zan Chen and David Bolduc and Daniel R Dempsey and Yousang Hwang and James Wells and Philip A Cole},

doi = {10.1038/nmeth.4004},

issn = {1548-7105},

year  = {2016},

date = {2016-11-01},

journal = {Nat Methods},

volume = {13},

number = {11},

pages = {925-927},

abstract = {Expressed protein ligation is a valuable method for protein semisynthesis that involves the reaction of recombinant protein C-terminal thioesters with N-terminal cysteine (N-Cys)-containing peptides, but the requirement of a Cys residue at the ligation junction can limit the utility of this method. Here we employ subtiligase variants to efficiently ligate Cys-free peptides to protein thioesters. Using this method, we have more accurately determined the effect of C-terminal phosphorylation on the tumor suppressor protein PTEN.},

keywords = {Animals, Bacillus subtilis, Blotting, Catalytic Domain, Cells, Cultured, Cysteine, Escherichia coli, Fibroblasts, Mice, Mutagenesis, Peptide Fragments, Peptide Synthases, Phosphorylation, Post-Translational, Protein Processing, PTEN Phosphohydrolase, Recombinant Proteins, Site-Directed, Subtilisins, Western},

pubstate = {published},

tppubtype = {article}

}

@article{1299966,

title = {Molecular Features of Phosphatase and Tensin Homolog (PTEN) Regulation by C-terminal Phosphorylation},

author = {Zan Chen and Daniel R Dempsey and Stefani N Thomas and Dawn Hayward and David M Bolduc and Philip A Cole},

doi = {10.1074/jbc.M116.728980},

issn = {1083-351X},

year  = {2016},

date = {2016-07-01},

journal = {J Biol Chem},

volume = {291},

number = {27},

pages = {14160-9},

abstract = {PTEN is a tumor suppressor that functions to negatively regulate the PI3K/AKT pathway as the lipid phosphatase for phosphatidylinositol 3,4,5-triphosphate. Phosphorylation of a cluster of Ser/Thr residues (amino acids 380-385) on the C-terminal tail serves to alter the conformational state of PTEN from an open active state to a closed inhibited state, resulting in a reduction of plasma membrane localization and inhibition of enzyme activity. The relative contribution of each phosphorylation site to PTEN autoinhibition and the structural basis for the conformational closure is still unclear. To further the structural understanding of PTEN regulation by C-terminal tail phosphorylation, we used protein semisynthesis to insert stoichiometric and site-specific phospho-Ser/Thr(s) in the C-terminal tail of PTEN. Additionally, we employed photo-cross-linking to map the intramolecular PTEN interactions of the phospho-tail. Systematic evaluation of the PTEN C-tail phospho-cluster showed autoinhibition, and conformational closure was influenced by the aggregate effect of multiple phospho-sites rather than dominated by a single phosphorylation site. Moreover, photo-cross-linking suggested a direct interaction between the PTEN C-tail and a segment in the N-terminal region of the catalytic domain. Mutagenesis experiments provided additional insights into how the PTEN phospho-tail interacts with both the C2 and catalytic domains.},

keywords = {Amino Acid Sequence, Humans, Phosphorylation, PTEN Phosphohydrolase},

pubstate = {published},

tppubtype = {article}

}

@article{1299967,

title = {Histone deacetylase inhibitors decrease NHEJ both by acetylation of repair factors and trapping of PARP1 at DNA double-strand breaks in chromatin},

author = {Carine Robert and Pratik K Nagaria and Nisha Pawar and Adeoluwa Adewuyi and Ivana Gojo and David J Meyers and Philip A Cole and Feyruz V Rassool},

doi = {10.1016/j.leukres.2016.03.007},

issn = {1873-5835},

year  = {2016},

date = {2016-06-01},

journal = {Leuk Res},

volume = {45},

pages = {14-23},

abstract = {Histone deacetylase inhibitors (HDACi) induce acetylation of histone and non-histone proteins, and modulate the acetylation of proteins involved in DNA double-strand break (DSB) repair. Non-homologous end-joining (NHEJ) is one of the main pathways for repairing DSBs. Decreased NHEJ activity has been reported with HDACi treatment. However, mechanisms through which these effects are regulated in the context of chromatin are unclear. We show that pan-HDACi, trichostatin A (TSA), causes differential acetylation of DNA repair factors Ku70/Ku80 and poly ADP-ribose polymerase-1 (PARP1), and impairs NHEJ. Repair effects are reversed by treatments with p300/CBP inhibitor C646, with significantly decreased acetylation of PARP1. In keeping with these findings, TSA treatment significantly increases PARP1 binding to DSBs in chromatin. Notably, AML patients treated with HDACi entinostat (MS275) in vivo also show increased formation of poly ADP-ribose (PAR) that co-localizes with DSBs. Further, we demonstrate that PARP1 bound to chromatin increases with duration of TSA exposure, resembling PARP "trapping". Knockdown of PARP1 inhibits trapping and mitigates HDACi effects on NHEJ. Finally, combination of HDACi with potent PARP inhibitor talazoparib (BMN673) shows a dose-dependent increase in PARP "trapping", which correlates with increased apoptosis. These results provide a mechanism through which HDACi inhibits deacetylation and increases binding of PARP1 to DSBs, leading to decreased NHEJ and cytotoxicity of leukemia cells.},

keywords = {Acetylation, Acute, Benzamides, Chromatin, Cultured, DNA Breaks, DNA End-Joining Repair, Double-Stranded, Histone Deacetylase Inhibitors, Humans, Ku Autoantigen, Leukemia, Myeloid, Poly (ADP-Ribose) Polymerase-1, Pyridines, Tumor Cells},

pubstate = {published},

tppubtype = {article}

}

@article{1299963,

title = {Modulation of p300/CBP Acetylation of Nucleosomes by Bromodomain Ligand I-CBP112},

author = {B. E. Zucconi and B. Luef and W. Xu and R. A. Henry and I. M. Nodelman and G. D. Bowman and A. J Andrews and P. A. Cole},

doi = {10.1021/acs.biochem.6b00480},

issn = {1520-4995},

year  = {2016},

date = {2016-00-00},

journal = {Biochemistry},

volume = {55},

number = {27},

pages = {3727-34},

abstract = {The histone acetyltransferase (HAT) enzymes p300 and CBP are closely related paralogs that serve as transcriptional coactivators and have been found to be dysregulated in cancer and other diseases. p300/CBP is a multidomain protein and possesses a highly conserved bromodomain that has been shown to bind acetylated Lys residues in both proteins and various small molecules, including I-CBP112 and CBP30. Here we show that the ligand I-CBP112 can stimulate nucleosome acetylation up to 3-fold while CBP30 does not. Activation of p300/CBP by I-CBP112 is not observed with the isolated histone H3 substrate but requires a nucleosome substrate. I-CBP112 does not impact nucleosome acetylation by the isolated p300 HAT domain, and the effects of I-CBP112 on p300/CBP can be neutralized by CBP30, suggesting that I-CBP112 likely allosterically activates p300/CBP through bromodomain interactions. Using mass spectrometry and Western blots, we have found that I-CBP112 particularly stimulates acetylation of Lys18 of histone H3 (H3K18) in nucleosomes, an established in vivo site of p300/CBP. In addition, we show that I-CBP112 enhances H3K18 acetylation in acute leukemia and prostate cancer cells in a concentration range commensurate with its antiproliferative effects. Our findings extend the known pharmacology of bromodomain ligands in the regulation of p300/CBP and suggest a novel approach to modulating histone acetylation in cancer.},

keywords = {Acetylation, Bromine Compounds, Cell Proliferation, Crystallography, Cultured, E1A-Associated p300 Protein, Histones, Humans, Leukemia, Male, Models, Molecular, Mutagenesis, Nucleosomes, p300-CBP Transcription Factors, Prostatic Neoplasms, Protein Binding, Protein Conformation, Site-Directed, Tumor Cells, X-Ray},

pubstate = {published},

tppubtype = {article}

}

@article{1299968,

title = {YcgC represents a new protein deacetylase family in prokaryotes},

author = {Shun Tu and Shu-Juan Guo and Chien-Sheng Chen and Cheng-Xi Liu and He-Wei Jiang and Feng Ge and Jiao-Yu Deng and Yi-Ming Zhou and Daniel M Czajkowsky and Yang Li and Bang-Ruo Qi and Young-Hoon Ahn and Philip A Cole and Heng Zhu and Sheng-Ce Tao},

doi = {10.7554/eLife.05322},

issn = {2050-084X},

year  = {2015},

date = {2015-12-01},

journal = {Elife},

volume = {4},

abstract = {Reversible lysine acetylation is one of the most important protein posttranslational modifications that plays essential roles in both prokaryotes and eukaryotes. However, only a few lysine deacetylases (KDACs) have been identified in prokaryotes, perhaps in part due to their limited sequence homology. Herein, we developed a ’clip-chip’ strategy to enable unbiased, activity-based discovery of novel KDACs in the Escherichia coli proteome. In-depth biochemical characterization confirmed that YcgC is a serine hydrolase involving Ser200 as the catalytic nucleophile for lysine deacetylation and does not use NAD(+) or Zn(2+) like other established KDACs. Further, in vivo characterization demonstrated that YcgC regulates transcription by catalyzing deacetylation of Lys52 and Lys62 of a transcriptional repressor RutR. Importantly, YcgC targets a distinct set of substrates from the only known E. coli KDAC CobB. Analysis of YcgC’s bacterial homologs confirmed that they also exhibit KDAC activity. YcgC thus represents a novel family of prokaryotic KDACs.},

keywords = {Amidohydrolases, Escherichia coli, Escherichia coli Proteins, Lysine, Post-Translational, Protein Processing, Substrate Specificity, Transcription Factors},

pubstate = {published},

tppubtype = {article}

}

@article{1299970,

title = {Mechanistic analysis of ghrelin-O-acyltransferase using substrate analogs},

author = {Martin S Taylor and Daniel R Dempsey and Yousang Hwang and Zan Chen and Nam Chu and Jef D Boeke and Philip A Cole},

doi = {10.1016/j.bioorg.2015.07.003},

issn = {1090-2120},

year  = {2015},

date = {2015-10-01},

journal = {Bioorg Chem},

volume = {62},

pages = {64-73},

abstract = {Ghrelin-O-Acyltransferase (GOAT) is an 11-transmembrane integral membrane protein that octanoylates the metabolism-regulating peptide hormone ghrelin at Ser3 and may represent an attractive target for the treatment of type II diabetes and the metabolic syndrome. Protein octanoylation is unique to ghrelin in humans, and little is known about the mechanism of GOAT or of related protein-O-acyltransferases HHAT or PORC. In this study, we explored an in vitro microsomal ghrelin octanoylation assay to analyze its enzymologic features. Measurement of Km for 10-mer, 27-mer, and synthetic Tat-peptide-containing ghrelin substrates provided evidence for a role of charge interactions in substrate binding. Ghrelin substrates with amino-alanine in place of Ser3 demonstrated that GOAT can catalyze the formation of an octanoyl-amide bond at a similar rate compared with the natural reaction. A pH-rate comparison of these substrates revealed minimal differences in acyltransferase activity across pH 6.0-9.0, providing evidence that these reactions may be relatively insensitive to the basicity of the substrate nucleophile. The conserved His338 residue was required both for Ser3 and amino-Ala3 ghrelin substrates, suggesting that His338 may have a key catalytic role beyond that of a general base.},

keywords = {Acyltransferases, Amino Acid Sequence, Animals, Baculoviridae, Biotin, Cell Line, Enzyme Assays, Genetic Vectors, Ghrelin, Hydrogen-Ion Concentration, Mice, Models, Molecular},

pubstate = {published},

tppubtype = {article}

}

@article{1299971,

title = {Synthetic approaches to protein phosphorylation},

author = {Zan Chen and Philip A Cole},

doi = {10.1016/j.cbpa.2015.07.001},

issn = {1879-0402},

year  = {2015},

date = {2015-10-01},

journal = {Curr Opin Chem Biol},

volume = {28},

pages = {115-22},

abstract = {Reversible protein phosphorylation is critically important in biology and medicine. Hundreds of thousands of sites of protein phosphorylation have been discovered but our understanding of the functions of the vast majority of these post-translational modifications is lacking. This review describes several chemical and biochemical methods that are under development and in current use to install phospho-amino acids and their mimics site-specifically into proteins. The relative merits of total chemical synthesis, semisynthesis, and nonsense suppression strategies for studying protein phosphorylation are discussed in terms of technical simplicity, scope, and versatility.},

keywords = {Animals, Humans, Mutagenesis, Phosphoproteins, Phosphorylation, Protein Transport, Recombinant Proteins, Site-Directed},

pubstate = {published},

tppubtype = {article}

}

@article{1299972,

title = {Switching immune signals on and off},

author = {Nam Chu and Philip A Cole},

doi = {10.7554/eLife.07204},

issn = {2050-084X},

year  = {2015},

date = {2015-04-01},

journal = {Elife},

volume = {4},

keywords = {Animals, Phytic Acid, Protein-Tyrosine Kinases},

pubstate = {published},

tppubtype = {article}

}

@article{1299973,

title = {Protein lysine acetylation by p300/CBP},

author = {Beverley M Dancy and Philip A Cole},

doi = {10.1021/cr500452k},

issn = {1520-6890},

year  = {2015},

date = {2015-03-01},

journal = {Chem Rev},

volume = {115},

number = {6},

pages = {2419-52},

keywords = {Acetylation, Animals, Humans, Lysine, Models, Molecular, p300-CBP Transcription Factors},

pubstate = {published},

tppubtype = {article}

}

@article{1299969,

title = {CBP Binding Outside of Promoters and Enhancers in Drosophila Melanogaster},

author = {P. Philip and A. Boija and R. Vaid and A. M. Churcher and D. J. Meyers and P. A. Cole and M. Mannervik and P. Stenberg},

doi = {10.1186/s13072-015-0042-4},

issn = {1756-8935},

year  = {2015},

date = {2015-00-00},

urldate = {2015-00-00},

journal = {Epigenetics Chromatin},

volume = {8},

pages = {48},

abstract = {BACKGROUND: CREB-binding protein (CBP, also known as nejire) is a transcriptional co-activator that is conserved in metazoans. CBP plays an important role in embryonic development and cell differentiation and mutations in CBP can lead to various diseases in humans. In addition, CBP and the related p300 protein have successfully been used to predict enhancers in both humans and flies when they occur with monomethylation of histone H3 on lysine 4 (H3K4me1). 

RESULTS: Here, we compare CBP chromatin immunoprecipitation sequencing data from Drosophila S2 cells with modENCODE data and show that CBP is bound at genomic sites with a wide range of functions. As expected, we find that CBP is bound at active promoters and enhancers. In addition, we find that the strongest CBP sites in the genome are found at Polycomb response elements embedded in histone H3 lysine 27 trimethylated (H3K27me3) chromatin, where they correlate with binding of the Pho repressive complex. Interestingly, we find that CBP also binds to most insulators in the genome. At a subset of these, CBP may regulate insulating activity, measured as the ability to prevent repressive H3K27 methylation from spreading into adjacent chromatin. 

CONCLUSIONS: We conclude that CBP could be involved in a much wider range of functions than has previously been appreciated, including Polycomb repression and insulator activity. In addition, we discuss the possibility that a common role for CBP at all functional elements may be to regulate interactions between distant chromosomal regions and speculate that CBP is controlling higher order chromatin organization.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1299978,

title = {Using S-adenosyl-L-homocysteine capture compounds to characterize S-adenosyl-L-methionine and S-adenosyl-L-homocysteine binding proteins},

author = {Lindsey J Brown and Matthias Baranowski and Yun Wang and Anna K Schrey and Thomas Lenz and Sean D Taverna and Philip A Cole and Michael Sefkow},

doi = {10.1016/j.ab.2014.08.013},

issn = {1096-0309},

year  = {2014},

date = {2014-12-01},

journal = {Anal Biochem},

volume = {467},

pages = {14-21},

abstract = {S-Adenosyl-l-methionine (SAM) is recognized as an important cofactor in a variety of biochemical reactions. As more proteins and pathways that require SAM are discovered, it is important to establish a method to quickly identify and characterize SAM binding proteins. The affinity of S-adenosyl-l-homocysteine (SAH) for SAM binding proteins was used to design two SAH-derived capture compounds (CCs). We demonstrate interactions of the proteins COMT and SAHH with SAH-CC with biotin used in conjunction with streptavidin-horseradish peroxidase. After demonstrating SAH-dependent photo-crosslinking of the CC to these proteins, we used a CC labeled with a fluorescein tag to measure binding affinity via fluorescence anisotropy. We then used this approach to show and characterize binding of SAM to the PR domain of PRDM2, a lysine methyltransferase with putative tumor suppressor activity. We calculated the Kd values for COMT, SAHH, and PRDM2 (24.1 ± 2.2 μM, 6.0 ± 2.9 μM, and 10.06 ± 2.87 μM, respectively) and found them to be close to previously established Kd values of other SAM binding proteins. Here, we present new methods to discover and characterize SAM and SAH binding proteins using fluorescent CCs.},

keywords = {Catechol O-Methyltransferase, DNA-Binding Proteins, Fluorescence Polarization, Histone-Lysine N-Methyltransferase, Humans, Hydrolases, Nuclear Proteins, S-Adenosylhomocysteine, S-Adenosylmethionine, Transcription Factors},

pubstate = {published},

tppubtype = {article}

}

@article{1299975,

title = {Dissecting the binding mode of low affinity phage display peptide ligands to protein targets by hydrogen/deuterium exchange coupled to mass spectrometry},

author = {Ulrike Leurs and Brian Lohse and Shonoi Ming and Philip A Cole and Rasmus P Clausen and Jesper L Kristensen and Kasper D Rand},

doi = {10.1021/ac503137u},

issn = {1520-6882},

year  = {2014},

date = {2014-12-01},

journal = {Anal Chem},

volume = {86},

number = {23},

pages = {11734-41},

abstract = {Phage display (PD) is frequently used to discover peptides capable of binding to biological protein targets. The structural characterization of peptide-protein complexes is often challenging due to their low binding affinities and high structural flexibility. Here, we investigate the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize interactions of low affinity peptides with their cognate protein targets. The HDX-MS workflow was optimized to accurately detect low-affinity peptide-protein interactions by use of ion mobility, electron transfer dissociation, nonbinding control peptides, and statistical analysis of replicate data. We show that HDX-MS can identify regions in the two epigenetic regulator proteins KDM4C and KDM1A that are perturbed through weak interactions with PD-identified peptides. Two peptides cause reduced HDX on opposite sides of the active site of KDM4C, indicating distinct binding modes. In contrast, the perturbation site of another PD-selected peptide inhibiting the function of KDM1A maps to a GST-tag. Our results demonstrate that HDX-MS can validate and map weak peptide-protein interactions and pave the way for understanding and optimizing the binding of peptide scaffolds identified through PD and similar ligand discovery approaches.},

keywords = {Binding Sites, Deuterium Exchange Measurement, Histone Demethylases, Humans, Jumonji Domain-Containing Histone Demethylases, Ligands, Mass Spectrometry, Models, Molecular, Molecular Structure, Peptides},

pubstate = {published},

tppubtype = {article}

}

@article{1299979,

title = {Two histone/protein acetyltransferases, CBP and p300, are indispensable for Foxp3+ T-regulatory cell development and function},

author = {Yujie Liu and Liqing Wang and Rongxiang Han and Ulf H Beier and Tatiana Akimova and Tricia Bhatti and Haiyan Xiao and Philip A Cole and Paul K Brindle and Wayne W Hancock},

doi = {10.1128/MCB.00919-14},

issn = {1098-5549},

year  = {2014},

date = {2014-11-01},

journal = {Mol Cell Biol},

volume = {34},

number = {21},

pages = {3993-4007},

abstract = {T-regulatory (Treg) cells are important to immune homeostasis, and Treg cell deficiency or dysfunction leads to autoimmune disease. A histone/protein acetyltransferase (HAT), p300, was recently found to be important for Treg function and stability, but further insights into the mechanisms by which p300 or other HATs affect Treg biology are needed. Here we show that CBP, a p300 paralog, is also important in controlling Treg function and stability. Thus, while mice with Treg-specific deletion of CBP or p300 developed minimal autoimmune disease, the combined deletion of CBP and p300 led to fatal autoimmunity by 3 to 4 weeks of age. The effects of CBP and p300 deletion on Treg development are dose dependent and involve multiple mechanisms. CBP and p300 cooperate with several key Treg transcription factors that act on the Foxp3 promoter to promote Foxp3 production. CBP and p300 also act on the Foxp3 conserved noncoding sequence 2 (CNS2) region to maintain Treg stability in inflammatory environments by regulating pCREB function and GATA3 expression, respectively. Lastly, CBP and p300 regulate the epigenetic status and function of Foxp3. Our findings provide insights into how HATs orchestrate multiple aspects of Treg development and function and identify overlapping but also discrete activities for p300 and CBP in control of Treg cells.},

keywords = {Animals, Cell Survival, Colitis, CREB-Binding Protein, Cyclic AMP Response Element-Binding Protein, E1A-Associated p300 Protein, Epigenesis, Female, Forkhead Transcription Factors, GATA3 Transcription Factor, Genetic, Humans, Inbred C57BL, Male, Mice, Promoter Regions, Regulatory, Sequence Deletion, T-Lymphocytes},

pubstate = {published},

tppubtype = {article}

}

@article{1299977,

title = {Regulation of S-adenosylhomocysteine hydrolase by lysine acetylation},

author = {Yun Wang and Jennifer M Kavran and Zan Chen and Kannan R Karukurichi and Daniel J Leahy and Philip A Cole},

doi = {10.1074/jbc.M114.597153},

issn = {1083-351X},

year  = {2014},

date = {2014-11-01},

journal = {J Biol Chem},

volume = {289},

number = {45},

pages = {31361-72},

abstract = {S-Adenosylhomocysteine hydrolase (SAHH) is an NAD(+)-dependent tetrameric enzyme that catalyzes the breakdown of S-adenosylhomocysteine to adenosine and homocysteine and is important in cell growth and the regulation of gene expression. Loss of SAHH function can result in global inhibition of cellular methyltransferase enzymes because of high levels of S-adenosylhomocysteine. Prior proteomics studies have identified two SAHH acetylation sites at Lys(401) and Lys(408) but the impact of these post-translational modifications has not yet been determined. Here we use expressed protein ligation to produce semisynthetic SAHH acetylated at Lys(401) and Lys(408) and show that modification of either position negatively impacts the catalytic activity of SAHH. X-ray crystal structures of 408-acetylated SAHH and dually acetylated SAHH have been determined and reveal perturbations in the C-terminal hydrogen bonding patterns, a region of the protein important for NAD(+) binding. These crystal structures along with mutagenesis data suggest that such hydrogen bond perturbations are responsible for SAHH catalytic inhibition by acetylation. These results suggest how increased acetylation of SAHH may globally influence cellular methylation patterns.},

keywords = {Acetylation, Adenosylhomocysteinase, Amino Acid, Amino Acid Sequence, Catalysis, Crystallography, Humans, Hydrogen Bonding, Lysine, Methylation, Models, Molecular, Molecular Sequence Data, Mutagenesis, NAD, Plasmids, Post-Translational, Protein Binding, Protein Processing, Protein Structure, Recombinant Proteins, Sequence Homology, Site-Directed, Structure-Activity Relationship, Tertiary, X-Ray},

pubstate = {published},

tppubtype = {article}

}

@article{1299976,

title = {How IGF-1 activates its receptor},

author = {Jennifer M Kavran and Jacqueline M McCabe and Patrick O Byrne and Mary Katherine Connacher and Zhihong Wang and Alexander Ramek and Sarvenaz Sarabipour and Yibing Shan and David E Shaw and Kalina Hristova and Philip A Cole and Daniel J Leahy},

doi = {10.7554/eLife.03772},

issn = {2050-084X},

year  = {2014},

date = {2014-09-01},

journal = {Elife},

volume = {3},

abstract = {The type I insulin-like growth factor receptor (IGF1R) is involved in growth and survival of normal and neoplastic cells. A ligand-dependent conformational change is thought to regulate IGF1R activity, but the nature of this change is unclear. We point out an underappreciated dimer in the crystal structure of the related Insulin Receptor (IR) with Insulin bound that allows direct comparison with unliganded IR and suggests a mechanism by which ligand regulates IR/IGF1R activity. We test this mechanism in a series of biochemical and biophysical assays and find the IGF1R ectodomain maintains an autoinhibited state in which the TMs are held apart. Ligand binding releases this constraint, allowing TM association and unleashing an intrinsic propensity of the intracellular regions to autophosphorylate. Enzymatic studies of full-length and kinase-containing fragments show phosphorylated IGF1R is fully active independent of ligand and the extracellular-TM regions. The key step triggered by ligand binding is thus autophosphorylation.},

keywords = {Amino Acid Sequence, Animals, Conserved Sequence, HEK293 Cells, Humans, IGF Type 1, Insulin, Insulin-Like Growth Factor I, Ligands, Mice, Models, Molecular, Molecular Sequence Data, Mutation, Phosphorylation, Protein Binding, Protein Multimerization, Protein Structure, Receptor, Tertiary},

pubstate = {published},

tppubtype = {article}

}

@article{1299981,

title = {Substrate- and cofactor-independent inhibition of histone demethylase KDM4C},

author = {Ulrike Leurs and Brian Lohse and Kasper D Rand and Shonoi Ming and Erik S Riise and Philip A Cole and Jesper L Kristensen and Rasmus P Clausen},

doi = {10.1021/cb500374f},

issn = {1554-8937},

year  = {2014},

date = {2014-09-01},

journal = {ACS Chem Biol},

volume = {9},

number = {9},

pages = {2131-8},

abstract = {Inhibition of histone demethylases has within recent years advanced into a new strategy for treating cancer and other diseases. Targeting specific histone demethylases can be challenging, as the active sites of KDM1A-B and KDM4A-D histone demethylases are highly conserved. Most inhibitors developed up-to-date target either the cofactor- or substrate-binding sites of these enzymes, resulting in a lack of selectivity and off-target effects. This study describes the discovery of the first peptide-based inhibitors of KDM4 histone demethylases that do not share the histone peptide sequence or inhibit through substrate competition. Through screening of DNA-encoded peptide libraries against KDM1 and -4 histone demethylases by phage display, two cyclic peptides targeting the histone demethylase KDM4C were identified and developed as inhibitors by amino acid replacement, truncation, and chemical modifications. Hydrogen/deuterium exchange mass spectrometry revealed that the peptide-based inhibitors target KDM4C through substrate-independent interactions located on the surface remote from the active site within less conserved regions of KDM4C. The sites discovered in this study provide a new approach of targeting KDM4C through substrate- and cofactor-independent interactions and may be further explored to develop potent selective inhibitors and biological probes for the KDM4 family.},

keywords = {Amino Acid Sequence, Catalytic Domain, Cell Line, Coenzymes, Deuterium Exchange Measurement, Enzyme Inhibitors, High-Throughput Screening Assays, Histone Demethylases, Humans, Inhibitory Concentration 50, Jumonji Domain-Containing Histone Demethylases, Molecular Sequence Data, Peptide Library},

pubstate = {published},

tppubtype = {article}

}

@article{1299980,

title = {Structural basis of nSH2 regulation and lipid binding in PI3Kα},

author = {Michelle S Miller and Oleg Schmidt-Kittler and David M Bolduc and Evan T Brower and Daniele Chaves-Moreira and Marc Allaire and Kenneth W Kinzler and Ian G Jennings and Philip E Thompson and Philip A Cole and L Mario Amzel and Bert Vogelstein and Sandra B Gabelli},

doi = {10.18632/oncotarget.2263},

issn = {1949-2553},

year  = {2014},

date = {2014-07-01},

journal = {Oncotarget},

volume = {5},

number = {14},

pages = {5198-208},

abstract = {We report two crystal structures of the wild-type phosphatidylinositol 3-kinase α (PI3Kα) heterodimer refined to 2.9 Å and 3.4 Å resolution: the first as the free enzyme, the second in complex with the lipid substrate, diC4-PIP$_2$, respectively. The first structure shows key interactions of the N-terminal SH2 domain (nSH2) and iSH2 with the activation loop that suggest a mechanism by which the enzyme is inhibited in its basal state. In the second structure, the lipid substrate binds in a positively charged pocket adjacent to the ATP-binding site, bordered by the P-loop, the activation loop and the iSH2 domain. An additional lipid-binding site was identified at the interface of the ABD, iSH2 and kinase domains. The ability of PI3Kα to bind an additional PIP$_2$ molecule was confirmed in vitro by fluorescence quenching experiments. The crystal structures reveal key differences in the way the nSH2 domain interacts with wild-type p110α and with the oncogenic mutant p110αH1047R. Increased buried surface area and two unique salt-bridges observed only in the wild-type structure suggest tighter inhibition in the wild-type PI3Kα than in the oncogenic mutant. These differences may be partially responsible for the increased basal lipid kinase activity and increased membrane binding of the oncogenic mutant.},

keywords = {Amino Acid Sequence, Animals, Binding Sites, Boron Compounds, Models, Molecular, Molecular Sequence Data, Phosphatidylinositol 3-Kinases, Protein Binding, Protein Conformation, Sf9 Cells, Signal Transduction, Spodoptera, src Homology Domains},

pubstate = {published},

tppubtype = {article}

}

@article{1299983,

title = {A selective phenelzine analogue inhibitor of histone demethylase LSD1},

author = {Polina Prusevich and Jay H Kalin and Shonoi A Ming and Manuela Basso and Jeffrey Givens and Xin Li and Jianfei Hu and Martin S Taylor and Anne M Cieniewicz and Po-Yuan Hsiao and Rong Huang and Heather Roberson and Nkosi Adejola and Lindsay B Avery and Robert A Casero and Sean D Taverna and Jiang Qian and Alan J Tackett and Rajiv R Ratan and Oliver G McDonald and Andrew P Feinberg and Philip A Cole},

doi = {10.1021/cb500018s},

issn = {1554-8937},

year  = {2014},

date = {2014-06-01},

journal = {ACS Chem Biol},

volume = {9},

number = {6},

pages = {1284-93},

abstract = {Lysine-specific demethylase 1 (LSD1) is an epigenetic enzyme that oxidatively cleaves methyl groups from monomethyl and dimethyl Lys4 of histone H3 (H3K4Me1, H3K4Me2) and can contribute to gene silencing. This study describes the design and synthesis of analogues of a monoamine oxidase antidepressant, phenelzine, and their LSD1 inhibitory properties. A novel phenelzine analogue (bizine) containing a phenyl-butyrylamide appendage was shown to be a potent LSD1 inhibitor in vitro and was selective versus monoamine oxidases A/B and the LSD1 homologue, LSD2. Bizine was found to be effective at modulating bulk histone methylation in cancer cells, and ChIP-seq experiments revealed a statistically significant overlap in the H3K4 methylation pattern of genes affected by bizine and those altered in LSD1-/- cells. Treatment of two cancer cell lines, LNCaP and H460, with bizine conferred a reduction in proliferation rate, and bizine showed additive to synergistic effects on cell growth when used in combination with two out of five HDAC inhibitors tested. Moreover, neurons exposed to oxidative stress were protected by the presence of bizine, suggesting potential applications in neurodegenerative disease.},

keywords = {Animals, Blotting, Cell Survival, Cells, Cultured, DNA Methylation, Embryo, Enzyme Inhibitors, Fetus, Histone Demethylases, Histones, Humans, Mammalian, Monoamine Oxidase, Neurons, Phenelzine, Rats, Sprague-Dawley, Western},

pubstate = {published},

tppubtype = {article}

}