@article{1665792,

title = {A central role for regulated protein stability in the control of TFE3 and MITF by nutrients},

author = {C. Nardone and B. A. Palanski and D. C. Scott and R. T. Timms and K. W. Barber and X. Gu and A. Mao and Y. Leng and E. V. Watson and B. A. Schulman and P. A. Cole and S. J. Elledge},

url = {https://www.sciencedirect.com/science/article/pii/S1097276522011704?via%3Dihub},

year  = {2023},

date = {2023-01-01},

journal = {Mol. Cell},

volume = {83},

pages = {57-73},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wang2023,

title = {Structural Basis of Sirtuin 6-Catalyzed Nucleosome Deacetylation},

author = {Z. A. Wang and J. W. Markert and S. D. Whedon and M. Yapa-Abeywardana and K. Lee and H. Jiang and C. Suarez and H. Li and L. Farnung and P. A. Cole},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {J. Am. Chem. Soc.},

volume = {145},

pages = {6811-6822},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1684906,

title = {Semisynthetic Approach to the Analysis of Tumor Suppressor PTEN Ubiquitination},

author = {R. Iwase and D. R. Dempsey and S. D. Whedon and H. Jiang and B. A. Palanski and B. Deng and P. A. Cole},

url = {https://pubs.acs.org/doi/abs/10.1021/jacs.2c13871},

year  = {2023},

date = {2023-01-01},

journal = {J. Am. Chem. Soc.},

volume = {145},

pages = {6039–6044},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1650158,

title = {Distinct biochemical properties of the class I histone deacetylase complexes},

author = {K. Lee and S. D. Whedon and Z. A. Wang and P. A. Cole},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

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

volume = {70},

pages = {102179},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1650156,

title = {Enzymatic Analysis of WWP2 E3 Ubiquitin Ligase Using Protein Microarrays Identifies Autophagy-Related Substrates},

author = {H. Jiang and C. Chiang and Z. Chen and S. Nathan and G. D’Agostino and J. Paulo and G. Song and H. Zhu and S. B. Gabelli and P. A. Cole},

year  = {2022},

date = {2022-01-01},

journal = {J. Biol. Chem.},

volume = {298},

pages = {101854},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1650157,

title = {PH domain-mediated autoinhibition and oncogenic activation of Akt},

author = {H. Bae and T. Viennet and E. Park and N. Chu and A. Salguero and M. J. Eck and H. Arthanari and P. A. Cole},

year  = {2022},

date = {2022-01-01},

journal = {eLife},

volume = {11},

pages = {e80148},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1624374,

title = {Epigenetic Silencing of BMP6 by Sin3A-HDAC1/2 Repressor Complex Drives Melanoma Metastasis via FAM83G/PAWS1},

author = {D. Min and J. Byun and E. H. Lee and A. A. Khan and C. Liu and O. Loudig and W. Hu and Y. Zhao and M. Herlyn and B. Tycko and P. A. Cole and B. Ryu},

year  = {2022},

date = {2022-01-01},

journal = {Mol. Cancer Res.},

volume = {20},

pages = {217-230},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1650155,

title = {Histone H2B Deacylation Selectivity: Exploring Chromatin’s Dark Matter with an Engineered Sortase},

author = {Z. A. Wang and S. D. Whedon and M. Wu and S. Weng and E. A. Brown and A. Anmangandla and L. Regan and K. Lee and J. Du and J. Y. Hong and L. Fairall and T. Kay and H. Lin and Y. Zhao and J. W. R. Schwabe and P. A. Cole},

year  = {2022},

date = {2022-01-01},

journal = {J. Am. Chem. Soc.},

volume = {144},

pages = {3360-3364},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1665791,

title = {KATs off: Biomedical insights from lysine acetyltransferase inhibitors},

author = {S. D. Whedon and P. A. Cole},

url = {https://www.sciencedirect.com/science/article/pii/S1367593122001405?via%3Dihub},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

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

volume = {72},

pages = {102255},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1624376,

title = {Multifaceted Regulation of Akt by Diverse C-terminal Post-translational Modifications},

author = {A. Salguero and M. Chen and A. Balana and N. Chu and H. Jiang and H. Bae and B. A. Palanski and K. Wright and S. Nathan and H.Zhu and S. Gabelli and M. Pratt and P. A. Cole},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {ACS Chem. Biol.},

volume = {17},

pages = {68-76},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1624366,

title = {Chemical Screen Identifies Diverse and Novel Histone Deacetylase Inhibitors as Repressors of NUT Function: Implications for NUT Carcinoma Pathogenesis and Treatment},

author = {H. Shiota and A. A. Alekseyenko and Z. A Wang and I. Filic and T. M. Knox and N. M. Luong and Y. Huang and D. A. Scott and K. L. Jones and P. C. Gokhale and M. E. Lemieux and P. A. Cole and M. I. Kuroda and C. A. French},

doi = {10.1158/1541-7786.MCR-21-0259},

issn = {1557-3125},

year  = {2021},

date = {2021-11-01},

urldate = {2021-11-01},

journal = {Mol. Cancer Res.},

volume = {19},

number = {11},

pages = {1818-1830},

abstract = {NUT carcinoma (NC), characterized most commonly by the BRD4-NUTM1 fusion, is a rare, aggressive variant of squamous carcinoma with no effective treatment. BRD4-NUT drives growth and maintains the poorly differentiated state of NC by activating pro-growth genes such as MYC, through the formation of massive, hyperacetylated, superenhancer-like domains termed megadomains. BRD4-NUT-mediated hyperacetylation of chromatin is facilitated by the chromatin-targeting tandem bromodomains of BRD4, combined with NUT, which recruits the histone acetyltransferase, p300. Here, we developed a high-throughput small-molecule screen to identify inhibitors of transcriptional activation by NUT. In this dCAS9-based GFP-reporter assay, the strongest hits were diverse histone deacetylase (HDAC) inhibitors. Two structurally unrelated HDAC inhibitors, panobinostat and the novel compound, IRBM6, both repressed growth and induced differentiation of NC cells in proportion to their inhibition of NUT transcriptional activity. These two compounds repressed transcription of megadomain-associated oncogenic genes, such as MYC and SOX2, while upregulating pro-differentiation, non-megadomain-associated genes, including JUN, FOS, and key cell-cycle regulators, such as CDKN1A. The transcriptional changes correlate with depletion of BRD4-NUT from megadomains, and redistribution of the p300/CBP-associated chromatin acetylation mark, H3K27ac, away from megadomains toward regular enhancer regions previously populated by H3K27ac. In NC xenograft models, we demonstrated that suppression of tumor growth by panobinostat was comparable with that of bromodomain inhibition, and when combined they improved both survival and growth suppression. IMPLICATIONS: The findings provide mechanistic and preclinical rationale for the use of HDAC inhibitors, alone or combined with other agents, in the treatment of NUT carcinoma.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1624365,

title = {The structural basis of PTEN regulation by multi-site phosphorylation},

author = {D. R. Dempsey and T. Viennet and R. Iwase and E. Y. Park and S. Henriquez and Z. Chen and J. R. Jeliazkov and B. A. Palanski and K. L. Phan and P. Coote and J. J. Gray and M. J. Eck and S. B. Gabelli and H. Arthanari and P. A. Cole},

doi = {10.1038/s41594-021-00668-5},

issn = {1545-9985},

year  = {2021},

date = {2021-10-28},

urldate = {2021-10-28},

journal = {Nat. Struct. Mol. Biol.},

volume = {28},

number = {10},

pages = {858-868},

abstract = {Phosphatase and tensin homolog (PTEN) is a phosphatidylinositol-3,4,5-triphosphate (PIP3) phospholipid phosphatase that is commonly mutated or silenced in cancer. PTEN’s catalytic activity, cellular membrane localization and stability are orchestrated by a cluster of C-terminal phosphorylation (phospho-C-tail) events on Ser380, Thr382, Thr383 and Ser385, but the molecular details of this multi-faceted regulation have remained uncertain. Here we use a combination of protein semisynthesis, biochemical analysis, NMR, X-ray crystallography and computational simulations on human PTEN and its sea squirt homolog, VSP, to obtain a detailed picture of how the phospho-C-tail forms a belt around the C2 and phosphatase domains of PTEN. We also visualize a previously proposed dynamic N-terminal α-helix and show that it is key for PTEN catalysis but disordered upon phospho-C-tail interaction. This structural model provides a comprehensive framework for how C-tail phosphorylation can impact PTEN’s cellular functions.},

keywords = {Animals, Ciona intestinalis, Crystallography, Fluorescence Polarization, Humans, Magnetic Resonance Spectroscopy, Molecular Docking Simulation, Phosphorylation, PTEN Phosphohydrolase, X-Ray},

pubstate = {published},

tppubtype = {article}

}

@article{1624369,

title = {The regulatory enzymes and protein substrates for the lysine β-hydroxybutyrylation pathway},

author = {H. Huang and D. Zhang and Y. Weng and K. Delaney and Z. Tang and C. Yan and S. Qi and C. Peng and P. A. Cole and R. G. Roeder and Y. Zhao},

doi = {10.1126/sciadv.abe2771},

issn = {2375-2548},

year  = {2021},

date = {2021-02-01},

urldate = {2021-02-01},

journal = {Sci. Adv.},

volume = {7},

number = {9},

abstract = {Metabolism-mediated epigenetic changes represent an adapted mechanism for cellular signaling, in which lysine acetylation and methylation have been the historical focus of interest. We recently discovered a β-hydroxybutyrate-mediated epigenetic pathway that couples metabolism to gene expression. However, its regulatory enzymes and substrate proteins remain unknown, hindering its functional study. Here, we report that the acyltransferase p300 can catalyze the enzymatic addition of β-hydroxybutyrate to lysine (Kbhb), while histone deacetylase 1 (HDAC1) and HDAC2 enzymatically remove Kbhb. We demonstrate that p300-dependent histone Kbhb can directly mediate in vitro transcription. Moreover, a comprehensive analysis of Kbhb substrates in mammalian cells has identified 3248 Kbhb sites on 1397 substrate proteins. The dependence of histone Kbhb on p300 argues that enzyme-catalyzed acylation is the major mechanism for nuclear Kbhb. Our study thus reveals key regulatory elements for the Kbhb pathway, laying a foundation for studying its roles in diverse cellular processes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1573454,

title = {Ubiquitin Ligase Activities of WWP1 Germline Variants K740N and N745S},

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

doi = {10.1021/acs.biochem.0c00869},

issn = {1520-4995},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Biochemistry},

abstract = {WWP1 is an E3 ubiquitin ligase that has been reported to target the tumor suppressor lipid phosphatase PTEN. K740N and N745S are recently identified germline variants of WWP1 that have been linked to PTEN-associated cancers [Lee, Y. R., et al. (2020) ]. These WWP1 variants have been suggested to release WWP1 from its native autoinhibited state, thereby promoting enhanced PTEN ubiquitination as a mechanism for driving cancer. Using purified proteins and enzymatic assays, we investigate the possibility that K740N and N745S WWP1 possess enhanced ubiquitin ligase activity and demonstrate that these variants are similar to the wild type (WT) in both autoubiquitination and PTEN ubiquitination. Furthermore, K740N and N745S WWP1 show dependencies similar to those of WT in terms of allosteric activation by an engineered ubiquitin variant, upstream E2 concentration, and substrate ubiquitin concentration. Transfected WWP1 WT and mutants demonstrate comparable effects on cellular PTEN levels. These findings challenge the idea that K740N and N745S WWP1 variants promote cancer by enhanced PTEN ubiquitination.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1573455,

title = {N-Terminal Protein Labeling with N-Hydroxysuccinimide Esters and Microscale Thermophoresis Measurements of Protein-Protein Interactions Using Labeled Protein},

author = {H. Jiang and P. A. Cole},

doi = {10.1002/cpz1.14},

issn = {2691-1299},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Curr. Protoc. Mol. Bio.},

pages = {e14},

abstract = {Protein labeling strategies have been explored for decades to study protein structure, function, and regulation. Fluorescent labeling of a protein enables the study of protein-protein interactions through biophysical methods such as microscale thermophoresis (MST). MST measures the directed motion of a fluorescently labeled protein in response to microscopic temperature gradients, and the protein’s thermal mobility can be used to determine binding affinity. However, the stoichiometry and site specificity of fluorescent labeling are hard to control, and heterogeneous labeling can generate inaccuracies in binding measurements. Here, we describe an easy-to-apply protocol for high-stoichiometric, site-specific labeling of a protein at its N-terminus with N-hydroxysuccinimide (NHS) esters as a means to measure protein-protein interaction affinity by MST. This protocol includes guidelines for NHS ester labeling, fluorescent-labeled protein purification, and MST measurement using a labeled protein. As an example of the entire workflow, we additionally provide a protocol for labeling a ubiquitin E3 enzyme and testing ubiquitin E2-E3 enzyme binding affinity. These methods are highly adaptable and can be extended for protein interaction studies in various biological and biochemical circumstances. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Labeling a protein of interest at its N-terminus with NHS esters through stepwise reaction Alternate Protocol: Labeling a protein of interest at its N-terminus with NHS esters through a one-pot reaction Basic Protocol 2: Purifying the N-terminal fluorescent-labeled protein and determining its concentration and labeling efficiency Basic Protocol 3: Using MST to determine the binding affinity of an N-terminal fluorescent-labeled protein to a binding partner. Basic Protocol 4: NHS ester labeling of ubiquitin E3 ligase WWP2 and measurement of the binding affinity between WWP2 and an E2 conjugating enzyme by the MST binding assay.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1624370,

title = {P300 Suppresses the Transition of Myelodysplastic Syndrome to Acute Myeloid Leukemia},

author = {M. Na and G. M. Martin and D. L. Karl and J. Sun and M. Torres-Martin and H. Itonaga and C. Martinez and S. Chen and Y. Xu and S. Duffort and P. -J. Hamard and C. Chen and L. Cimmino and F. -C. Yang and B. Zucconi and P. A. Cole and M. Xu and M. E. Figueroa and S. D. Nimer},

year  = {2021},

date = {2021-01-01},

journal = {JCI Insights},

volume = {6},

pages = {e138478},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{1624375,

title = {Site-specific 5-Formyl Cytosine Mediated DNA-Histone Crosslinks: Synthesis and Polymerase Bypass by Human DNA Polymerase η},

author = {S. S Pujari and M. Wu and J. Thomforde and Z. A. Wang and C. Chao and N. Olson and L. Erber and W. Pomerantz and P. A. Cole and N. Tretyakova},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Angew. Chem. Int. Ed.},

volume = {60},

pages = {26489-26494},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32541877,

title = {The protein kinase Akt acts as a coat adaptor in endocytic recycling},

author = {J. W. Hsu and M. Bai and K. Li and J. S. Yang and N. Chu and P. A. Cole and M. J. Eck and J. Li and V. W. Hsu},

year  = {2020},

date = {2020-08-01},

journal = {Nat. Cell Biol.},

volume = {22},

number = {8},

pages = {927–933},

abstract = {Coat proteins have a central role in vesicular transport by binding to cargoes for their sorting into intracellular pathways. Cargo recognition is mediated by components of the coat complex known as adaptor proteins1-3. We previously showed that Arf-GAP with coil-coil, ANK repeat and PH domain-containing protein 1 (ACAP1) functions as an adaptor for a clathrin coat complex that has a function in endocytic recycling4-6. Here, we show that the protein kinase Akt acts as a co-adaptor in this complex, and is needed in conjunction with ACAP1 to bind to cargo proteins to promote their recycling. In addition to advancing the understanding of endocytic recycling, we uncover a fundamentally different function in which a kinase acts, as Akt in this case is an effector rather than a regulator in a cellular event.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32744507,

title = {The Structural Determinants of PH Domain-Mediated Regulation of Akt Revealed by Segmental Labeling},

author = {N. Chu and T. Viennet and H. Bae and A. Salguero and A. Boeszoermenyi and H. Arthanari and P. A. Cole},

year  = {2020},

date = {2020-08-01},

journal = {Elife},

volume = {9},

abstract = {Akt is a critical protein kinase that governs cancer cell growth and metabolism. Akt appears to be autoinhibited by an intramolecular interaction between its N-terminal pleckstrin homology (PH) domain and kinase domain, which is relieved by C-tail phosphorylation, but the precise molecular mechanisms remain elusive. Here we use a combination of protein semisynthesis, NMR, and enzymological analysis to characterize structural features of the PH domain in its autoinhibited and activated states. We find that Akt autoinhibition depends on the length/flexibility of the PH-kinase linker. We identify a role for a dynamic short segment in the PH domain that appears to regulate autoinhibition and PDK1-catalyzed phosphorylation of Thr308 in the activation loop. We determine that Akt allosteric inhibitor MK2206 drives distinct PH domain structural changes compared to baseline autoinhibited Akt. These results highlight how the conformational plasticity of Akt governs the delicate control of its catalytic properties.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}