@article {2525,
	title = {Detection and assignment of phosphoserine and phosphothreonine residues by C-13-P-31 spin-echo difference NMR spectroscopy},
	journal = {Journal of Biomolecular Nmr},
	volume = {43},
	number = {1},
	year = {2009},
	note = {ISI Document Delivery No.: 379QKTimes Cited: 0Cited Reference Count: 31McIntosh, Lawrence P. Kang, Hyun-Seo Okon, Mark Nelson, Mary L. Graves, Barbara J. Brutscher, Bernhard},
	month = {Jan},
	pages = {31-37},
	type = {Article},
	abstract = {A simple NMR method is presented for the identification and assignment of phosphorylated serine and threonine residues in C-13- or C-13/N-15-labeled proteins. By exploiting modest (similar to 5 Hz) 2- and 3-bond C-13-P-31 scalar couplings, the aliphatic H-1-C-13 signals from phosphoserines and phosphothreonines can be detected selectively in a P-31 spin-echo difference constant time H-1-C-13 HSQC spectrum. Inclusion of the same P-31 spin-echo element within the C-13 frequency editing period of an intraHNCA or HN(CO)CA experiment allows identification of the amide H-1(N) and N-15 signals of residues (i) for which C-13(alpha)(i) or C-13(alpha)(i - 1), respectively, are coupled to a phosphate. Furthermore, P-31 resonance assignments can be obtained by applying selective low power cw P-31 decoupling during the spin-echo period. The approach is demonstrated using a PNT domain containing fragment of the transcription factor Ets-1, phosphorylated in vitro at Thr38 and Ser41 with the MAP kinase ERK2.},
	keywords = {ASSIGNMENT, CENTER-DOT-OP, CONSTANT-TIME, Ets-1, MAP kinase, NUCLEIC-ACIDS, OP HYDROGEN-BONDS, P-31-C-13 scalar coupling, Phosphoprotein, PHOSPHORYLATION, POINTED DOMAIN, PROTEIN, QUANTITATIVE J-CORRELATION, RESONANCE, SCALAR COUPLINGS, TRANSCRIPTION FACTOR},
	isbn = {0925-2738},
	url = {<Go to ISI>://000261411100004},
	author = {McIntosh, L. P. and Kang, H. S. and Okon, M. and Nelson, M. L. and Graves, B. J. and Brutscher, B.}
}
@article {2120,
	title = {Identification and structural characterization of a CBP/p300-binding domain from the ETS family transcription factor GABP alpha},
	journal = {Journal of Molecular Biology},
	volume = {377},
	number = {3},
	year = {2008},
	note = {ISI Document Delivery No.: 293ZPTimes Cited: 5Cited Reference Count: 60Kang, Hyun-Seo Nelson, Mary L. Mackereth, Cameron D. Scharpf, Manuela Graves, Barbara J. McIntosh, Lawrence P.},
	month = {Mar},
	pages = {636-646},
	type = {Article},
	abstract = {Using NMR spectroscopy, we identified and characterized a previously unrecognized structured domain near the N-terminus (residues 35-121) of the ETS family transcription factor GABP alpha. The monomeric domain folds as a five-stranded beta-sheet crossed by a distorted helix. Although globally resembling ubiquitin, the GABP(x fragment differs in its secondary structure topology and thus appears to represent a new protein fold that we term the OST (On-SighT) domain. The surface of the GABP alpha OST domain contains two predominant clusters of negatively-charged residues suggestive of electrostatically driven interactions with positively-charged partner proteins. Following a best-candidate approach to identify such a partner, we demonstrated through NMR-monitored titrations and glutathione S-transferase pulldown assays that the OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300. This provides a direct structural link between GABP and a central component of the transcriptional machinery. (C) 2008 Elsevier Ltd. All rights reserved.},
	keywords = {BACKBONE DYNAMICS, C-13-LABELED PROTEINS, CREB-BINDING-PROTEIN, ESCHERICHIA-COLI, HIGH-RESOLUTION, HYPOXIA-INDUCIBLE FACTOR-1-ALPHA, LARGER PROTEINS, NEUROMUSCULAR-JUNCTION, NMR, NMR EXPERIMENTS, protein-protein interaction, RESIDUAL DIPOLAR COUPLINGS, SPECTROSCOPY, TRANSCRIPTION FACTOR, UBIQUITIN},
	isbn = {0022-2836},
	url = {<Go to ISI>://000255374200006},
	author = {Kang, H. S. and Nelson, M. L. and Mackereth, C. D. and Scharpf, M. and Graves, B. J. and McIntosh, L. P.}
}
@article {1518,
	title = {Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast},
	journal = {Cell},
	volume = {126},
	number = {3},
	year = {2006},
	note = {ISI Document Delivery No.: 075KITimes Cited: 111Cited Reference Count: 68Parsons, Ainslie B. Lopez, Andres Givoni, Inmar E. Williams, David E. Gray, Christopher A. Porter, Justin Chua, Gordon Sopko, Richelle Brost, Renee L. Ho, Cheuk-Hei Wang, Jiyi Ketela, Troy Brenner, Charles Brill, Julie A. Fernandez, G. Esteban Lorenz, Todd C. Payne, Grego S. Ishihara, Satoru Ohya, Yoshikazu Andrews, Brenda Hughes, Timothy R. Frey, Brendan J. Graham, Todd R. Andersen, Raymond J. Boone, Charles},
	month = {Aug},
	pages = {611-625},
	type = {Article},
	abstract = {Discovering target and off-target effects of specific compounds is critical to drug discovery and development. We generated a compendium of "chemical-genetic interaction" profiles by testing the collection of viable yeast haploid deletion mutants for hypersensitivity to 82 compounds and natural product extracts. To cluster compounds with a similar mode-of-action and to reveal insights into the cellular pathways and proteins affected, we applied both a hierarchical clustering and a factorgram method, which allows a gene or compound to be associated with more than one group. In particular, tamoxifen, a breast cancer therapeutic, was found to disrupt calcium homeostasis and phosphatidylserine (PS) was recognized as a target for papuamide B, a cytotoxic lipopeptide with anti-HIV activity. Further, the profile of crude extracts resembled that of its constituent purified natural product, enabling detailed classification of extract activity prior to purification. This compendium should serve as a valuable key for interpreting cellular effects of novel compounds with similar activities.},
	keywords = {1, 3-BETA-D-GLUCAN SYNTHASE, BREAST-CANCER CELLS, DELETION MUTANTS, drug, EXPRESSION, GENOME-WIDE ANALYSIS, HAPLOINSUFFICIENCY, INDUCED, SACCHAROMYCES-CEREVISIAE, THEONELLA-SWINHOEI, TRANSCRIPTION FACTOR},
	isbn = {0092-8674},
	url = {<Go to ISI>://000239883400019},
	author = {Parsons, A. B. and Lopez, A. and Givoni, I. E. and Williams, D. E. and Gray, C. A. and Porter, J. and Chua, G. and Sopko, R. and Brost, R. L. and Ho, C. H. and Wang, J. Y. and Ketela, T. and Brenner, C. and Brill, J. A. and Fernandez, G. E. and Lorenz, T. C. and Payne, G. S. and Ishihara, S. and Ohya, Y. and Andrews, B. and Hughes, T. R. and Frey, B. J. and Graham, T. R. and Andersen, R. J. and Boone, C.}
}
@article {934,
	title = {Diversity in structure and function of the Ets family PNT domains},
	journal = {Journal of Molecular Biology},
	volume = {342},
	number = {4},
	year = {2004},
	note = {ISI Document Delivery No.: 855WLTimes Cited: 17Cited Reference Count: 86},
	month = {Sep},
	pages = {1249-1264},
	type = {Article},
	abstract = {The PNT (or Pointed) domain, present within a subset of the Ets family of transcription factors, is structurally related to the larger group of SAM domains through a common tertiary arrangement of four alpha-helices. Previous studies have shown that, in contrast to the PNT. domain from Tel, this domain from Ets-1 contains an additional N-terminal helix integral to its folded structure. To further investigate the structural plasticity of the PNT domain, we have used NMR spectroscopy to characterize this domain from two additional Ets proteins, Erg and GABPalpha. These studies both define the conserved and variable features of the PNT domain, and demonstrate that the additional N-terminal helix is also present in GABPa, but not Erg. In contrast to Tel and Yan, which self-associate to form insoluble polymers, we also show that the isolated PNT domains from Ets-1, Ets-2, Erg, Fli-1, GABPalpha, and Pnt-P2 are monomeric in solution. Furthermore, these soluble PNT domains do not associate in any pair-wise combination. Thus these latter Ets family PNT domains likely mediate interactions with additional components of the cellular signaling or transcriptional machinery. (C) 2004 Elsevier Ltd. All rights reserved.},
	keywords = {ALPHA-MOTIF SAM, ASSIGNMENT, AUTOMATED, CHEMICAL-SHIFT, DIPOLAR COUPLINGS, ENDOTHELIAL-CELL DIFFERENTIATION, Erg, GABP, GENE, NMR-SPECTRA, POINTED DOMAIN, protein interactions, PROTEIN-KINASE, SAM domain, TRANSCRIPTION FACTOR},
	isbn = {0022-2836},
	url = {<Go to ISI>://000224005500015},
	author = {Mackereth, C. D. and Scharpf, M. and Gentile, L. N. and Macintosh, S. E. and Slupsky, C. M. and McIntosh, L. P.}
}
@article {541,
	title = {Inhibitory module of Ets-1 allosterically regulates DNA binding through a dipole-facilitated phosphate contact},
	journal = {Journal of Biological Chemistry},
	volume = {277},
	number = {3},
	year = {2002},
	note = {ISI Document Delivery No.: 514CWTimes Cited: 21Cited Reference Count: 50},
	month = {Jan},
	pages = {2225-2233},
	type = {Article},
	abstract = {DNA binding of the transcription factor Ets-1 is negatively regulated by three inhibitory helices that lie near the ETS domain. The current model suggests that this negative regulation, termed autoinhibition, is caused by the energetic expense of a DNA-induced structural transition that includes the unfolding of one inhibitory helix. This report investigates the role of helix H1 of the ETS domain in the autoinhibition mechanism. Previous structural studies modeled the inhibitory helices packing together and connecting with helix H1, suggesting a role of this helix in the configuration of an inhibitory module. Recently, high-resolution structures of the ETS domain-DNA interface indicate that the N terminus of helix H1 directly contacts DNA. The contact, which is augmented by the macrodipole of helix H1, consists of a hydrogen bond between the amide NH of leucine 337 in helix HI and the oxygen of a corresponding phosphate. We propose that this hydrogen bond positions helix H1 to be a link between autoinhibition and DNA binding. Four independent approaches tested this hypothesis. First, the hydrogen bond was disrupted by removal of the phosphate in a missing phosphate analysis. Second, base pairs that surround the helix HI-contacting phosphate and appear to dictate DNA backbone conformation were mutated. Next, a hydrophobic residue in helix H1 that is expected to position the N terminus of the helix was altered. Finally, a residue on the surface of helix 111 that may contact the inhibitory elements was changed. In each case DNA binding and autoinhibition was affected. Taken together, the results demonstrate the role of the dipole-facilitated phosphate contact in DNA binding. Furthermore, the findings support a model in which helix H1 links the inhibitory elements to the ETS domain. We speculate that this helix, which is conserved in all Ets proteins, provides a common route to regulation.},
	keywords = {ALPHA-HELIX, AUTO-INHIBITION, COMPLEX, DOMAIN, FACTORS ELK-1, INDIRECT READOUT, MURINE ETS-1, PROTEINS, RECOGNITION, TRANSCRIPTION FACTOR},
	isbn = {0021-9258},
	url = {<Go to ISI>://000173421300083},
	author = {Wang, H. and McIntosh, L. P. and Graves, B. J.}
}
@article {480,
	title = {Oligomerization-dependent association of the SAM domains from Schizosaccharomyces pombe Byr2 and Ste4},
	journal = {Journal of Biological Chemistry},
	volume = {277},
	number = {42},
	year = {2002},
	note = {ISI Document Delivery No.: 605EATimes Cited: 21Cited Reference Count: 46},
	month = {Oct},
	pages = {39585-39593},
	type = {Article},
	abstract = {SAM (sterile alpha motif) domains are protein-protein interaction modules found in a large number of regulatory proteins. Byr2 and Ste4 are two SAM domain-containing proteins in the mating pheromone response pathway of the fission yeast, Schizosaccharomyces pombe. Byr2 is a mitogen-activated protein kinase kinase kinase that is regulated by Ste4. Tu et al (Tu, H., Barr, M., Dong, D. L., and Wigler, M. (1997) Mol. Cell. Biol. 17, 5876-5887) showed that the isolated SAM domain of Byr2 binds a fragment of Ste4 that contains both a leucine zipper (Ste4-LZ) domain as well as a SAM domain, suggesting that Byr2-SAM and Ste4-SAM may form a hetero-oligomer. Here, we show that the individual SAM domains of Ste4 and Byr2 are monomeric at low concentrations and bind to each other in a 1:1 stoichiometry with a relatively weak dissociation constant of 56 +/- 3 mum. Inclusion of the Ste4-LZ domain, which determines the oligomeric state of Ste4, has a dramatic effect on binding affinity, however. We find that the Ste4-LZ domain is trimeric and, when included with the Ste4-SAM domain, yields a 3:1 Ste4-LZ-SAM:Byr2-SAM complex with a tight dissociation constant of 19 +/- 4 nm. These results suggest that the Ste4-LZ-SAM protein may recognize multiple binding sites on Byr2-SAM, indicating a new mode of oligomeric organization for SAM domains. The fact that high affinity binding occurs only with the addition of an oligomerization domain suggests that it may be necessary to include ancillary oligomerization modules when searching for binding partners of SAM domains.},
	keywords = {CRYSTAL-STRUCTURE, HUMAN LEUKEMIA, IDENTIFICATION, KINASE, LAC REPRESSOR, PROTEIN-KINASE, RECEPTOR, TEL, TRANSCRIPTION FACTOR, TYROSINE, YEAST},
	isbn = {0021-9258},
	url = {<Go to ISI>://000178662500069},
	author = {Ramachander, R. and Kim, C. A. and Phillips, M. L. and Mackereth, C. D. and Thanos, C. D. and McIntosh, L. P. and Bowie, J. U.}
}
@article {4406,
	title = {Assigning the NMR spectra of aromatic amino acids in proteins: analysis of two Ets pointed domains},
	journal = {Biochemistry and Cell Biology-Biochimie Et Biologie Cellulaire},
	volume = {76},
	number = {2-3},
	year = {1998},
	note = {ISI Document Delivery No.: 157QRTimes Cited: 11Cited Reference Count: 34},
	pages = {379-390},
	type = {Article},
	abstract = {The measurement of interproton nuclear Overhauser enhancements (NOEs) and dihedral angle restraints of aromatic amino acids is a critical step towards determining the structure of a protein. The complete assignment of the resonances from aromatic rings and the subsequent resolution and identification of their associated NOEs, however, can be a difficult task. Shown here is a strategy for assigning the H-1,C-13, and N-15 signals from the aromatic side chains of histidine, tryptophan, tyrosine, and phenylalanine using a suite of homo- and hetero-nuclear scalar and NOE correlation experiments, as well as selective deuterium isotope labelling. In addition, a comparison of NOE information obtained from homonuclear NOE spectroscopy (NOESY) and C-13-edited NOESY - heteronuclear single quantum correlation experiments indicates that high-resolution homonuclear two-dimensional NOESY spectra of selectively deuterated proteins are invaluable for obtaining distance restraints to the aromatic residues.},
	keywords = {ACTIVE-SITE, ANGLE, aromatic residue, BACKBONE H-1, C-13-LABELED PROTEINS, CHEMICAL-SHIFTS, dihedral, DNA-BINDING, HETERONUCLEAR NMR, HISTIDINE-RESIDUES, MAGNETIC-RESONANCE SPECTROSCOPY, NMR assignment, NOE, pH titration, PHENYLALANINE RESIDUES, TRANSCRIPTION FACTOR},
	isbn = {0829-8211},
	url = {<Go to ISI>://000078073600026},
	author = {Slupsky, C. M. and Gentile, L. N. and McIntosh, L. P.}
}
