@article {2141,
	title = {The affinity of Ets-1 for DNA is modulated by phosphorylation through transient interactions of an unstructured region},
	journal = {Journal of Molecular Biology},
	volume = {382},
	number = {4},
	year = {2008},
	note = {ISI Document Delivery No.: 359YPTimes Cited: 3Cited Reference Count: 42Lee, Gregory M. Pufall, Miles A. Meeker, Charles A. Kang, Hyun-Seo Graves, Barbara J. McIntosh, Lawrence P.},
	month = {Oct},
	pages = {1014-1030},
	type = {Article},
	abstract = {Binding of the transcription factor Ets-1 to DNA is allosterically regulated by a serine-rich region (SRR) that modulates the dynamic character of the adjacent structured DNA-binding ETS domain and its flanking autoinhibitory elements. Multi-site phosphorylation of the flexible SRR in response to Ca2+ signaling mediates variable regulation of Ets-1 DNA-binding affinity. In this study, we further investigated the mechanism of this regulation. First, thermal and urea denaturation experiments demonstrated that phosphorylation of the predominantly unstructured SRR imparts enhanced thermodynamic stability on the well-folded ETS domain and its inhibitory module. We next identified a minimal fragment (residues 279-440) that exhibits both enhanced autoinhibition of Ets-1 DNA-binding and allosteric reinforcement by phosphorylation. To test for intramolecular interactions between the SRR and the rest of the fragment that were not detectable by H-1-H-1 NOE measurements, paramagnetic relaxation enhancements were performed using Cu2+ bound to the N-terminal ATCUN motif. Increased relaxation detected for specific amide and methyl groups revealed a preferential interaction surface for the flexible SRR extending from the inhibitory module to the DNA-binding interface. Phosphorylation enhanced the localization of the SRR to this surface. We therefore hypothesize that the positioning of the SRR at the DNA-binding interface and its role in shifting Ets-1 to an inhibited conformation are linked. In particular, transient interactions dampen the conformational flexibility of the ETS domain and inhibitory module required for high-affinity binding, as well as possibly occlude the DNA interaction site. Surprisingly, the phosphorylation-dependent effects were relatively insensitive to changes in ionic strength, suggesting that electrostatic forces are not the dominant mechanism for mediating these interactions. The results of this study highlight the role of flexibility and transient binding in the variable regulation of Ets-1 activity. (C) 2008 Elsevier Ltd. All rights reserved.},
	keywords = {allosteric regulation, ATCUN MOTIF, AUTOINHIBITION, BINDING, CHEMICAL-SHIFTS, DISORDERED PROTEIN, DOMAIN, DYNAMICS, GROUP HYDROGEN-EXCHANGE, NMR, paramagnetic relaxation, PARAMAGNETIC RELAXATION ENHANCEMENT, protein dynamics, SPECTROSCOPY, transcription},
	isbn = {0022-2836},
	url = {<Go to ISI>://000260024500017},
	author = {Lee, G. M. and Pufall, M. A. and Meeker, C. A. and Kang, H. S. and Graves, B. J. and McIntosh, L. P.}
}
@article {750,
	title = {DFT calculation of core-electron binding energies},
	journal = {Journal of Electron Spectroscopy and Related Phenomena},
	volume = {133},
	number = {1-3},
	year = {2003},
	note = {ISI Document Delivery No.: 754ZWTimes Cited: 40Cited Reference Count: 70},
	month = {Nov},
	pages = {69-76},
	type = {Article},
	abstract = {A total of 59 core-electron binding energies (CEBEs) were studied with the Amsterdam Density Functional Program (ADF) program and compared with the observed values. The results indicate that a polarized triple-zeta basis set of Slater-type orbitals is adequate for routine assessment of the performance of each method of computation. With such a basis set, seven density functionals were tested. In addition, the performance of 21 energy density functionals were computed from the density calculated with the statistical average of orbital potentials (SAOP). Among all the choices tested, the best density functional for core-electron binding energies of C to F turns out to be the combination of Perdew-Wang (1986) functional for exchange and the Perdew-Wang (1991) functional for correlation, confirming earlier studies based on contracted Gaussian-type orbitals. For this best functional, five Slater-type orbital basis sets were examined, ranging from polarized double-zeta quality to the largest set available in the ADF package. For the best functional with the best basis set, the average absolute deviation (AAD) of the calculated value from experiment is only 0.16 eV (C) 2003 Elsevier B.V. All rights reserved.},
	keywords = {ADF, BASIS-SETS, CEBE, CHEMICAL-SHIFTS, CONJUGATED, core-electron binding energy, CORRECT ASYMPTOTIC-BEHAVIOR, DENSITY-FUNCTIONAL CALCULATION, DFF, ESCA, EXCHANGE-ENERGY, GENERALIZED GRADIENT APPROXIMATION, MOLECULAR CALCULATIONS, MOLECULES, PHOTOELECTRON-SPECTROSCOPY, X-RAY-EMISSION, XPS},
	isbn = {0368-2048},
	url = {<Go to ISI>://000187364200010},
	author = {Takahata, Y. and Chong, D. P.}
}
@article {496,
	title = {Site-specific characterization of the association of xylooligosaccharides with the CBM13 lectin-like xylan binding domain from Streptomyces lividans xylanase 10A by NMR spectroscopy},
	journal = {Biochemistry},
	volume = {41},
	number = {13},
	year = {2002},
	note = {ISI Document Delivery No.: 538ARTimes Cited: 12Cited Reference Count: 53},
	month = {Apr},
	pages = {4255-4263},
	type = {Article},
	abstract = {Endo-beta-1,4-xylanase 10A (Xyn10A) from Streptomyces lividans includes an N-terminal catalytic module and a 130-residue C-terminal family 13 carbohydrate-binding module (CBM13). This latter domain adopts a beta-trefoil structure with three potential binding sites (alpha, beta, and gamma) for a variety of small sugars, xylooligosaccharides, and xylan polymers. To investigate the role of this multivalency in carbohydrate binding, we have used NMR spectroscopy to characterize the interaction of isolated CBM13 with a series of sugars. We have assigned resonances from the main chain nuclei of CBM13 using heteronuclear NMR experiments. Analysis of N-15 NMR relaxation data using the extended model free formalism reveals that CBM13 tumbles as an oblate ellipsoid (D-\/D-perpendicular to = 0.80+/-0.02) and that its backbone is relatively rigid on the sub-nanosecond time scale. In particular, the three binding sites show no distinct patterns of increased internal mobility. Ligand-induced chemical shift changes in the H-1-N-15 HSQC spectra of CBM13 were monitored as a function of increasing concentrations Of L-arabinose, lactose, D-xylose, xylobiose, xylotetraose, and xylohexaose. Patterns of shift perturbations for well-resolved resonances demonstrate that all of these sugars associate independently with the three binding sites of CBM13. On the basis of the site-specific association constants derived from a quantitative analysis of these titration data, we show that L-arabinose, lactose, and D-xylose preferentially bind to the alpha site of CBM13, xylobiose binds equally well to all three sites, and xylotetraose and xylohexaose prefer binding to the beta site. Inspection of the crystallographic structure of CBM13 [Notenboom, V., Boraston, A. B., Williams, S. J., Kilburn, D. G., and Rose, D. R. (2002) Biochemistry 41, 4246-4254] provides a rationalization for these results.},
	keywords = {BACKBONE DYNAMICS, CELLULOMONAS-FIMI CENC, CHEMICAL-SHIFTS, CRYSTAL-STRUCTURES, E-86, IMPROVED SENSITIVITY, INSOLUBLE LIGANDS, LIGAND SPECIFICITY, NUCLEAR-MAGNETIC-RESONANCE, OLIVACEOVIRIDIS, ROTATIONAL DIFFUSION},
	isbn = {0006-2960},
	url = {<Go to ISI>://000174792300010},
	author = {Scharpf, M. and Connelly, G. P. and Lee, G. M. and Boraston, A. B. and Warren, R. A. J. and McIntosh, L. P.}
}
@article {4971,
	title = {Hyperfine structure in the rotational spectrum of GaF: A comparison of experimental and calculated spin-rotation and electric field gradient tensors},
	journal = {Journal of Molecular Spectroscopy},
	volume = {204},
	number = {2},
	year = {2000},
	note = {ISI Document Delivery No.: 380JBTimes Cited: 18Cited Reference Count: 74},
	month = {Dec},
	pages = {184-194},
	type = {Article},
	abstract = {{The high-resolution pure rotational spectrum of Gal; has been measured using a Balle-Flygare-type Fourier transform spectrometer. improved nuclear quadrupolar coupling constants and rotational constants have been obtained along with the first reported fluorine spin-rotation constant for gallium fluoride, C-I ((GaF)-Ga-69-F-19},
	keywords = {ab initio calculations, CHEMICAL-SHIFTS, CONSTANTS, electric field gradient tensors, FINITE BASIS-SET, gallium fluoride, group-13 fluorides, HARTREE-FOCK CALCULATIONS, hyperfine structure, LASER-ABLATION, MICROWAVE-SPECTRUM, MILLIMETER, MOLECULES, MONOFLUORIDE, NMR, nuclear magnetic shielding tensors, quadrupolar coupling, QUADRUPOLE COUPLING-CONSTANTS, rotational spectroscopy, SPECTROSCOPY, spin-rotation constants},
	isbn = {0022-2852},
	url = {<Go to ISI>://000165697100003},
	author = {Wasylishen, R. E. and Bryce, D. L. and Evans, C. J. and Gerry, M. C. L.}
}
@article {4828,
	title = {Lattice energy-minimization calculation in the further investigation of XRD and NMR studies of zeolite frameworks},
	journal = {Chemistry of Materials},
	volume = {12},
	number = {2},
	year = {2000},
	note = {ISI Document Delivery No.: 287JNTimes Cited: 6Cited Reference Count: 29},
	month = {Feb},
	pages = {336-342},
	type = {Article},
	abstract = {A knowledge of the local structure of zeolite frameworks is an important prerequisite for a detailed and quantitative understanding of e.g, catalytic processes. In the present work the sensitivity of 1D and 2D MAS NMR experiments to the local order of framework T atoms and energy-minimization calculations for the geometrical analysis of the complete zeolite framework structure are combined to provide a most detailed view of their structural properties. Correlations of the chemical shifts, delta(Si-29), with the mean distance between Si and its neighboring Si T atoms, (d) over bar(Si-Si), are presented for the three materials MFI, MEL, and MTT. Excellent agreement between experimental and computational results was obtained. In the case of MFI, this most complicated structure was used to demonstrate the viability of the method. The MTT and MEL systems showed that it is possible to deduce the unique assignment of the NMR spectra from energy-minimized structures when it is not possible using the available structural data from X-ray structure analysis. Taken together, all three investigations also demonstrate that improved structural data are obtained from lattice energy minimizations compared to those from Rietveld analysis as long as the topology of the framework is known.},
	keywords = {3-DIMENSIONAL BONDING CONNECTIVITIES, CHEMICAL-SHIFTS, HIGH-TEMPERATURE, NUCLEAR MAGNETIC-RESONANCE, ORTHORHOMBIC FRAMEWORK, SI-29 MAS-NMR, SILICA POLYMORPHS, SOLID-STATE NMR, X-RAY-DIFFRACTION, ZSM-11},
	isbn = {0897-4756},
	url = {<Go to ISI>://000085502900017},
	author = {Hochgrafe, M. and Gies, H. and Fyfe, C. A. and Feng, Y. and Grondey, H.}
}
@article {4217,
	title = {Accurate density functional calculations of core XPS spectra: simulating chemisorption and intermolecular effects on real systems?},
	journal = {Journal of Electron Spectroscopy and Related Phenomena},
	volume = {88},
	year = {1998},
	note = {ISI Document Delivery No.: ZK716Times Cited: 4Cited Reference Count: 297th International Conference on Electron SpectroscopySEP 08-12, 1997CHIBA, JAPAN},
	month = {Mar},
	pages = {657-663},
	type = {Proceedings Paper},
	abstract = {We present recent methods based on the density functional theory of electronic structures in which computed CEBEs are in remarkable agreement with experiment, with average absolute deviations from experiment of the order of 0.2-0.3 eV. These procedures take advantage of the speed and CPU time scaling of DFT as a function of system size: they are computationally tractable, even for surprisingly large systems such as condensed phases or molecules chemisorbed on metallic surfaces. Two examples are examined herein to illustrate this point. (C) 1998 Elsevier Science B.V.},
	keywords = {APPROXIMATION, BASIS-SET, CHEMICAL-SHIFTS, ELECTRON BINDING-ENERGIES, GAS},
	isbn = {0368-2048},
	url = {<Go to ISI>://000073354200111},
	author = {Bureau, C. and Chong, D. P.}
}
@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.}
}
@article {3799,
	title = {Characterization of a buried neutral histidine residue in Bacillus circulans xylanase: NMR assignments, pH titration, and hydrogen exchange},
	journal = {Protein Science},
	volume = {5},
	number = {11},
	year = {1996},
	note = {ISI Document Delivery No.: VQ786Times Cited: 41Cited Reference Count: 63},
	month = {Nov},
	pages = {2319-2328},
	type = {Article},
	abstract = {Bacillus circulans xylanase contains two histidines, one of which (His 156) is solvent exposed, whereas the other (His 149) is buried within its hydrophobic core. His 149 is involved in a network of hydrogen bonds with an internal water and Ser 130, as well as a potential weak aromatic-aromatic interaction with Tyr 105. These three residues, and their network of interactions with the bound water, are conserved in four homologous xylanases. To probe the structural role played by His 149, NMR spectroscopy was used to characterize the histidines in BCX. Complete assignments of the H-1, C-13, and N-15 resonances and tautomeric forms of the imidazole rings were obtained from two-dimensional heteronuclear correlation experiments. An unusual spectroscopic feature of BCX is a peak near 12 ppm arising from the nitrogen bonded H-1(epsilon 2) of His 149. Due to its solvent inaccessibility and hydrogen bonding to an internal water molecule, the exchange rate of this proton (4.0 X 10(-5) s(-1) at pH* 7.04 and 30 degrees C) is retarded by > 10(6)-fold relative to an exposed histidine. The pK(a) of His 156 is unperturbed at similar to 6.5, as measured from the pH dependence of the N-15- and H-1-NMR spectra of BCX. In contrast, His 149 has a pK(a) < 2.3, existing in the neutral (NH)-H-epsilon 2 tautomeric state under all conditions examined. BCX unfolds at low pH and 30 degrees C, and thus His 149 is never protonated significantly in the context of the native enzyme. The structural importance of this buried histidine is confirmed by the destablizing effect of substituting a phenylalanine or glutamine at position 149 in BCX.},
	keywords = {ACTIVE-SITE, ALPHA-HELICES, AQUEOUS-SOLUTION, CHEMICAL-SHIFTS, ESCHERICHIA-COLI, GLYCOSYL HYDROLASES, H-1-NMR SPECTRUM, HYDROGEN-DEUTERIUM EXCHANGE, IMIDAZOLE, internal water, L-ALA-OH, NUCLEAR MAGNETIC-RESONANCE, pH titration, pK(alpha), PROTEIN HYDRATION, protein stability},
	isbn = {0961-8368},
	url = {<Go to ISI>://A1996VQ78600018},
	author = {Plesniak, L. A. and Connelly, G. P. and Wakarchuk, W. W. and McIntosh, L. P.}
}
@article {3708,
	title = {Interaction of soluble cellooligosaccharides with the N-terminal cellulose-binding domain of Cellulomonas fimi CenC .2. NMR and ultraviolet absorption spectroscopy},
	journal = {Biochemistry},
	volume = {35},
	number = {44},
	year = {1996},
	note = {ISI Document Delivery No.: VR098Times Cited: 68Cited Reference Count: 46},
	month = {Nov},
	pages = {13895-13906},
	type = {Article},
	abstract = {The N-terminal cellulose-binding domain (CBDN1) from Cellulomonas fimi beta-1,4-glucanase CenC binds amorphous but not crystalline cellulose. To investigate the structural and thermodynamic bases of cellulose binding, NMR and difference ultraviolet absorbance spectroscopy were used in parallel with calorimetry (Tomme, P., Creagh, A. L., Kilburn, D. G., \& Haynes, C. A., (1996) Biochemistry 35, 13885-13894] to characterize the interaction of soluble cellooligosaccharides with CBDN1 Association constants, determined from the dependence of the amide H-1 and N-15 chemical shifts of CBDN1 upon added sugar, increase from 180 +/- 60 M(-1) for cellotriose to 4 200 +/- 720 M(-1) for cellotetraose, 34 000 +/- 7 600 M(-1) for cellopentaose, and an estimate of 50 000 M(-1) for cellohexaose. This implies that the CBDN1 cellulose-binding site spans approximately five glucosyl units, On the basis of the observed patterns of amide chemical shift changes, the cellooligosaccharides bind along a five-stranded beta-sheet that forms a concave face of the jelly-roll beta-sandwich structure of CBDN1. This beta-sheet contains a strip of hydrophobic side chains flanked on both sides by polar residues, NMR and difference ultraviolet absorbance measurements also demonstrate that tyrosine, but not tryptophan, side chains may be involved in oligosaccharide binding. These results lead to a model in which CBDN1 interacts with soluble cellooligosaccharides and, by inference, with single polysaccharide chains in regions of amorphous cellulose, primarily through hydrogen bonding to the equatorial hydroxyl groups of the pyranose rings. Van der against the apolar side chains may augment binding. CBDN1 stands in marked contrast to previously characterized CBDs that absorb to crystalline cellulose via a flat binding surface dominated by exposed aromatic rings.},
	keywords = {BACKBONE H-1, CHEMICAL-SHIFTS, ESCHERICHIA-COLI, EXPRESSION, HIGH-LEVEL, NUCLEAR-MAGNETIC-RESONANCE, PROTEIN, REESEI CELLOBIOHYDROLASE-I, SEQUENCE, TRICHODERMA-REESEI, TRYPTOPHAN RESIDUES},
	isbn = {0006-2960},
	url = {<Go to ISI>://A1996VR09800005},
	author = {Johnson, P. E. and Tomme, P. and Joshi, M. D. and McIntosh, L. P.}
}
@article {3800,
	title = {Secondary structure and NMR assignments of Bacillus circulans xylanase},
	journal = {Protein Science},
	volume = {5},
	number = {6},
	year = {1996},
	note = {ISI Document Delivery No.: UP617Times Cited: 23Cited Reference Count: 74},
	month = {Jun},
	pages = {1118-1135},
	type = {Article},
	abstract = {Bacillus circulans xylanase (BCX) is a member of the family of low molecular weight endo-beta-(1,4)-xylanases. The main-chain H-1, C-13, and N-15 resonances of this 20.4-kDa enzyme were assigned using heteronuclear NMR experiments recorded on a combination of selectively and uniformly labeled protein samples. Using chemical shift, NOE, J coupling, and amide hydrogen exchange information, 14 beta-strands, arranged in a network of three beta-sheets, and a single cy-helix were identified in BCX. The NMR-derived secondary structure and beta-sheet topology agree closely with that observed in the crystal structure of this protein. The H-N of Ile 118 has a strongly upfield-shifted resonance at 4.03 ppm, indicative of a potential amide-aromatic hydrogen bond to the indole ring of Trp 71. This interaction, which is conserved in all low molecular weight xylanases of known structure, may play an important role in establishing the active site conformation of these enzymes. Following hen egg white and bacteriophage T4 lysozymes, B. circulans xylanase represents the third family of beta-glycanases for which extensive NMR assignments have been reported. These assignments provide the background for detailed studies of the mechanism of carbohydrate recognition and hydrolysis by this bacterial xylanase.},
	keywords = {amide-aromatic hydrogen bond, AMINO-ACID, ASSIGNMENTS, BACKBONE AMIDE, beta-glycanase, C-13-LABELED PROTEINS, C-ALPHA, chemical shift index, CHEMICAL-SHIFTS, COUPLING-CONSTANTS, LARGER PROTEINS, NMR, NUCLEAR-MAGNETIC-RESONANCE, SECONDARY STRUCTURE, SIDE-CHAIN RESONANCES, SOLVENT, SUPPRESSION, XYLANASE},
	isbn = {0961-8368},
	url = {<Go to ISI>://A1996UP61700014},
	author = {Plesniak, L. A. and Wakarchuk, W. W. and McIntosh, L. P.}
}
