NMR Facility Operations at NYSBC © NYSBC 7 Sep 2006 1 NYSBC Introduction The New York Structural Biology Center is an independent corporation acting as a resource facility for its ten Member Institutions. Albert Einstein College of Medicine of Yeshiva University City University of New York Columbia University Memorial Sloan Kettering Cancer Center Mount Sinai School of Medicine New York University Rockefeller University State University of New York Wadsworth Center, NYS Dept. Health/HRI Weill Cornell Medical College of Cornell University © NYSBC 7 Sep 2006 2 NYSBC operates cryo-electron microscopy resources, two beam lines at NSLS/BNL, and a large NMR facility. There are investigator- headed laboratories, including the protein preparation lab for the New York Consortium for Membrane Protein Structure, funded by NIGMS-PSI. The resources are predominantly available to the Member Institutions, including investigators: Aneel Aggarwal Mark E. Girvin Carlos A. Meriles Ruth Stark David Allis Paul Gottlieb Gaetano Montelione Thomas Szyperski Clay Bracken Steve Greenbaum Tom Muir Maria Luisa Tasayco Esther Breslow Clare Grey Fred Naider Peter Tonge David Cowburn Swapna V. Gurla Arthur G. Palmer Iban Ubarretxena-Belandia Samuel J. Danishefsky Griselda Hernandez Dinshaw Patel Chunyu Wang Seth Darst Barry H. Honig Brian Phillips Milton H. Werner David Eliezer Alexej Jerschow Daniel Raleigh Stanislaus Wong John Spencer Evans Tarun Kapoor Thomas P. Sakmar Lei Zeng Jack H. Freed David LeMaster Nicole Sampson Ming-Ming Zhou Nicholas Geacintov Chin Lin Alexander Shekhtman Martine Ziliox Ranajeet Ghose Min Lu Samuel Singer Lane Gilchrist Ann McDermot Steven Smith Investigators listed are both direct users of the Facility and those collaborating with direct users. Users from outside the NYSBC member institutions are co-PIs or users of the 900 MHz Structural Biology Resource funded by NIH GM-66354 © NYSBC 7 Sep 2006 3 NMR Resources Approximately 35 research groups with about 90 operators use the instruments shown in tables below, plus 700, 600 & 500 systems. 0.1% 2mM Sucrose Spectrometer Probe Ethylbenzene Anomeric 1H S/N S/N 900 #1 cp TCI 8707:1 1006:1 900 US2 #2 TCI 2440:1 495:1 800 US2 #1 cp TCI 7450:1 915:1 800 US2 #2 cp TCI 9011:1 851:1 800 conv cp TXI 7050:1 940:1 90% B1 LowerTemp. Probes Tuning Fields, kHz. S/N(1,2) Homogeneity Range, oC(3) 750 MHz Range, MHz 1H/13C/15N Volume 10kHz/15kHz HXY X: 150-200 13C 160:1 120/50/50 35-40 μl -40/-30 wide bore Y:70-130 15N: 30:1 HFX 13C 240:1 X:35-225 120/50/50 35-40 μl -40/-30 wide bore 15N: 30:1 HCN 13C 180:1 standard narrowband 120/50/50 35-40 μl -15/-5 15N: 30:1 bore HRMAS 90o pulse: narrowband 1H : 250:1 35-40 μl n.a. HCND 6μs/8μs/15μs (1) CPMAS probes: sensitivity is measured on a fully packed natural abundance glycine sample, 4 scans, 1H-13C cross polarization experiment. (2) HRMAS probes: sensitivity is measured on 60 μ volume sample of 0.1% ethylbenzene solution in CDCl3. (3) These probes have reliably achieved the sample temperatures at the indicated spinning speeds using either an Airjet cooler or Bruker Cooling unit as the source of cold gas. © NYSBC 7 Sep 2006 4 Spectrometer Performance Heteronuclear spin-echo difference test is run on a sample The lineshape stability test is run on a non-spinning containing 500 mM Sucrose in 100% D2O. In this test the sample of 0.3% CHCl3 in Acetone-D6. The lineshape is 12C center-band of the sucrose anomeric protons is described by the hump numbers (linewidth at 0.55%/0.11% suppressed in two scans, below the intensity of natural of the carbon satellite peaks and half height of the main abundance 13C side-bands in a series of 20 consecutive chloroform peak). In this test the hump numbers should experiments. not degrade by more than 10% over a period of 12 Hrs. Protein Solid State Performance Characteristic solid state spectra (left) on labeled ubiqutin. left – CP 13C/ 1H; center, double CP 13C/15N/1H; right, 2-D double CP 13C/15N/1H © NYSBC 7 Sep 2006 5 NMR Environment Constructing a Center in Manhattan with minimal interference from the outside environment presents challenges. Red surface are at the 5 G contour © NYSBC 7 Sep 2006 6 To achieve excellent vibration isolation, we choose to take advantage of Manhattan geology, and provide linkage of all critical NMR and CEM sites to the local hard schist bedrock. For the 800’s and 750 on a suspended floor, this involved constructing four c. 3 m diameter columns sunk to bedrock, up to 15 m high (left – picture of one column). © NYSBC 7 Sep 2006 7 © NYSBC 7 Sep 2006 8 NMR Results Publications. (2005-6) see http://www.nysbc.org/papers • Poget SF, Krueger-Koplin ST, Krueger-Koplin RD, Cahill SM, Chandra Shekar S, Girvin ME 'NMR Assignment of the Dimeric S. aureus Small Multidrug-Resistance Pump in LPPG Micelles.' J Biomol NMR 2006 Feb 2 • Shekar, S.C., Wu, H., Fu, Z., Yip, S.C., Cahill, S.M., Girvin, M.E., Backer, J.M. (2005) Mechanism of constitutive PI 3-kinase activation by oncogenic mutants of the p85 regulatory subunit. J Biol Chem 280, 27850-27855 • Yu, G. Vengadesan, H., Wang, L., Jashi, T. Yefremov, S. Tian, V. Gaba, I. Shomer and R. E. Stark, “Magic-Angle Spinning NMR Studies of Cell Wall- Bound Aromatic-Aliphatic Biopolyesters Associated with Strengthening of Intercellular Adhesion in Potato ( Solanum Tuberosum L.) Tuber Parenchyma,” Biomacromolecules 7, 937-944. Pujato M, Navarro A, Versace R, Mancusso R, Ghose R, Tasayco ML 'The pH-dependence of amide chemical shift of Asp/Glu reflects its pK(a) in intrinsically disordered proteins with only local interactions.' Biochim Biophys Acta 2006 May 13 • Meriles, CA, Dong W. "Indirect detection of nuclear magnetic resonance via geometrically induced long-range dipolar fields" J. Magn. Res. In Press, Corrected Proof • Marulanda, D, Tasayco, M.L., Cataldi, M., Arriaran, V., Polenova, P. (2005) Resonance Assignments and Secondary Structure Analysis of E. coli Thioredoxin by Magic Angle Spinning Solid-State NMR Spectroscopy. Journal of Physical Chemistry B. 109, 18135-18145. • Pujato, M.; Bracken, C.; Mancusso, R.; Cataldi, M.; Tasayco, M. L. pH-Dependence of Amide Chemical Shifts in Natively Disordered Polypeptides Detects Medium-Range Interactions with Ionizable Residues. Biophysical Journal 89, 3293-3302. • Edwards , T.A., Butterwick, J.A., Zeng, L., Gupta, Y.K., Wang, X, Wharton, R.P., Palmer, A.G., Aggarwal, A.K. Solution Structure of the Vts1 SAM Domain in the Presence of RNA J. Mol. Biol. 356, 1065-1072. • Tang Y, Grey MJ, McKnight J, Palmer AG, Raleigh DP 'Multistate Folding of the Villin Headpiece Domain.' J Mol Biol 355, 1066-1072. • Grey, M.J., Tang, Y, Alexov, E, McKnight, C.J., Raleigh, D.P.,Palmer, A.G. (2006) Characterizing a Partially Folded Intermediate of the Villin Headpiece Domain Under Non-denaturing Conditions: Contribution of His41 to the pH-dependent Stability of the N-terminal Subdomain . Journal of Molecular Biology 355, 1078-1094. • Valentine, E. R., and Palmer, A. G., 3rd (2005). Microsecond-to-Millisecond Conformational Dynamics Demarcate the GluR2 Glutamate Receptor Bound to Agonists Glutamate, Quisqualate, and AMPA. Biochemistry 44, 3410-3417 • Zech, S.J., Wand, A.J., McDermott, A.E. Protein Structure Determination by high resolution solid-state NMR spectroscopy: Application to microcrystalline ubiquitin. J Am Chem Soc 127, 8618-8626. • Li H, Ilin S, Wang W, Duncan EM, Wysocka J, Allis CD, Patel DJ 'Molecular basis for site-specific read-out of histon H3K4me3 by the BPTF PHD finger of NURF' Nature 442, 31-32 • Teplova M, Yuan YR, Phan AT, Malinina L, Teplov A, Patel DJ 'Structural Basis for recognition and sequestration of UUU(OH) 3' termini of nascent RNA polymerase II transcripts by LA, a rheumatic diseaase autoanitgen' Mol. Cell 21 75-85 • Phan A.T., Kuryavyi V., Gaw H.Y., Patel D.J. (2005). Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter. Nature Chemical Biology, 1, 167-173. • Zhang N., Phan A.T., Patel D.J. (2005). (3+1) assembly of three human telomeric repeats into an asymmetric dimeric G-quadruplex. J. Am. Chem. Soc., 127, 17277-17285. • Zhang, N., Lin, C., Huang, X., Kolbanovskiy, A., Hingerty, B. E., Amin, S., Broyde, S., Geacintov, N. E., and Patel, D. J. (2005). Methylation of Cytosine at C5 in a CpG Sequence Context Causes a Conformational Switch of a Benzo[a]pyrene diol epoxide-N(2)-guanine Adduct in DNA from a Minor Groove Alignment to Intercalation with Base Displacement. J Mol Biol 346, 951-965. • Phan A.T., Kuryavyi V., Ma J.B., Faure A., Andréola M.L., Patel D.J. (2005). An interlocked dimeric parallel-stranded DNA quadruplex: A potent inhibitor of HIV-1 integrase. Proc. Natl. Acad. Sci. USA, 102, 634-639. • Phan A.T., Modi Y.S., Patel D.J. (2004). Propeller-type parallel-stranded G-quadruplexes in the human c-myc promoter. J. Am. Chem. Soc. , 126, 8710-8716. • Serganov A., Yuan Y.R., Pikovskaya O., Polonskaia A., Malinina L., Phan A.T., Hobartner C., Micura R., Breaker R.R., Patel D.J. (2004) Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol. , 11, 1729-1741. • Qian C, Zhang Q, Li S, Zeng L, Walsh MJ, Zhou MM. (2005)Structure and chromosomal DNA binding of the SWIRM domain. Nat Struct Mol Biol. 2005 12 (12):1078-85. Edwards, TA, Butterwick, JA, Zeng, Z, Gupta, YK, Wang, X, Wharton, RP, Palmer, AG, Aggarwal, AK.