PUBLICATIONS ASSOCIATED WITH THE NEW YORK STRUCTURAL BIOLOGY CENTER BY MEMBER INSTITUTION ^c

PUBLICATIONS ASSOCIATED WITH THE NEW YORK STRUCTURAL BIOLOGY CENTER BY MEMBER INSTITUTION ^c

This list is updated approximately quarterly. More recent information is available at Recent Preprints And Reprints.

Albert Einstein College of Medicine, Yeshiva University

2008 Zhong J, Frases S, Wang H, Casadevall A, Stark RE. (2008) Following Fungal Melanin Biosynthesis with Solid-State NMR: Biopolymer Molecular Structures and Possible Connections to Cell-Wall Polysaccharides. Biochemistry, 47, 4701-4710

Chattopadhyay, K., Ramagopal, U.A., Brenowitz, M., Nathenson, S.G. and Almo, S.C. (2008) Evolution of GITRL immune function: murine GITRL exhibits unique structural and biochemical properties within the TNF superfamily. Proc Natl Acad Sci U S A, 105, 635-640.

Zhang Q, Atreya HS, Kamen DE, Girvin ME, Szyperski T. (2008) GFT projection NMR based resonance assignment of membrane proteins: application to subunit C of E. coli F(1)F (0) ATP synthase in LPPG micelles. J Biomol NMR, 40, 157-63.

Nguyen TT, Brown S, Fedorov AA, Fedorov EV, Babbitt PC, Almo SC, Raushel FM. (2008). At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate. Biochemistry, 47, 1194-206.

2007 Poget, S.F. and Girvin, M.E. (2007) Solution NMR of membrane proteins in bilayer mimics: Small is beautiful, but sometimes bigger is better. Biochim Biophys Acta, 1768, 3098-3106.

Chattopadhyay, K., Ramagopal, U.A., Mukhopadhaya, A., Malashkevich, V.N., Dilorenzo, T.P., Brenowitz, M., Nathenson, S.G. and Almo, S.C. (2007) Assembly and structural properties of glucocorticoid-induced TNF receptor ligand: Implications for function. Proceedings of the National Academy of Sciences of the United States of America, 104, 19452-19457.

Rakus, J.F., Fedorov, A.A., Fedorov, E.V., Glasner, M.E., Vick, J.E., Babbitt, P.C., Almo, S.C. and Gerlt, J.A. (2007) Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans. Biochemistry, 46, 12896-12908.

Hermann, J.C., Marti-Arbona, R., Fedorov, A.A., Fedorov, E., Almo, S.C., Shoichet, B.K. and Raushel, F.M. (2007) Structure-based activity prediction for an enzyme of unknown function. Nature, 448, 775-779.

Song, L., Kalyanaraman, C., Fedorov, A.A., Fedorov, E.V., Glasner, M.E., Brown, S., Imker, H.J., Babbitt, P.C., Almo, S.C., Jacobson, M.P. and Gerlt, J.A. (2007) Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nature chemical biology, 3, 486-491.

Girvin, M. Faculty of 1000 Evaluation for Douglas SM et al 'DNA-nanotube-induced alignment of membrane proteins for NMR structure determination' Proc Natl Acad Sci U S A 104 6644-8.

Poget SF, Cahill SM, Girvin ME 'Isotropic Bicelles Stabilize the Functional Form of a Small Multidrug-Resistance Pump for NMR Structural Studies.' J Am Chem Soc 129: 2432-2433

Kamen, D.E., Cahill, S.M. and Girvin, M.E. (2007) Multiple alignment of membrane proteins for measuring residual dipolar couplings using lanthanide ions bound to a small metal chelator. Journal of the American Chemical Society, 129, 1846-1847.

2006 Akana, J, Federov, A, Federov, E, Novak, W, Babbitt, P, Almo, S, Gerlt, J. D-Ribulose 5-Phosphate 3-Epimerase: Functional and Structural Relationships to Members of the Ribulose-Phosphate Binding (β/α)β-Barrel Superfamily. Biochemistry 45, 2493-2503

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 36 10-10 Suppl. 1.

2005 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

2003 Tian, S., Garcia-Rivera, J., Yan, B., Casadevall, A., and Stark, R. E. Unlocking the molecular structure of fungal melanin using ¹³C biosynthetic labeling and solid-state NMR. Biochemistry 42, 8105-8109. ^a

City University of New York

Ferrage F, Piserchio A, Cowburn D, Ghose R. (2008) On the Measurement of 15N-{1H} Nuclear Overhauser Effects. J Mag Res, 192, 302-313.

Yang J, Tasayco ML, Polenova T. (2008) Magic Angle Spinning NMR Experiments for Structural Studies of Differentially Enriched Protein Interfaces and Protein Assemblies. J Am Chem Soc, 30, 5798-807.

2007 He, X. Yang, H. Wang, R. Estephan, F. Francis, S. Kodukula, J. Storch, and R. E. Stark, Solution-State Molecular Structure of Apo and Oleate-Liganded Liver Fatty Acid-Binding Protein, Biochemistry 46:12543-12556

Quijada J, Lopez G, Versace R, Ramirez L, Tasayco ML 'On the NMR analysis of pK(a) values in the unfolded state of proteins by extrapolation to zero denaturant.' Biophys Chem 129:242-50

Dong W, Meriles, CA, 'Indirect detection of NMR via geometry-dependent dipolar fields, revisited' Journal of Magnetic Resonance 186, 330-336

Nicotera, I., McLachlan, G. D., Bennett, G. D., Plitz, I., Badway, F., Amatucci, G. G., Greenbaum, S. G., Solid-State NMR Characterization of Electrolyte Breakdown Products iin Nonaqueous Asymmetric Hybrid Supercapacitors. Electrochemical and Solid-State Letters (2007) 10(1) A5-A8

2006 Natarayan, A., Ghose, R., M. Hill, J., Structure and Dynamics of ASC2, A Pyrin Domain-Only Protein that Regulates Inflammatory Signalling. J Biol Chem. 281 31863-31875

Del Rio, A., Dutta K., Chavez J., Ubarretxena-Belandia, I., Ghose, R., Solution Structure and Dynamics of the N-terminal Cytosolic Domain of Rhomboid Intramembrane Protease from Pseudomonas aeruginosa: Insights into a Functional Role in Intramembrane Proteolysis. 2006 J Mol Biol 365: 109-122. ^a

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 7, 1227-33

Meriles, CA, Dong W. "Indirect detection of nuclear magnetic resonance via geometrically induced long-range dipolar fields" J. Magn. Res. 181(2) 331-335

2005 Alimova, A, Katz, A, Podder, R, Minko, G, Wei, H, Berriman, J, Alfano, R.R., Gottlieb, P. Virus Particles and Receptor Interaction Monitored by Fluorescence Spectroscopy. Photochemistry and Photobiology 81, 879-883

Marulanda, D, Tasayco, M.L., Cataldi, M., Arriaran, V., Polenova, P. 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

2004 Marulanda, D., Tasayco, M.L., McDermott, A., Cataldi, M., Arriaran, V., and Polenova, T., Magic Angle Spinning and Solid-State NMR Spectroscopy for Structural Studies of Protein Interfaces. Resonance Assignments of Differentially Enriched Escherichia coli Thioredoxin Reassembled by Fragment Complementation. J. Am. Chem. Soc. 126, 16608-16620. ^a

Dutta K, Shi HH, Cruz-Chu ER, Kami K, Ghose R. (2004) Dynamic influences on a high-affinity, high-specificity interaction involving the C-terminal SH3 domain of P67(phox) Biochemistry 43 8094-8106 ^a

2002 Wang, H., He, Y., Kroenke, C. D., Kodukula, S., Storch, J., Palmer, A. G., and Stark, R. E. Titration and exchange studies of liver fatty acid-binding protein with ¹³C-labeled long-chain fatty acids. Biochemistry 41, 5453-5461. ^a

Columbia University

2008 Cheung J, Bingman CA, Reyngold M, Hendrickson WA, Waldburger CD. (2008) Crystal structure of a functional dimer of the PhoQ^? sensor domain. J Biol Chem, 283, 13762-70.

Shen Y, Tong L. (2008) Structural Evidence for Direct Interactions between the BRCT Domains of Human BRCA1 and a Phospho-peptide from Human ACC1. Biochemistry, 47, 5767-73.

Forouhar F, Abashidze M, Xu H, Grochowski L L, Seetharaman J, Hussain M, Kuzin A, Chen Y, Zhou W, Xiao R, Acton T B, Montelione G T, Galinier A, White R H,Tong L. (2008) Molecular insights into the biosynthesis of the F420 coenzyme. J Biol Chem, 283, 1183211840.

Koehnke J, Jin X, Trbovic N, Katsamba PS, Brasch J, Ahlsen G, Scheiffele P, Honig B, Palmer AG 3rd, Shapiro L. (2008) Crystal Structures of beta-Neurexin 1 and beta-Neurexin 2 Ectodomains and Dynamics of Splice Insertion Sequence 4. Structure, 16, 410-21.

2007 Hendrickson WA 'Impact of structures from the protein structure initiative.' Structure 15:1528-9

Varga K, Tian L, McDermott AE. 'Solid-state NMR study and assignments of the KcsA potassium ion channel of S. lividans.' Biochim Biophys Acta 1604-1613, 1604-13.

Amodeo GA, Rudolph MJ, Tong L 'Crystal structure of the heterotrimer core of Saccharomyces cerevisiae AMPK homologue SNF1.' Nature 449, 492-5.

Tao, X, Tong, L. Crystal Structure of the MAP Kinase Binding Domain and the Catalytic Domain of Human MKP5. Protein Sci. 16: 880

Yin C, Khan JA, Swapna GV, Ertekin A, Krug RM, Tong L, Montelione GT. Conserved surface features form the double-stranded RNA-binding site of non-structural protein 1 (NS1) from influenza A and B viruses.' J Biol Chem 282, 20584 - 20592.

Liu Q, Hendrickson WA 'Insights into hsp70 chaperone activity from a crystal structure of the yeast hsp110 sse1.' Cell 131,106-20.

Benach J, Wang L, Chen Y, Ho CK, Lee S, Seetharaman J, Xiao R, Acton TB, Montelione GT, Deng H, Sun R, Tong L. 'Structural and functional studies of the abundant tegument protein ORF52 from murine gammaherpesvirus-68.' J. Biol. Chem 282, 31534-31541.

Li J, Mao X, Dong LQ, Liu F, Tong L 'Crystal Structures of the BAR-PH and PTB Domains of Human APPL1.' Structure 15, 525-33.

Valentine ER, Ferrage F, Massi F, Cowburn D, and Palmer AG 'Joint Composite-Rotation Adiabatic-Sweep Isotope Filtration' J. Biomol. NMR 38, 11-22.

Williams JC, Roulhac PL, Roy AG, Vallee RB, Fitzgerald MC, Hendrickson WA. Structural and thermodynamic characterization of a cytoplasmic dynein light chain-intermediate chain complex. Proc Natl Acad Sci U S A ,*104*, 1002810033.

Yin C, Khan JA, Swapna GV, Ertekin A, Krug RM, Tong L, Montelione GT Conserved surface features form the double-stranded RNA-binding site of non-structural protein 1 (NS1) from influenza A and B viruses.' J Biol Chem 282, 20584 - 20592.

Forouhar F, Kuzin A, Seetharaman J, Lee I, Zhou W, Abashidze M, Chen Y, Yong W, Janjua H, Fang Y, Wang D, Cunningham K, Xiao R, Acton TB, Pichersky E, Klessig DF, Porter CW, Montelione GT, Tong L. 'Functional insights from structural genomics.' J Struct Funct Genomics, 2-3, 37 - 44.

Martinez-Hackert, E, Hendrickson, WA. Structures of and interactions between domains of trigger factor from Thermotoga maritima. Acta Crystallogr D Biol Crystallogr 63, 536-47.

Vorobiev SM, Neely H, Seetharaman J, Ma LC, Xiao R, Acton TB, Montelione GT, Tong L 'Crystal structure of AGR_C_4470p from Agrobacterium tumefaciens.' Protein Sci 16, 535-8.

Bai Y, Auperin TC, Tong L 'The use of in situ proteolysis in the crystallization of murine CstF?-77.' Acta Crystallograph Sect F Struct Biol Cryst Commun 2007 Feb 1; 63 (Pt 2),135-8.

Bai Y, Auperin T, Chou C, Chang G, Manley J, Tong L. Crystal Structure of Murine CstF-77: Dimeric Association and Implications for Polyadenylation of mRNA Precursors, Mol. Cell 25, 863-875.

Goldbourt A, Gross BJ, Day LA, McDermott AE 'Filamentous Phage Studied by Magic-Angle Spinning NMR: Resonance Assignment and Secondary Structure of the Coat Protein in Pf1.' J Am Chem Soc 129, 2338-2344.

Townley R, Shapiro L 'Crystal Structures of the Adenylate Sensor from Fission Yeast AMP-Activated Protein Kinase.' Science 315, 1726-1729.

Forouhar F, Anderson JL, Mowat CG, Vorobiev SM, Hussain A, Abashidze M, Bruckmann C, Thackray SJ, Seetharaman J, Tucker T, Xiao R, Ma LC, Zhao L, Acton TB, Montelione GT, Chapman SK, Tong L. Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase. Proc Natl Acad Sci U S A 104 473-78

Rudolph M, Amodeo G, Iram S, Hong S, Pirio G, Carlson M, Tong L, Structure of the Bateman2 Domain of Yeast Snf4: Dimeric Association and Relevance for AMP Binding. Structure 15: 65-74

Xiang S, Usunow G, Lange G, Busch M, Tong L 'Crystal structure of 1-deoxy-D-xylulose 5-phosphate synthase (DXS), a crucial enzyme for isoprenoids biosynthesis.' J Biol Chem 282, 2676-2682

Mandel CR, Kaneko S, Zhang H, Gebauer D, Vethantham V, Manley JL, Tong L 'Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease.' Nature 282, 953-956

2006 Joel A. Butterwick and Arthur G. Palmer, III "An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H" Protein Sci. 2006 15 2697-2707

Armstrong N, Jasti J, Beich-Frandsen M, Gouaux E 'Measurement of Conformational Changes accompanying Desensitization in an Ionotropic Glutamate Receptor.' Cell 127:85-97

Jingshi Shen, David C. Tareste, Fabienne Paumet, James E. Rothman and Thomas J. Melia, 'Selective Activation of Cognate SNAREpins by Sec1/Munc18 Proteins' Cell 128 183-195

Mandel CR, Gebauer D, Zhang H, Tong L 'A serendipitous discovery that in situ proteolysis is essential for the crystallization of yeast CPSF-100 (Ydh1p).' Acta Crystallograph Sect F Struct Biol Cryst Commun 62:1041-5

Massi F, Wang C, Palmer AG. Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase. Biochemistry 36 10787-94

Lorieau JL, McDermott AE. 'Conformational flexibility of a microcrystalline globular protein: order parameters by solid-state NMR spectroscopy.' J Am Chem Soc 128,11505-12

Shen, Y., Chou, C.Y., Chang, G.G., Tong, L. Is dimerization required for the catalytic activity of bacterial biotin carboxylase? Molecular Cell 22, 807-818.

Lim, D., Gregorio, G.G., Bingman, C., Martinez-Hackert, E., Hendrickson, W.A., Goff, S.P. Crystal Structure of the Moloney Murine Leukemia Virus RNase H Domain. J Virol 80, 8379-8389.

Kawate, T, Gouaux, E. Fluorescence-Detectino Size-Exclusion Chromatography for Precrystallization Screening of Integral Membrane Proteins. Structure 14, 673-681.

Hsiao YS, Jogl G, Tong L 'Crystal structures of murine carnitine acetyltransferase in ternary complexes with its substrates.' J Biol Chem 281, 28480-28497

Yu, B. Edstrom, W.C., Benach, J., Hamuro, Y., Weber, P.C., Gibney, B.R., Hunt, J.F. (2006) Crystal structures of catlytic Complexes of the oxidative DNA/RNA repair enzyme AlkB. Nature 439 879-884

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. ^a

Tang Y, Grey MJ, McKnight J, Palmer AG, Raleigh DP 'Multistate Folding of the Villin Headpiece Domain.' J Mol Biol 355, 1066-1072. ^a

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. ^a

Forouhar, F.; Hussain, M.; Farid, R.; Benach, J.; Abashidze, M.; Edstrom, W. C.; Vorobiev, S. M.; Xiao, R.; Acton, T. B.; Fu, Z.; Kim, J. J.; Miziorko, H. M.; Montelione, G. T.; Hunt, J. F., Crystal structures of two bacterial 3-hydroxy-3-methylglutaryl-CoA lyases suggest a common catalytic mechanism among a family of TIM barrel metalloenzymes cleaving carbon-carbon bonds. J Biol Chem 2006, 281, 7533-45.

2005 Furukawa, H, Singh, S, K, Mancusso, R, Gouaux,E, Subunit arrangement and function in NMDA receptors. Nature 438, 185-92.

Benach, J.; Edstrom, W. C.; Lee, I.; Das, K.; Cooper, B.; Xiao, R.; Liu, J.; Rost, B.; Acton, T. B.; Montelione, G. T.; Hunt, J. F., The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism. Acta Crystallogr D Biol Crystallogr 61 589-98.

Forouhar, F.; Lee, I. S.; Vujcic, J.; Vujcic, S.; Shen, J.; Vorobiev, S. M.; Xiao, R.; Acton, T. B.; Montelione, G. T.; Porter, C. W.; Tong, L., Structural and functional evidence for Bacillus subtilis PaiA as a novel N1-spermidine/spermine acetyltransferase. J Biol Chem 280, 40328-36.

Khan, J, Dunn, B, Tong, L. Crystal Structure of Human Taspase1, a Crucial Protease Regulating the Function of MLL. Structure 13, 1443-1452.

Gorman J, Shapiro L. Crystal structures of the tryptophan repressor binding protein WrbA and complexes with flavin mononucleotide.' Protein Sci 12, 3004-3012.

Fan Q., Hendrickson, W. Structure of Human Follicle-Stimulating Hormone in Complex with its Receptor. Nature 433 269-277

Gorman, J, Shapiro, L. Crystal structures of the tryptophan repressor binding protein WrbA and complexes with flavin mononucleotide. Protein Sci 12 3004-12.

Valentine, E. R., and Palmer, A. G., 3rd. Microsecond-to-Millisecond Conformational Dynamics Demarcate the GluR2 Glutamate Receptor Bound to Agonists Glutamate, Quisqualate, and AMPA. Biochemistry 44, 3410-3417

Forouhar, F., Yang, Y., Kumar, D., Chen, Y., Fridman, E., Park, S.W., Chiang, Y., Acton, T.B., Montelione, G.T., Pichersky, E., Klessig, D.F., Tong, L. Structural and Biochemical Studies Identify Tabacco SABP2 as a Methyl Salicylate Esterase and Implicate it it Plant Innate Immunity. Proc Natl Acad Sci USA 102: 1773-1778

Inanobe, A., Furukawa, H., Gouaux, E. Mechanism of Partial Agonist Action at the NR1 Subunit of NMDA Receptors. Neuron. 47: 71-84

Jogl, G., Hsiao, Y., Tong, L. Crystal Structure of Mouse Carnitine Octanoyltransferase and Molecular Determinants of Substrate Selectivitiy. J. Biol. Chem. 280: 738-744

Marina A, Waldburger CD, Hendrickson WA. (2005) Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein. EMBO J 24, 4247-4259.

Olson, R., Gouaux, E. Crystal Structure of the Vibrio cholerae Cytolysin(VCC) Pro-toxin and its Assembly into a Heptameric Transmembrane Pore. J. Mol. Biol. 350, 997-1016

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.

Huang,C.C., Stricher, F., Martin,L., Decker, J.M., Majeed, S., Barthe, P., Hendrickson,W.A., Robinson,J., Roumestand, C., Sodroski,J. , Wyatt,R., Shaw, G.M, Vita ,C. , Kwong, P.D, Scorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120: crystal structures, molecular mimicry, and neutralization breadth. Structure 13, 755-768 (2005).

Williams, J.C. , Sue,C., Banting,G.S., Yang, H. , Glerum, D.M., Hendrickson, W.A. and Schon, E.A. (2005) Crystal Structure of Human SCO1: Implications for Redox Signaling by Mitochondrial Cytochrome c Oxidase "Assembly" Protein. J. Biol. Chem. 280, 15202-15211

Williams, J.C. , Xie, H., and Hendrickson, W.A. Crystal Structure of Dynein Light Chain TcTex-1. J. Biol. Chem. 280, 21981-21986

2004 Forouhar, F., Lee, I., Benach, J., Kulkarni, K., Xiao, R., Acton, T., Montelione, G., Tong, L. A Novel Nad-Binding Protein Revealed by the Crystal Structure of 2,3-Diketo-L-Gulonate Reductase (YIAK). J. Biol. Chem. 279 13148-13155

Yernool, D., Boudker, O., Jin, Y., Gouaux, E. (2004) Structure of a Glutamate Transporter Homologue From Pyrococcus Horikoshii. Nature 431 811

Kovall, R., Hendrickson, W. Crystal Structure of the Nuclear Effector of Notch Signaling, CSL, Bound to DNA. EMBO J. 23 3441-3451

Zhang,H., Tweel, B., Li, J., Tong, L. Crystal Structure of the Carboxyltransferase Domain of Acetyl-Coenzyme A Carboxylase in Complex with CP-640186. Structure 12 1683-1691

Mancia, F. , Patel, S.D., Rajala, M.W., Scherer, P.E., Nemes, A., Schieren, I., Hendrickson , W.A., and Shapiro, L. Optimization of Protein Production in Mammalian Cells with a Coexpressed Fluorescent Marker. Structure 12, 1355-1360

Blankenfeldt, W., Kuzin, A., Skarina, T., Korniyenko, Y., Tong, L., Bayer, P., Janning, P., Thomashow, L., Mavrodi, D. Structure and Function of the Phenazine Biosynthetic Protein PhzF from Pseudomonas Fluorescens. Proc Natl Acad Sci USA 101 16431-16436

Chen, Y., Li, M., Zhang, Y., He, L., Yamada, Y., Fitzmaurice, A., Shen, Y., Zhang, H., Tong, L., Yang, Y Structural Basis of the α 1-β Subunit Interaction of Voltage-Gated Ca²⁺ Channels. Nature 429 675

Huang, C.C., Venturi, M., Majeed, S., Moore, M. J., Phogat, S., Zhang, M. Y., Dimitrov, D. S., Hendrickson, W., Robinson, J., Sodroski, J., Wyatt, R., Choe, H., Farzan, M., Kwong, P.D. Structural Basis of Tyrosine Sulfation and VH-gene Usage in Antibodies that Recognize the HIV Type 1 Coreceptor-Binding Site on gp120. Proc Natl Acad Sci USA 101 2706-2711

Patel, S, Rajala, M, Rossetti, L, Scherer, P, Shapiro, L. Disulfide-Dependent Multimeric Assembly of Resistin Family Hormones. Science 304: 1154-1158

Jogl, G.,Tong, L.. Crystal Structure of Yeast Acetyl-Coenzyme A Synthetase in Complex with AMP. Biochemistry 43 1425-1431

Goldsmith-Fischman, S., Kuzin, A., Edstrom, A., Benach, J., Shastry, R., Xiao, R., Acton, T., Honig, B., Montelione, G., Hunt, J. The SufE Sulfur-Acceptor Protein Contains a Conserved Core Structure that Mediates Interdomain Interactions in a Variety of Redox Protein Complexes. J. Mol. Biol. 344 549-565

Shen, Y., Volrath, S., Weatherly, S., Elich, T., Tong, L. A Mechanism for the Potent inhibition of Eukaryotic Acetyl Coenzyme A Carboxylase by Soraphen A, a Macrocyclic Polyketide Natural Product. Mol. Cell 16 881-891

Gebauer, J., Li, J., Jogl, G., Shen, Y., Myszka, D., Tong, L. Crystal structure of the PH-BEACH domains of human LRBA/BGL. Biochemistry 43 14873-14880

Khan, K., Brint, E., O'Neill, L., Tong, L. Crystal Structure of the Toll/interleukin-1 Receptor (TIR) Domain of IL-1RAPL. J. Biol. Chem. 279 31664-31670

Hsiao, Y., Jogl, G., Tong, L. Structural and Biochemical Studies of the Substrate Selectivity of Carnitine Acetyltransferase. J. Biol. Chem. 279 31584-31589

Zhang, H., Tweel, B., Tong, L. Molecular Basis for the Inhibition of the Carboxyltransferase Domain of Acetyl-coenzyme-A Carboxylase by Haloxyfop and Diclofop. Proc Natl Acad Sci USA 101 5910-5915

Galdiero, S., Gouaux, E. High Resolution Crystallographic Studies of α-HemolysinPhospholipid Complexes Define HeptamerLipid Head Group Interactions: Implication for Understanding ProteinLipid Interactions. Protein Sci. 13 1503-1511

Marulanda, D., Tasayco, M.L., McDermott, A., Cataldi, M., Arriaran, V., and Polenova, T. Magic Angle Spinning and Solid-State NMR Spectroscopy for Structural Studies of Protein Interfaces. Resonance Assignments of Differentially Enriched Escherichia coli Thioredoxin Reassembled by Fragment Complementation. J. Am. Chem. Soc. 126, 16608-16620. ^a

Wang, C., Karpowich, N., Hunt, J. F., Rance, M., and Palmer, A. G. Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy transduction in ABC transporters. J Mol Biol 342, 525-537.

Butterwick, J. A., Patrick Loria, J., Astrof, N. S., Kroenke, C. D., Cole, R., Rance, M., and Palmer, A. G., 3rd . Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes. J Mol Biol 339, 855-871.

Zech, S. G., Olejniczak, E., Hajduk, P., Mack, J., and McDermott, A. E. Characterization of protein-ligand interactions by high-resolution solid-state NMR spectroscopy. J Am Chem Soc 126, 13948-13953.

2003 Wang, C., Rance, M., and Palmer, A. G. Mapping chemical exchange in proteins with MW > 50 kD. J Am Chem Soc 125, 8968-8969.

Memorial Sloan Kettering Cancer Center

2007 Phan AT, Kuryavyi V, Luu KN, Patel DJ 'Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution.' Nucleic Acids Res 35:6517-25

Phan AT, Kuryavyi V, Burge S, Neidle S, Patel DJ 'Structure of an Unprecedented G-Quadruplex Scaffold in the Human c-kit Promoter.' J Am Chem Soc 129; 4386-4392

Rodrguez FA, Cai Y, Lin C, Tang Y, Kolbanovskiy A, Amin S, Patel DJ, Broyde S, Geacintov NE. 'Exocyclic amino groups of flanking guanines govern sequence-dependent adduct conformations and local structural distortions for minor groove-aligned benzo[a]pyrenyl-guanine lesions in a GG mutation hotspot context.' Nucleic Acids Res 35 15551568 ^a

2006 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, 31-2

Phan A.T., Luu K.N., Patel D.J. Different loop arrangements of intramolecular human telomeric (3+1) G-quadruplexes in K⁺ solution. Nucleic Acids Res., 34, 5715-5719.

Luu K.N., Phan A.T., Kuryavyi V., Lacroix L., Patel D.J. Structure of the human telomere in K⁺ solution: an intramolecular (3 + 1) G-quadruplex scaffold. J. Am. Chem. Soc., 128, 9963-9970.

Teplova M., Yuan Y.R., Phan A.T., Malinina L., Ilin S., Teplov A., Patel D.J. 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.

Yunus AA, Lima CD 'Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway.' Nat Struct Mol Biol 13, 491

2005 Phan A.T., Kuryavyi V., Gaw H.Y., Patel D.J. Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter. Nat. Chem. Biol., 1, 167-173.

Zhang N., Phan A.T., Patel D.J. (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. 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. ^a

Lois, L.M., and Lima, C.D. Structures of the Small Ubiquitin-like MOdifier E1 activating enzyme provide insights into SUMO activation and the mechanism for E2 recruitment to E1. EMBO J. 24, 439-451. ^c

Phan A.T., Kuryavyi V., Ma J.B., Faure A., Androla M.L., Patel D.J. . An interlocked dimeric parallel-stranded DNA quadruplex: A potent inhibitor of HIV-1 integrase. Proc. Natl. Acad. Sci. USA, 102, 634-639.

Reverter, D., Wu, K., Erdene, T.G., Pan, Z.-Q., Wilkinson, K.D., and Lima, C.D. Structure of the complex between the Ulp/Senp protease family member Den1 and Nedd8. J. Mol. Biol. 345, 141-151. ^c

2004 Cheng, Y., Patel, D. (2004) Crystallographic Structure of the Nuclease Domain of 3'hExo, A DEDDh Family Member, Bound to rAMP. J. Mol. Biol. 343: 305-312

Phan A.T., Modi Y.S., Patel D.J. 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. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol. , 11, 1729-1741.

Gu, M., Fabrega, C., Liu, D., Liu, H., Kiledjian, M., Lima, C. Insights into the Structure , Mechanism and Regulation of Scavenger mRNA Decapping Activity. Mol. Cell 14 67-80

Fabrega, C., Hausmann, S., Shen, V., Shuman, S., Lima, C. Structure and Mechanism of the mRNA (guanine-N7) cap Methyltransferase. Mol. Cell 13 77-89

Reverter, D., Lima, C. A Basis for SUMO Protease Specificity Provided by Analysis of Human Senp2 and a Senp2-SUMO Complex. Structure 12 1519-1531

Ho, C., Wang, L., Lima, C., Shuman, S. Structure and Mechanism of RNA Ligase. Structure 12 327-339

Buglino, J., Onwueme, K., Ferreras, J., Quadri, L., Lima, C. Crystal Structure of PapA5 , a Phthiocerol Dimycocerosyl Transferase from Mycobacterium Tuberculosis. J. Biol. Chem. 279 30634-30642

Mount Sinai School of Medicine

2008 Zeng L, Yap KL, Ivanov AV, Wang X, Mujtaba S, Plotnikova O, Rauscher Iii FJ, Zhou MM. (2008) Structural insights into human KAP1 PHD finger-bromodomain and its role in gene silencing. Nat Struct Mol Biol., 6, 626-33.

Gupta YK, Nair DT, Wharton RP, Aggarwal AK. (2008) Structures of Human Pumilio with Noncognate RNAs Reveal Molecular Mechanisms for Binding Promiscuity. Structure, 16, 549-557.

Zeng L, Zhang Q, Gerona-Navarro G, Moshkina N, Zhou MM. (2008) Structural Basis of Site-Specific Histone Recognition by the Bromodomains of Human Coactivators PCAF and CBP/p300. Structure, 16 , 643-52.

Cunha L, Kuti M, Bishop DF, Mezei M, Zeng L, Zhou MM, Desnick RJ. (2007) Human uroporphyrinogen III synthase: NMR-based mapping of the active site.' Proteins, 71, 855-873.

2007 Vink M, Derr K, Love J, Stokes DL, Ubarretxena-Belandia I. (2007) A high-throughput strategy to screen 2D crystallization trials of membrane proteins. J Struct Biol, 160, 295-304.

Vanamee ES, Berriman J, Aggarwal AK. An EM view of the FokI synaptic complex by single particle analysis. J Mol Biol 370 207-12

2005 Qian C, Zhang Q, Li S, Zeng L, Walsh MJ, Zhou MM. Structure and chromosomal DNA binding of the SWIRM domain. Nat Struct Mol Biol. 2005 12:1078-85.

Edwards, TA, Butterwick, JA, Zeng, Z, Gupta, YK, Wang, X, Wharton, RP, Palmer, AG, Aggarwal, AK. Solution Structure of the Vts1 SAM Domain in the Presence of RNA J. Mol. Biol. 365, 1065-1072. ^a

2004 Capili, A. D., Edghill, E. L., Wu, K., and Borden, K. L. Structure of the C-terminal RING finger from a RING-IBR-RING/TRIAD motif reveals a novel zinc-binding domain distinct from a RING. J Mol Biol 340, 1117-1129

2003 Yan, K. S., Yan, S., Farooq, A., Han, A., Zeng, L., and Zhou, M. M. Structure and conserved RNA binding of the PAZ domain. Nature 426, 468-474.

NYU

2008 George EA, Novick RP, Muir TW. (2008) Cyclic Peptide Inhibitors of Staphylococcal Virulence Prepared by Fmoc-Based Thiolactone Peptide Synthesis. J Am Chem Soc, 130, 4914-24.

Wu CC, Rice WJ, Stokes DL. (2008) Structure of a copper pump suggests a regulatory role for its metal-binding domain. Structure 16, 976-85.

Owen GR, Acehan D, Derr KD, Rice WJ, Stokes DL. (2008) Cryoelectron tomography of isolated desmosomes. Biochem Soc Trans, 36, 173-9.

Liu J, Wang D, Zheng Q, Lu M, Arora PS. (2008) Atomic structure of a short alpha-helix stabilized by a main chain hydrogen-bond surrogate. -J Am Chem Soc.-, 130, 4334-7.

Wu J, Tseng YD, Xu CF, Neubert TA, White MF, Hubbard SR. (2008) Structural and biochemical characterization of the KRLB region in insulin receptor substrate-2. Nat Struct Mol Biol, 15, 251-8.

2007 Vink M, Derr K, Love J, Stokes DL, Ubarretxena-Belandia I. (2007) A high-throughput strategy to screen 2D crystallization trials of membrane proteins. J Struct Biol, 160, 295-304.

Stokes DL 'Desmosomes from a structural perspective.' Curr Opin Cell Biol 19:565-71

Hu GB, Rice WJ, Drose S, Altendorf K, Stokes DL 'Three-dimensional structure of the KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals.' J Struct Biol 2007 Epub Sep 18

Chen H, Ma J, Li W, Eliseenkova AV, Xu C, Neubert TA, Miller WT, Mohammadi M 'A molecular brake in the kinase hinge region regulates the activity of receptor tyrosine kinases.' Mol Cell 27, 717-30

2006 Stiegler AL, Burden SJ, Hubbard SR 'Crystal Structure of the Agrin-responsive immunoglobulin-like Domains 1 and 2 of the Receptor Tyrosine Kinase MuSK.' J Mol Biol 364: 424-433

Bergamin, E., Wu, J., Hubbard, S.R. Structural basis for phosphotyrosine recognition by suppressor of cytokine signaling-3. Structure 14, 1285-1292.

N. Mller, A. Jerschow. Nuclear Spin Noise Imaging. Proc. Natl. Acad. Sci. USA 2006 103. 6790-6792.

Rice WJ, Kovalishin A, Stokes DL 'Role of metal-binding domains of the copper pump from Archaeoglobus fulgidus.' Biochem Biophys Res Commun 348, 124-131

Stokes, D.L., A.J. Pomfret, W.J. Rice, J.P. Glaves, H.S.Young. 2006. Interactions between Ca²⁺-ATPase and the pentameric form of phospholamban in two-dimensional co-crystals. Biophys. J. 90, 42134223. ^a

Chen, Z., B.L. Akin , D.L. Stokes , L.R. Jones. 2006. Cross-linking of C-terminal residues of phospholamban to the Ca²⁺ pump of cardiac sarcoplasmic reticulum to probe spatial and functional interactions within the transmembrane domain. J. Biol. Chem 281, 14163-14172. ^a

Olsen, S, Li, J, Eliseenkova, A, Ibrahimi, O, Lao, Z, Zhang, F, Linhardt, R, Joyner, A, Mohammadi, M. Structural Basis by Which Alternative Splicing Modulates the Organizer Activity of FGF8 in the Brain. Genes Dev, 20, 185-198.

2005 Depetris, R.S., Hu, J., Gimpelevich, I., Holt, L.J., Daly, R.J., and Hubbard, S.R. Structural basis for inhibition of the insulin receptor by the adaptor protein Grb14. Mol. Cell 20, 325-333.

Stokes, D.L., F. Delavoie, W.J. Rice, P. Champeil, D.B. McIntosh, J.-J. Lacapere, 2005. Structural Studies of a Stabilized Phosphoenzyme Intermediate of Ca²⁺-ATPase. J. Biol. Chem. 280 18063-18072. ^a

Hu, J. and Hubbard, S.R. Structural characterization of a novel Cbl phosphotyrosine-recognition motif in the APS family of adapter proteins J. Biol. Chem. 280, 18943-18949.

Ibrahimi OA, Yeh BK, Eliseenkova AV, Zhang F, Olsen SK, Igarashi M, Aaronson SA, Linhardt RJ, Mohammadi M. Analysis of mutations in fibroblast growth factor (FGF) and a pathogenic mutation in FGF receptor (FGFR) provides direct evidence for the symmetric two-end model for FGFR dimerization. Mol Cell Biol 25: 671-84.

Kumar, R., Ling, W., Schoefberger, W., and Jerschow, A. Separated quadrupolar field experiment. J Magn Reson 172, 209-213.

Li, S., Depetris, R.S., Barford, D., Chernoff, J., and Hubbard, S.R. Crystal structure of a complex between protein tyrosine phosphatase 1B and the insulin receptor tyrosine kinase. Structure 13, 1643-1651.

2004 Liu, J., Yong, W., Deng, Y., Kallenbach, N., Lu, M. Atomic Structure of a Tryptophan-Zipper Pentamer. Proc Natl Acad Sci USA 101 16156-16161^a

Olsen, S.K., Ibrahimi, O.A., Raucci, A., Zhang, F., Eliseenkova, A.V., Yayon, A., Basilico, C., Linhardt, R.J., Schlessinger, J., Mohammadi, M. Insights into the Molecular Basis for Fibroblast Growth Factor Receptor Autoinhibition and Ligand-Binding Promiscuity. Proc Natl Acad Sci USA 101, 935-940 (2004)

Ibrahimi, O., Zhang, F., Eliseenkova, A., Linhardt, R., Mohammadi, M. Proline to Arginine Mutations in FGF Receptors 1 and 3 Result in Pfeiffer and Muenke Craniosynostosis Syndromes Through Enhancement of FGF Binding Affinity. Hum. Mol. Genet. 13 69-78

2003 He, W., Cowin, P., and Stokes, D. L. Untangling desmosomal knots with electron tomography. Science 302, 109-113. ^{a, b}

Rockefeller University

2008 George EA, Novick RP, Muir TW. (2008) Cyclic Peptide Inhibitors of Staphylococcal Virulence Prepared by Fmoc-Based Thiolactone Peptide Synthesis. J Am Chem Soc, 130, 4914-24.

Banerjee S, Huber T, and Sakmar TP. (2008) Rapid Incorporation of Functional Rhodopsin into Nanoscale Apolipoprotein Bound Bilayer (NABB) Particles. Journal of Molecular Biology, 377, 1067-1081.

2007 Ottesen JJ, Bar-Dagan M, Giovani B, Muir TW 'An amalgamation of solid phase peptide synthesis and ribosomal peptide synthesis.' Biopolymers 2007 Jul 17 Epub

	Wei Y, Liu S, Lausen J, Woodrell C, Cho S, Biris N, Kobayashi N, Wei Y, Yokoyama S, Werner MH. 'A TAF4-homology domain from the corepressor ETO is a docking platform for positive and negative regulators of transcription.' Nat Struct Mol Biol. 14: 653-61.

Wei Y, Liu S, Lausen J, Woodrell C, Cho S, Biris N, Kobayashi N, Wei Y, Yokoyama S, Werner MH. 'A TAF4-homology domain from the corepressor ETO is a docking platform for positive and negative regulators of transcription.' Nat Struct Mol Biol. 14: 653-61.

2006

	Li H, Ilin S, Wang W, Duncan EM, Wysocka J, Allis CD, Patel DJ 'Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF' Nature 442, 91-95 ^a

Li H, Ilin S, Wang W, Duncan EM, Wysocka J, Allis CD, Patel DJ 'Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF' Nature 442, 91-95 ^a

	Carrington PE, Sandu C, Wei Y, Hill JM, Morisawa G, Huang T, Gavathiotis W, Yu W, Werner MH "The structure of FADD and its mode of interaction with procaspase-8" Mol. Cell 22 599-610

Carrington PE, Sandu C, Wei Y, Hill JM, Morisawa G, Huang T, Gavathiotis W, Yu W, Werner MH "The structure of FADD and its mode of interaction with procaspase-8" Mol. Cell 22 599-610

Ji, H., Shekhtman, A., McDonnell, J., Ghose, R., Cowburn D. (2006) "NMR determination that an extended BH3 motif of pro-apoptotic BID is specifically bound to BCL-X_L " Magnetic Res. Chem. 44 101-6 ^a

	Muralidharan V., Dutta K., Cho J., Vila-Perello M., Raleigh DP., Cowburn D., Muir TW 'Solution Structure and Folding Characteristics of the C-Terminal SH3 Domain of c-Crk-II' Biochemistry 45, 8874-8884 ^a

Muralidharan V., Dutta K., Cho J., Vila-Perello M., Raleigh DP., Cowburn D., Muir TW 'Solution Structure and Folding Characteristics of the C-Terminal SH3 Domain of c-Crk-II' Biochemistry 45, 8874-8884 ^a

2004 Romanelli, A., Shekhtman, A., Cowburn, D., and Muir, T. W. Semisynthesis of a segmental isotopically labeled protein splicing precursor: NMR evidence for an unusual peptide bond at the N-extein-intein junction. Proc Natl Acad Sci U S A 101, 6397-6402. ^a

Lambert, L. J., Wei, Y., Schirf, V., Demeler, B., and Werner, M. H. T4 AsiA blocks DNA recognition by remodeling σ(70) region 4. EMBO J 23, 2952-2962.

Cowburn D, Shekhtman A, Xu R, Ottesen JJ, Muir TW. Segmental isotopic labeling for structural biological applications of NMR. Methods Mol Biol. 278 47-56. ^a

2003 Ottesen, J. J., Blaschke, U. K., Cowburn, D., and Muir, T. W. Segmental isotopic labeling: Prospects for a new tool to study the structure-function relationships in multidomain proteins. In Biological Magnetic Resonance, R. N. Krishna, and L. J. Berliner, eds. (New York, Kluwer), pp. 35-51. ^a,b

2002 Camarero, J. A., Shekhtman, A., Campbell, E. A., Chlenov, M., Gruber, T. M., Bryant, D. A., Darst, S. A., Cowburn, D., and Muir, T. W. (2002). Autoregulation of a bacterial sigma factor explored by using segmental isotopic labeling and NMR. Proc Natl Acad Sci U S A 99, 8536-8541.^a,b

Shekhtman, A., and Cowburn, D. A ubiquitin-interacting motif from Hrs binds to and occludes the ubiquitin surface necessary for polyubiquitination in monoubiquitinated proteins. Biochem Biophys Res Commun 296, 1222-1227. ^a,b

Shekhtman, A., Ghose, R., Goger, M., and Cowburn, D. NMR structure determination and investigation using a reduced proton (REDPRO) labeling strategy for proteins. FEBS Lett 524, 177-182. ^a,b

2001 Ghose, R., Shekhtman, A., Goger, M. J., Ji, H., and Cowburn, D. A novel, specific interaction involving the Csk SH3 domain and its natural ligand. Nat Struct Biol 8, 998-1004.^a,b

McDonnell, J. M., Calvert, R., Beavil, R. L., Beavil, A. J., Henry, A. J., Sutton, B. J., Gould, H. J., and Cowburn, D. The structure of the IgE Cε2 domain and its role in stabilizing the complex with its high-affinity receptor FcεRIα. Nat Struct Biol 8, 437-441.^a,b

Shekhtman, A., Ghose, R., Wang, D., Cole, P. A., and Cowburn, D. Novel mechanism of regulation of the non-receptor protein tyrosine kinase Csk: insights from NMR mapping studies and site-directed mutagenesis. J Mol Biol 314, 129-138. ^a,b

State University of New York

2008 Zhang Q, Atreya HS, Kamen DE, Girvin ME, Szyperski T. (2008) GFT projection NMR based resonance assignment of membrane proteins: application to subunit C of E. coli F(1)F (0) ATP synthase in LPPG micelles. J Biomol NMR, 40, 157-63.

2007 Yakubovskaya E, Lukin M, Chen Z, Berriman J, Wall JS, Kobayashi R, Kisker C, Bogenhagen DF. The EM structure of human DNA polymerase gamma reveals a localized contact between the catalytic and accessory subunits. EMBO J. 26:4283-91

Kempf, J. G.; Jung, J-y.; Ragain, C.; Sampson, N. S.; Loria, J. P. Dynamic Requirements for a functional protein hinge. 2007 J. Mol. Biol 368: 131-149

2006 Lemaster DM, Hernandez G 'Residue cluster additivity of thermodynamic stability in the hydrophobic core of mesophile vs. hyperthermophile rubredoxins.' Biophys Chem 125: 483-489

Burz, D.S., Dutta, K., Cowburn, D., Shekhtman, A. (2006) Mapping structural interactions in proteins using NMR (STINT-NMR). Nature Methods 3, 93-95 ^a

Burz, D.S., Dutta, K., Cowburn, D., Shekhtman, A. (2006) Mapping structural interactions in proteins using NMR (STINT-NMR). Nature Protocols, 1, 146-152. ^a

Tang Y, Grey MJ, McKnight J, Palmer AG. Raleigh DP Multistate Folding of the Villin Headpiece Domain. J Mol Biol 355, 1066-1072.^a

Tang Y, Goger MJ, Raleigh DP 'NMR Characterization of a Peptide Model Provides Evidence for Significant Structure in the Unfolded State of the Villin Headpiece Helical Subdomain.' Biochemistry 45:6940-6946 ^a

2005 Kempf, JG, Jung, J, Ragain, CM, Sampson, NS, Loria, JP. Entropic Control in Catalysis from the Functional Dynamics of a Protein Hinge. 46th Experimental NMR Conference, Providence, RI (1015 Apr 2005)

Peng, L., Liu, Y., Kim, N., Readman, J.E., and Grey, C.P. Detection of Brnsted acid sites in zeolite HY with high-field ¹⁷O-MAS-NMR techniques. Nature Materials 4 216-219

Wadsworth Center, NYS Health Dept. / Health Research Inc.

2007 Lemaster DM, Hernandez G 'Residue cluster additivity of thermodynamic stability in the hydrophobic core of mesophile vs. hyperthermophile rubredoxins.' Biophys Chem 125 (2-3), 483-489

2006 Bennett MT, Rodgers MT, Hebert AS, Ruslander LE, Eisele L, Drohat AC 'Specificity of Human Thymine DNA Glycosylase Depends on N-Glycosidic Bond Stability.' J Am Chem Soc 128, 12510-12519

Weill Medical College of Cornell University

2008 Malgieri G, Eliezer D. (2008) Structural effects of Parkinson's disease linked DJ-1 mutations. Protein Sci., 17, 855-68.

Paleologou KE, Schmid AW, Rospigliosi CC, Kim HY, Lamberto GR, Fredenburg RA, Lansbury PT Jr, Fernandez CO, Eliezer D, Zweckstetter M, Lashuel HA. (2008) Phosphorylation at S129, but not the phosphomimics S129E/D inhibits the fibrilization of α -synuclein. J Biol Chem, 283, 16895-16905.

Liu J, Wang D, Zheng Q, Lu M, Arora PS. (2008) Atomic structure of a short alpha-helix stabilized by a main chain hydrogen-bond surrogate. -J Am Chem Soc.-, 130, 4334-7.

2007 Sung YH, Eliezer D 'Residual Structure, Backbone Dynamics, and Interactions within the Synuclein Family.' J Mol Biol 372:689-707

Lu M, Lin SC, Huang Y, Kang YJ, Rich R, Lo YC, Myszka D, Han J, Wu H. XIAP Induces NF-kappaB Activation via the BIR1/TAB1 Interaction and BIR1 Dimerization. Mol Cell. 26 689-702

2006 Zheng Q, Deng Y, Liu J, Hoek LV, Berkhout B, Lu M 'Core Structure of S2 from the Human Coronavirus NL63 Spike Glycoprotein(,).' Biochemistry 45:15205-15215

Liu, J, Deng, Y, Zheng, Q, Cheng, CS, Kallenbach, NR, Lu, M. A Parallel Coiled-Coil Tetramer with Offset Helices. Biochemistry 45: 15224-15231

Liu J, Zheng Q, Deng Y, Cheng CS, Kallenbach NR, Lu M 'A seven-helix coiled coil.' Proc Natl Acad Sci U S A 103 15457-15462

Barré P, Eliezer D 'Folding of the repeat domain of tau upon binding to lipid surfaces' J. Mol. Biol. 362 312-26

Park HH, Wu H 'Crystal Structure of RAIDD Death Domain Implicates Potential Mechanism of PIDDosome Assembly.' J Mol Biol 357, 358-364.

Sung, Y, Rospigliosi, C, Eliezer, D NMR mapping of copper binding sites in α-synuclein. Biochim. Biophys. Acta 1764, 5-12.

Sung, Y, Eliezer, D, Secondary structure and dynamics of micelle bound β- and γ-synuclein. Prot Sci, 15,1162-1174.

Cordero-Morales, J, Cuello, L, Zhao, Y, Jogini, V, Cortes, D, Roux, B, Perozo, E. Molecular Determinants of Gating at the Potassium-Channel Selectivity Filter. Nat. Struct. Mol. Biol, 13 311.

Deng, Y, Liu, J, Zheng, Q, Eliezer, D, Kallenbach, N, Lu, M. Antiparallel Four-Stranded Coiled Coil Specified by a 3-3-1 Hyrdrophobic Heptad Repeat. Structure 14 247-255. ^a

Deng, Y, Liu, J, Zheng, Q, Yong, W, Lu, M. Structures and Polymorphic Interactions of Two Heptad-Repeat Regions of the SARS Virus S2 Protein. Structure 14, 889-899.

2005 Bussell, R Jr, Ramlall, T F, Eliezer, D. Helix Periodicity, Topology and Dynamics of Membrane-Associated alpha-Synuclein. Prot Sci 14, 862-872.

Eliezer, D, Barr, P, Kobaslija, M, Chan, D, Li, X, Heend, L. Residual structure in the repeat domain of tau: Echoes of microtubule binding and paired helical filament formation. Biochemistry 44, 1026-1036.

Steegborn C., Litvin T. N., Hess K. C., Capper A. B., Taussig R., Buck J., Levin L.R., Wu H. A novel mechanism for adenylyl cyclase inhibition from the crystal structure of its complex with catechol estrogen. J Biol Chem 280 31754-9.

Yang, JK, Wang,L, Zheng, L, Wan, F, Ahmed, M, Lenardo,MJ , Wu, H. Crystal Structure of MC159 Reveals Molecular Mechanism of DISC Assembly and FLIP Inhibition. Mol Cell 20, 939-949

Naik, M.T., Lee, H., Bracken, C. and Breslow, E., NMR Investigation of Main-Chain Dynamics of the H80E Mutant of Bovine Neurophysin-I: Demonstration of Dimerization-Induced Changes at the Hormone-Binding Site, Biochemistry 44, 11766-11776

Steegborn, C., Litvin, T., Levin, L., Buck, J., Wu, H. Biocarbonate Activation of Adenylyl Cyclase via Promotion of Catalytic Active Site Closure and Metal Recruitment. Nat. Struct. Mol. Biol. 12 32

2004 Liu, J., Yong, W., Deng, Y., Kallenbach, N., Lu, M. Atomic Structure of a Tryptophan-Zipper Pentamer. Proc Natl Acad Sci USA 101 16156-16161 ^a

Dai, J., Liu, J., Deng, Y., Smith, T., Lu, M. Structure and Protein Design of a Human Platelet Function Inhibitor. Cell 116 649-659

Ye, H., Chen, T., Xu, X., Pennycooke, M., Wu, H., Steegborn, C. Crystal Structure of the Putative Adapter Protein MTH1859. J. Struct. Biol. 148 251-256

NYSBC (as an institutional contributor or otherwise acknowledged)

Laboratory of Physical Biochemistry

2008 Liu D, Xu R, Dutta K, Cowburn D. (2008) N-terminal cysteinyl proteins can be prepared using thrombin cleavage. FEBS letts , 582, 1163-7.

Xiong X, Cui P, Hossain S, Xu R, Warner B, Guo X, An X, Debnath A, Cowburn D, Kotula L. (2008) . Allosteric Inhibition of the nonMyristoylated c-Abl Tyrosine Kinase by Phosphopeptides Derived from Abi1/Hssh3bp1. BBA Molecular Cell Research, 1783, 737-47.

Bhattacharya S, Zhang H, Debnath AK, Cowburn D. (2008) Solution structure of a hydrocarbon stapled peptide inhibitor in complex with monomeric C-terminal domain of HIV-1 capsid. J Biol Chem, 283, 16274-8.

Ferrage F, Piserchio A, Cowburn D, Ghose R. (2008) On the Measurement of 15N-{1H} Nuclear Overhauser Effects. J Mag Res, 192, 302-313.

Zhang H, Zhao Q, Bhattacharya S, Waheed A, Tong X, Hong A, Heck S, Curreli F, Goger M, Cowburn D, Freed E, Debnath A. (2008) A Cell-penetrating Helical Peptide as a Potential HIV-1 Inhibitor. J Miol Biol, 378, 565-80

2007 Valentine ER, Ferrage F, Massi F, Cowburn D, and Palmer AG 'Joint Composite-Rotation Adiabatic-Sweep Isotope Filtration' J. Biomol. NMR 38 11-22

Cowburn D 'Moving parts: how the adaptor protein CRK is regulated, and regulates.' Nat Struct Mol Biol 14:465-6

2006 Burz, D.S., Dutta, K., Cowburn, D., Shekhtman, A. (2006) Mapping structural interactions in proteins using NMR (STINT-NMR). Nature Methods 3, 93-95 ^a

Burz, D.S., Dutta, K., Cowburn, D., Shekhtman, A. (2006) Mapping structural interactions in proteins using NMR (STINT-NMR). Nature Protocols, 1, 146-152. ^a

Mukherjee, M., Dutta, K., White, M.A., Cowburn, D., Fox, R.O. (2006) "NMR solution structure and backbone dynamics of domain III of the E protein of tick-borne Langat flavivirus, suggests a potential site for molecular recognition" Protein Science 15 1342-1355.

Ferrage, F., Pelupessey P., Cowburn D., Bodenhausen G. "Intra-residue dipolar cross-relaxation rates between ¹³Cα and ¹³C' as a measure of internal dynamics in proteins by NMR Spectroscopy" J. Am. Chem. Soc. 128 11072-8

2005 Salmon, J.B., Dubrocq, C., Tabeling, P., Charier, S., Alcor, D., Jullien, L., Ferrage, F. (2005) An Approach To Extract Rate Constants from Reaction-Diffusion Dynamics in a Microchannel Anal. Chem. 77, 3417-3424

2004 Mukherjee, M., Dutta, K., Pascal, S., Fox, R. Letter to the Editor: Backbone and side chain resonance assignments of domain III of the tick-borne Langat flavivirus envelope protein. Journal of Biomolecular NMR. 29, 535 - 536

Romanelli, A., Shekhtman, A., Cowburn, D., and Muir, T. W. (2004). Semisynthesis of a segmental isotopically labeled protein splicing precursor: NMR evidence for an unusual peptide bond at the N-extein-intein junction. Proc Natl Acad Sci U S A 101, 6397-6402. ^a

Cowburn D, Shekhtman A, Xu R, Ottesen JJ, Muir TW. (2004) Segmental isotopic labeling for structural biological applications of NMR. Methods Mol Biol. 278 47-56. ^a

2003 Fushman, D., and Cowburn, D. (2003). Characterization of Inter-Domain Orientation in Solution using the NMR relaxation approach. In Biological Magnetic Resonance, R. N. Krishna, and L. J. Berliner, eds. (New York, Kluwer), pp. 53-77. ^b

Goger, M., McDonnell, J. M., and Cowburn, D. (2003). Using cryoprobes to decrease acquisition times of triple resonance experiments used for protein resonance assignments. Spectroscopy 17, 161-167. ^b

Ottesen, J. J., Blaschke, U. K., Cowburn, D., and Muir, T. W. (2003). Segmental isotopic labeling: Prospects for a new tool to study the structure-function relationships in multidomain proteins. In Biological Magnetic Resonance, R. N. Krishna, and L. J. Berliner, eds. (New York, Kluwer), pp. 35-51. ^{a, b}

Shekhtman, A., and Cowburn, D. (2002). A ubiquitin-interacting motif from Hrs binds to and occludes the ubiquitin surface necessary for polyubiquitination in monoubiquitinated proteins. Biochem Biophys Res Commun 296, 1222-1227. ^{a, b}

Shekhtman, A., Ghose, R., Goger, M., and Cowburn, D. (2002). NMR structure determination and investigation using a reduced proton (REDPRO) labeling strategy for proteins. FEBS Lett 524, 177-182. ^{a, b}

2001 Fushman, D., and Cowburn, D. (2001). Nuclear magnetic resonance relaxation in determination of residue-specific ¹⁵N chemical shift tensors in proteins in solution: protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Methods Enzymol 339, 109-126. ^{a, b}

Ghose, R., Shekhtman, A., Goger, M. J., Ji, H., and Cowburn, D. (2001). A novel, specific interaction involving the Csk SH3 domain and its natural ligand. Nat Struct Biol 8, 998-1004. ^{a, b}

McDonnell, J. M., Calvert, R., Beavil, R. L., Beavil, A. J., Henry, A. J., Sutton, B. J., Gould, H. J., and Cowburn, D. (2001). The structure of the IgE Cε2 domain and its role in stabilizing the complex with its high-affinity receptor FcεRIα. Nat Struct Biol 8, 437-441. ^{a, b}

Shekhtman, A., Ghose, R., Wang, D., Cole, P. A., and Cowburn, D. (2001). Novel mechanism of regulation of the non-receptor protein tyrosine kinase Csk: insights from NMR mapping studies and site-directed mutagenesis. J Mol Biol 314, 129-138. ^{a, b}

Other

2008 Wu CC, Rice WJ, Stokes DL. (2008) Structure of a copper pump suggests a regulatory role for its metal-binding domain. Structure 16, 976-85.

Owen GR, Acehan D, Derr KD, Rice WJ, Stokes DL. (2008) Cryoelectron tomography of isolated desmosomes. Biochem Soc Trans, 36, 173-9.

2007 Vink M, Derr K, Love J, Stokes DL, Ubarretxena-Belandia I. (2007) A high-throughput strategy to screen 2D crystallization trials of membrane proteins. J Struct Biol, 160, 295-304.

Stokes DL 'Desmosomes from a structural perspective.' Curr Opin Cell Biol 19:565-71

Vanamee ES, Berriman J, Aggarwal AK. An EM view of the FokI synaptic complex by single particle analysis. J Mol Biol 370 207-12

Li Y, Brodsky B, Baum J. NMR shows hydrophobic interactions replace glycine packing in the triple helix at a natural break in the (Gly-X-Y)n repeat. J Biol Chem 282:22699-706

Yakubovskaya E, Lukin M, Chen Z, Berriman J, Wall JS, Kobayashi R, Kisker C, Bogenhagen DF. The EM structure of human DNA polymerase gamma reveals a localized contact between the catalytic and accessory subunits. EMBO J. 26:4283-91

2006 Pomfret, A.J., Rice, W.J., Stokes, D.L. Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases. Journal of Structural Biology, 157, 106-116.

Hinsen, K., Reuter, N., Navaza, J., Stokes, D.L., Lacapere, J.J. Normal mode-based fitting of atomic structure into electron density maps: Application to sarcoplasmic reticulum Ca-ATPase. Biophysical Journal 88, 818-827.

Wood, M.A., Meredith, D.O., Owen, G.R., Richards, R.G., Riehle, M.O. Utilizing atomic number contrast for FESEM imaging of colloidal nanotopography underlying biological cells. Nanotechnology 16, 1433-1439.

Rao, K.N., Kumaran, D., Seetharaman, J., Bonanno, J.B., Burley, S.K., Swaminathan, S. Crystal structure of trehalose-6-phosphate phosphatase-related protein: Biochemical and biological implications. Protein Science 15, 1735-1744.

Greig, S.L., Berriman, J.A., O'Brien, J.A., Taylor, J.A., Bellamy, A.R., Yeager, M.J., Mitra, A.K. Structural determinants of rotavirus subgroup specificity mapped by cryo-electron microscopy. Journal of Molecular Biology 356, 209-221.

Rice WJ, Kovalishin A, Stokes DL 'Role of metal-binding domains of the copper pump from Archaeoglobus fulgidus.' Biochem Biophys Res Commun 348, 124-131

2005 Stokes, D.L., F. Delavoie, W.J. Rice, P. Champeil, D.B. McIntosh, J.-J. Lacapere, 2005. Structural Studies of a Stabilized Phosphoenzyme Intermediate of Ca²⁺-ATPase. J. Biol. Chem. 280 18063-18072. ^a

2003 He, W., Cowin, P., and Stokes, D. L. (2003). Untangling desmosomal knots with electron tomography. Science 302, 109-113. ^{a, b}

Notes

a This publication has two or more Member Institutional affiliations.

b This publication has NYSBC as an institutional affiliation because of support for investigators Cowburn or Stokes, and preceded scientific use of the facilities.

c Publications using the beamline X4A are taken from the NSLS site http://www.nsls.bnl.gov/beamlines/beamline.asp?blid=X4A, for 2004 on. Before that date, X4A was operated by HHMI. Others are nominated to this list by an author and/or contain a specific reference to NYSBC.

d RPI has access to NYSBC resources by arrangements with Wadsworth Center.

-- JasperShahn - 8 Jul 2005

This topic: Main > NysbcPubs

History: r77 - 16 Jul 2008 - 10:55:41 - JasperShahn

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PUBLICATIONS ASSOCIATED WITH THE NEW YORK STRUCTURAL BIOLOGY CENTER BY MEMBER INSTITUTION c

Other

Notes

a This publication has two or more Member Institutional affiliations.

b This publication has NYSBC as an institutional affiliation because of support for investigators Cowburn or Stokes, and preceded scientific use of the facilities.

c Publications using the beamline X4A are taken from the NSLS site http://www.nsls.bnl.gov/beamlines/beamline.asp?blid=X4A, for 2004 on. Before that date, X4A was operated by HHMI. Others are nominated to this list by an author and/or contain a specific reference to NYSBC.

d RPI has access to NYSBC resources by arrangements with Wadsworth Center.

PUBLICATIONS ASSOCIATED WITH THE NEW YORK STRUCTURAL BIOLOGY CENTER BY MEMBER INSTITUTION ^c