Publications-2008

--- Year 2008 ---

2. Aggarwal, R., Burley, S.K., Swaminathan, S. (2008)(14)
A novel mode of dimerization via formation of a glutamate anhydride crosslink in a protein crystal structure.
Proteins 71: 1038-1041

3. Lucas M Velloso, Shyam S Bhaskaran, Raymond Schuch, Vincent A Fischetti & C Erec Stebbins (2008) (153_RUg)
A structural basis for the allosteric regulation of non-hydrolysing UDP-GlcNAc 2-epimerases.
EMBO Reports. 9, 199 - 205 Published online: 11 January 2008 [premier].

4. Hanna, R.A., Campbell, R.L., Davies, P.L. (2008)(185)
Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin.
Nature, 456:409-12 [premier].

5. Yang, M, K Horii, AB Herr, TL Kirley.(2008) (77)
Characterization and importance of the dimer interface of human calcium-activated nucleotidase.
Biochemistry 47:771-778

6. Benarroch D, Smith P, Shuman S. (2008) (153_SKIb,c)
Characterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domain.
Structure 16:501-12

7. Liliana Marín-García, Bernardo A. Frontana-Uribe, Juan Pablo Reyes-Grajeda, Vivian Stojanoff, Hugo Javier Serrano-Posada & Abel Moreno. (2008)(87)
Chemical recognition of carbonate anions by proteins involved in biomineralization processes and their influence on calcite crystal growth.
Cryst. Growth Des. 8: 1340-1345

8. Qian, J., Cuerrier, D., Davies, P.L., Li, Z., Powers, J.C., Campbell, R.L. (2008)(185)
Cocrystal structures of primed side-extending alpha-ketoamide inhibitors reveal novel calpain-inhibitor aromatic interactions.
J. Med. Chem. 51: 5264-5270

9. Eugenio De la Mora Lugo y Enrique Rudiño Piñera (2008)(174)
Cristales, difracción y desplazamiento atómicos: ¿es posible usar datos cristalográficos para extraer movimientos.
XXXII Mensaje Bioquímico, Facultad de Medicina, UNAM.
ISSN-0188-137X, pp.135-148.

11. N. B. Olivier and B. Imperiali B. (2008) (173)
Crystal structure and catalytic mechanism of PglD from Campylobacter jejuni.
J. Biol. Chem. 283:27937-46

13. Di Costanzo, L., Drury, J.E., Penning, T.M., Christianson, D.W. (2008) (229)
Crystal Structure of Human Liver {Delta}4-3-Ketosteroid 5{beta}-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis.
J. Biol. Chem. 283: 16830-16839

14. Kelly V. Jamieson, Jinhua Wu, Stevan R. Hubbard, and Daniel Meruelo (2008) (193)
Crystal structure of the human laminin receptor precursor.
J. Biol. Chem. 283: 3002 - 3005

15. S. Biswas, M. M. Mohammad, L. Movileanu and B. van den Berg, B. (2008) (110b)
Crystal Structure of the Outer Membrane Protein OpdK from Pseudomonas aeruginosa.
Structure 16: 1027-1035

16. Xiang, S., Tong, L. (2008) (162)
Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction.
Nat. Struct. Mol. Biol. 15: 295-302 [premier].

17. Cortajarena AL, Yi F, Regan L. (2008) (27a)
Designed TPR modules as novel anticancer agents.
ACS Chem Biol. 3:161-6

18. James Q. Boedicker, Liang Li, Timothy R. Kline, and Rustem F. Ismagilov (2008) (199)
Detecting bacteria and determining their susceptibility to antibiotics by stochastic confinement in nanoliter droplets using plug-based microfluidics.
Lab Chip 8: 1265-1272

19. Bacha, U., Barrila, J., Gabelli, S.B., Kiso, Y., Amzel, L.M., Freire, E. (2008) (204)
Development of Broad-Spectrum Halomethyl Ketone Inhibitors Against Coronavirus Main Protease 3CLpro
Chem. Biol. Drug. Des. 72: 34-49

20. Yobana Pérez, Désir Eid, Francisco Acosta, Liliana Marín-García, Jean Jakoncic, Vivian Stojanoff, Bernardo A. Frontana-Uribe, Abel Moreno (2008)(84)
Electrochemically Assisted Protein Crystallization of Commercial Cytochrome C without Previous Purification.
Cryst. Growth Des. 8:2493-2496

21. Tang, Y., Holbert, M.A., Wurtele, H., Meeth, K., Rocha, W., Gharib, M., Jiang, E., Thibault, P., Verrault, A., Cole, P.A., Marmorstein, R.(2008) (203)
Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP.
Nat. Struct. Mol. Biol. 15: 738-745 [premier].

22. N Mirkin, J Jakoncic, V Stojanoff and A Moreno (2008) (84)
High Resolution X-ray Crystallographic Structure of Bovine Heart Cytochrome C and its Application to the Design of an Electron Transfer Biosensor
Proteins: Struc. Func. Bioinformatics 70:83-92

23. Zhaocai Zhou, Xiaomin Song, Alan Berezov, Geng Zhang, Yanjing Li, Hongtao Zhang, Ramachandran Murali, Bin Li, and Mark I. Greene (2008)(117a)
Human glucocorticoid-induced TNF receptor ligand regulates its signaling activity through multiple oligomerization states
Proc. Natl. Acad. Sci. 105:5465-5470 [premier].

24. C. H. Huang, D. Mandelker, S. B. Gabelli and L. M. Amzel (2008)(195)
Insights into the oncogenic effects of /PIK3CA/ mutations from the structure of p110alpha/p85alpha.
Cell Cycle 7:1151-6 [premier].

25. Rinaldo-Matthis, A., Murkin, A.S., Ramagopal, U.A., Clinch, K., Mee, S.P., Evans, G.B., Tyler, P.C., Furneaux, R.H., Almo, S.C., Schramm, V.L. (2008) (153_AECOMe)
L-Enantiomers of transition state analogue inhibitors bound to human purine nucleoside phosphorylase.
J. Am. Chem. Soc. 130: 842-844 [premier].

26. Grove TZ, Cortajarena AL, Regan L.(2008) (27a)
Ligand binding by repeat proteins: natural and designed.
Curr. Opin. Struct. Biol. 18:507-1 [premier].

27. Mitrousis, G., Olia, S.A., Walker-Kopp,N. and Cingolani, G. (2008) (65)
Molecular basis for the recognition of snurportin 1 by importin b.
J. Biol. Chem. 283: 7877-7884

28. Hearn, E.M., Patel, D.R., van den Berg, B. (2008)(47a, 110a)
Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation
Proc. Natl. Acad. Sci. 105: 8601-8606; published online on June 16, 2008 [premier].

29. Coureux, P.D., Fan, Z.P., Stojanoff, V., Genick, U.K. (2008) (63) Picometer-scale conformational heterogeneity separates functional from nonfunctional States of a photoreceptor protein.
Structure 16: 863-872

30. Friedmann, D.R., Wilson, J.J., Kovall, R.A. (2008) (57)
RAM-induced Allostery Facilitates Assembly of a Notch Pathway Active Transcription Complex.
J. Biol. Chem. 283: 14781-14791

31. Tatiana Y. Zakharian, Luigi Di Costanzo and David W. Christianson (2008)(188)
(S)-2-Amino-6-nitrohexanoic Acid Binds to Human Arginase I through Multiple Nitro−Metal Coordination Interactions in the Binuclear Manganese Cluster
J. Am. Chem. Soc., 130(51):17254–17255 [premier].

32. deLivron, M. A., and Robinson, V. L. (2008) (55)
Salmonella enterica Serovar Typhimurium BipA Exhibits Two Distinct Ribosome Binding Modes.
J. Bacteriol. 190(17): 5944-5952,

33. Liang Li, Sigrid Nachtergaele, Annela M. Seddon, Valentina Tereshko, Nina Ponomarenko, and Rustem F. Ismagilov, (2008) (199)
Simple Host-Guest Chemistry To Modulate the Process of Concentration and Crystallization of Membrane Proteins by Detergent Capture in a Microfluidic Device.
J. Am. Chem. Soc. 130: 14324-14328 [premier].

34. Chen Yunting, Jakoncic Jean, Wang Jin, Zheng Xiliang, Carpino Nick, Nassar Nicolas (2008)(211)
Structural and Functional Characterization of the C-Terminal Domain of the Ecdysteroid Phosphate Phosphatase from Bombyx mori Reveals a New Enzymatic Activity.
Biochemistry 47:12135-12145

36. Brent, M.M., Anand, R., Marmorstein, R. (2008) (211)
Structural Basis for DNA Recognition by FoxO1 and Its Regulation by Posttranslational Modification.
Structure 16: 1407-1416

37. Stouffer, A.L., Acharya, R., Salom, D., Levine, A.S., Costanzo, L.D., Soto, C.S., Tereshko, V., Nanda, V., Stayrook, S., DeGrado, W.F. (2008)(169,123)
Structural basis for the function and inhibition of an influenza virus proton channel
Nature 451: 596-600 [premier].

38. J. J. Adams, K. Gregg, E. A. Bayer, A. B. Boraston & S. P. Smith (2008) (130)
Structural basis for a novel mode of Clostridium perfringens toxin complex formation.
Proc. Natl. Acad. Sci. (Track II). 105, 12194-12199 [premier].

39. Critton, D.A., Tortajada, A., Stetson, G., Peti, W., Page, R. (2008) (150)
Structural basis of substrate recognition by Hematopoietic Tyrosine Phosphatase (HePTP).
Biochemistry, 47:13336–45

40. V Thai, P Renesto, C Fowler, D Brown, T Davis, W Gu, D Pollock, D Kern, D Raoult, and E Eisenmesser (2008) (132)
Structural, Biochemical, and in Vivo Characterization of the First Virally Encoded Cyclophilin from the Mimivirus.
J. Mol. Biol. 378:71-86

41. Nan Zhao, Jean-Luc Ferrer, Jeannine Ross, Ju Guan, Yue Yang, Eran Pichersky, Joseph P. Noel, and Feng Chen (2008) (12d)
Structural, Biochemical and Phylogenetic Analyses Suggest that Indole-3-acetic Acid Methyltransferase Is An Evolutionarily Ancient Member of the SABATH Family
Plant Physiol. 146: 455-467 [premier].

42. L. M. Amzel, C. H. Huang, D. Mandelker, C. Lengauer, S. B. Gabelli and B. Vogelstein (2008)(195)
Structural comparisons of class I phosphoinositide 3-kinases.
Nat. Rev. Cancer 8:665-669 Epub 2008 Jul 17 [premier].

43. Brohawn, S.G., Leksa, N.C., Spear, E.D., Rajashankar, K.R., Schwartz, T.U. (2008) (236)
Structural evidence for common ancestry of the nuclear pore complex and vesicle coats.
Science 322: 1369-1373 [premier].

44. Valverde R, Edwards L, Regan L.(2008) (107)
Structure and function of KH domains.
FEBS J. 275:2712-26

46. Qian C, Li S, Jakoncic J, Zeng L, Walsh MJ, Zhou MM. (2008) (213)
Structure and Hemimethylated CpG Binding of the SRA Domain from Human UHRF1.
J. Biol. Chem. 2008 283:34490-4. Epub 2008 Oct 22.

47. Xie, P., Williams, D.S., Atilla-Gokcumen, G.E., Milk, L., Xiao, M., Smalley, K.S., Herlyn, M., Meggers, E., Marmorstein, R. (2008)(263)
Structure-based design of an organoruthenium phosphatidyl-inositol-3-kinase inhibitor reveals a switch governing lipid kinase potency and selectivity.
ACS Chem. Biol. 3: 305-316

48. Malashkevich, V.N., Varney, K.M., Garrett, S.C., Wilder, P.T., Knight, D., Charpentier, T.H., Ramagopal, U.A., Almo, S.C., Weber, D.J., Bresnick, A.R. (2008) (153_AECOMb)
Structure of Ca(2+)-Bound S100A4 and Its Interaction with Peptides Derived from Nonmuscle Myosin-IIA.
Biochemistry 47: 5111-5126

49. Kim, J., Tsai, P.C., Chen, S.L., Himo, F., Almo, S.C., Raushel, F.M. (2008) (153_AECOMd)
Structure of diethyl phosphate bound to the binuclear metal center of phosphotriesterase.
Biochemistry 47: 9497-9504

50. Loll, P. J., Swain, E., Chen, Y, Turner, B. T., and Zhang, J. F. (2008)(97b)
Structure of the SH3 domain of rat endophilin A2.
Acta Crystallogr. F64:243-246

51. Gillis, A.J., Schuller, A.P., Skordalakes, E.(2008)(180)
Structure of the Tribolium castaneum telomerase catalytic subunit TERT.
Nature 455: 633-637 [premier].

55. Zakharian, T.Y., Di Costanzo, L., Christianson, D.W. (2008)(188)
Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I
Org. Biomol. Chem. 6: 3240-3243

56. M. A. Adams, Y. Luo, B. Hove-Jensen, S. He, L. M. Dryden, D. Zechel and Z. Jia(2008) (105)
The crystal structure of PhnH: a necessary component of C-P lyase in Escherichia coli.
J. Bacteriol. 190:1072-1083

57. Liu, X., Wang, L., Zhao, K., Thompson, P.R., Hwang, Y., Marmorstein, R., Cole, P.A. (2008)(165)
The structural basis of protein acetylation by the p300/CBP transcriptional coactivator
Nature 451: 846-850 [premier]

--- Year 2008 (NO Project) ---

1. J Cannon, R Haire, A Magis, D Eason, K Winfrey, J Hernandez Prada, K Bailey, J Jakoncic, G Litman and D Ostrov,(UNKNOWN)
A Bony Fish Immunological Receptor of the NITR Multigene Family Mediates Allogeneic Recognition
Immunity, 29:228-237 [premier]

10. A Magis, K Bailey, E Kurenova, J Hernandez Prada, W Cance, D Ostrov (2008)(UNKNOWN) Crystallization of the Focal Adhesion Kinase Targeting (FAT) Domain in a Primitive Orthorhombic Space Group
Acta Cryst. F, 64, 564-566

12. Moiseeva, N., Bau, R., Swenson, S.D., Markland, F.S., Choe, J.-Y., Liu, Z.-J., Allaire, M. (2008) (UNKNOWN)
Crystal structure of acostatin, a dimeric disintegrin from southern copperhead (Agkistrodon contortrix contortrix) at 1.7 A resolution
Acta Crystallogr.,Sect.D 64: 466-470

35. M Bianchet, A Hafiz, G Vasta and M Amzel (2008) (UNKNOWN)
Structural Aspects of Lectin-Ligand Interactions, Animal Lectins: A Functional View, p. 13-47, CRC Press, Boca Raton, London, New York.

52. Tang, Y., Meeth, K., Jiang, E., Luo, C., Marmorstein, R. (2008) (UNKNOWN)
Structure of Vps75 and implications for histone chaperone function.
Proc.Natl.Acad.Sci.Usa 105: 12206-12211 [premier]

53. A. Patel, V. Dharmarajan and M. Cosgrove (2008) (UNKNOWN)
Structure of WDR5 bound to Mixed Lineage Leukemia protein-1 peptide,
J. Biol. Chem. 283:32158-32161

54. Y Gupta, D Nair, R Wharton, A Aggarwal (2008)(UNKNOWN)
Structures of Human Pumilio with Noncognate RNAs Reveal Molecular Mechanisms for Binding Promiscuity
Structure, 16(4): 549-57

--- Year 2008 (Thesis Publications) ---

35. S Messing
Structure and Function of the RNA Pyrophosphohydrolase BdRppH and the 9-cis-epoxy Carotenoid Dioxygenase VP14 , Ph.D Thesis. Johns Hopkins University, Baltimore (2008).