Publications-2007

--- Year 2007 ---

1. Katherine A. Henzler-Wildman, Ming Lei, Vu Thai, S. Jordan Kerns, Martin Karplus, Dorothee Kern (2007) (16)
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis.
Nature. 450: 913-916

2. Kun Qian and Vivian Stojanoff (2007)
An integrated web environment for fast access and easy management of a synchrotron beam line.
Nuclear Inst. and Methods in Physics Research, A. 582: 199-201

3. Gunther, S., Varma, A.K., Moza, B., Kasper, K.J., Wyatt, A.W., Zhu, P., Rahman, A.K., Li, Y., Mariuzza, R.A., McCormick, J.K., Sundberg, E.J. (2007) (152)
A novel loop domain in superantigens extends their T cell receptor recognition site .
J.Mol.Biol. 371: 210-221

4. Mikhkylik a., Ford b., Keller j., Chen y, Nassar n, Carpino n (2007) (139)
A phosphatase activity of Sts-1 contributes to the suppression of TCR signaling.
Mol Cell. 27(3): 486-97

5. A. Jain and V. Stojanoff, 2007
Are you centered? An automatic crystal-centering method for high-throughput macromolecular crystallography
J. Synchrotron Rad, 14: 355-360 [ Read Article ]

6. Coureux, Pierre-Damien; Genick, Ulrich K (2007) (63)
Chapter Book Publication Methods in Enzymology 422( A) 305-337

7. Fuentes-Silva, D., Mendoza-Hernandez, G., Stojanoff, V., Palomares, L.A., Zenteno, E., Torres-Larios, A., Rodriguez-Romero, A. (2007) (159)
Crystallization and identification of the glycosylated moieties of two isoforms of the main allergen Hev b 2 and preliminary X-ray analysis of two polymorphs of isoform II.
Acta Cryst.F 63: pp.787-791

9. Parry, C.S., Gorski, J., Stern, L.J. (2007) (59)
Crystallographic Structure of the Human Leukocyte Antigen DRA, DRB3*0101: Models of a Directional Alloimmune Response and Autoimmunity.
J.Mol.Biol. v371: pp.435-446

10. L Di Costanzo, M Pique, D Christianson. (2007) (188)
Crystal Structure of Human Arginase l Complexed with Thiosemicarbazide Reveals an Unusual Thiocarbonly u-Sulfide Ligand in the Binuclear Manganese Cluster.
J. Am. Chem. Soc., 129: 6388-6389

11. Zhu, W., Chance, M.R., Manjasetty, B.A. (2007)(153_CWRUa)
Crystal Structure of Mn2+-bound Escherichia coli L-arabinose Isomerase (ECAI) and Implications in Protein Catalytic Mechanism and Thermo-Stability.
The Journal of Young Investigators 17: 1-1

12. Napetschnig, J., Blobel, G., Hoelz, A. (2007) (153_RUc)
Crystal structure of the N-terminal domain of the human protooncogene Nup214/CAN.
Proc.Natl.Acad.Sci.Usa v104: 1783-1788

13. Kull, F.J., DeSilva, R.S., Kovacikova, G., Lin, W., Taylor, R.K., Skorupski, K. (2007) (108)
Crystal structure of the Vibrio cholerae Quorum-Sensing Regulatory Protein HapR.
J.BACTERIOL. v189 : pp. 5683-5691

14. Crichlow, G.V., Zhou, H., Hsiao, H-H., Frederick, K.B., Debrosse, M., Yang, Y., Folta-Stogniew, E.J., Chung, H-J., Fan, C., De La Cruz, E.M., Levens, D., Lolis , E., Braddock, D. (2007) (163)
Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition.
EMBO J. 27: 277-289.

15. J. Parker, M.A. Bianchet, D. Krosky, J Friedman, L.M. Amzel & J Stivers (2007) (231)
Enzymatic capture of an extrahelical thymine in the search for uracil in DNA. Nature 449(7161):433-437

16. Valverde, Roberto, Pozdnyakova, Irina, Kajander, Tommi, Venkatraman, Janani, and Regan, Lynne. (2007) (107)
Fragile X Mental Retardation Syndrome: Structure of the KH1-KH2 Domains of Fragile X Mental Retardation Protein.
Structure. 15: 1090-1098.

17. Samer Lone, Sharon A. Townson, Sacha N. Uljon, Robert E. Johnson, Amrita Brahma, Deepak T. Nair, Satya Prakash, Louise Prakash, and Aneel K. Aggarwal (2007) (62)
Human DNA Polymerase Kappa Encircles DNA: Implications for Mismatch Extension and Lesion Bypass.
Molecular Cell 25: 601-614

18. Katherine A. Henzler-Wildman, Vu Thai, Ming Lei, Maria Ott, Magnus Wolf-Watz, Tim Fenn, Ed Pozharski, Mark A. Wilson, Gregory A. Petsko, Martin Karplus, Christian G. Hubner, Dorothee Kern (2007) (16)
Intrinsic motions along an enzymatic reaction trajectory.
Nature 450: 838-844

19. Varbanova M, Yamaguchi S, Yang Y, McKelvey K, Hanada A, Borochov R, Yu F, Jikumaru Y, Ross J, Cortes D, Je Ma C, Noel JP, Mander L, Shula ev V, Kamiya Y, Rodermel S, Weiss D, Pichersky E. (2007) (12a,12d)
Methylation of Gibberellins by Arabidopsis GAMT1 and GAMT2.
Plant Cell. 19:32-45

20. A Moreno, B Quiroz-Garcia, F Yokaichiya, V Stojanoff, P Rudolph (2007) (230) Protein Crystal Growth in Gels and Stationary Magnetic Fields.
Cryst. Res. Technol. 42: 231-236

21. Bajaj, M. and Moriyama, H. (2007) (61d)
Purification, crystallization, and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana.
Acta Crystallographica F. 63: 409-411.

22. J. P. Reyes-Grajeda, L. Marin-Garcia, V. Stojanoff and A. Moreno (2007) (87)
Purification, crystallization and preliminary X-ray analysis of struthiocalcin 1 from ostrich (Struthio camelus) eggshell.
Acta Crystallographica F. 63: 987-989

23. R Daber, S Stayrook, A Rosenberg, M Lewis(2007) (122)
Structural Analysis of Iac Repressor Bound to Allosteric Effectors.
J. Mol. Biol., 370: 609-619

24. P Sapienza, J Rosenberg, L Jen-Jacobson. (2007) (234)
Structural and Thermodymamic Basis for Enhanced DNA Binding by a Promiscuous Mutant EcoRI Endonuclease.
Structure 15: 1368-1382

25. Yuzawa, S., Opatowsky, Y., Zhang, Z., Mandiyan, V., Lax, I., Schlessinger, J. (2007) (140)
Structural Basis for Activation of the Receptor Tyrosine Kinase KIT by Stem Cell Factor.
Cell(Cambridge,Mass.) v130: pp. 323-334

26. Sanders, B.D., Zhao, K., Slama, J.T. and Marmorstein, R. (2007) (73) Structural basis for nicotinamide inhibition and base exchange in Sir2 enzymes.
Mol. Cell, 25: 463-472.

27. Lew, E.D., Bae, J.H., Rohmann, E., Wollnik, B., Schlessinger, J. (2007) (137)
Structural basis for reduced FGFR2 activity in LADD syndrome: Implications for FGFR autoinhibition and activation.
PNAS 104: 19802-19807

28. Korczynska M, Mukhtar TA, Wright GD, Berghuis AM. (2007) (125)
Structural basis for streptogramin B resistance in Staphylococcus aureus by virginiamycin B lyase.
Proc Natl Acad Sci U S A. 104(25) : 10388-93

29. Aleshin, A.E., Shiryaev, S.A., Strongin, A.Y., Liddington, R.C. (2007) (92 PDB:2GGV)
Structural evidence for regulation and specificity of flaviviral proteases and evolution of the Flaviviridae fold.
Protein Sci. 16: 795-806

30. Almo, S.C., Bonanno, J.B., Sauder, J.M., Emtage, S., Dilorenzo, T.P., Malashkevich, V., Wasserman, S.R., Swaminathan, S., Eswaramoorthy, S., Agarwal, R., Kumaran, D., Madegowda, M., Ragumani, S., Patskovsky, Y., Alvarado, J., Ramagopal, U.A., Faber-Barata, J., Chance, M.R., Sali, A., Fiser, A., Zhang, Z.Y., Lawrence, D.S., Burley, S.K. (2007) (153_AECOMc)
Structural genomics of protein phosphatases.
J Struct Funct Genomics. 8: 121-140

31. Biswas, S, Mohammad, MM, Patel, DR, Movileanu, L and van den Berg, B (2007) (110b)
Structural Insight into OprD Substrate specifity.
NSMB 14: 1108-1109.

32. Ferraro, D.J., Brown, E.N., Yu, C.L., Parales, R.E., Gibson, D.T., Ramaswamy, S. (2007) (22)
Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1.
Bmc Struct.Biol. 7: 10-10

33. Burk, D.L., Hwang, J., Kwok, E., Marrone, L., Goodfellow, V., Dmitrienko, G.I., Berghuis, A.M. (2007)(168) Structural Studies of the Final Enzyme in the alpha-Aminoadipate Pathway-Saccharopine Dehydrogenase from Saccharomyces cerevisiae
J.Mol.Biol. 373: 745-754

34. Gabelli, S.B., Bianchet, M.A., Xu, W.L., Dunn, C.A., Niu, Z.-D., Amzel, L.M., Bessman, M.J. (2007) (170a)
Structure and Function of the E. coli Dihydroneopterin Triphosphate Pyrophosphatase: A Nudix Enzyme Involved in Folate Biosynthesis.
Structure. 15: 1014-1022

35. Lee, J., Page, R., Garcia-Contreras, R., Palermino, J.M., Zhang, X.S., Doshi, O., Wood, T.K., Peti, W. (2007) (150)
Structure and Function of the Escherichia coli Protein YmgB: A Protein Critical for Biofilm Formation and Acid-resistance.
J.Mol.Biol. 373: 11-26

36. Kajander T, Cortajarena AL, Mochrie S, Regan L. (2007) (27a)
Structure and stability of designed TPR protein superhelices: unusual crystal packing and implications for natural TPR proteins.
Acta Crystallogr D Biol Crystallogr. D63: 800-801

37. Genick UK. (2007) (63)
Structure-factor extrapolation using the scalar approximation: theory, applications and limitations.
Acta Crystallogr D Biol Crystallogr. 63:1029-41

38. Olia, A.S., Casjens, S.R., Cinglani, G. (2007) (155)
Structure of Phage P22 Cell Envelope Penetrating Needle.
Nature Structural Biology. 14: 1221-1226

39. Olia, S.A., Casjens, S. and Cingolani, G. (2007) (93)
Structure of Tail Needle gp26 bound to Xenon gas.
Acta Cryst D. Submitted

40. S. Wang, J. Engohang-Ndong, and I. Smith. (2007) (94)
Structure of the DNA-binding domain of the response regulator PhoP from Mycobacterium tuberculosis.
Biochemistry. 46: 14751-14761

41. Primo ME, Klinke S, Sica MP, Goldbaum FA, Jakoncic J, Poskus E, Ermacora MR. (2007) (154)
Structure of the mature ectodomain of the human receptor-type protein-tyrosine phosphatase IA-2.
J Biol Chem. 283: 4674-4681

42. Susan Rouda and Emmanuel Skordalakes (2007) (209)
Structure of the RNA-Binding Domain of Telomerase: Implications for RNA Recognition and Binding.
Structure. 15: 1403-1412

43. J. Jakoncic , Y. Jouanneau, C. Meyer and V. Stojanoff. (2007) (50)
The catalytic pocket of the ring-hydroxylating dioxygenase from Spingomonas CHY1.
Biochemical and Biophysical Research Communications(2007) 352 : 861-866

44. Jean Jakoncic, Yves Jouanneau, Christine Meyer, Vivian Stojanoff (2007) (50)
The crystal structure of the ring-hydroxylating dioxygenase from Spingomonas CHY-1.
FEBS Journal (2007) 274: 2470-2481

45. Abbott, D.W., Boraston, A.B. (2007) (146)
The Structural Basis for Exopolygalacturonase Activity in a Family 28 Glycoside Hydrolase.
J.Mol.Biol. 368: 1215-1222

46. Chuan-Hsiang Huang, Diana Mandelker, Oleg Schmidt-Kittler, Yardena Samuels, Victor E. Velculescu, Kenneth W. Kinzler, Bert Vogelstein, Sandra B. Gabelli, and L. Mario Amzel (195)
The Structure of a Human p110{alpha}/p85{alpha} Complex Elucidates the Effects of Oncogenic PI3K{alpha} Mutations.
Science (Cover). 318: 1744-1748.

47. Liang Li, James Q. Boedicker, and Rustem F. Ismagilov (2007) (199) Using a Multijunction Microfluidic Device To Inject Substrate into an Array of Preformed Plugs without Cross-Contamination: Comparing Theory and Experiments.
Anal. Chem. 79: 2756-2761

48. N. Moiseeva and M. Allaire. (2007)
Using barium ions for heavy-atom derivatization and phasing of xylanase II from Trichoderma longibrachiatum.
Acta Cryst. D. 63: 1025-1028

49. Delai L. Chen, Liang Li, Sebastian Reyes, David N. Adamson, and Rustem F. Ismagilov (2007) (199) Using Three-Phase Flow of Immiscible Liquids To Prevent Coalescence of Droplets in Microfluidic Channels: Criteria To Identify the Third Liquid and Validation with Protein Crystallizations
Langmuir 23: 2255-2260

50. Aoyagi M, Zhai D, Jin C, Aleshin AE, Stec B, Reed JC, Liddington RC. (2007) (95)
Vaccinia virus N1L protein resembles a B cell lymphoma-2 (Bcl-2) family protein.
Protein Sci. 16(1):118-24

51. Lu, M., Lin, S.C., Huang, Y., Kang, Y.J., Rich, R., Lo, Y.C., Myszka, D., Han, J., Wu, H. (2007) (114)
XIAP Induces NF-kappaB Activation via the BIR1/TAB1 Interaction and BIR1 Dimerization.
Mol.Cell 26: 689-702

--- Year 2007 (NO Project) ---

8. D Ostrov, J Hernandez Prada, R Haire, J Cannon, A Magis, K Bailey, G Litman (2007)(UNKNOWN)
Crystallization and X-ray Diffraction Analysis of a Novel Immune-Type Receptor from Ictalurus punctatus and Phasing by Selenium Anomalous Dispersion Methods
Acta Cryst. F, 63, 1035-1037