Novel uncomplexed and complexed structures of plasmepsin II, an aspartic protease from Plasmodium falciparum

Journal of Molecular Biology

Volumn 327, Issue 1, 2003, Pages 173-181

  Asojo, Oluwatoyin A ^a   Gulnik, Sergei V ^a,c   Afonina, Elena ^a,c   Yu, Betty ^a,c   Ellman, Jonathan A ^b   Haque, Tasir S ^b   Silva, Abelardo M ^a,c  

^a NATIONAL CANCER INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Sequoia Pharmaceuticals Inc   (United States)

Author keywords

Aspartic protease; Crystal structure; Malaria; Plasmepsin; Plasmodium falciparum

Indexed keywords

ASPARTIC PROTEINASE; ENZYME INHIBITOR; MONOMER; N [3 [(2 BENZO[1,3]DIOXOL 5 YL ETHYL) 3 (1 METHYL 3 OXO 1,3 DIHYDROISOINDOL 2 YL)PROPIONYL]AMINO] 1 BENZYL 2 (HYDROXYPROPYL) 4 BENZYLOXY 3,5 DIMETHOXYBENZAMIDE; PEPSTATIN; PLASMEPSIN II; UNCLASSIFIED DRUG;

ANALYTICAL PARAMETERS; ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; CRYSTAL STRUCTURE; CRYSTALLIZATION; CRYSTALLOGRAPHY; ENZYME STRUCTURE; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL;

PLASMODIUM FALCIPARUM;

EID: 0037436389     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00036-6     Document Type: Article

References (36)

1. Control of Tropical Diseases: Malaria Control. 1995;WHO Office of Information, Geneva, Switzerland.
2. Francis S.E., Sullivan D.J. Jr, Goldberg D.E. Hemoglobin metabolism in the malaria parasite Plasmodium falciparum. Annu. Rev. Microbiol. 51:1997;97-123.
3. Gluzman I.Y., Francis S.E., Oksman A., Smith C.E., Duffin K.L., Goldberg D.E. Order and specificity of the Plasmodium falciparum hemoglobin degradation pathway. J. Clin. Invest. 93:1994;1602-1608.
4. Glodberg D.E., Slater A.F., Beavis R., Chait B., Cerami A., Henderson G. Hemoglobin degradation in the human malaria pathogen Plasmodium falciparum: a catabolic pathway initiated by a specific aspartic protease. J. Exp. Med. 173:1991;961-969.
5. Francis S.E., Gluzman I.Y., Oksman A., Banerjee D., Goldberg D.E. Characterization of native falcipain, an enzyme involved in Plasmodium falciparum hemoglobin degradation. Mol. Biochem. Parasitol. 83:1996;189-200.
6. Banerjee R., Liu J., Beatty W., Pelosof L., Klemba M., Goldberg D.E. Four plasmepsins are active in the Plasmodium falciparum food vacuole, including a protease with an active-site histidine. Proc. Natl Acad. Sci. USA. 99:2002;990-995.
7. Francis S.E., Gluzman I.Y., Oksman A., Knickerbocker A., Mueller R., Bryant M.L., et al. Molecular characterization and inhibition of a Plasmodium falciparum aspartic hemoglobinase. EMBO J. 13:1994;306-317.
8. Silva A.M., Lee A.Y., Gulnik S.V., Maier P., Collins J., Bhat T.N., et al. Structure and inhibition of plasmepsin II, a hemoglobin degrading enzyme from Plasmodium falciparum. Proc. Natl Acad. Sci. USA. 93:1996;10034-10039.
9. Bernstein N.K., Cherney M.M., Loetscher H., Ridley R.G., James M.N. Crystal structure of the novel aspartic proteinase zymogen proplasmepsin II from Plasmodium falciparum. Nature Struct. Biol. 6:1990;32-37.
10. Asojo O.A., Afonina E., Gulnik S.V., Yu B., Erickson J., Randad R., et al. Crystal Structures of ser 205 mutant plasmepsin II from Plasmodium falciparum at 1.8 Å in complex with the inhibitors rs367 and rs370. Acta Crystallog. sect. D. 58:2002;2001-2008.
11. Silva A.M., Lee A.Y., Erickson J.W., Goldberg D.E. Structural analysis of plasmepsin II. A comparison with human aspartic proteases. Advan. Exp. Med. Biol. 436:1998;363-373.
12. Westling J., Cipullo P., Hung S.H., Saft H., Dame J.B., Dunn B.M. Active site specificity of plasmepsin II. Protein Sci. 8:1999;2001-2009.
13. Haque T.S., Skillman A.G., Lee C.E., Habashita H., Gluzman I.Y., Ewing T.J., et al. Potent, low-molecular-weight non-peptide inhibitors of malarial aspartyl protease plasmepsin II. J. Med. Chem. 42:1999;1428-1440.
14. Carroll C.D., Johnson T.O., Tao S., Lauri G., Orlowski M., Gluzmanm I.Y., et al. Evaluation of a structure-based statine cyclic diamino amide encoded combinatorial library against plasmepsin II and cathepsin D. Bioorg. Med. Chem. Letters. 8:1998;3203-3206.
15. Carroll C.D., Patel H., Johnson T.O., Guo T., Orlowski M., He Z.M., et al. Identification of potent inhibitors of Plasmodium falciparum plasmepsin II from an encoded statine combinatorial library. Bioorg. Med. Chem. Letters. 8:1998;2315-2320.
16. Carroll C.D., Orlowski M. Screening aspartyl proteases with combinatorial libraries. Advan. Exp. Med. Biol. 436:1998;375-380.
17. Goldberg D.E. Plasmodial hemoglobin degradation: an ordered pathway in a specialized organelle. Infect. Agents Dis. 1:1992;207-211.
18. Baldwin E.T., Bhat T.N., Gulnik S., Hosur M.V., Sowder R.C. II, Cachau R.E., et al. Crystal structures of native and inhibited forms of human cathepspin D: implications for lysosomal targeting and drug design. Proc. Natl Acad. Sci. USA. 90:1993;6796-6800.
19. Sussman J.L., Lin D., Jiang J., Manning N.O., Prilusky J., Ritter O., Abola E.E. Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallog. sect. D. 54:1998;1078-1084.
20. Subramanian E., Swan I.D., Liu M., Davies D.R., Jenkins J.A., Tickle I.J., Blundell T.L. Homology among acid proteases: comparison of crystal structures at 3 Å resolution of acid proteases from Rhizopus chinensis and Endothia Parasitica. Proc. Natl Acad. Sci. USA. 74:1997;556-559.
21. Janin J. Surface and inside volumes in globular proteins. Nature. 277:1997;491-492.
22. Gulnik S.V., Afonina E.I., Gustchina E., Yu B., Silva A.M., Kim Y., Erickson J.W. Utility of (his)(6) tag for purification and refolding of proplasmepsin-2 and mutants with altered activation properties. Protein Expr. Purif. 24:2002;412-419.
23. Otwinowski Z. DENZO: An Oscillation Data Processing Program for Macromolecular Crystallography. 1993;Yale University Press, New Haven, CT.
24. Otwinowski Z. SCALEPACK: Software for the Scaling Together of Integrated Intensities Measured on a Number of Separate Diffraction Images. 1993;Yale University Press, New Haven.
25. Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallog. sect. A. 50:1994;157-163.
26. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard G. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A. 47:1991;110-119.
27. Brunger A.T., Krukowski A., Erickson J. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallog. sect. A. 46:1990;585-593.
28. Brunger A.T., Adams P.D., Rice L.M. New applications of simulated annealing in X-ray crystallography and solution NMR. Structure. 5:1997;325-336.
29. Adams P.D., Pannu N.S., Read R.J., Brunger A.T. Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc. Natl Acad. Sci. USA. 94:1997;5018-5023.
30. Brunger A.T. The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature. 355:1992;472-474.
31. Brunger A.T. X-PLOR: A System for X-ray Crystallography and NMR. 1992;Yale University Press, New Haven, CT.
32. Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta. Crystallog. sect. A. 32:1976;922-923.
33. Merritt E.A., Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524.
34. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
35. Esnouf R.M. An extensively modified version of MOLSCRIPT that includes greatly enhanced coloring capabilities. J. Mol. Graph. Model. 15:1997;132-134.
36. Christopher J.A. SPOCK: The Structural Properties Observations and Calculation Kit. 1998;The Center for Macromolecular Design, Texas A&M University, College Station, TX.