The solution structure and dynamics of human neutrophil gelatinase-associated lipocalin

Journal of Molecular Biology

Volumn 289, Issue 1, 1999, Pages 139-157

  Coles, Murray ^a   Diercks, Tammo ^a   Muehlenweg, Bernd ^b   Bartsch, Stefan ^b   Zölzer, Volker ^b   Tschesche, Harald ^b   Kessler, Horst ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b BIELEFELD UNIVERSITY   (Germany)

Author keywords

Human neutrophil gelatinase associated lipocalin; NMR; Protein dynamics; Protein structure; Protein protein interactions

Indexed keywords

BACTERIAL PROTEIN; CELL SURFACE RECEPTOR; CHEMOTACTIC PEPTIDE; CYSTEINE; GELATINASE; GELATINASE B; INHIBITOR PROTEIN; LIPOCALIN; NITROGEN 15;

ARTICLE; BINDING SITE; CELL TRANSPORT; COMPLEX FORMATION; DISULFIDE BOND; EXTRACELLULAR SPACE; GRANULOCYTE; HUMAN; HYDROPHOBICITY; LIGAND BINDING; MOLECULAR DYNAMICS; NEUTROPHIL; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FAMILY; PROTEIN PROTEIN INTERACTION; PROTEIN QUATERNARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE;

EID: 0033612221     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2755     Document Type: Article

References (54)

1. Arii S., Mise M., Harada T., Furutani M., Ishigami S., Niwano M., Mizumoto M., Fukumoto M., Imamura M. Overexpression of matrix metalloproteinase-9 gene in hepatocellular carcinoma with invasive potential. Hepatology. 24:1996;316-322.
2. 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible. Biochemistry. 31:1992;5269-5278.
3. Bocskei Z., Groom C. R., Flower D. R., Wright C. E., Phillips S. E., Cavaggioni A., Findlay J. B., North A. C. Pheromone binding to two rodent urinary proteins revealed by X-ray crystallography. Nature. 360:1992;186-188.
4. Brownlow S., Cabral J. H. M., Cooper R., Flower D. R., Yewdall S. J., Polikarpov I., North A. C., Sawyer L. Bovine β-lactoglobulin at 1.8 Å resolution-still an enigmatic lipocalin. Structure. 5:1997;481-495.
5. Brunger A. T. X-PLOR, Version 3.1. A System for X-ray Crystallography and NMR. 1992;Yale University Press, New Haven.
6. Chu S.-T., Lin H.-J., Chen Y.-H. Complex formation between a formyl peptide and 24p3 protein with a blocked N-terminus of pyrroglutamate. J. Pept. Res. 49:1997;582-585.
7. Clore G. M., Szabo A., Bax A., Kay L. E., Driscoll P. C., Gronenborn A. M. Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J. Am. Chem. Soc. 112:1990;4989-4991.
8. Edwards D. R., Murphy G. Proteases-invasion and more. Nature. 394:1998;527-528.
9. Elneihoum A. M., Falke P., Hedblad B., Lindgarde F., Ohlsson K. Leukocyte activation in atherosclerosis: correlatation with risk factors. Atherosclerosis. 131:1997;79-84.
10. Flower D. R. The lipocalin protein family: structure and function. Biochem. J. 318:1996;1-14.
11. Flower D. R., North A. C. T., Attwood T. K. Mouse oncogene protein 24p3 is a member of the lipocalin protein family. Biochem. Biophys. Res. Commun. 180:1991;69-74.
12. Furutani M., Arii S., Mizumoto M., Kato M., Imamura M. Identification of a neutrophil-associated lipocalin mRNA in human pancreatic cancers using a modified signal sequence trap method. Cancer Letters. 122:1998;209-214.
13. Garcia de la Torre J., Bloomfield V. A. Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications. Quart. Rev. Biophys. 14:1981;81-139.
14. αH coupling constants on protein structure determination by NMR. J. Magn. Reson. ser. B. 104:1994;99-103.
15. Gemmecker G., Jahnke W., Kessler H. Measurement of fast proton exchange rates in isotopically labelled compounds. J. Am. Chem. Soc. 115:1993;11620-11621.
16. Gilson M., Sharp K., Honig B. Calculating the electrostatic potential of molecules in solution: method and error assessment. J. Comput. Chem. 9:1988;327-355.
17. Huber R., Schneider M., Mayr I., Mueller R., Deutzmann R., Suter F., Zuber H., Falk H., Kayser H. Molecular structure of the bilin binding protein (BBP) from Pieris brassicae after refinement at 2.0 Å resolution. J. Mol. Biol. 198:1987;499-513.
18. 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry. 28:1989;8972-8979.
19. Keatings V. M., Barnes P. J. Granulocyte activation markers in induced sputum: comparison between chronic obstructive pulmonary disease, asthma, and normal subjects. Am. J. Respir. Crit. Care Med. 155:1997;449-453.
20. Kjeldsen L., Bainton D. F., Sengelov H., Borregaard N. Structural and functional heterogeneity among peroxidase-negative granules in human neutrophils: identification of a distinct gelatinase-containing granule subset by combined immunocytochemistry and subcellular fractionation. Blood. 82:1993;3183-3191.
21. Kjeldsen L., Bainton D. F., Sengelov H., Borregaard N. Identification of neutrophil gelatinase-associated lipocalin as a novel matrix protein of specific granules in human neutrophils. Blood. 83:1994;799-807.
22. 15N-labelled peptide. J. Biomol. NMR. 6:1995;306-312.
23. Kolkenbrock H., Hecker-Kia A., Orgel D., Kinawi A., Ulbrich N. Progelatinase B forms from human neutrophils. Complex formation of monomer/lipocalin with TIMP-1. Biol. Chem. 377:1996;529-533.
24. Kraulis P. J. MOLSCRIPT-a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
25. 13Cβ chemical shifts on protein structure determination by NMR. J. Magn. Reson. ser. B. 106:1995a;92-96.
26. Kuszewski J., Gronenborn A. M., Clore G. M. The impact of direct refinement against proton chemical shifts on protein structure determination by NMR. J. Magn. Reson. ser. B. 107:1995b;293-297.
27. Kuszewski J., Gronenborn A. M., Clore G. M. A potential involving multiple proton chemical-shift restraints for non-stereospecifically assigned methyl and methylene protons. J. Magn. Reson. ser. B. 112:1996a;78-91.
28. Kuszewski J., Gronenborn A. M., Clore G. M. Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases. Protein Sci. 5:1996b;1067-1080.
29. Kuszewski J., Gronenborn A. M., Clore G. M. Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids. J. Magn. Reson. 125:1997;171-177.
30. Laskowski R. A., MacArthur M. W., Moss D. S., Thornton J. M. PROCHECK: a Program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-289.
31. Leutner M., Gschwind R. M., Liermann J., Schwarz C., Gemmecker G., Kessler H. Automated backbone assignment of labelled proteins using the threshold accepting algorithm. J. Biomol. NMR. 11:1998;31-43.
32. Lipari G., Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104:1982;4546-4559.
33. Liu W. M. Shear numbers of protein beta- barrels: definition refinements and statistics. J. Mol. Biol. 275:1998;541-545.
34. 2NCO-E. COSY, a simple method for the stereospecific assignment of side-chain amide protons in proteins. J. Magn. Reson. 124:1997;255-258.
35. Merritt E. A., Murphy M. E. P. Raster3D version 2.0-a program for photorealistic molecular graphics. Acta Crystallog. sect. D. 50:1994;869-873.
36. Nagata A., Suzuki Y., Igarashi M., Eguchi N., Toh H., Urade Y., Hayaishi O. Human brain prostaglandin D synthase has been evolution arily differentiated from lipophilic-ligand carrier proteins. Proc. Natl Acad. Sci. USA. 88:1991;4020-4024.
37. Newcomer M. E., Jones T. A., Aqvist J., Sundelin J., Eriksson U., Rask L., Peterson P. A. The three-dimensional structure of retinol-binding protein. EMBO J. 3:1984;1451-1454.
38. Nicholls A., Sharp K., Honig B. Protein folding and association: insights from interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11:1991;281-296.
39. Orekhov V. Y., Nolde D. E., Golovanov A. P., Korzhnev D. M., Arseniev A. S. Processing of heteronuclear NMR relaxation data with the new software DASHA. Appl. Magn. Reson. 9:1995;581-588.
40. Richardson J. S. The anatomy and taxonomy of protein structure. Advan. Protein Chem. 34:1981;167-339.
41. Schettler A., Thorn H., Jockusch B. M., Tschesche H. Release of proteinases from stimulated polymorphonuclear leukocytes. Evidence for subclasses of the main granule types and their association with cytoskeletal components. Eur. J. Biochem. 197:1991;197-202.
42. Schurr J. M., Babcock H. P., Fujimoto B. S. A test of the model-free formulas. Effects of anisotropic rotational diffusion and dimerization. J. Magn. Reson. ser. B. 105:1994;211-224.
43. Seveus L., Amin K., Peterson C. G., Roomans G. M., Venge P. Human neutrophil lipocalin (HNL) is a specific granule constituent of the neutrophil granulocyte. studies in bronchial and lung parenchymal tissue and peripheral blood cells. Histochem. Cell Biol. 107:1997;423-432.
44. Sivaprasadarao A., Findlay B. C. Structure-function studies on human retinol binding protein using site-directed mutagenesis. Biochem. J. 300:1994;437-442.
45. Spinelli S., Ramoni R., Grolli S., Bonicel B., Cambillau C., Tegoni M. The structure of monomeric porcine odorant binding protein sheds light on the domain swapping mechanism. Biochemistry. 37:1998;7913-7918.
46. Stack M. S., Ellerbroek S. M., Fishman D. A. The role of proteolytic enzymes in the pathology of epithelial ovarian carcinoma. Int. J. Oncol. 12:1998;569-576.
47. Sundaram M., Sivaprasadarao A., DeSousa M., Findlay B. C. The transfer of retinol from serum retinol-binding protein to cellular retinol-binding protein is mediated by a membrane receptor. J. Biol. Chem. 273:1998;3336-3342.
48. 15N spin relaxation times. J. Biomol. NMR. 3:1993;151-164.
49. Triebel S., Bläser J., Reinke H., Tschesche H. A 25 kDa alpha2-microglobulin-related protein is a component of the 125 kDa form of human gelatinase. FEBS Letters. 314:1992;386-388.
50. Weichsel A., Andersen J. F., Champagne D. E., Walker F. A., Montfort W. R. Crystal structure of a nitric oxide transport protein from a blood sucking insect. Nature Struct. Biol. 5:1998;304-309.
51. 13C chemical-shift data. J. Biomol. NMR. 4:1994;171-180.
52. Wishart D. S., Sykes B. D., Richards F. M. The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry. 31:1992;1647-1651.
53. Young L., Jernigan R. L., Covell D. G. A role for surface hydrophobicity in protein-protein recognition. Protein Sci. 3:1994;717-729.
54. Zanotti G., Berni R., Monaco H. L. Crystal structure of liganded and unliganded forms of bovine plasma retinol binding protein. J. Biol. Chem. 268:1993;10728-10738.