Mouse ApoM displays an unprecedented seven-stranded lipocalin fold: Folding decoy or alternative native fold?

Journal of Molecular Biology

Volumn 404, Issue 3, 2010, Pages 363-371

  Sevvana, Madhumati ^a   Kassler, Kristin ^a   Ahnström, Josefin ^b   Weiler, Sigrid ^a   Dahlbäck, Björn ^b   Sticht, Heinrich ^a   Muller, Yves A ^a  

^a UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

^b LUND UNIVERSITY   (Sweden)

Author keywords

Alternative conformations; Apolipoprotein; Lipocalin; Misfolding; Refolding

Indexed keywords

APOLIPOPROTEIN M; LIPOCALIN;

AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; STRUCTURE ANALYSIS;

EID: 78349307798     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.09.062     Document Type: Article

References (43)

1. Anfinsen C.B. Principles that govern the folding of protein chains. Science 1973, 181:223-230.
2. Dobson C.M. Protein folding and misfolding. Nature 2003, 426:884-890.
3. Dill K.A., Chan H.S. From Levinthal to pathways to funnels. Nat. Struct. Biol. 1997, 4:10-19.
4. Gettins P.G. Serpin structure, mechanism, and function. Chem. Rev. 2002, 102:4751-4804.
5. Klieber M.A., Underhill C., Hammond G.L., Muller Y.A. Corticosteroid-binding globulin, a structural basis for steroid transport and proteinase-triggered release. J. Biol. Chem. 2007, 282:29594-29603.
6. Solomatin S.V., Greenfeld M., Chu S., Herschlag D. Multiple native states reveal persistent ruggedness of an RNA folding landscape. Nature 2010, 463:681-684.
7. Chow M.K., Amin A.A., Fulton K.F., Whisstock J.C., Buckle A.M., Bottomley S.P. REFOLD: an analytical database of protein refolding methods. Protein Expression Purif. 2006, 46:166-171.
8. Xu N., Dahlback B. A novel human apolipoprotein (apoM). J. Biol. Chem. 1999, 274:31286-31290.
9. Zhang X.Y., Jiao G.Q., Hurtig M., Dong X., Zheng L., Luo G.H., et al. Expression pattern of apolipoprotein M during mouse and human embryogenesis. Acta Histochem. 2004, 106:123-128.
10. Sevvana M., Ahnstrom J., Egerer-Sieber C., Lange H.A., Dahlback B., Muller Y.A. Serendipitous fatty acid binding reveals the structural determinants for ligand recognition in apolipoprotein M. J. Mol. Biol. 2009, 393:920-936.
11. Flower D.R., North A.C., Attwood T.K. Structure and sequence relationships in the lipocalins and related proteins. Protein Sci. 1993, 2:753-761.
12. Deakin J.E., Papenfuss A.T., Belov K., Cross J.G., Coggill P., Palmer S., et al. Evolution and comparative analysis of the MHC class III inflammatory region. BMC Genomics 2006, 7:281.
13. Faber K., Axler O., Dahlback B., Nielsen L.B. Characterization of apoM in normal and genetically modified mice. J. Lipid Res. 2004, 45:1272-1278.
14. Ahnstrom J., Faber K., Axler O., Dahlback B. Hydrophobic ligand binding properties of the human lipocalin apolipoprotein M. J. Lipid Res. 2007, 48:1754-1762.
15. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 1993, 26:795-800.
16. McCoy A.J. Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr. Sect. D 2007, 63:32-41.
17. Terwilliger T.C. Using prime-and-switch phasing to reduce model bias in molecular replacement. Acta. Crystallogr. Sect. D 2004, 60:2144-2149.
18. Murshudov G.N., Vagin A.A., Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. Sect. D 1997, 53:240-255.
19. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. Sect. D 2004, 60:2126-2132.
20. Perrakis A., Morris R., Lamzin V.S. Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 1999, 6:458-463.
21. DeLano W. The PyMOL Molecular Graphics System 2003, DeLano Scientific LLC, San Carlos, CA.
22. Fuentes-Prior P., Noeske-Jungblut C., Donner P., Schleuning W.D., Huber R., Bode W. Structure of the thrombin complex with triabin, a lipocalin-like exosite-binding inhibitor derived from a triatomine bug. Proc. Natl Acad. Sci. USA 1997, 94:11845-11850.
23. Flower D.R. The lipocalin protein family: structure and function. Biochem. J. 1996, 318:1-14.
24. Flower D.R., North A.C., Sansom C.E. The lipocalin protein family: structural and sequence overview. Biochim. Biophys. Acta 2000, 1482:9-24.
25. Greene L.H., Chrysina E.D., Irons L.I., Papageorgiou A.C., Acharya K.R., Brew K. Role of conserved residues in structure and stability: tryptophans of human serum retinol-binding protein, a model for the lipocalin superfamily. Protein Sci. 2001, 10:2301-2316.
26. Duan J., Dahlback B., Villoutreix B.O. Proposed lipocalin fold for apolipoprotein M based on bioinformatics and site-directed mutagenesis. FEBS Lett. 2001, 499:127-132.
27. Homeyer N., Essigke T., Meiselbach H., Ullmann G.M., Sticht H. Effect of HPr phosphorylation on structure, dynamics, and interactions in the course of transcriptional control. J. Mol. Model. 2007, 13:431-444.
28. Wartha F., Horn A.H.C., Meiselbach H., Sticht H. Molecular dynamics simulations of HIV-1 protease suggest different mechanisms contributing to drug resistance. J. Chem. Theory Comput. 2005, 1:315-324.
29. Humphrey W., Dalke A., Schulten K. VMD: Visual Molecular Dynamics. J. Mol. Graphics 1996, 14:33-38. 27-38.
30. Fiser A., Do R.K., Sali A. Modeling of loops in protein structures. Protein Sci. 2000, 9:1753-1773.
31. Fiser A., Sali A. ModLoop: automated modeling of loops in protein structures. Bioinformatics 2003, 19:2500-2501.
32. Schulenburg C., Weininger U., Neumann P., Meiselbach H., Stubbs M.T., Sticht H., et al. Impact of the C-terminal disulfide bond on the folding and stability of onconase. ChemBioChem 2010, 11:978-986.
33. Remaut H., Rose R.J., Hannan T.J., Hultgren S.J., Radford S.E., Ashcroft A.E., Waksman G. Donor-strand exchange in chaperone-assisted pilus assembly proceeds through a concerted beta strand displacement mechanism. Mol. Cell 2006, 22:831-842.
34. Remaut H., Waksman G. Protein-protein interaction through beta-strand addition. Trends Biochem. Sci. 2006, 31:436-444.
35. Baldwin R.L. On-pathway versus off-pathway folding intermediates. Fold. Des. 1996, 1:R1-R8.
36. Robert V., Volokhina E.B., Senf F., Bos M.P., Van Gelder P., Tommassen J. Assembly factor Omp85 recognizes its outer membrane protein substrates by a species-specific C-terminal motif. PLoS Biol. 2006, 4:e377.
37. Knowles T.J., Jeeves M., Bobat S., Dancea F., McClelland D., Palmer T., et al. Fold and function of polypeptide transport-associated domains responsible for delivering unfolded proteins to membranes. Mol. Microbiol. 2008, 68:1216-1227.
38. Rousseau F., Schymkowitz J.W., Itzhaki L.S. The unfolding story of three-dimensional domain swapping. Structure 2003, 11:243-251.
39. Schoch G.A., D'Arcy B., Stihle M., Burger D., Bar D., Benz J., et al. Molecular switch in the glucocorticoid receptor: active and passive antagonist conformations. J. Mol. Biol. 2010, 395:568-577.
40. Grishin N.V. Fold change in evolution of protein structures. J. Struct. Biol. 2001, 134:167-185.
41. Zanotti G., Berni R., Monaco H.L. Crystal structure of liganded and unliganded forms of bovine plasma retinol-binding protein. J. Biol. Chem. 1993, 268:10728-10738.
42. Kleywegt G.J., Bergfors T., Senn H., Le Motte P., Gsell B., Shudo K., Jones T.A. Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid. Structure 1994, 2:1241-1258.
43. Murzin A.G. How far divergent evolution goes in proteins. Curr. Opin. Struct. Biol. 1998, 8:380-387.