Nano-structure of the laminin γ-1 short arm reveals an extended and curved multidomain assembly

Matrix Biology

Volumn 29, Issue 7, 2010, Pages 565-572

  Patel, Trushar R ^a   Morris, Gordon A ^b   Zwolanek, Daniela ^c   Keene, Douglas R ^d   Li, Jianhua ^e   Harding, Stephen E ^b   Koch, Manuel ^c   Stetefeld, Jörg ^a  

^a UNIVERSITY OF MANITOBA   (Canada)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^c UNIVERSITY OF COLOGNE   (Germany)

^d SHRINERS HOSPITAL FOR CHILDREN   (United States)

^e RIGAKU CORPORATION   (Japan)

Author keywords

Ab initio modeling; Analytical ultracentrifugation; Dynamic light scattering; Laminin; Rotary shadowing; Small angle X ray scattering

Indexed keywords

LAMININ GAMMA1; NANOMATERIAL;

ARTICLE; ELECTRON MICROSCOPY; LIGHT SCATTERING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; ULTRACENTRIFUGATION; X RAY CRYSTALLOGRAPHY;

HUMANS; HYDRODYNAMICS; LAMININ; LIGHT; MICROSCOPY, ELECTRON, TRANSMISSION; MODELS, MOLECULAR; MOLECULAR WEIGHT; PARTICLE SIZE; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; SCATTERING, RADIATION; SCATTERING, SMALL ANGLE; SHADOWING (HISTOLOGY); SOFTWARE; ULTRACENTRIFUGATION; X-RAY DIFFRACTION;

EID: 77957754110     PISSN: 0945053X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.matbio.2010.07.004     Document Type: Article

References (48)

1. Ang S., Kogulanathan J., Morris G., Kök M., Shewry P., Tatham A., Adams G., Rowe A., Harding S. Structure and heterogeneity of gliadin: a hydrodynamic evaluation. Eur. Biophys. J. 2010, 39:255-261.
2. Aumailley M., Bruckner-Tuderman L., Carter W.G., Deutzmann R., Edgar D., Ekblom P., Engel, Engvall E., Hohenester E., Jones J.C.R., Kleinman H.K., Marinkovich M.P., Martin G.R., Mayer U., Meneguzzi G., Miner J.H., Miyazaki K., Patarroyo M., Paulsson M., Quaranta V., Sanes J.R., Sasaki T., Sekiguchi K., Sorokin L.M., Talts J.F., Tryggvason K., Uitto J., Virtanen I., von der Mark K., Wewer U.M., Yamada Y., Yurchenco P.D. A simplified laminin nomenclature. Matrix Biol. 2005, 24:326-332.
3. Brookes E., Demeler B., Rosano C., Rocco M. The implementation of SOMO (SOlution MOdeller) in the UltraScan analytical ultracentrifugation data analysis suite: enhanced capabilities allow the reliable hydrodynamic modeling of virtually any kind of biomacromolecule. Eur. Biophys. J. 2010, 39:423-435.
4. Bruce A., Dennis B., Julian L., Martin R., Keith R., Watson J.D. Molecular Biology of the Cell 1994, Garland Publishing, a member of the Taylor & Francis Group, New York. 3 ed.
5. Burchard W. Static and dynamic light scattering approaches to structure determination of biopolymers. Laser Light Scattering in Biochemistry 1992, 3-22. Royal Society of Chemistry, Cambdrige. S.E. Harding, D.B. Sattelle, V.A. Bloomfield (Eds.).
6. Cardinali B., Profumo A., Aprile A., Byron O., Morris G., Harding S.E., Stafford W.F., Rocco M. Hydrodynamic and mass spectrometry analysis of nearly-intact human fibrinogen, chicken fibrinogen, and of a substantially monodisperse human fibrinogen fragment X. Arch. Biochem. Biophys. 2010, 493:157-168.
7. Cheng Y.-S., Champliaud M.-F., Burgeson R.E., Marinkovich M.P., Yurchenco P.D. Self-assembly of laminin isoforms. J. Biol. Chem. 1997, 272:31525-31532.
8. Colognato H., Yurchenco P.D. Form and function: the laminin family of heterotrimers. Dev. Dyn. 2000, 218:213-234.
9. Cooper A.R., Kurkinen M., Taylor A., Hogan B.L.M. Studies on the biosynthesis of laminin by murine parietal endoderm cells. Eur. J. Biochem. 1981, 119:189-197.
10. Dam J., Schuck P. Calculating sedimentation coefficient distributions by direct modeling of sedimentation velocity concentration profiles in methods in enzymology. Numerical Computer Methods, Part E 2004, vol. 384:185-212. Academic Press. M.L. Johnson, L. Brand (Eds.).
11. Demeler B. UltraScan a comprehensive data analysis software package for analytical ultracentrifugation experiments. Modern Analytical Ultracentrifugation: Techniques and Methods 2005, 210-229. Royal Society of Chemistry, London. D.J. Scott, S.E. Harding, A.J. Rowe (Eds.).
12. Engel J., Odermatt E., Engel A. Shapes, domain organizations and felxibility of laminin and fibronectin, two mulfifunctional proteins of the extracellular matrix. J. Mol. Biol. 1981, 150:97-120.
13. Franke D., Svergun D.I. DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J. Appl. Crystallogr. 2009, 42:342-346.
14. GarcÌa de la Torre J., Huertas M.L., Carrasco B. Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys. J. 2000, 78:719-730.
15. Gerl M., Mann K., Aumailley M., Timpl R. Localization of a major nidogen-binding site to domain III of laminin B2 chain. Eur. J. Biochem. 1991, 202:167-174.
16. Giebeler R. The Optima XL-A: a new analytical ultracentrifuge with a novel precision absorption optical system. Analytical Ultracentrifugation in Biochemistry and Polymer Science 1992, 16-25. Royal Society of Chemistry, Cambridge, United Kingdom. S.E. Harding, A.J. Rowe, J.C. Horton (Eds.).
17. Gralén N. Sedimentation and Diffusion Measurements on Cellulose and Cellulose Derivatives 1944, University of Uppsala, Uppsala, Sweden.
18. Guinier A., Fourner G. Small Angle Scattering of X-rays 1955, Wiley, New York.
19. Harding S.E. Photon correlation spectroscopy. Encyclopedia of Molecular Biology 1999, 1847-1849. John Wiley and Sons, New York. T.E. Creighton (Ed.).
20. Harding S.E., Colfen H., Aziz Z. The ELLIPS suit of whole-body protein conformation algorithms for Microsoft Windows. Analytical Ultracentrifugation Techniques and Methods 2005, 468-483. Royal Society of Chemistry, Cambridge, United Kingdom. D.J. Scott, S.E. Harding, A.J. Rowe (Eds.).
21. Kalluri R. Basement membranes: structure, assembly and role in tumour angiogenesis. Nat. Rev. Cancer 2003, 3:422-433.
22. Konarev P.V., Volkov V.V., Sokolova A.V., Koch M.H.J., Svergun D.I. PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J. Appl. Crystallogr. 2003, 36:1277-1282.
23. Kozin M.B., Svergun D. Automated matching of high- and low-resolution structural models. J. Appl. Crystallogr. 2001, 34:33-41.
24. Kumaran, D., Bonanno, J., Romero, R., Burley, S.K., Swaminathan, S., to be published. Crystal structure of a glycosyl hydrolases family 2 protein from Bacteroides thetaiotaomicron.
25. Kurkinen M., Barlow D.P., Jenkins J.R., Hogan B.L. In vitro synthesis of laminin and entactin polypeptides. J. Biol. Chem. 1983, 258:6543-6548.
26. Laue T.M., Shah B.D., Ridgeway T.M., Pelletier S.L. Computer-aided interpretation of analytical sedimentation data for proteins. Analytical Ultracentrifugation in Biochemistry and Polymer Science 1992, 90-125. Royal Society of Chemistry, Cambridge, United Kingdom. S.E. Harding, A.J. Rowe, J.C. Horton (Eds.).
27. Mercurio A.M., Rabinovitz I. Towards a mechanistic understanding of tumor ≤-141.
28. Miner J.H., Yurchenco P.D. Laminin functions in tissue morphogenesis. Annu. Rev. Cell. Dev. Biol. 2004, 20:255-284.
29. Odenthal U., Haehn S., Tunggal P., Merkl B., Schomburg D., Frie C., Paulsson M., Smyth N. Molecular analysis of laminin N-terminal domains mediating self-interactions. J. Biol. Chem. 2004, 279:44504-44512.
30. Petoukhov M.V., Svergun D.I. Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys. J. 2005, 89:1237-1250.
31. Pusey P.N. Photon Correlation and Light Beating Spectroscopy 1974, 387-428. Plenum Press, New York. H.Z. Cummings, E.R. Pike (Eds.).
32. Ralston G. Introduction to analytical ultracentrifugation 1993, Beckman Instruments, Inc., Fullerton.
33. Rehmann H., Das J., Knipscheer P., Wittinghofer A., Bos J.L. Structure of the cyclic-AMP-responsive exchange factor Epac2 in its auto-inhibited state. Nature 2006, 439:625-628.
34. Rousselle P., Keene D.R., Ruggiero F., Champliaud M.-F., Rest M.v.d., Burgeson R.E. Laminin 5 binds the NC-1 domain of type VII collagen. J. Cell Biol. 1997, 138:719-728.
35. Rowe A.J. The concentration dependence of transport processes: a general description applicable to the sedimentation, translational diffusion and viscosity coefficients of macromolecular solutes. Biopolymers 1977, 16:2595-2611.
36. Schuck P. Sedimentation analysis of noninteracting and self-associating solutes using numerical solutions to the Lamm equation. Biophys. J. 1998, 75:1503-1512.
37. Stetefeld J., Mayer U., Timpl R., Huber R. Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin [gamma]1 chain harboring the nidogen binding site. J. Mol. Biol. 1996, 257:644-657.
38. Stetefeld J., Mayer U., Timpl R., Huber R. Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin g1 chain harboring the nidogen binding site. J. Mol. Biol. 1996, 257:644-657.
39. Svedberg T., Pedersen K.O. The Ultracentrifuge 1940, Oxford University Press, Oxford.
40. Svergun D. Determination of the regularisation parameter in indirect transform using perceptual criteria. J. Appl. Crystallogr. 1992, 25:495-503.
41. Svergun D. CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 1995, 28:768-773.
42. Svergun D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 1999, 76:2879-2886.
43. Svergun D.I., Petoukhov M.V., Koch M.H.J. Determination of domain structure of proteins from X-ray solution scattering. Biophys. J. 2001, 80:2946-2953.
44. Takagi J., Yang Y., Liu J.-h., Wang J.-h., Springer T.A. Complex between nidogen and laminin fragments reveals a paradigmatic [beta]-propeller interface. Nature 2003, 424:969-974.
45. Tanford C. Physical Chemistry of Macromolecules 1961, John Wiley & Sons, Inc., New York.
46. Tzu J., Marinkovich M.P. Bridging structure with function: structural, regulatory, and developmental role of laminins. Int. J. Biochem. Cell. Biol. 2008, 40:199-214.
47. Volkov V.V., Svergun D.I. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crystallogr. 2003, 36:860-864.
48. Yurchenco P., Cheng Y., Colognato H. Laminin forms an independent network in basement membranes [published erratum appears in J Cell Biol 1992 Jun;118(2):493]. J. Cell Biol. 1992, 117:1119-1133.