Snapshot of protein structure evolution reveals conservation of functional dimerization through intertwined folding

Structure

Volumn 12, Issue 8, 2004, Pages 1489-1494

  Chirgadze, Dimitri Y ^a   Demydchuk, Mykhaylo ^a   Becker, Marion ^a   Moran, Stephen ^a   Paoli, Massimo ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MUTANT PROTEIN; PROTEIN P50;

ARTICLE; CRYSTALLIZATION; DIMERIZATION; GENE MUTATION; MOLECULAR CLONING; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ANIMALS; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; EVOLUTION, MOLECULAR; HUMANS; HYDROPHOBICITY; MODELS, MOLECULAR; MUTATION; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN-SERINE-THREONINE KINASES;

EUKARYOTA;

EID: 4143141894     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.06.011     Document Type: Article

References (30)

1. Atwell S., Ultsch M., De Vos A.M., Wells J.A. Structural plasticity at a remodelled protein-protein interface. Science. 278:1997;1125-1128
2. Baldwin A.S. The NF-κB and IκB proteins. new discoveries and insights Annu. Rev. Immunol. 14:1996;649-681
3. Bennett M.J., Choe S., Eisenberg D. Domain swapping. entangling alliances between proteins Proc. Natl. Acad. Sci. USA. 91:1994;3127-3131
4. Bogan A.A., Thorn K.S. Anatomy of hot spots in protein interfaces. J. Mol. Biol. 280:1998;1-9
5. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., et al. Crystallography and NMR system. a new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54:1998;905-921
6. Calarese D.A., Scanlan C.N., Zwick M.B., Deechongkit S., Mimura Y., Kunert R., Zhu P., Wormald M.R., Stanfield R.L., Roux K.H., et al. Antibody domain exchange is an immunological solution to carbohydrate cluster recognition. Science. 300:2003;2065-2071
7. CCP4 Collaborative Computational Project, Number 4) The CCP4 suite. programs for protein crystallography Acta Crystallogr. D Biol. Crystallogr. 50:1994;760-763
8. Chen F.E., Huang D.B., Chen Y.Q., Ghosh G. Crystal structure of p50/p65 heterodimer of transcription factor NF-κB bound to DNA. Nature. 391:1998;410-413
9. Clackson T., Wells J.A. A hot spot of binding energy in a hormone-receptor interface. Science. 267:1995;383-386
10. Cordes M.H.J., Walsh N.P., McKnight C.J., Sauer R.T. Evolution of a protein fold in vitro. Science. 284:1999;325-327
11. Frank M.K., Dyda F., Dobrodumov A., Gronenborn A.M. Core mutations switch monomeric protein GB1 into an intertwined tetramer. Nat. Struct. Biol. 9:2002;877-885
12. Ghosh G., van Duyne G., Ghosh S., Sigler P.B. Structure of NF-κB p50 homodimer bound to a kB site. Nature. 373:1995;303-310
13. Hart D.J., Speight R.E., Sutherland J.D., Blackburn J.M. Analysis of the NF-κB p50 dimer interface by diversity screening. J. Mol. Biol. 310:2001;563-575
14. Huang D.B., Huxford T., Chen Y.Q., Ghosh G. The role of DNA in the mechanism of NF-κB dimer formation. crystal structures of the dimerisation domains of the p50 and p65 subunits Structure. 5:1997;1427-1436
15. Janin J. Wet and dry interfaces. the role of solvent in protein-protein and protein-DNA recognition Structure. 7:1999;R277-R279
16. Larsen T.A., Olson A.J., Goodsell D.S. Morphology of protein-protein interfaces. Structure. 6:1998;421-427
17. 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. Crystallogr. 26:1993;283-291
18. Liu J., Eisenberg D. 3D domain swapping. as domains continue to swap Protein Sci. 11:2002;1285-1299
19. McRee D.E. XtalView/Xfit. a versatile program for manipulating atomic coordinates and electron density J. Struct. Biol. 125:1999;156-165
20. Morris R.J., Perrakis A., Lamzin V.S. ARP/wARP's model-building algorithms. I. The main chain. Acta Crystallogr. D Biol. Crystallogr. 58:2002;968-975
21. Muller C.W., Rey F.A., Sodeoka M., Verdine G.L., Harrison S.C. Structure of the NF-κB p50 homodimer bound to DNA. Nature. 373:1995;311-317
22. Murshudov G.N., Vagin A.A., Dodson E.J. Refinement of macromolecular structures by maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53:1997;240-255
23. Navaza J. AMoRe. an automated package for molecular replacement Acta Crystallogr. A. 50:1994;157-163
24. Nooren I.M.A., Thornton J. Diversity of protein-protein interactions. EMBO J. 22:2003;3486-3492
25. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326
26. Schlunegger M.P., Bennett M.J., Eisenberg D. Oligomer formation by 3D domain swapping. a model for protein assembly and misassembly Adv. Protein Chem. 50:1997;61-122
27. Thome M., Tschopp J. TCR-induced NF-κB activation. a crucial role for Carma1, Bcl10 and MALTI Trends Immunol. 24:2003;419-424
28. Tranier S., Iobbi-Nivol C., Birck C., Ilbert M., Mortier-Barriere I., Mejean V., Samama J.P. A novel protein fold and extreme domain swapping in the dimeric TorD chaperone from Shewanella massilia. Structure. 11:2003;165-174
29. Wells J.A. Binding in the growth hormone receptor complex. Proc. Natl. Acad. Sci. USA. 93:1996;1-6
30. Winn M.D., Isupov M.N., Murshudov G.N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D Biol. Crystallogr. 57:2001;122-133