Core mutations switch monomeric protein GB1 into an intertwined tetramer

Nature Structural Biology

Volumn 9, Issue 11, 2002, Pages 877-885

  Frank, M Kirsten ^a   Dyda, Fred ^a   Dobrodumov, Anatoliy ^a   Gronenborn, Angela M ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MUTANT PROTEIN; PROTEIN G; PROTEIN G B1; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL MUTATION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POINT MUTATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; WILD TYPE; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BINDING SITES, ANTIBODY; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS;

BACTERIA (MICROORGANISMS);

EID: 0036829597     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb854     Document Type: Article

References (41)

1. Gronenborn, A.M. et al. A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science 253, 657-661 (1991).
2. Gallagher, T., Alexander, P., Bryan, P. Gilliland, G.L. Two crystal structures of the β1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR. Biochemistry 33, 4721-4729 (1994).
3. Tcherkasskaya, O., Knutson, J. R., Bowley, S.A., Frank, M.K. Gronenborn, A.M. Nanosecond dynamics of the single tryptophan reveals multi-state equilibrium unfolding of protein GB1. Biochemistry 39, 11216-11226 (2000).
4. Malakauskas, S.M. Mayo, S.L. Design, structure and stability of a hyperthermophilic protein variant. Nature Struct. Biol. 5, 470-475 (1998).
5. Gronenborn, A.M., Frank, M.K. Clore, G.M. Core mutants of the immunoglobulin binding domain of streptococcal protein G: Stability and structural integrity. FEBS Lett. 398, 312-316 (1996).
6. Achari, A. et al. 1.67 Å X-ray structure of the B2 immunoglobulin-binding domain of streptococcal protein G and comparison to the NMR structure of the B1 domain. Biochemistry 31, 10449-10457 (1992).
7. Gronenborn, A.M. Clore, G.M. Rapid screening for structural integrity of expressed proteins by heteronuclear NMR spectroscopy. Protein Sci. 5, 174-177 (1996).
8. Clore, G.M. Gronenborn, A.M. Structures of larger proteins in solution: Three- and four-dimensional heteronuclear NMR spectroscopy. Science 252, 1390-1399 (1991).
9. Bax, A. Grzesiek, S. Methodological advances in protein NMR. Acc. Chem. Res. 26, 131-138 (1993).
10. Clore, G. M. Gronenborn, A. M. Determining structures of larger proteins and protein complexes by NMR. Trends Biotechnol. 16 22-34 (1998).
11. Omichinski, J.G. et al. NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. Science 261, 438-446 (1993).
12. Annila, A., Aittio, H., Thulin, E. Drakenberg, T. Recognition of protein folds via dipolar couplings. J. Biol. NMR 14, 223-230 (1999).
13. 15N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N. J. Biomol. NMR 19, 289-290 (2001).
14. Cornilescu, G., Marquardt, J.L., Ottiger, M. Bax, A. Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J. Am. Chem. Soc. 120, 6836-6837 (1998).
15. Nilges, M., Clore, G.M Gronenborn, A.M. Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett. 229, 317-324 (1988).
16. Brünger, A.T. et al. Crystallography and NMR system (CNS): A new software system for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
17. Hendrickson, W.A. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 254, 51-58 (1991).
18. Kuhlman, B., O'Neill, J.W., Kim, D.E., Zhang, K.Y.J. Baker, D. Conversion of monomeric protein L to an obligate dimer by computational protein design. Proc. Natl. Acad. Sci. USA 98, 10687-10691 (2001).
19. Bennett, M.J., Choe, S. Eisenberg, D. Domain swapping - Entangling alliances between proteins. Proc. Natl. Acad. Sci. USA 91, 3127-3131 (1994).
20. Delaglio, F. et al. NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293 (1995).
21. Garrett, D.S., Powers, R., Gronenborn, A.M. Clore, G.M. A common sense approach to peak picking in two-, three- and four-dimensional spectra using automatic computer analysis of contour diagrams. J. Magn. Reson. 94, 214-220 (1991).
22. Cornilescu, G., Delaglio, F. Bax, A. Protein backbone angle restraints from searching a database for protein chemical shift and sequence homology. J. Biomol. NMR 13, 289-302 (1999).
23. Warren, J.J. Moore, P.B. A maximum likelihood method for determining Da and R for sets of dipolar coupling data. J. Magn. Reson. 149, 271-275 (2001).
24. 1H NMR. Proteins Struct. Funct. Genet. 17, 297-309 (1993).
25. O'Donoghue, S.I., King, G.F. Nilges, M. Calculation of symmetric multimer structures from NMR data using a priori knowledge of the monomer structure, co-monomer restraints, and interface mapping: The case of leucine zippers. J. Biomol. NMR 8, 193-206 (1996).
26. Ramachandran, G. N., Ramakrishnan, C. Sasisekharan, V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7, 95-99 (1963).
27. Laskowski, R.A., MacArthur, M.W., Moss, D.S. Thornton, J.W. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291 (1993).
28. Koradi, R., Billeter, M. Wüthrich, K. A program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55 (1996).
29. Carson, M. RIBBONS 2.0. J. Appl. Crystallogr. 24, 958-961 (1991).
30. Jancarik, J. Kim, S.-H. Sparse matrix sampling: A screening method for crystallization of proteins. J. Appl. Crystallogr. 24, 409-411 (1991).
31. Otwinowski, Z. Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
32. Sheldrick, G. M. in Direct Methods for Solving Macromolecular Structures (ed. Fortier, S.) 401-411 (Kluwer Academic Publications, Dordrecht; 1998).
33. Ramakrishnan, V., Finch, J. T., Graziano, V., Lee, P. L. Sweet, R. M. Crystal structure of globular domain of histone HS and its implications for nucleosome binding. Nature 362, 219-223 (1993).
34. Wang, B.-C. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115, 90-112 (1985).
35. Jones, T.A., Zou, J.-Y., Cowan, S.W. Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119 (1991).
36. Furey, W. Swaminathan, S. PHASES-95: A program package for processing and analyzing diffraction data from macromolecules. Methods Enzymol. 277, 590-620 (1997).
37. Brünger, A.T. X-PLOR: A System for X-ray Crystallography and NMR (Yale University Press, New Haven; 1993).
38. Navaza, J. Saludjian, P. AMoRe: An automated molecular replacement program package. Methods Enzymol. 276, 581-594 (1997).
39. Brünger, A.T. Free R value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475 (1992).
40. Tronrud, D.E. Knowledge-based B-factor restraints for the refinement of proteins. J. Appl. Crystallogr. 29, 100-104 (1996).
41. Brooks, B. R. et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4, 187-217 (1983).