NMR-detected conformational exchange observed in a computationally designed variant of protein Gβ1

Protein Engineering, Design and Selection

Volumn 21, Issue 9, 2008, Pages 577-587

  Crowhurst, Karin A ^a,c   Mayo, Stephen L ^a,b  

^a California Institute of Technology HHMI   (United States)

^b California Institute of Technology   (United States)

^c CALIFORNIA STATE UNIVERSITY   (United States)

Author keywords

Backbone dynamics; Computational protein design; Conformational exchange; ORBIT; Protein G 1

Indexed keywords

AROMATIC COMPOUNDS; BINDING ENERGY; BINDING SITES; BIOCHEMISTRY; DYNAMICS; HYDROGEN; NONMETALS; NUCLEAR MAGNETIC RESONANCE; PROTEINS;

BACKBONE DYNAMICS; BIOPHYSICAL CHARACTERIZATION; BIOPHYSICAL PROPERTIES; COMPUTATIONAL PROTEIN DESIGN; CONFORMATIONAL EXCHANGE; FUTURE DESIGNS; HYDROGEN EXCHANGE; MULTI-NUCLEAR NMR; MULTIPLE BINDING SITES; ORBIT; PROTEIN DYNAMICS; PROTEIN G; SIDE CHAINS; STACKING INTERACTIONS; STRUCTURAL PROPERTIES; TIME SCALING; WILD-TYPE;

NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

HYDROGEN; PROTEIN G; STREPTOCOCCAL PROTEIN G BETA1;

ARTICLE; CONFORMATIONAL TRANSITION; DIFFUSION; HYDROPHOBICITY; MOTION; MUTATION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN SYNTHESIS; WILD TYPE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; COMPUTER SIMULATION; ESCHERICHIA COLI; ISOTOPES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS;

EID: 49749132270     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzn035     Document Type: Article

References (51)

1. Åkerud,T., Thulin,E., Van Etten,R.L. and Akke,M. (2002) J. Mol. Biol., 322, 137-152.
2. Bai,Y., Milne,J.S., Mayne,L. and Englander,S.W. (1993) Proteins, 17, 75-86.
3. Burley,S.K. and Petsko,G.A. (1985) Science, 229, 23-28.
4. Choy,W.Y., Mulder,F.A., Crowhurst,K.A., Muhandiram,D.R., Millett,I.S., Doniach,S., Forman-Kay,J.D. and Kay,L.E. (2002) J. Mol. Biol., 316, 101-112.
5. Dahiyat,B.I. and Mayo,S.L. (1997) Science, 278, 82-87.
6. Delaglio,F. (1995) NMRDraw (v. 1.8) [Software]. Bethesda, MD: NIH Laboratory of Chemical Physics.
7. DeLano,W.L. (2002) The PyMOL Molecular Graphics System (v. 0.99) [Software]. Palo Alto, CA: DeLano Scientific.
8. Dempsey,C.E. (2001) Prog. Nucl. Mag. Res. Sp., 39, 135-170.
9. Desjarlais,J.R. and Handel,T.M. (1999) J. Mol. Biol., 290, 305-318.
10. Dobson,N., Dantas,G., Baker,D. and Varani,G. (2006) Structure, 14, 847-856.
11. Eisenmesser,E.Z., Millet,O., Labeikovsky,W., Korzhnev,D.M., Wolf-Watz,M., Bosco,D.A., Skalicky,J.J., Kay,L.E. and Kern,D. (2005) Nature, 438, 117-121.
12. Farrow,N.A., Muhandiram,R., Singer,A.U., Pascal,S.M., Kay,C.M., Gish,G., Shoelson,S.E., Pawson,T., Forman-Kay,J.D. and Kay,L.E. (1994) Biochemistry, 33, 5984-6003.
13. Farrow,N.A., Zhang,O., Szabo,A., Torchia,D.A. and Kay,L.E. (1995) J. Biomol. NMR, 6, 153-162.
14. Foulkes-Murzycki,J.E., Scott,W.R. and Schiffer,C.A. (2007) Structure, 15, 225-233.
15. Gillespie,B., Vu,D.M., Shah,P.S., Marshall,S.A., Dyer,R.B., Mayo,S.L. and Plaxco,K.W. (2003) J. Mol. Biol., 330, 813-819.
16. Hanson,W.M., Beeser,S.A., Oas,T.G. and Goldenberg,D.P. (2003) J. Mol. Biol., 333, 425-441.
17. Harbury,P.B., Plecs,J.J., Tidor,B., Alber,T. and Kim,P.S. (1998) Science, 282, 1462-1467.
18. Hass,M.A. and Led,J.J. (2006) Magn. Reson. Chem., 44, 761-769.
19. Hwang,T.-L., Mori,S. and Shaka,A.J. (1997) J. Am. Chem. Soc., 119, 6203-6204.
20. Hwang,T.-L., van Zijl,P.C.M. and Mori,S. (1998) J. Biomol. NMR, 11, 221-226.
21. Jarymowycz,V.A. and Stone,M.J. (2006) Chem. Rev., 106, 1624-1671.
22. Johnson,B.A. and Blevins,R.A. (1994a) J. Biomol. NMR, 4, 603-614.
23. Johnson,B.A. and Blevins,R. (1997) Merck and Co, Whitehouse Station, NJ, 4.1.2 ed.;
24. Johnson,B.H. and Hecht,M.H. (1994b) Bio/Technology, 12, 1357-1360.
25. Johnson,E.C., Lazar,G.A., Desjarlais,J.R. and Handel,T.M. (1999) Structure, 7, 967-976.
26. Kay,L.E., Keifer,P. and Saarinen,T. (1992) J. Am. Chem. Soc., 114, 10663-10665.
27. Kroenke,C.D., Loria,J.P., Lee,L.K., Rance,M. and Palmer,A.G., III (1998) J. Am. Chem. Soc., 120, 7905-7915.
28. Kuhlman,B., Dantas,G., Ireton,G.C., Varani,G., Stoddard,B.L. and Baker,D. (2003) Science, 302, 1364-1368.
29. Larson,S.M., England,J.L., Desjarlais,J.R. and Pande,V.S. (2002) Protein Sci., 11, 2804-2813.
30. Lee,G.M., Donaldson,L.W., Pufall,M.A., Kang,H.S., Pot,I., Graves,B.J. and McIntosh,L.P. (2005) J. Biol. Chem., 280, 7088-7099.
31. Lefèvre,J.-F., Dayie,K.T., Peng,J.W. and Wagner,G. (1996) Biochemistry, 35, 2674-2686.
32. Lipari,G. and Szabo,A. (1982a) J. Am. Chem. Soc., 104, 4546-4559.
33. Lipari,G. and Szabo,A. (1982b) J. Am. Chem. Soc., 104, 4559-4570.
34. Looger,L.L., Dwyer,M.A., Smith,J.J. and Hellinga,H.W. (2003) Nature, 423, 185-190.
35. Mayer,K.L., Earley,M.R., Gupta,S., Pichumani,K., Regan,L. and Stone,M.J. (2003) Nat. Struct. Biol., 10, 962-965.
36. McCammon,J.A. (2005) Biochim. Biophys. Acta, 1754, 221-224.
37. Muhandiram,D.R. and Kay,L.E. (1994) J. Magn. Reson. Ser. B, 103, 203-216.
38. Palmer,A.G., III (1998) Columbia University, New York, 1.3 ed.;
39. Pfuhl,M., Chen,H.A., Kristensen,S.M. and Driscoll,P.C. (1999) J. Biomol. NMR, 14, 307-320.
40. Ross,S.A., Sarisky,C.A., Su,A. and Mayo,S.L. (2001) Protein Sci., 10, 450-454.
41. Santoro,J. and King,G.C. (1992) J. Magn. Reson., 97, 202-207.
42. SPSS. (2001) SigmaPlot (v. 7.0) [Software]. San Jose, CA: Systat Software, Inc.
43. Spyracopoulos,L. (2006) J. Biomol. NMR, 36, 215-224.
44. Su,A. and Mayo,S.L. (1997) Protein Sci., 6, 1701-1707.
45. Tang,K.E. and Dill,K.A. (1998) J. Biomol. Struct. Dyn., 16, 397-411.
46. Ventura,S., Vega,M.C., Lacroix,E., Angrand,I., Spagnolo,L. and Serrano,L. (2002) Nat. Struct. Biol., 9, 485-493.
47. Walsh,S.T.R., Lee,A.L., DeGrado,W.F. and Wand,A.J. (2001) Biochemistry, 40, 9560-9569.
48. Wand,A.J. (2001) Nat. Struct. Biol., 8, 926-931.
49. Wolfram Research. (2005) Mathematica (v. 5.2) [Software]. Champaign, Illinois: Wolfram Research, Inc.
50. Zavodszky,M.I., Lei,M., Thorpe,M.F., Day,A.R. and Kuhn,L.A. (2004) Proteins, 57, 243-261.
51. Zwahlen,C., Legault,P., Vincent,S.J.F., Greenblatt,J., Konrat,R. and Kay,L.E. (1997) J. Am. Chem. Soc., 119, 6711-6721.