NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein

Journal of Molecular Biology

Volumn 274, Issue 2, 1997, Pages 152-159

  Penkett, Christopher J ^a   Redfield, Christina ^a   Dodd, Ian ^b   Hubbard, Julia ^b   McBay, Diane L ^b   Mossakowska, Danuta E ^b   Smith, Richard A G ^b   Dobson, Christopher M ^a   Smith, Lorna J ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b GLAXOSMITHKLINE   (United Kingdom)

Author keywords

Coupling constant; Nuclear magnetic resonance; Protein data base; Random coil; Structural propensities

Indexed keywords

BINDING PROTEIN; FIBRONECTIN; FIBRONECTIN BINDING PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; DATA BASE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PH; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STAPHYLOCOCCUS AUREUS; STEREOCHEMISTRY;

EID: 0030726550     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1369     Document Type: Editorial

References (55)

1. Baldwin R. L. α-Helix formation by peptides of defined sequence. Biophys. Chem. 55:1995;127-135.
2. Barton G. J. Protein secondary structure prediction. Curr. Opin. Struct. Biol. 5:1995;372-376.
3. Blaber M., Zhang X. J., Matthews B. W. Structural basis of amino-acid α-helix propensity. Science. 260:1993;1637-1640.
4. Bolin K. A., Pitkeathly M., Miranker A., Smith L. J., Dobson C. M. Insight into a random coil conformation and an isolated helix: structural and dynamical characterisation of the C-helix peptide from hen lysozyme. J. Mol. Biol. 262:1996;443-453.
5. 15. J. Am. Chem. Soc. 116:1994;8466-8469.
6. Burnham M. K., Chopra I., Critchley I. A., Knowles D. J. C. Patent; International publication number: W0 94/18327. 1994.
7. Bystroff C., Simons K. T., Han K. F., Baker D. Local sequence-structure correlations in proteins. Curr. Opin. Biotechnol. 7:1996;417-421.
8. Chakrabartty A., Kortemme T., Baldwin R. L. Helix propensities of the amino-acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 3:1994;843-852.
9. Cordes M., Davidson A. R., Sauer R. T. Sequence space, folding and protein design. Curr. Opin. Struct. Biol. 6:1996;3-10.
10. Dobson C. M. Flexible friends. Curr. Biol. 3:1993;530-532.
11. Driscoll P. C., Clore G. M., Marion D., Wingfield P. T., Gronenborn A. M. Complete resonance assignment for the polypeptide backbone of interleukin-1-β using 3-dimensional heteronuclear NMR spectroscopy. Biochemistry. 29:1990;3542-3556.
12. 13. J. Biomol. NMR. 2:1992;583-590.
13. Fiebig K. M., Schwalbe H., Buck M., Smith L. J., Dobson C. M. Towards a description of the conformation of denatured states of proteins. Comparison of a random coil model with NMR measurements. J. Phys. Chem. 100:1996;2661-2666.
14. Frenkiel T., Bauer C., Carr M. D., Birdsall B., Feeney J. HMQC-NOESY-HMQC, a 3-dimensional NMR experiment which allows detection of nuclear Overhauser effects between protons with overlapping signals. J. Magn. Reson. 90:1990;420-425.
15. Gast K., Damaschun H., Eckert K., Schulze-Forster K., Maurer H. R., Müller-Frohne M., Zirwer D., Czarnecki J., Damaschun G. Prothymosin α: a biologically active protein with a random coil conformation. Biochemistry. 34:1995;13211-13218.
16. Harper E. T., Rose G. D. Helix stop signals in proteins and peptides-the capping box. Biochemistry. 32:1993;7605-7609.
17. Hernández M. A., Avila J., Andreu J. M. Physicochemical characterization of the heat-stable microtubule-associated protein MAP2. Eur. J. Biochem. 154:1986;41-48.
18. Horovitz A., Matthews J. M., Fersht A. R. α-Helix stability in proteins. II. Factors that influence stability at an internal position. J. Mol. Biol. 227:1992;560-568.
19. House-Pompeo K., Xu Y., Joh D., Speziale P., Höök M. Conformational changes in the fibronectin binding MSCRAMMs are induced by ligand binding. J. Biol. Chem. 271:1996;1379-1384.
20. Ikura M., Bax A., Clore G. M., Gronenborn A. M. Detection of nuclear Overhauser effects between degenerate amide proton resonances by heteronuclear 3-dimensional nuclear-magnetic-resonance spectroscopy. J. Am. Chem. Soc. 112:1990;9020-9022.
21. Karplus M. Contact electron-spin coupling of nuclear magnetic moments. J. Chem. Phys. 30:1959;11-15.
22. 15. J. Magn. Reson. 86:1990;110-126.
23. Kay L. E., Marion D., Bax A. Practical aspects of 3D heteronuclear NMR of proteins. J. Magn. Reson. 84:1989;72-84.
24. 1. J. Mol. Biol. 230:1993;312-322.
25. (waf1/cip1/sdi1). Proc. Natl Acad. Sci. USA. 93:1996;11504-11509.
26. Kuboniwa H., Grzesiek S., Delaglio F., Bax A. Measurement of HN,Hα J-couplings in calcium-free calmodulin using new 2D and 3D water-flip-back methods. J. Biomol. NMR. 4:1994;871-878.
27. Lyu P. C., Wemmer D. E., Zhou H. X., Pinker R. J., Kallenbach N. R. Capping interactions in isolated α-helices - position dependent substitution effects and structure of a serine-capped peptide helix. Biochemistry. 32:1993;421-425.
28. 1115. Biochemistry. 28:1989;6150-6156.
29. 1. J. Biomol. NMR. 5:1995;14-24.
30. Minor D. L., Kim P. S. Context is a major determinant of β-sheet propensity. Nature. 371:1994;264-267.
31. Moore G. J. Designing peptide mimetics. Trends Pharmacol. Sci. 15:1994;124-129.
32. Moult J. The current state-of-the-art in protein-structure prediction. Curr. Opin. Biotechnol. 7:1996;422-427.
33. Munoz V., Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. II. Helix macrodipole effects and rational modification of the helical content of natural peptides. J. Mol. Biol. 245:1995;275-296.
34. Munoz V., Blanco F. J., Serrano L. The hydrophobic-staple motif and a role for loop-residues in α-helix stability and protein-folding. Nature Struct. Biol. 2:1995;380-385.
35. HNα. J. Mol. Biol. 180:1984;741-751.
36. Ramirezalvarado M., Blanco F. J., Serrano L. De-novo design and structural-analysis of a model β-hairpin peptide system. Nature Struct. Biol. 3:1996;604-612.
37. Redfield C., Smith L. J., Boyd J., Lawrence G. M. P., Edwards R. G., Smith R. A. G., Dobson C. M. Secondary structure and topology of human interleukin-4 in solution. Biochemistry. 30:1991;11029-11033.
38. Regan L. Protein-structure - born to be beta. Curr. Biol. 4:1994;656-658.
39. Richardson J. S., Richardson D. C. Amino-acid preferences for specific locations at the ends of alpha-helices. Science. 240:1988;1648-1652.
40. Schwalbe H., Fiebig K. M., Buck M., Jones J. A., Grimshaw S. B., Spencer A., Glasser S. J., Smith L. J., Dobson C. M. Structural and dynamical properties of lysozyme denatured in 8 M urea. Heteronuclear 3D NMR experiments and theoretical simulations. Biochemistry. 36:1997;8977-8991.
41. Schweers O., Schönbunn-Hanebeck E., Marx A., Mandelkow E. Structural studies of tau protein and Alzheimer paired helical filaments show no evidence for β-structure. J. Biol. Chem. 269:1994;24290-24297.
42. Searle M. S., Williams D. H., Gerhard U. Partitioning of free-energy contributions in the estimation of binding constants - residual motions and consequences for amide-amide hydrogen-bond strengths. J. Am. Chem. Soc. 114:1992;10697-10704.
43. Seip S., Balbach J., Kessler H. Determination of backbone conformation of isotopically enriched proteins based on coupling-constants. J. Magn. Reson. Series B. 104:1994;172-179.
44. Serrano L. Comparison between the φ distribution of amino acids in the protein data base and NMR data indicates that amino acids have various φ propensities in the random coil conformation. J. Mol. Biol. 254:1995;322-333.
45. Signäs C., Raucci G., Jönsson K., Lindgren P. E., Anantharamaiah G. M., Höök M., Lindberg M. Nucleotide sequence of the gene for a fibronectin-binding protein fromStaphylococcus aureus. Proc. Natl Acad. Sci. USA. 86:1989;699-703.
46. Smith C. K., Withka J. M., Regan L. A thermodynamic scale for the β-sheet forming tendencies of the amino-acids. Biochemistry. 33:1994;5510-5517.
47. Smith L. J., Fiebig K. M., Schwalbe H., Dobson C. M. The concept of a random coil. Residual structure in peptides and denatured proteins. Folding and Design. 1:1996a;R95-R106.
48. Smith L. J., Bolin K. A., Schwalbe H., MacArthur M. W., Thornton J. M., Dobson C. M. Analysis of main chain torsion angles in proteins. Prediction of NMR coupling constants for native and denatured conformations. J. Mol. Biol. 255:1996b;494-506.
49. Spolar R. S., Record M. T. Coupling of local folding to site-specific binding of proteins to DNA. Science. 263:1994;777-784.
50. Swindells M. B., MacArthur M. W., Thornton J. M. Intrinsic φ,ψ propensities of amino acids derived from the coil region of known structures. Nature Struct. Biol. 2:1995;596-603.
51. Wang A. C., Bax A. Determination of the backbone dihedral angles φ in human ubiquitin from reparametrized empirical Karplus equations. J. Am. Chem. Soc. 118:1996;2483-2494.
52. Weinreb P. H., Zhen W., Poon A. W., Conway K. A., Lansbury P. T. NACP, a protein implicated in Alzheimer's disease and learning is natively unfolded. Biochemistry. 35:1996;13709-13715.
53. Wishart D. S., Sykes B. D., Richards F. M. Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J. Mol. Biol. 222:1991;311-333.
54. 11315. J. Biomol. NMR. 5:1995;67-81.
55. Yao J., Feher V. A., Espejo B. F., Reymond M. T., Wright P. E., Dyson H. J. Stabilization of a type VI turn in a family of linear peptides in water solution. J. Mol. Biol. 243:1994;736-753.