The unfolded protein state revisited

Water and the Cell

Volumn , Issue , 2006, Pages 235-252

  Carvajal, Patricio A ^a,b   Lanier, Tyre C ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b PONTIFICIA UNIVERSIDAD CATÓLICA DE VALPARAÍSO   (Chile)

Author keywords

AFGP; PPII; Protein Hydration; Protein Unfolding

Indexed keywords

EID: 84900284041     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/1-4020-4927-7_11     Document Type: Chapter

References (76)

1. Adzhubei A, SternbergM(1993) Left-handed polyproline II helices commonly occur in globular proteins. J Mol Biol 229:472-493
2. Asher SA, Mikhonin AV, Bykov S (2004) UV Raman demonstrates that alpha-helical polyalanine peptides melt to polyproline II conformations. J Am Chem Soc 126:8433-8440
3. Baldwin R (2002) A new perspective on unfolded proteins. Adv Protein Chem 62:361-367
4. Barron LD, Blanch EW, Hecht L (2002) Unfolded proteins studied by raman optical activity. Adv Prot Chem 62:51-90
5. Bella J, Eaton M, Brodsky B, Berman HM (1994) Crystal-structure and molecular-structure of a collagenlike peptide at 1.9-Angstrom resolution. Science 266:75-81
6. Bella J, Brodsky B, Berman HM (1995) Hydration structure of a collagen peptide. Structure 3:893-906
7. Ben RN (2001) Antifreeze glycoproteins - Preventing the growth of ice. Chembiochem 2:161-166
8. Berisio R, Vitagliano L, Mazzarella L, Zagari A (2002) Crystal structure of a collagen triple helix model (Pro-Pro-Gly)-3. Protein Sci 11:262-270
9. Blanch EW, Morozova-Roche LA, Cochran DA, Doig AJ, Hecht L, Barron LD (2000) Is polyproline II helix the killer conformation? A Raman optical activity study of the amyloidogenic prefibrillar intermediate of human lysozyme. J Mol Biol 301:553-563
10. Blanch EW, Kasarda DD, Hecht L, Nielsen K, Barron LD (2003) New insight into the solution structures of wheat gluten proteins from Raman optical activity. Biochemistry 42:5665-5673
11. Bokor M, Csizmok V, Kovacs D, Banki P, Friedrich P, Tompa P, Tompa K (2005) NMR relaxation studies on the hydrate layer of intrinsically unstructured proteins. Biophysical J 88:2030-2037
12. Bolen DW, Baskakov IV (2001) The osmophobic effect: Natural selection of a thermodynamic force in protein folding. J Mol Biol 310:955-963
13. Bond CJ, Wong KB, Clarke J, Fersht AR, Daggett V (1997) Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: Description of the folding pathway. Proc Natl Acad Sci USA 94:13409-13413
14. Brant DA, Flory PA (1965) Configuration of random polypeptide chains 2: Theory. J Am Chem Soc 87:2791-2800
15. Brodsky B, Ramshaw JAM (1997) The collagen triple-helix structure. Matrix Biol 15(8-9):545-554
16. Burcham TS, Osuga DT, Rao BNN, Bush CA, Feeney RE (1986) Purification and primary sequences of the major arginine-containing antifreeze glycopeptides from the fish eleginus-gracilis. J Biol Chem 261:6384-6389
17. Bush CA, Feeney RE (1986) Conformation of the glycotripeptide repeating unit of antifreeze glycoprotein of polar fish as determined from the fully assigned proton NMR-spectrum. Int J Pept Protein Res 28(4):386-397
18. Chang JY, Ballatore A (2000) The structure of denatured bovine pancreatic trypsin inhibitor (BPTI). Febs Lett 473:183-187
19. Chellgren BW, Creamer TP (2004) Short sequences of non-proline residues can adopt the polyproline II helical conformation. Biochemistry 43:5864-5869
20. Counterman AE, Clemmer DE (2004) Anhydrous polyproline helices and globules. J Phys Chem B 108:4885-4898
21. Creamer TP, Campbell MN (2002) Determinants of the polyproline II helix from modeling studies. Adv Protein Chem 62:263-282
22. DeVries AL, Komatsu SK, Feeney RE (1970) Chemical and physical properties of freezing pointdepressing glycoproteins from Antarctic fishes. J Biol Chem 245:2901-2908
23. Drozdov AN, Grossfield A, Pappu RV (2004) Role of solvent in determining conformational preferences of alanine dipeptide in water. J Am Chem Soc 126:2574-2581
24. Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P et al. (2001) Intrinsically disordered protein. J Mol Graph Model 19:26-59
25. Dunker AK, Brown CJ, Lawson JD, Lakoucheva LM, Obradovic Z (2002) Intrinsic disorder and protein function. Biochemistry 41:6573-6582
26. Eker F, Cao X, Nafie LA, Schweitzer-Stenner R (2002) Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study. J Am Chem Soc 124:14330-14341
27. Eker F, Griebenow K, Schweitzer-Stenner R (2003) Stable conformations of tripeptides in aqueous solution studied by UV circular dichroism spectroscopy. J Am Chem Soc 125:878-885
28. Eker F, Griebenow R, Cao X, Nafie LA, Schweitzer-Stenner R (2004) Tripeptides with ionizable side chains adopt a perturbed polyproline II structure in water. Biochemistry 43:613-621
29. Farrell HM, Qi PX, Wickham ED, Unruh JJ (2002) Secondary structural studies of bovine caseins: Structure and temperature dependence of beta-casein phosphopeptide (1-25) as analyzed by circular dichroism, FTIR spectroscopy, and analytical ultracentrifugation. J Protein Chem 21:307-321
30. Garcia AE (2004) Characterization of non-Alpha helical conformations in Ala peptides. Polymer 45:669-676
31. Giesemann T, Rathke-Hartlieb S, Rothkegel M, Bartsch JW, Buchmeier S, Jockusch BM, Jockusch H (1999) A role for polyproline motifs in the spinal muscular atrophy protein SMN - Profilins bind to and colocalize with SMN in nuclear gems. J Biol Chem 274:37908-37914
32. Graether SP, Jia Z (2001) Modeling Pseudomonas syringae ice-nucleation protein as -rfaut-helical protein. Biophys J 80:1169-1173
33. Harding MM, Anderberg PI, Haymet ADJ (2003) Antifreeze glycoproteins from polar fish. Eur J Biochem 270:1381-1392
34. Jardetzky TS, Brown JH, Gorga JC, Stern LJ, Urban RG, Strominger JL, Wiley DC (1996) Crystallographic analysis of endogenous peptides associated with HLA-DR1 suggests a common, polyproline II-like conformation for bound peptides. Proc Natl Acad Sci USA 93:734-738
35. Kakinoki S, Hirano V, Oka M (2005) On the stability of Polyproline I and II structures of proline oligopeptides. Polymer Bull 53:109-115
36. Kay BK, Williamson MP, Sudol M(2000) The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains. FASEB J 14:231-241
37. Keiderling TA, Silva RA, Yoder G, Dukor RK (1999) Vibrational circular dichroism spectroscopy of selected oligopeptide conformations. Bioorg Med Chem 7:133-141
38. Kelly MA, Chellgren BW, Rucker AL, Troutman JM, Fried MG (2001) Host-guest study of left-handed polyproline II helix formation. Biochemistry 40:14376-14383
39. Kentsis A, Mezei M, Gindin T, Osman R (2004) Unfolded state of polyalanine is a segmented polyproline II helix. Prot Struct Funct Bio 55:493-501
40. Kindahl L, Sandstrom C, Norberg T, Kenne L (2000) H-1 NMR studies of hydroxy protons of Asn- and Ser-linked disaccharides in aqueous solution. J Carbohydrate Chem 19:1291-1303
41. Klein-Seetharaman J, Oikawa M, Grimshaw SB, Wirmer J, Duchardt E et al Long-range interactions within a nonnative protein. Science 295:1719-1722
42. Kramer RZ, Vitagliano L, Bella J, Berisio R, Mazzarella L, Brodsky B, Zagari A, Berman HM (1998) X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (Pro-Pro- Gly). J Mol Biol 280:623-638
43. Linder S, Hufner K, Wintergerst U, Aepfelbacher M (2000) Microtubule-dependent formation of podosomal adhesion structures in primary human macrophages. J Cell Sci 113:4165-4176
44. Mahoney NM, Janmey PA, Alamo SC (1997) Structure of the profiling-poly-L-proline complex involved in morphogenesis and cytoskeletal regulation. Nat Struct Biol 4:953-960
45. Maiti NC, Apetri MM, Zagorski MG, Carey PR, Anderson VE (2004) Raman spectroscopic characterization of secondary structure in natively unfolded proteins: alpha-synuclein. J Am Chem Soc 126:2399-2408
46. Mezei M, Fleming PJ, Srinivasan R, Rose GD (2004) Polyproline II helix is the preferred conformation for unfolded polyalanine in water. Prot Struct Funct Bio 55:502-507
47. Mimura Y, Yamamoto Y, Inoue Y, Chujo R (1992) NMR-study of interaction between sugar and peptide moieties in mucin-type model glycopeptides. Int J Biol Macromol 14:242-248
48. Naganagowda GA, Gururaja TL, Satyanarayana J, Levine MJ (1999) NMR analysis of human salivary mucin (MUC7) derived O-linked model glycopeptides: comparison of structural features and carbohydrate-peptide interactions. J Pept Res 54:290-310
49. Nguyen DH, Colvin ME, Yeh Y, Feeney RE, Fink WH (2002) The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoproteins. Biophysical J 82:2892-2905
50. Pollack GH (2002) The cell as a biomaterial. J Mater Sci Mater Med 13:811-821
51. Poon CD, Samulski ET, Weise CF, Weisshaar JC (2002) Do bridging water molecules dictate the structure of a model dipeptide in aqueous solution? J Am Chem Soc 122:5642-5643
52. Reiersen H, Rees AR (2001) The hunchback and its neighbours: proline as an environmental modulator. Trends Biochem Sci 26:679-684
53. Rucker AL, Creamer TP (2002) Polyproline II helical structure in protein unfolded states: Lysine peptides revisited. Protein Sci 11:980-985
54. Rucker AL, Pager CT, Campbell MN, Qualls JE, Creamer TP (2003) Host-guest scale of left handed polyproline II helix formation. Protein Struct Funct Genet 53:68-73
55. Schrag JD, Ogrady SM, DeVries A (1982) The relationship of amino acid composition and molecularweight of antifreeze glycopeptides to non-colligative freezing point depression. Biochim Biophys Acta 717:322-326
56. Schweers O, Schnbrunn-Hanebeck E, Marx A, Mandelkow E (1994) Structural studies of tau protein and Alzheimer paired helical filaments show no evidence for -structure. J Biol Chem 269:24290-24297
57. Schweitzer-Stenner R, Eker F, Perez A, Griebenow K, Cao X, Nafie LA (2003) The structure of triproline in water probed by polarized Raman, Fourier transform infrared, vibrational circular dichroism, and electric ultraviolet circular dichroism spectroscopy. Biopolymers 71:558-568
58. Schweitzer-Stenner R, Eker F, Griebenow K, Cao X, Nafie L (2004) The conformation of tetra-Alanine in water determined by polarized Raman, FT-IR and VCD spectroscopy. J Am Chem Soc 126:2768-2776
59. Shah NK et al. (1996) A host-guest set of triple-helical peptides: Stability of Gly-X-Y triplets containing common nonpolar residues. Biochemistry 35:10262-10268
60. Shi ZS, Olson CA, Rose GD, Baldwin RL, Kallenbach NR (2002) Polyproline II structure in a sequence of seven alanine residues. Proc Natl Acad Sci USA 99:9190-9195
61. Shortle D (1996) The denatured state (the other half of the folding equation) and its role in protein stability. Faseb J 10:27-34
62. Smyth E, Syme CD, Blanch EW, Hecht L, Vasak M, Barron LD (2001) Solution structure of native proteins with irregular folds from Raman optical activity. Biopolymers 58:138-151
63. Sreerama N, Woody RW (1994) Poly(Pro) II helices in globular proteins: identification and circular dichroism analysis. Biochemistry 33:10022-10025
64. Stapley BJ, Creamer TP (1999) A survey of left-handed polyproline II helices. Prot Sci 8:587-595
65. Syme CD, Blanch EW, Holt C, Jakes R, Goedert M, Hecht L, Barron LD (2002) A Raman optical activity study of rheomorphism in caseins, synucleins and tau - New insight into the structure and behaviour of natively unfolded proteins. Eur J Biochem 269:148-156
66. Tachibana Y, Fletcher GL, Fujitani N, Tsuda S, Monde K, Nishimura SI (2004a) Antifreeze glycoproteins: Elucidation of the structural motifs that are essential for antifreeze activity. Angew Chem Int Ed Engl 43:856-862
67. Tachibana Y, Monde K, Nishimura SI (2004b) Sequential glycoproteins: Practical method for the synthesis of antifreeze glycoprotein models containing base labile groups. Macromolecules 37:6771-6779
68. Tiffany ML, Krimm S (1968) New chain conformations of poly(glutamic acid) and polylysine. Biopolymers 6:1379-1383
69. Tiffany ML, Krimm S (1972) Effect of temperature on circular-dichroism spectra of polypeptides in extended state. Biopolymers 11:2309-2316
70. Tiffany ML, Krimm S (1973) Extended conformations of polypeptides and proteins in urea and guanidine hydrochloride. Biopolymers 12:575-587
71. Tompa P (2002) Intrinsically unstructured proteins. Trends Biochem Sci 27:527-533
72. Uversky VN, Fink AL (2002) The chicken egg scenario of protein folding revisited. Febs Lett 515:79-83
73. Weinreb PH, Zhen W, Poon AW, Conway KA, Lansbury PT (1996) NACP, a protein implicated in Alzheimers disease and learning, is natively unfolded. Biochemistry 35:13709-13715
74. Woutersen S, Hamm P (2001) Isotope-edited two-dimensional vibrational spectroscopy of trialanine in aqueous solution. J Chem Phys 114:2727-2737
75. Wright PE, Dyson HJ (1999) Intrinsically unstructured proteins: re-Assessing the protein structurefunction paradigm. J Mol Biol 293:321-331
76. Yeh Y, Feeney RE (1996) Antifreeze proteins: Structures and mechanisms of function. Chemical Reviews 96:601-617