Polyproline II structure in proteins: Identification by chiroptical spectroscopies, stability, and functions

Chirality

Volumn 14, Issue 10, 2002, Pages 782-792

  Bochicchio, Brigida ^a   Tamburro, Antonio Mario ^a  

^a UNIVERSITY OF BASILICATA   (Italy)

Author keywords

Chiroptical spectroscopies; Elasticity; PPII; Recognition

Indexed keywords

ELASTOMER; PROLINE DERIVATIVE; PROTEIN;

AMINO ACID ANALYSIS; CELL MOTILITY; CHIRALITY; CIRCULAR DICHROISM; ELASTICITY; GENETIC TRANSCRIPTION; HUMAN; HYDROGEN BOND; IMMUNE RESPONSE; MOLECULAR RECOGNITION; NONHUMAN; OPTICAL ROTATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; RAMAN SPECTROMETRY; RELIABILITY; REVIEW; SIGNAL TRANSDUCTION; SPECTROSCOPY;

CIRCULAR DICHROISM; ELASTICITY; PEPTIDES; PROTEIN CONFORMATION; SPECTRUM ANALYSIS;

EID: 0036035968     PISSN: 08990042     EISSN: None     Source Type: Journal    
DOI: 10.1002/chir.10153     Document Type: Review

References (95)

1. Kelly MA, Chellgren BW, Rucker AL, Troutman JM, Fried MG, Miller AF, Creamer TP. Host-guest study of left-handed polyproline II helix formation. Biochemistry 2001;40:14376-14383.
2. Siligardi G, Drake AF. The importance of extended conformations and, in particular, the PPII conformation for the molecular recognition of peptides. Biopolymers 1995;37:281-292.
3. Traub W, Shmueli U. Structure of poly-L-proline (I). Nature 1963;198: 1165-1166.
4. Woody RW. Circular dichroism and conformation of unordered polypeptides. Adv Biophys Chem 1992;2:37-79.
5. Wütrich K. NMR of Proteins and Nucleic Acids. New York: Wiley-Interscience; 1986.
6. Blanch E, Morozova-Roche LA, Cochran DAE, Doig AJ, Hecht L, Barron LD. Is polyproline II helix the killer conformation? A Raman optical activity study of the amyloidogenic prefibrillar intermediate of human lysozyme. J Mol Biol 2000;301:553-563.
7. Drake AF, Siligardi G, Gibbons WA. Reassessment of the electronic circular dichroism criteria for random coil conformations of poly(L-lysine) and the implications for the protein folding and denaturation studies. Biophys Chem 1988;31:143-146.
8. Venugopal MG, Ramshaw JAM, Braswell E, Zhu D, Brodsky B. Electrostatic interactions in collagen-like triple helical peptides. Biochemistry 1994;33:7948-7956.
9. Nielsen EB, Shellman IA. The absorption spectra of simple amides and peptides. J Phys Chem 1967;71:2297-2304.
10. Greenfield N, Fasman GD. Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 1969;8:4108-4116.
11. Johnson WC Jr, Tinoco I Jr. Circular dichroism of polypeptide solutions in the vacuum ultraviolet. J Am Chem Soc 1972;94:4389-4392.
12. Gilbert SM, Wellner N, Belton PS, Greenfield JA, Siligardi G, Shewry PR, Tatham AS. Expression and characterisation of a highly repetitive peptide derived from a wheat seed storage protein. Biochim Biophys Acta 2000;1479:135-146.
13. Tiffany ML, Krimm S. Circular dichroism of poly-L-proline in an unordered conformation. Biopolymers 1968;6:1767-1770.
14. Yasui SC, Keiderling TA. Vibrational circular dichroism of polypeptides. Poly(lysine) conformations as a function of pH in aqueous solution. J Am Chem Soc 1986;108:5576-5581.
15. Paterlini MG, Freedman TB, Nafie LA. Vibrational circular dichroism of spectra of three conformationally distinct states and an unordered state of poly(L-lysine) in deuterated aqueous solution. Biopolymers 1986;25:1751-1765.
16. Bienkiewicz EA, Woody AY, Woody RW. Conformation of the RNA polymerase II C-terminal domain: Circular dichroism of long and short fragments. J Mol Biol 2000;297:119-133.
17. Tonelli AE. Calculated rotatory properties of random coil poly-L-alanine. Macromolecules 1969;2:635-637.
18. Ronish EW, Krimm S. Theoretical calculation of the circular dichroism of unordered polypeptide chains. Biopolymers 1972;11:1919-1928.
19. Dungan JM III, Hooker TM Jr. Conformation of peptides in solution. Circular dichroism studies of N-acetyl-L-alanine N-methylamide and N-acetyl-L-Serine N-methylamide. Macromolecules 1981;14:1812-1822.
20. Siemion IZ, Wieland T, Pook KH. Effect of the distance of proline carbonyl from β and γ carbons on the position of the carbon-13 NMR signals. Angew Chem Int Ed 1975;14:702-703.
21. Mizushima S, Shimanouchi T, Tsuboi M, Arakawa TJ. Near-infrared spectra of compounds with two peptide bonds and the configuration of a polypeptide chain. VI. Further evidence of the internal hydrogen bonding and an estimation of its energy. J Am Chem Soc 1957;79:5357-5361.
22. Portnova SL, Bystrov VF, Tsetlin VI, Ivanov VI, Ovchinnikov Yu A. Conformational states of peptide systems. I. Quantitative evaluation of intramolecular hydrogen bonding in alanine dipeptides by infrared spectroscopy. Zh Obshch Khim 1968;38:428-439.
23. Bystrov VF, Portnova SL, Tsetlin VI, Ovchinnikov Yu A. Conformational studies of peptide systems. Rotational states of the NH-CH fragment of alanine dipeptides by nuclear magnetic resonance. Tetrahedron 1969;25:493-515.
24. Marraud M, Néel J, Avignon M, Huong PV. Conformational study of dipeptides in solution. J Chim Phys Phys-Chim Biol 1970;67:959-964.
25. Avignon M, Huong PV, Lascombe J, Marraud M, Néel J. Infrared spectroscopic study of the conformation of some model peptide compounds. Biopolymers 1969;8:69-89.
26. Avignon M, Huong PV. A method of quantitative determination of stereoisomers of dipeptides in solution by infrared spectroscopy. Biopolymers 1970;9:427-432.
27. Burgess AW, Scheraga HA. Stable conformations of dipeptides. Biopolymers 1973;12:2177-2183.
28. Cung MT, Marraud M, Néel J. In: Bergmann ED, Pulmann B, editors. Conformation of Biological Molecules and Polymers. New York: Academic Press; 1973. p 69-86.
29. Maxfield FR, Leach SJ, Stimson ER, Powers SP, Scheraga HA. Infrared spectra of the N-acetyl-N′-methylamides of glycine, L-alanine, and L-leucine in dilute solutions of chloroform and carbon tetrachloride. Biopolymers 1979;18:2507-2521.
30. Ramachandran GN, Chandrasekaran R. Conformational energy map of a dipeptide unit in relation to infrared and nuclear magnetic resonance. Biopolymers 1971;10:935-939.
31. Aebersold D, Pysh ES. Optical properties of amorphous polypeptides. I. One state solutions. J Chem Phys 1970;53:2156-2163.
32. Zubkov VA, Birshtein TM, Milevskaya IS, Volkenstein MV. Circular dichroism of random coil polypeptide chains. Biopolymers 1971;10: 2051-2061.
33. Madison V, Schelmann J. Optical activity of polypeptides and proteins. Biopolymers 1972;11;1041-1076.
34. Pysh ES. The calculated ultraviolet optical properties of poly-L-proline I and II. J Mol Biol 1967;23:587-599.
35. Pysh ES. Scalar spectral characteristics of one-dimensional solids. J Chem Phys 1970;52:4723-4733.
36. Tterlikkis L, Loxsom FM, Rhodes W. Theoretical optical properties of poly-L-proline. Biopolymers 1973;12:675-684.
37. Pysh ES. Random-phase calculation of poly-L-proline II circular dichroism. Biopolymers 1974;13:1563-1571.
38. Applequist J. Theoretical π-π* circular dichroic spectra of helical polyglycine and poly-L-alanine as functions of backbone torsion angles. Biopolymers 1981;20:2311-2322.
39. Manning MC, Woody RW. Theoretical CD studies of polypeptides helices: Examination of important electronic and geometric factors. Biopolymers 1991;31:569-586.
40. Tinoco I Jr. Electronic spectroscopy of rigid polymers. J Am Chem Soc 1964;86:297-298.
41. Ronish EW, Krimm S. The calculated circular dichroism of polyproline II in the polarizability approximation. Biopolymers 1974;13:1635-1651.
42. Mandel R, Holzwarth G. Ultraviolet circular dichroism of polyproline and oriented collagen. Biopolymers 1973;12:655-674.
43. Viguera AR, Arrondo JL, Musacchio A, Saraste M, Serrano L. Characterization of the interaction of natural proline rich peptides with five different SH3 domains. Biochemistry 1994;33:10925-10933.
44. Tatham AS, Drake AF, Shewry PR. Conformational studies of a synthetic peptide corresponding to the repeat motif of C hordein. Biochem J 1989;259:471-476.
45. Dukor RK, Keiderling TA. Reassessment of the random coil conformation: Vibrational CD study of proline oligopeptides and related polypeptides. Biopolymers 1991;31:1747-1761.
46. Keiderling TA, Silva RA, Yoder G, Dukor RK. Vibrational circular dichroism spectroscopy of selected oligopeptide conformations. Bioorg Med Chem 1999;7:133-141.
47. Smyth E, Syme CD, Blanch EW, Hecht L, Vasàk M, Barron LD. Solution structure of native proteins with irregular folds from Raman optical activity. Biopolymers 2001;58:138-151.
48. Syme CD, Blanch EW, Holt C, Ross J, Goedert M, Hecht L, Barron LD. A Raman optical activity study of rheomorphism in caseins, synucleins and tau. Eur J Biochem 2002;269:148-156.
49. Cowan PM, McGavin S. Structure of poly-L-proline. Nature 1955;176: 501-503.
50. Crick FHC, Rich A. Structure of polyglycine II. Nature 1955;176:780-781.
51. Sreerama N, Woody R. Molecular dynamics simulations of polypeptide conformations in water. A comparison of α, β, and poly(pro)II conformations. Proteins 1999;36:400-406.
52. Martino M, Bavoso A, Guantieri V, Coviello A, Tamburro AM. On the occurrence of polyproline II structure in elastin. J Mol Struct 2000;519;173-189.
53. Rich A, Crick FHC. The molecular structure of collagen. J Mol Biol 1961;3:483-506.
54. Ramachandran GN, Sasisekharan V. Structure of collagen. Nature 1961;190:1004-1005.
55. Piez KA, Eigner EA, Lewis MS. Chromatographic separation and aminoacid composition of the subunits of several collagens. Biochemistry 1963;2:58-66.
56. Piez KA. Characterization of a collagen from codfish skin containing three chromatographically different alpha-chains. Biochemistry 1965; 4:2590-2596.
57. 10. J Biom Struct Dyn 1998;15:1029-1037.
58. Stapley BJ, Creamer TP. A survey of left-handed polyproline II helices. Protein Sci 1999;223:1121-1138.
59. Makarov AA, Lobachov VM, Adzhubei IA, Esipova NG. Natural polypeptides in left-handed helical conformation. FEBS Lett 1992;306:63-65.
60. Adzhubei AA, Sternberg MJE. Left-handed polyproline II helices commonly occur in globular proteins. J Mol Biol 1993;229:472-493.
61. Labeit S, Kolmerer B. Titins: Giant proteins in charge of muscle ultrastructure and elasticity. Science 1995;270:293-296.
62. Gutierrez-Cruz G, Van Heerden AH, Wang K. Modular motif, structural folds and affinity profiles of the PEVK segment of human fetal skeletal muscle titin. J Biol Chem 2001;276:7442-7449.
63. MacArthur MW, Thornton JM. Influence of proline residues on protein conformation. J Mol Biol 1991;218:397-412.
64. Kan MaKL, Wang K. Polyproline II helix is a key structural motif of the elastic PEVK segment of titin. Biochemistry 2001;40:3427-3438.
65. Wang Cao Q, Bayley H. Sequence of abductin, the molluscan 'rubber' protein. Curr Biol 1997;7:677-678.
66. Royce PM, Steinmann B (editors). Connective Tissue and its Heritable Disorders. New York: Wiley-Liss; 1993.
67. Tamburro AM, Davidson JM (editors). Elastin: Chemical and Biological Aspects. Galatina, Italy: Congedo; 1990.
68. Sandberg LB, Gray WR, Franzblau C (editors). Elastin and Elastic Tissue. New York: Plenum Press; 1977.
69. Flory J. Principles of Polymer Chemistry. Ithaca, NY: Cornell University Press; 1953.
70. Villani V, D'Alessio L, Tamburro AM. Contribution of GXGG sequences to elastin elasticity. Development of the transition to chaos mechanism of elasticity. In: Tamburro AM, editor. Elastin and Elastic Tissue. Potenza, Italy: Armento; 1996. p 31-37.
71. Villani V, D'Alessio L, Tamburro AM. Conformational non linear dynamical behavior of the peptide Boc-Gly-Leu-Gly-Gly-Nme. J Chem Soc Perkin Trans 2 1997;2375-2385.
72. Debelle L, Tamburro AM. Elastin: Molecular description and function. Int J Biochem Cell Biol 1999;31:261-272.
73. Bonelli A, D'Alessio L, Ruffo S, Tamburro AM. Structural and dynamic complexity of an elastin-related peptide. In: Novak MM, editor. Emergent Nature. Singapore: World Scientific; 2002. p 33-44.
74. Bochicchio B, Tamburro AM. The exon-by-exon full synthesis of non-crosslinking sequences of human tropoelastin: CD studies. In: Alix AJP, editor. Elastin 2001. Reims University Press; 2002.
75. Bochicchio B, Pepe A, Tamburro AM. On (GGLGY) synthetic repeating sequences of lamprin and analogous sequences. Matrix Biol 2001; 20:243-250.
76. Robson P, Wright GM, Sitarrz E, Maiti A, Rawat M, Youson JH, Keeley FW. Characterization of lamprin, an unusual matrix protein from lamprey cartilage. J Biol Chem 1993;268:1440-1447.
77. Tamburro AM, Guantieri V, Pandolfo L, Scopa A. Synthetic fragments and analogues of elastin. II. Conformational studies. Biopolymers 1990; 29:855-870.
78. Knighton DR, Zheng J, Ten Eyck LF, Xoung N, Taylor SS, Sowadski IM. Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science 1991;253:414-420.
79. Renzoni DA, Pugh DJR, Siligardi G, Das P, Morton CJ, Rossi C, Waterfiel MD, Campbell ID, Ladbury JE. Structural and thermodynamic characterization of the interaction of the SH3 domain from Fyn with the poline-rich binding site on the p85 subunit of PI3-kinase. Biochemistry 1996;35:15646-15653.
80. Sudol M. Structure and function of the WW domain. Progr Biophys Mol Biol 1996;65:113-132.
81. Tanaka M, Shibata H. Poly (L-proline)-binding proteins from chick embryos are a profilin and profilactin. Eur J Biochem 1985;151:291-297.
82. Mahoney NM, Janmey PA, Almo SC. Structure of the profilin-poly-L-proline complex involved in morphogenesis and cytoskeletal regulation. Nat Struct Biol 1997;4:953-960.
83. Jardetsky TS, Brown JH, Gorga JC, Stern LJ, Urban RG, Strominger JL, Wiley DC. Crystallographic analysis of endogenous peptides associated with HLA-DR1 suggests a common, polyproline II-like conformation for bound peptides. Proc Natl Acad Sci USA 1996;93:734-738.
84. Stern LJ, Brown JH, Jardetsky TS, Gorga JC, Urban RG, Strominger JL, Wiley DC. Crystal structure of the human class II MHC protein HLA-DR1 completed with an influenza virus peptide. Nature 1994;368:215-221.
85. Spencer DIR, Missailidis S, Denton G, Murray A, Brady K, Matteis CID, Searle MS, Tendler SJB, Price MR. Structure/activity studies of the anti-MUC1 monoclonal antibody C595 and synthetic MUC1 mucin-core-related peptides and glycopeptides. Biospectroscopy 1999;5:79-91.
86. Torrent M, Geli MI, Ruiz-Avila M, Canals JM, Puigdomènech P, Ludevid MD. Role of structural domains for maize gamma-zein retention in Xenopus oocytes. Planta 1994;192:512-518.
87. Rabanal F, Ludevid MD, Pons M, Giralt E. CD of proline-rich polypeptides: Application to the study of the repetitive domain of maize glutelin-2. Biopolymers 1993;33:1019-1028.
88. Sherman SA, Gmeiner WH, Kirnarskiy L, Perini F, Ruddon WJ. A linear 23-residue peptide reveals a propensity to form an unusual native-like conformation. J Biomol Struct Dyn 1995;13:441-446.
89. Sreerama N, Woody RW. Poly(Pro)II helices in globular proteins: Identification and circular dichroic analysis. Biochemistry 1994;33:10022-10025.
90. Caldwell JW, Applequist J. Theoretical π-π absorption, circular dichroic, and linear dichroic spectra of collagen triple helices. Biopolymers 1984;10:1891-1904, and references therein.
91. Ramachandran GN, Sasisekharan V. Refinement of the structure of collagen. Biochim Biophys Acta 1965;109:314-316.
92. Lee CH, Kominos D, Jacques S, Margolis B, Schlessinger J, Shoelson SE, Kuriyan J. Crystal structures of peptide complexes of the aminoterminal SH2 domain of the Syp tyrosine phosphatase. Structure 1994; 2:423-438.
93. Musacchio A, Saraste M, Wilmanns M. High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides. Nat Struct Biol 1994;8:546-551.
94. Lim WA, Richards FM, Fox RO. Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature 1994;372:375-379.
95. Brown JH, Jardetzky TS, Gorga JC, Stern LJ, Urban RG, Strominger JL, Wiley DC. Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 1993;364:33-39.