Raman optical activity of proteins, carbohydrates and glycoproteins

Chirality

Volumn 18, Issue 2, 2006, Pages 103-115

  Zhu, Fujiang ^a   Isaacs, Neil W ^a   Hecht, Lutz ^a   Tranter, George E ^b   Barron, Laurence D ^a  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Carbohydrates; Glycoproteins; Pattern recognition; Proteins; Raman optical activity; Structural genomics; Vibrational optical activity

Indexed keywords

CARBOHYDRATE; GLYCOPROTEIN; PROTEIN;

ALPHA HELIX; BETA SHEET; CHIRALITY; CONFERENCE PAPER; HYDRATION; MATHEMATICAL MODEL; NEODYMIUM LASER; PATTERN RECOGNITION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; RAMAN SPECTROMETRY; STEREOCHEMISTRY; STRUCTURAL GENOMICS; SYNCHROTRON RADIATION; X RAY CRYSTALLOGRAPHY;

ANIMALS; CARBOHYDRATE SEQUENCE; CARBOHYDRATES; CATTLE; GENOMICS; GLYCOPROTEINS; HUMANS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SPECTRUM ANALYSIS, RAMAN; STEREOISOMERISM;

EID: 31644443201     PISSN: 08990042     EISSN: 1520636X     Source Type: Journal    
DOI: 10.1002/chir.20225     Document Type: Conference Paper

References (63)

1. Pusey ML, Liu ZJ, Tempel W, Praissman J, Lin D, Wang BC, Gavira JA, Ng JD. Life in the fast lane for protein crystallization and X-ray crystallography. Prog Biophys Mol Biol 2005;88:359-386.
2. Sue SC, Chang CF, Huang YT, Chou CY, Huang TH. Challenges in NMR-based structural genomics. Physica A 2005;350:12-27.
3. Uversky VN. Natively unfolded proteins: a point where biology waits for physics. Protein Sci 2002;11:739-756.
4. Dyson HJ, Wright PE. Intrinsically unstructured proteins and their functions. Nat Rev 2005;6:197-208.
5. Dwek RA. Toward understanding the function of sugars. Chem Rev 1996;96:683-720.
6. Lapthorn AJ, Harris DC, Littlejohn A, Lustbader JW, Canfield RE, Machin KJ, Morgan FJ, Isaacs NW. Crystal structure of human chorionic gonadotropin. Nature 1994;369:455-461.
7. Wormald MR, Petrescu AJ, Pao Y-L, Glithero A, Elliot T, Dwek RA. Conformational studies of oligosaccharides and glycopeptides: complementarity of NMR, X-ray crystallography, and molecular modelling. Chem Rev 2002;102:371-386.
8. Barth A, Zscherp C. What vibrations tell us about proteins. Q Rev Biophys 2002;35:369-430.
9. Miura T, Thomas Jr GJ. Raman spectroscopy of proteins and their assemblies. In: Biswas BB, Roy S, editors. Subcellular biochemistry. Vol 24. Proteins: structure, function and engineering. New York: Plenum Press; 1995. p 55-99.
10. Tuma R. Raman spectroscopy of proteins: from peptides to large assemblies. J Raman Spectrosc 2005;36:307-319.
11. Fasman GD (editor). Circular dichroism and the conformational analysis of biomolecules. New York: Plenum Press; 1996.
12. Wallace BA, Wien F, Miles AJ, Lees JG, Hoffmann SV, Evans P, Wistow GJ, Slingsby C. Biomedical applications of synchrotron radiation circular dichroism spectroscopy: identification of mutant proteins associated with disease and development of a reference database for fold motifs. Faraday Discuss 2004;126:237-243.
13. Keiderling TA. Peptide and protein conformational studies with vibrational circular dichroism and related spectroscopies. In: Berova N, Nakanishi K, Woody RW, editors. Circular dichroism. Principles and applications. New York: Wiley-VCH; 2000. p 621-666.
14. Hug W. Raman optical activity. In: Chalmers JM, Griffiths PR, editors. Handbook of vibrational spectroscopy, Vol. 1. Chichester, U.K: John Wiley & Sons; 2002. p 745-758.
15. Barron LD. Molecular light scattering and optical activity, 2nd edition. Cambridge, England: Cambridge University Press; 2004.
16. Barron LD, Hecht L, Blanch EW, McColl IH. Raman optical activity comes of age. Mol Phys 2004;102:731-744.
17. Barron LD, Bogaard MP, Buckingham AD. Raman scattering of circularly polarized light by optically active molecules. J Am Chem Soc 1973;95:603-605.
18. Barron LD, Hecht L, Blanch EW, Bell AF. Solution structure and dynamics of biomolecules from Raman optical activity. Prog Biophys Mol Biol 2000;73:1-49.
19. Barron LD, Zhu F, Hecht L, Barron LD. Structure and behavior of proteins from Raman optical activity. In: Uversky VN, Permyakov EA, editors. Protein structures: methods in protein structure and stability. New York: Nova Science Publishers; 2006.
20. Blanch EW, Hecht L, Syme CD, Volpetti V, Lomonossoff GP, Nielsen K, Barron LD. Molecular structures of viruses from Raman optical activity. J Gen Virol 2002;83:2593-2600.
21. Hug W, Hangartner G. A novel high-throughput Raman spectrometer for polarization difference measurements. J Raman Spectrosc 1999;30:841-852.
22. Hug W. Virtual enantiomers as the solution of optical activity's deterministic offset problem. Appl Spectrosc 2003;57:1-13.
23. Atkins PW, Barron LD. Rayleigh scattering of polarized photons by molecules. Mol Phys 1969;16:453-466.
24. Barron LD, Buckingham AD. Rayleigh and Raman scattering from optically active molecules. Mol Phys 1971;20:1111-1119.
25. Hecht L, Barron LD, Hug W. Vibrational Raman optical activity in backscattering. Chem Phys Lett 1989;158:341-344.
26. Hecht L, Barron LD. An analysis of modulation experiments for Raman optical activity. Appl Spectrosc 1990;44:483-491.
27. Polavarapu PL. Ab initio vibrational Raman and Raman optical activity spectra. J Phys Chem 1990;94:8106-8112.
28. Zuber G, Hug W. Rarified basis sets for the calculation of optical tensors. 1. The importance of gradients on hydrogen atoms for the Raman scattering tensor. J Phys Chem A 2004;108:2108-2118.
29. Hecht L, Barron LD, Blanch EW, Bell AF, Day LA. Raman optical activity instrument for studies of biopolymer structure and dynamics. J Raman Spectrosc 1999;30:815-825.
30. Zhu F, Isaacs NW, Hecht L, Barron LD. Raman optical activity: a tool for protein structure analysis. Structure 2005;13:1409-1419.
31. Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24:946-950.
32. Tu AT. Peptide backbone conformation and microenvironment of protein side chains. Adv Spectrosc 1986;13:47-112.
33. Diem M. Modern vibrational spectroscopy. New York: John Wiley & Sons; 1993.
34. Schweitzer-Stenner R, Eker F, Huang Q, Griebenow K, Mroz PA, Kozlowski PM. Structure analysis of dipeptides in water by exploring and utilizing the structural sensitivity of amide III by polarized visible Raman, FTIR-spectroscopy and DFT based normal coordinate analysis. J Phys Chem B 2002;106:4294-4304.
35. McColl IH, Blanch EW, Hecht L, Barron LD. A study of α-helix hydration in polypeptides, proteins and viruses using vibrational Raman optical activity. J Am Chem Soc 2004;126:8181-8188.
36. McColl IH, Blanch EW, Gill AC, Rhie AGO, Ritchie MA, Hecht L, Nielsen K, Barron LD. A new perspective on β-sheet structures using vibrational Raman optical activity: from poly(L-lysine) to the prion protein. J Am Chem Soc 2003;125:10019-10026.
37. Holt C, Sawyer L. Caseins as rheomorphic proteins: interpretation of primary and secondary structures of the αS1-, β- and κ-caseins. J Chem Soc Faraday Trans 1993;89:2683-2692.
38. Syme CD, Blanch EW, Holt C, Jakes R, Goedert M, Hecht L, Barron LD. A Raman optical activity study of rheomorphism in caseins, synucleins and tau protein: implications for fibrillogenic propensity. Eur J Biochem 2002;269:148-156.
39. Shi Z, Woody RW, Kallenbach N. Is polyproline II a major backbone conformation in unfolded proteins? Adv Protein Chem 2002;62:163-240.
40. McColl IH, Blanch EW, Hecht L, Kallenbach NR, Barron LD. Vibrational Raman optical activity characterization of poly(L-proline) II helix in alanine oligopeptides. J Am Chem Soc 2004;126:5076-5077.
41. Shi Z, Olson CA, Rose GD, Baldwin RL, Kallenbach NR. Polyproline II structure in a sequence of seven alanine residues. Proc Natl Acad Sci USA 2002;99:9190-9195.
42. Blundell T, Barlow D, Borkakoti N, Thornton J. Solvent-induced distortions and the curvature of α-helices. Nature 1983;306:281-283.
43. Sundaralingham M, Sekharudu YC. Water inserted α-helical segments implicate reverse turns as folding intermediates. Science 1989;244:1333-1337.
44. Blanch EW, 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.
45. Macleod NA, Butz P, Simons JP, Grant GH, Baker CM, Tranter GE. Structure, electronic circular dichroism and Raman optical activity in the gas phase and in solution: a computational and experimental investigation. Phys Chem Chem Phys 2005;7:1432-1440.
46. Blanch EW, Hecht L, Day LA, Pederson DM, Barron LD. Tryptophan absolute stereochemistry in viral coat proteins from Raman optical activity. J Am Chem Soc 2001;123:4863-4864.
47. Adzhubei AA, Sternberg MJE. Left-handed polyproline II helices commonly occur in globular proteins. J Mol Biol 1993;229:472-493.
48. Creamer TP, Campbell MN. Determinants of the polyproline II helix from modelling studies. Adv Protein Chem 2002;62:263-282.
49. Bochicchio B, Tamburro AM. Polyproline II structure in proteins: identification by chiroptical spectroscopies, stability, and functions. Chirality 2002;14:782-792.
50. Barron LD, Blanch EW, Hecht L. Unfolded proteins studied by Raman optical activity. Adv Protein Chem 2002;62:51-90.
51. Blanch EW, Gill AC, Rhie AGO, Hope J, Hecht L, Nielsen K, Barron LD. Raman optical activity demonstrates poly(L-proline) II helix in the N-terminal region of the ovine prion protein: implications for function and misfunction. J Mol Biol 2004;343:467-476.
52. Wen ZQ, Barron LD, Hecht L. Vibrational Raman optical activity of monosaccharides. J Am Chem Soc 1993;115:285-292.
53. Bell AF, Barron LD, Hecht L. Vibrational Raman optical activity study of D-glucose. Carbohydr Res 1994;257:11-24.
54. Bell AF, Hecht L, Barron LD. Vibrational Raman optical activity of ketose monosaccharides. Spectrochim Acta A 1995;51:1367-1378.
55. Bell AF, Hecht L, Barron LD. Disaccharide solution stereochemistry from Vibrational Raman optical activity. J Am Chem Soc 1994;116:5155-5161.
56. Bell AF, Hecht L, Barron LD. Polysaccharide Vibrational Raman optical activity: laminarin and pullulan. J Raman Spectrosc 1995;26:1071-1074.
57. Bell AF, Hecht L, Barron LD. New evidence for conformational flexibility in cyclodextrins from vibrational Raman optical activity. Chem Eur J 1997;3:1292-1298.
58. Zhu F, Isaacs NW, Hecht L, Barron LD. Polypeptide and carbohydrate structure of an intact glycoprotein from Raman optical activity. J Am Chem Soc 2005;127:6142-6143.
59. Fournier T, Medjoubi-N N, Porquet D. Alpha-1-acid glycoprotein. Biochem Biophys Acta 2000;1482:157-171.
60. Kopecký Jr V , Ettrich R, Hofbauerová K, Baumrauk V. Structure of human α-acid glycoprotein and its high-affinity binding site. Biochem Biophys Res Commun 2003;300:41-46.
61. Brownlow S, Cabral JHM, Cooper R, Flower DR, Yewdall SJ, Polikarpov I, North ACT, Sawyer L. Bovine β-lactoglobulin at 1.8 Å resolution-still an enigmatic lipocalin. Structure 1997;5:481-495.
62. Krzanowski WJ. Principles of multivariate analysis, a user's perspective. Oxford Statistical Science Series 3. Oxford, England: Oxford University Press, Oxford Science Publications; 1998.
63. STATISTICA (data analysis software system), version 6 (www.statsoft. com). Tulsa, OK: StatSoft, Inc.; 2004.