Advertisement

Electronic Circular Dichroism Spectroscopy in Structural Analysis of Biomolecular Systems

  • Magdalena PeculEmail author
  • Wojciech Dzwolak
Chapter
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 14)

Abstract

In this chapter, the use of electronic circular dichroism (CD) in structural analysis of biological molecular systems is discussed. The quantum chemical theory of the phenomenon is briefly presented, and the applications of the CD spectroscopy in determination of spatial structure of proteins and nucleic acids, and of absolute configuration of small molecules of pharmacological significance are summarized. Some attention is also paid to the emerging technique related to CD—circularly polarized luminscence (CPL).

Keywords

electronic circular dichroism circularly polarized luminscence protein structure nucleic acid structure induced chirality 

References

  1. 1.
    1. Biot JB (1817) Mem Acad Roy Sci Inst France 2:41Google Scholar
  2. 2.
    2. Djerassi C (1960) Optical Rotatory Dispersion. McGraw-Hill, New YorkGoogle Scholar
  3. 3.
    Snatzke G (1968) Angew Chem Internat Edit 7:14Google Scholar
  4. 4.
    Haidinger W (1847) Poggendorfs Annalen 70, 531Google Scholar
  5. 5.
    Cotton AM (1896) Ann Chim Physique 8:347Google Scholar
  6. 6.
    Laur P (2012) Comprehensive chiroptical spectroscopy: Volume 1—instrumentation, methodologies, and theoretical simulations. Wiley, Hoboken. (Chap. The first decades after the discovery of CD and ORD by Aime Cotton in 1895)Google Scholar
  7. 7.
    Sreerama N, Woody RW (2000) Circular dichroism: Principles and applications. Wiley, New York, pp 601–620 (Chap. Circular Dichroism of Peptides and Proteins)Google Scholar
  8. 8.
    Cantor C, Schimmel P (1980) Biophysical Chemistry, Part 2: Techniques for the Study of Biological Structure and Function. W.H. Freeman and Company, New YorkGoogle Scholar
  9. 9.
    Rodger A, Norden B (1997) Circular Dichroism and Linear Dichroism. Oxford University Press, Oxford. (Oxford Chemistry Masters)Google Scholar
  10. 10.
    Woody RW (2012) Comprehensive chiroptical spectroscopy: Volume 2—applications in stere- ochemical analysis of synthetic compounds, natural products, and biomolecules. Wiley, Hoboken. (Chap. Electronic Circular Dichroism of Proteins)Google Scholar
  11. 11.
    Toniolo C, Formaggio F, Woody RW (2012) Comprehensive chiroptical spectroscopy: Volume 2—applications in stereochemical analysis of synthetic compounds, natural products, and biomolecules. Wiley, Hoboken. (Chap. Electronic Circular Dichroism of Peptides)Google Scholar
  12. 12.
    Kypr J, Kejnovska I, Bednarova K, Vorlickova M (2012) “Comprehensive chiroptical spectroscopy: Volume 1—applications in stereochemical analysis of synthetic compounds, natural products, and biomolecules. Wiley, Hoboken. (Chap. Electronic Circular Dichroism Spectroscopy of Nucleic Acids)Google Scholar
  13. 13.
    Gray DM (2012) Comprehensive chiroptical spectroscopy: Volume 2—applications in stere- ochemical analysis of synthetic compounds, natural products, and biomolecules. Wiley, Hoboken. (Chap. Circular Dichroism of Protein-Nucleic Acid Interactions)Google Scholar
  14. 14.
    Ellestad GA (2012) Comprehensive chiroptical spectroscopy: Volume 2—applications in stereochemical analysis of synthetic compounds, natural products, and biomolecules. Wiley, Hoboken. (Chap. Drug and Natural Product Binding to Nucleic Acids Analyzed by Electronic Circular Dichroism)Google Scholar
  15. 15.
    Bertucci C, Pistolozzi M (2012) Comprehensive chiroptical spectroscopy: Volume 2—applications in stereochemical analysis of synthetic compounds, natural products, and biomolecules. Wiley, Hoboken. (Chap. Electronic Circular Dichro- ism in Drug Discovery)Google Scholar
  16. 16.
    Kelly S, Price N (1997) BBA-Protein Struct M 1338:161Google Scholar
  17. 17.
    Bulheller B, Rodger A, Hirst J (2007) Phys Chem Chem Phys 9:2020Google Scholar
  18. 18.
    Kelly S, Jess T, Price N (2005) BBA-Proteins Proteom 1751:119Google Scholar
  19. 19.
    Miles A, Wallace B (2006) Chem Soc Rev 35:39Google Scholar
  20. 20.
    Karabencheva T, Christov C (2010) In: Donev R (ed) in Advances in Protein Chemistry and Structural Biology, Advances in Protein Chemistry and Structural Biology, vol 80, pp 85–115Google Scholar
  21. 21.
    Rosenfeld L (1928) Z Phys 52:161Google Scholar
  22. 22.
    Ruud K, Helgaker T (2002) Chem Phys Lett 352:533Google Scholar
  23. 23.
    Cheeseman JR, Frisch MJ, Devlin FJ, Stephens PJ (2000) J Phys Chem A 104:1039Google Scholar
  24. 24.
    Grimme S (1996) Chem. Phys. Lett. 259, 128Google Scholar
  25. 25.
    Grimme S, Waletzke M (1999) J. Chem. Phys. 111, 5645Google Scholar
  26. 26.
    Autschbach J, Ziegler T (2002) J Chem Phys 116:891Google Scholar
  27. 27.
    Yabana K, Bertsch GF (1999) Phys Rev A 60:1271Google Scholar
  28. 28.
    Pecul M, Ruud K, Rizzo A, Helgaker T (2004) J Phys Chem A 108:4269Google Scholar
  29. 29.
    Skomorowski W, Pecul M, Salek P, Helgaker T (2007) J Chem Phys 127:085102Google Scholar
  30. 30.
    Sebek J, Gyurcsik B, Sebestik J, Kejik Z, Bednarova L, Bour P (2007) J Phys Chem A 111:2750Google Scholar
  31. 31.
    Kaminsky J, Kubelka J, Bour P (2011) J Phys Chem A 115:1734Google Scholar
  32. 32.
    Brkljaca Z, Condic-Jurkic K, Smith A-S, Smith DM J Comp Theor CompGoogle Scholar
  33. 33.
    Shcherbin D, Ruud K (2008) Chem Phys 349:234Google Scholar
  34. 34.
    Pecul M, Ruud K, Helgaker T (2004) Chem Phys Lett 388:110Google Scholar
  35. 35.
    Hirst JD (1998) J Chem Phys 109:782Google Scholar
  36. 36.
    Woody RW, Sreerama N (1999) J Chem Phys 111:2844Google Scholar
  37. 37.
    Applequist J, Sundberg KR, Olson ML, Weiss LC (1979) J Chem Phys 70:1240Google Scholar
  38. 38.
    Woody RW (1968) J Chem Phys 49:4797Google Scholar
  39. 39.
    Bayley P, Nielsen E, Schellman J (1969) J Phys Chem 73:228Google Scholar
  40. 40.
    Liu HW, Nakanishi K (1981) J Am Chem Soc 103:5591Google Scholar
  41. 41.
    Liu HW, Nakanishi K (1982) J Am Chem Soc 104:1178Google Scholar
  42. 42.
    Harada N, Nakanishi K (1983) Circular Dichroic Spectroscopy – Exciton Coupling in Organic Stereochemistry. University Science Books, Mill ValleyGoogle Scholar
  43. 43.
    Hirst JD, Hirst DM, Brooks CL (1997) J Phys Chem A 101:4821Google Scholar
  44. 44.
    Besley NA, Hirst JD (1998) J Phys Chem A 102:10791Google Scholar
  45. 45.
    Sebek J, Kejik Z, Bour P (2006) J Phys Chem A 110:4702Google Scholar
  46. 46.
    Rogers D, Hirst J (2004) Chirality 16:234Google Scholar
  47. 47.
    Grishina I, Woody R, (1994) Faraday Discussion 99:245Google Scholar
  48. 48.
    Roy A, Bour P, Keiderling TA (2009) Chirality 21:E163Google Scholar
  49. 49.
    Malon P, Bednarova L, Straka M, Krejci L, Kumprecht L, Kraus T, Kubanova M, Baumruk V (2010) Chirality 22:E47Google Scholar
  50. 50.
    Bednarova L, Bour P, Malon P (2010) Chirality 22:514Google Scholar
  51. 51.
    Robin M (1975) Higher Excited States of Polyatomic Molecules. Academic Press, New YorkGoogle Scholar
  52. 52.
    Bulheller B, Miles A, Wallace B, Hirst J (2008) J Phys Chem B 112:1866Google Scholar
  53. 53.
    Bulheller B, Miles A, Wallace B, Hirst J (2008) J Phys Chem B 112:1866Google Scholar
  54. 54.
    Woody R (2010) Chirality 22:E22Google Scholar
  55. 55.
    Zako T, Sakono M, Hashimoto N, Ihara M, Maeda M (2009) Biophys J 96:3331Google Scholar
  56. 56.
    Pedersen J, Andersen C, Otzen D (2010) FEBS J 277:4591Google Scholar
  57. 57.
    Giiler G, Drafic E, Vorobev M, Vogel V, Mantele W (2011) Spectrochim Acta A 79:104Google Scholar
  58. 58.
    Vass E, Majer Z, Kohalmy K, Hollosi M (2010) Chirality 22:762Google Scholar
  59. 59.
    Greenfield N, Fasman G (1969) Biochem 10:41084116Google Scholar
  60. 60.
    Whitmore L, Wallace B (2004) Nucleic Acids Res 32:W668Google Scholar
  61. 61.
    Johnson W (1999) Proteins 35:307Google Scholar
  62. 62.
    Sreerama N, Woody R (2000) Anal Biochem 287:252Google Scholar
  63. 63.
    Louis-Jeune C, Andrade-Navarro M, Perez-Iratxeta C (2012) Proteins 80:374Google Scholar
  64. 64.
    Whitmore L, Wallace B (2008) Biopolym 89:392Google Scholar
  65. 65.
    Abdul-Gader A, Miles A, Wallace B (2011) Bioinforma 27:1630Google Scholar
  66. 66.
    Janes R, Miles A, Woollett B, Klose D, Wallace B (2012) Chirality 24:751Google Scholar
  67. 67.
    Rogers D, Hirst J (2004) Biochem 43:11092Google Scholar
  68. 68.
    Lala A, Kaul P (1992) J Biol Chem 267:19914Google Scholar
  69. 69.
    Dael HV (1993) Biochem 32:11886Google Scholar
  70. 70.
    Demarest S, Boice J, Fairman R, Raleigh D (1999) J Mol Biol 294:213Google Scholar
  71. 71.
    Gawronski J, Grajewski J (2003) Org Lett 5:3301Google Scholar
  72. 72.
    Zsila F (2003) FEBS Lett 539:85Google Scholar
  73. 73.
    Zsila F, Bikadi Z, Simonyi M (2003) Biochem Pharmacol 64:1651Google Scholar
  74. 74.
    Dzwolak W, Pecul M (2005) FEBS Letters 104:6601Google Scholar
  75. 75.
    Dzwolak W, Loksztejn A, Galinska-Rakoczy A, Adachi R, GotoY, Rupnicki L (2007) J Amer Chem Soc 129:7517Google Scholar
  76. 76.
    Loksztejn A, Dzwolak W (2008) J Mol Biol 379:9Google Scholar
  77. 77.
    Loksztejn A, Dzwolak W (2010) J Mol Biol 395:643Google Scholar
  78. 78.
    Babenko V, Harada T, Yagi H, Goto Y, Kuroda R, Dzwolak W (2011) Chirality 23:638Google Scholar
  79. 79.
    Johnson W (2000) Circular dichroism: Principles and applications. Wiley, New York, pp 703–718. (Chap. Circular Dichroism of Peptides and Proteins)Google Scholar
  80. 80.
    Maurizot J (2000) Circular dichroism: Principles and applications. Wiley, New York, pp 719–739. (Chap. Circular Dichroism of Peptides and Proteins)Google Scholar
  81. 81.
    Gray D (2000) Circular dichroism: Principles and applications. Wiley, New York, pp 769–796. (Chap. Circular Dichroism: Principles and Applications)Google Scholar
  82. 82.
    Kypr J, Kejnovska I, Renciuk D, Vorlickova M (2009) Nucleic Acids Res 37:1713Google Scholar
  83. 83.
    Riazance J, Baase W, Johnson W Jr, Hall K, Cruz P, Tinoco I (1985) Nucleic Acids Res 13:4983Google Scholar
  84. 84.
    Kwit M, Rozwadowska MD, Gawromiski J, Grajewska A (2009) J Org Chem 74:8051, pMID:19817355, http://pubs.acs.org/doi/pdf/10.1021/jo901175s
  85. 85.
    Berova N, Ellestad G, Harada N Comprehensive Natural Products II Chemistry and Biology, (Elsevier) Chap.Modern Methods in Natural Product Chemistry: Characterization by Circular Dichroism Spectroscopy, pp 91–147Google Scholar
  86. 86.
    Berova N, Bari LD, Pescitelli G (2007) Chem Soc Rev 36:914Google Scholar
  87. 87.
    Stephens PJ, Devlin FJ, Pan J-J (2008) Chirality 20:643Google Scholar
  88. 88.
    He Y ,Wang B, Dukor RK, Nafie LA (2011) Appl Spectrosc 65:699Google Scholar
  89. 89.
    Riehl JP, Richardson FS (1977) Chem Rev 77:773Google Scholar
  90. 90.
    Riehl JP, Richardson FS (1986) Chem Rev 86:1Google Scholar
  91. 91.
    Gafni A (1978) Biochemistry 17, 1301Google Scholar
  92. 92.
    Gafni A (1981) J Biol Chem 256:8875Google Scholar
  93. 93.
    Steinberg N, Wachtel EJ, Gafni A (1982) Biochem 21:2573Google Scholar
  94. 94.
    Tran CD, Drake AF (1981) Biochem Biophys Res Commun 101:76Google Scholar
  95. 95.
    Tran C, Beddard GS (1981) Biochem Biophys Acta 678:293Google Scholar
  96. 96.
    Tran C, Beddard GS (1982) J Am Chem Soc 104:6741Google Scholar
  97. 97.
    Brittain HM (1996) Chirality 8:357Google Scholar
  98. 98.
    Goto H, Sawada I, Nomura N (2010) Int J Pol Mat 59:786Google Scholar
  99. 99.
    Montgomery CP, Murray BS, New EJ, Pal R, Parker D (2009) Accounts of Chemical Research 42:925Google Scholar
  100. 100.
    Gussakovsky E (2010) Reviews in fluorescence 2008. Springer Science + Business Media, Mill Valley, pp 425–459 (Chap. Circularly Polarized Luminescence (CPL) of Proteins and Protein Complexes)Google Scholar
  101. 101.
    Riehl J, Muller G (2012) Comprehensive chiroptical spectroscopy: Volume 1—instrumentation, methodologies, and theoretical simulations. Wiley, Hoboken. (Chap. Circularly Polarized Luminscence Spectroscopy and Emission-Detected Circular Dichroism)Google Scholar
  102. 102.
    Pritchard B, Autschbach J (2010) Chem Phys Chem 11:2409Google Scholar
  103. 103.
    Pecul M, Ruud K (2011) Phys Chem Chem Phys 11:643Google Scholar
  104. 104.
    Nesgaard L, Hoffmann S, Andersen C, Malmendal A, Otzen D (2008) Biopolymers 89:779Google Scholar
  105. 105.
    Sreerama N, Manning M, Powers M, Zhang J, Goldenberg D, Woody R (1999) Biochemistry 38:10814Google Scholar
  106. 106.
    Crescitelli F, Mommaerts W, Shaw T (1966) P Natl Acad Sci USA 56:1729Google Scholar
  107. 107.
    Zsila F, Bikadi Z, Simonyi M (2003) Biochem Pharmacol 65:447Google Scholar
  108. 108.
    Nishii FTI, Kataoka M, Goto Y (1994) Biochemistry 33:4903Google Scholar
  109. 109.
    Babenko V, Dzwolak W (2011) Chem Commun 47:10686Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Faculty of ChemistryUniversity of WarsawWarszawaPoland

Personalised recommendations