242
B. Czarnik-Matusewicz and Y.M. Jung
and quantitative prediction of secondary structure from infrared spectra. Additionally, the strengths and weaknesses of these procedures are discussed.
Acknowledgments this work was supported by the National Research Foundation of Korea
(NRF) grant funded by the Korea government (mESt) (No. 2012R1A1A3011844) and the Korean
Federation of Science and technology Societies (KoFSt) grant funded by Korea government
(mESt, Basic Research Promotion Fund). BC-m is grateful to the National Science Centre for
research funding (grant no. 2012/05/B/St/02029).
References
1. Noda I, ozaki Y (2004) two-dimensional correlation spectroscopy: applications in vibrational and optical spectroscopy. John Wiley & Sons, Chichester
2. Baiz CR, Reppert m, tokmakoff A (2013) An introduction to protein 2d ir spectroscopy.
In: Fayer md (ed) ultrafast infrared vibrational spectroscopy, CRC Press. http://web.mit.
edu/~tokmakofflab/documents/Intro2dIR.pdf. Accessed 10 Apr 2013
3. Yang WJ, griffiths P, Byler dm, Susi h (1885) Protein conformation by infrared spectroscopy: resolution enhancement by fourier self-deconvolution. Appl Spectrosc 39(2):282–287
4. Jackson m, mantsch hh (1995) the use and misuse of FtIR spectroscopy in the determination of protein structure. Crit Rev Biochem mol Biol 30(2):95–120
5. Noda I (1986) two-dimensional infrared (2d IR) spectroscopy of synthetic and biopolymers.
Bull Am Phys Soc 31(3):520
6. Noda I (1993) generalized two-dimensional correlation method applicable to infrared, Raman, and other types of spectroscopy. Appl Spectrosc 47(9):1329–1336
7. Raval A, Piana S, Eastwood mP, dror Ro, Shaw dE (2012) Refinement of protein structure
homology models via long, all-atom molecular dynamics simulations. Proteins 80(8):2071–
2079
8. dobson Cm (2003) Protein folding and misfolding. Nature 426(6968):884–90
9. dill KA, macCallum JL (2012) the Protein-Folding Problem, 50 Years on. Science
338(6110):1042–1046
10. Xu m, Ermolenkov vv, uversky vN, Lednev IK (2008). hen egg white lysozyme fibrillation: a deep uv resonance Raman spectroscopic study. J Biophotonics 1(3):215–229
11. Cerf E, Sarroukh R, tamamizu-Kato S, Breydo L, derclaye S, dufrêne YF, Narayanaswami
V, Goormaghtigh E, Ruysschaert JM, Raussens V (2009) Antiparallel β-sheet: a signature
structure of the oligomeric amyloid β-peptide. Biochem J 421(3):415–423
12. Zandomeneghi g, Krebs mR, mcCammon mg, Fandrich m (2004) FtIR Reveals Structural
Differences between Native β-Sheet Proteins and Amyloid Fibrils. Protein Sci 13(12):3314–
3321
13. meier RJ (2005) vibrational spectroscopy: a ‘vanishing’ discipline? Chem Soc Rev
34(9):743–752
14. Noda I (2002) general theory of two-dimensional (2d) Analysis. In: Chalmers Jm, griffiths PR (eds) handbook of vibrational Spectroscopy, vol. 3. John Wiley & Sons, p 2123–
2134
15. ozaki Y (2002) 2d Correlation spectroscopy in vibrational spectroscopy. In: Chalmers
Jm, griffiths PR (eds) handbook of vibrational spectroscopy, vol. 3. John Wiley & Sons,
pp 2135–2172
16. Noda I (2008) generalized two-dimensional correlation spectroscopy. In: Laane J (ed) Frontiers of molecular spectroscopy. Elsevier Science, p 367–381
17. Noda I (2004) Advances in two-dimensional correlation spectroscopy. vib Spectrosc
36(2):143–165
B. Czarnik-Matusewicz and Y.M. Jung
and quantitative prediction of secondary structure from infrared spectra. Additionally, the strengths and weaknesses of these procedures are discussed.
Acknowledgments this work was supported by the National Research Foundation of Korea
(NRF) grant funded by the Korea government (mESt) (No. 2012R1A1A3011844) and the Korean
Federation of Science and technology Societies (KoFSt) grant funded by Korea government
(mESt, Basic Research Promotion Fund). BC-m is grateful to the National Science Centre for
research funding (grant no. 2012/05/B/St/02029).
References
1. Noda I, ozaki Y (2004) two-dimensional correlation spectroscopy: applications in vibrational and optical spectroscopy. John Wiley & Sons, Chichester
2. Baiz CR, Reppert m, tokmakoff A (2013) An introduction to protein 2d ir spectroscopy.
In: Fayer md (ed) ultrafast infrared vibrational spectroscopy, CRC Press. http://web.mit.
edu/~tokmakofflab/documents/Intro2dIR.pdf. Accessed 10 Apr 2013
3. Yang WJ, griffiths P, Byler dm, Susi h (1885) Protein conformation by infrared spectroscopy: resolution enhancement by fourier self-deconvolution. Appl Spectrosc 39(2):282–287
4. Jackson m, mantsch hh (1995) the use and misuse of FtIR spectroscopy in the determination of protein structure. Crit Rev Biochem mol Biol 30(2):95–120
5. Noda I (1986) two-dimensional infrared (2d IR) spectroscopy of synthetic and biopolymers.
Bull Am Phys Soc 31(3):520
6. Noda I (1993) generalized two-dimensional correlation method applicable to infrared, Raman, and other types of spectroscopy. Appl Spectrosc 47(9):1329–1336
7. Raval A, Piana S, Eastwood mP, dror Ro, Shaw dE (2012) Refinement of protein structure
homology models via long, all-atom molecular dynamics simulations. Proteins 80(8):2071–
2079
8. dobson Cm (2003) Protein folding and misfolding. Nature 426(6968):884–90
9. dill KA, macCallum JL (2012) the Protein-Folding Problem, 50 Years on. Science
338(6110):1042–1046
10. Xu m, Ermolenkov vv, uversky vN, Lednev IK (2008). hen egg white lysozyme fibrillation: a deep uv resonance Raman spectroscopic study. J Biophotonics 1(3):215–229
11. Cerf E, Sarroukh R, tamamizu-Kato S, Breydo L, derclaye S, dufrêne YF, Narayanaswami
V, Goormaghtigh E, Ruysschaert JM, Raussens V (2009) Antiparallel β-sheet: a signature
structure of the oligomeric amyloid β-peptide. Biochem J 421(3):415–423
12. Zandomeneghi g, Krebs mR, mcCammon mg, Fandrich m (2004) FtIR Reveals Structural
Differences between Native β-Sheet Proteins and Amyloid Fibrils. Protein Sci 13(12):3314–
3321
13. meier RJ (2005) vibrational spectroscopy: a ‘vanishing’ discipline? Chem Soc Rev
34(9):743–752
14. Noda I (2002) general theory of two-dimensional (2d) Analysis. In: Chalmers Jm, griffiths PR (eds) handbook of vibrational Spectroscopy, vol. 3. John Wiley & Sons, p 2123–
2134
15. ozaki Y (2002) 2d Correlation spectroscopy in vibrational spectroscopy. In: Chalmers
Jm, griffiths PR (eds) handbook of vibrational spectroscopy, vol. 3. John Wiley & Sons,
pp 2135–2172
16. Noda I (2008) generalized two-dimensional correlation spectroscopy. In: Laane J (ed) Frontiers of molecular spectroscopy. Elsevier Science, p 367–381
17. Noda I (2004) Advances in two-dimensional correlation spectroscopy. vib Spectrosc
36(2):143–165