Skip to main content
NCBI home page
Biophysical Journal logoLink to Biophysical Journal
. 2000 Feb;78(2):994–1000. doi: 10.1016/S0006-3495(00)76657-4

Do parallel beta-helix proteins have a unique fourier transform infrared spectrum?

R Khurana 1, A L Fink 1
PMCID: PMC1300702  PMID: 10653812

Abstract

Several polypeptides have been found to adopt an unusual domain structure known as the parallel beta-helix. These domains are characterized by parallel beta-strands, three of which form a single parallel beta-helix coil, and lead to long, extended beta-sheets. We have used ATR-FTIR (attenuated total reflectance-fourier transform infrared spectroscopy) to analyze the secondary structure of representative examples of this class of protein. Because the three-dimensional structures of parallel beta-helix proteins are unique, we initiated this study to determine if there was a corresponding unique FTIR signal associated with the parallel beta-helix conformation. Analysis of the amide I region, emanating from the carbonyl stretch vibration, reveals a strong absorbance band at 1638 cm(-1) in each of the parallel beta-helix proteins. This band is assigned to the parallel beta-sheet structure. However, components at this frequency are also commonly observed for beta-sheets in many classes of globular proteins. Thus we conclude that there is no unique infrared signature for parallel beta-helix structure. Additional contributions in the 1638 cm(-1) region, and at lower frequencies, were ascribed to hydrogen bonding between the coils in the loop/turn regions and amide side-chain interactions, respectively. A 13-residue peptide that forms fibrils and has been proposed to form beta-helical structure was also examined, and its FTIR spectrum was compared to that of the parallel beta-helix proteins.

Full Text

The Full Text of this article is available as a PDF (174.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bauer H. H., Müller M., Goette J., Merkle H. P., Fringeli U. P. Interfacial adsorption and aggregation associated changes in secondary structure of human calcitonin monitored by ATR-FTIR spectroscopy. Biochemistry. 1994 Oct 11;33(40):12276–12282. doi: 10.1021/bi00206a034. [DOI] [PubMed] [Google Scholar]
  2. Baumann U., Wu S., Flaherty K. M., McKay D. B. Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif. EMBO J. 1993 Sep;12(9):3357–3364. doi: 10.1002/j.1460-2075.1993.tb06009.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Benzinger T. L., Gregory D. M., Burkoth T. S., Miller-Auer H., Lynn D. G., Botto R. E., Meredith S. C. Propagating structure of Alzheimer's beta-amyloid(10-35) is parallel beta-sheet with residues in exact register. Proc Natl Acad Sci U S A. 1998 Nov 10;95(23):13407–13412. doi: 10.1073/pnas.95.23.13407. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Byler D. M., Susi H. Examination of the secondary structure of proteins by deconvolved FTIR spectra. Biopolymers. 1986 Mar;25(3):469–487. doi: 10.1002/bip.360250307. [DOI] [PubMed] [Google Scholar]
  5. Cabiaux V., Oberg K. A., Pancoska P., Walz T., Agre P., Engel A. Secondary structures comparison of aquaporin-1 and bacteriorhodopsin: a Fourier transform infrared spectroscopy study of two-dimensional membrane crystals. Biophys J. 1997 Jul;73(1):406–417. doi: 10.1016/S0006-3495(97)78080-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cascio M., Glazer P. A., Wallace B. A. The secondary structure of human amyloid deposits as determined by circular dichroism spectroscopy. Biochem Biophys Res Commun. 1989 Aug 15;162(3):1162–1166. doi: 10.1016/0006-291x(89)90795-x. [DOI] [PubMed] [Google Scholar]
  7. Caughey B. W., Dong A., Bhat K. S., Ernst D., Hayes S. F., Caughey W. S. Secondary structure analysis of the scrapie-associated protein PrP 27-30 in water by infrared spectroscopy. Biochemistry. 1991 Aug 6;30(31):7672–7680. doi: 10.1021/bi00245a003. [DOI] [PubMed] [Google Scholar]
  8. Dong A., Huang P., Caughey W. S. Protein secondary structures in water from second-derivative amide I infrared spectra. Biochemistry. 1990 Apr 3;29(13):3303–3308. doi: 10.1021/bi00465a022. [DOI] [PubMed] [Google Scholar]
  9. Dong A., Prestrelski S. J., Allison S. D., Carpenter J. F. Infrared spectroscopic studies of lyophilization- and temperature-induced protein aggregation. J Pharm Sci. 1995 Apr;84(4):415–424. doi: 10.1002/jps.2600840407. [DOI] [PubMed] [Google Scholar]
  10. Downing D. T. Molecular modeling indicates that homodimers form the basis for intermediate filament assembly from human and mouse epidermal keratins. Proteins. 1995 Oct;23(2):204–217. doi: 10.1002/prot.340230210. [DOI] [PubMed] [Google Scholar]
  11. Emsley P., Charles I. G., Fairweather N. F., Isaacs N. W. Structure of Bordetella pertussis virulence factor P.69 pertactin. Nature. 1996 May 2;381(6577):90–92. doi: 10.1038/381090a0. [DOI] [PubMed] [Google Scholar]
  12. Fink A. L., Oberg K. A., Seshadri S. Discrete intermediates versus molten globule models for protein folding: characterization of partially folded intermediates of apomyoglobin. Fold Des. 1998;3(1):19–25. doi: 10.1016/S1359-0278(98)00005-4. [DOI] [PubMed] [Google Scholar]
  13. Goormaghtigh E., Cabiaux V., Ruysschaert J. M. Secondary structure and dosage of soluble and membrane proteins by attenuated total reflection Fourier-transform infrared spectroscopy on hydrated films. Eur J Biochem. 1990 Oct 24;193(2):409–420. doi: 10.1111/j.1432-1033.1990.tb19354.x. [DOI] [PubMed] [Google Scholar]
  14. Goormaghtigh E., Raussens V., Ruysschaert J. M. Attenuated total reflection infrared spectroscopy of proteins and lipids in biological membranes. Biochim Biophys Acta. 1999 Jul 6;1422(2):105–185. doi: 10.1016/s0304-4157(99)00004-0. [DOI] [PubMed] [Google Scholar]
  15. Heffron S., Moe G. R., Sieber V., Mengaud J., Cossart P., Vitali J., Jurnak F. Sequence profile of the parallel beta helix in the pectate lyase superfamily. J Struct Biol. 1998;122(1-2):223–235. doi: 10.1006/jsbi.1998.3978. [DOI] [PubMed] [Google Scholar]
  16. Jackson M., Mantsch H. H. The use and misuse of FTIR spectroscopy in the determination of protein structure. Crit Rev Biochem Mol Biol. 1995;30(2):95–120. doi: 10.3109/10409239509085140. [DOI] [PubMed] [Google Scholar]
  17. Johnson W. C., Jr Protein secondary structure and circular dichroism: a practical guide. Proteins. 1990;7(3):205–214. doi: 10.1002/prot.340070302. [DOI] [PubMed] [Google Scholar]
  18. Krimm S., Bandekar J. Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. Adv Protein Chem. 1986;38:181–364. doi: 10.1016/s0065-3233(08)60528-8. [DOI] [PubMed] [Google Scholar]
  19. Langs D. A. Three-dimensional structure at 0.86 A of the uncomplexed form of the transmembrane ion channel peptide gramicidin A. Science. 1988 Jul 8;241(4862):188–191. doi: 10.1126/science.2455345. [DOI] [PubMed] [Google Scholar]
  20. Lazo N. D., Downing D. T. Amyloid fibrils may be assembled from beta-helical protofibrils. Biochemistry. 1998 Feb 17;37(7):1731–1735. doi: 10.1021/bi971016d. [DOI] [PubMed] [Google Scholar]
  21. Lazo N. D., Downing D. T. Beta-helical fibrils from a model peptide. Biochem Biophys Res Commun. 1997 Jun 27;235(3):675–679. doi: 10.1006/bbrc.1997.6863. [DOI] [PubMed] [Google Scholar]
  22. Lee D. C., Haris P. I., Chapman D., Mitchell R. C. Determination of protein secondary structure using factor analysis of infrared spectra. Biochemistry. 1990 Oct 2;29(39):9185–9193. doi: 10.1021/bi00491a012. [DOI] [PubMed] [Google Scholar]
  23. Manning M. C., Illangasekare M., Woody R. W. Circular dichroism studies of distorted alpha-helices, twisted beta-sheets, and beta turns. Biophys Chem. 1988 Aug;31(1-2):77–86. doi: 10.1016/0301-4622(88)80011-5. [DOI] [PubMed] [Google Scholar]
  24. Manning M. C. Underlying assumptions in the estimation of secondary structure content in proteins by circular dichroism spectroscopy--a critical review. J Pharm Biomed Anal. 1989;7(10):1103–1119. doi: 10.1016/0731-7085(89)80049-4. [DOI] [PubMed] [Google Scholar]
  25. Naik V. M., Krimm S. Vibrational analysis of the structure of gramicidin A. II. Vibrational spectra. Biophys J. 1986 Jun;49(6):1147–1154. doi: 10.1016/S0006-3495(86)83743-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Oberg K. A., Fink A. L. A new attenuated total reflectance Fourier transform infrared spectroscopy method for the study of proteins in solution. Anal Biochem. 1998 Feb 1;256(1):92–106. doi: 10.1006/abio.1997.2486. [DOI] [PubMed] [Google Scholar]
  27. Petersen T. N., Kauppinen S., Larsen S. The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix. Structure. 1997 Apr 15;5(4):533–544. doi: 10.1016/s0969-2126(97)00209-8. [DOI] [PubMed] [Google Scholar]
  28. Raetz C. R., Roderick S. L. A left-handed parallel beta helix in the structure of UDP-N-acetylglucosamine acyltransferase. Science. 1995 Nov 10;270(5238):997–1000. doi: 10.1126/science.270.5238.997. [DOI] [PubMed] [Google Scholar]
  29. Sieber V., Jurnak F., Moe G. R. Circular dichroism of the parallel beta helical proteins pectate lyase C and E. Proteins. 1995 Sep;23(1):32–37. doi: 10.1002/prot.340230105. [DOI] [PubMed] [Google Scholar]
  30. Steinbacher S., Seckler R., Miller S., Steipe B., Huber R., Reinemer P. Crystal structure of P22 tailspike protein: interdigitated subunits in a thermostable trimer. Science. 1994 Jul 15;265(5170):383–386. doi: 10.1126/science.8023158. [DOI] [PubMed] [Google Scholar]
  31. Susi H., Byler D. M. Fourier transform infrared study of proteins with parallel beta-chains. Arch Biochem Biophys. 1987 Nov 1;258(2):465–469. doi: 10.1016/0003-9861(87)90367-5. [DOI] [PubMed] [Google Scholar]
  32. Symmons M. F., Buchanan S. G., Clarke D. T., Jones G., Gay N. J. X-ray diffraction and far-UV CD studies of filaments formed by a leucine-rich repeat peptide: structural similarity to the amyloid fibrils of prions and Alzheimer's disease beta-protein. FEBS Lett. 1997 Jul 28;412(2):397–403. doi: 10.1016/s0014-5793(97)00809-0. [DOI] [PubMed] [Google Scholar]
  33. Venyaminov SYu, Baikalov I. A., Wu C. S., Yang J. T. Some problems of CD analyses of protein conformation. Anal Biochem. 1991 Nov 1;198(2):250–255. doi: 10.1016/0003-2697(91)90421-o. [DOI] [PubMed] [Google Scholar]
  34. Venyaminov SYu, Kalnin N. N. Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. I. Spectral parameters of amino acid residue absorption bands. Biopolymers. 1990;30(13-14):1243–1257. doi: 10.1002/bip.360301309. [DOI] [PubMed] [Google Scholar]
  35. Wallace B. A., Ravikumar K. The gramicidin pore: crystal structure of a cesium complex. Science. 1988 Jul 8;241(4862):182–187. doi: 10.1126/science.2455344. [DOI] [PubMed] [Google Scholar]
  36. Yoder M. D., Keen N. T., Jurnak F. New domain motif: the structure of pectate lyase C, a secreted plant virulence factor. Science. 1993 Jun 4;260(5113):1503–1507. doi: 10.1126/science.8502994. [DOI] [PubMed] [Google Scholar]
  37. de Jongh H. H., Goormaghtigh E., Ruysschaert J. M. The different molar absorptivities of the secondary structure types in the amide I region: an attenuated total reflection infrared study on globular proteins. Anal Biochem. 1996 Nov 1;242(1):95–103. doi: 10.1006/abio.1996.0434. [DOI] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES