Structural analysis and mapping of individual protein complexes by infrared nanospectroscopy

Nature Communications

Volumn 4, Issue , 2013, Pages

  Amenabar, Iban ^a   Poly, Simon ^a   Nuansing, Wiwat ^a   Hubrich, Elmar H ^b   Govyadinov, Alexander A ^a   Huth, Florian ^a,c   Krutokhvostov, Roman ^a   Zhang, Lianbing ^a   Knez, Mato ^a,d   Heberle, Joachim ^b   Bittner, Alexander M ^a,d   Hillenbrand, Rainer ^a,d  

^a CIC NANOGUNE   (Spain)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c Neaspec GmbH   (Germany)

^d BASQUE FOUNDATION FOR SCIENCE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID; FERRITIN; INSULIN;

DIFFRACTION; DISEASE INCIDENCE; FTIR SPECTROSCOPY; IMAGE RESOLUTION; INFRARED SPECTROSCOPY; MAPPING; MEMBRANE; NANOTECHNOLOGY; PROTEIN;

ALPHA HELIX; ARTICLE; BETA SHEET; FOURIER TRANSFORM INFRARED NANOSPECTROSCOPY; INFRARED SPECTROSCOPY; NONHUMAN; PROTEIN ANALYSIS; PROTEIN SECONDARY STRUCTURE; PURPLE MEMBRANE; TOBACCO MOSAIC VIRUS;

EQUIPMENT DESIGN; FERRITINS; HALOBACTERIUM SALINARUM; INSULIN; MODELS, MOLECULAR; NANOTECHNOLOGY; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; TOBACCO MOSAIC VIRUS;

EID: 84890131752     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms3890     Document Type: Article

References (53)

1. Venyaminov, S. Y. & Kalnin, N. N. Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. I. Spectral parameters of amino-acid residue absorption-bands. Biopolymers 30, 1243-1257 (1990).
2. Jackson, M. & Mantsch, H. H. The use and misuse of FTIR spectroscopy in the determination of protein-structure. Crit. Rev. Biochem. Mol. Biol. 30, 95-120 (1995).
3. Garczarek, F. & Gerwert, K. Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy. Nature 439, 109-112 (2006). (Pubitemid 43053638)
4. Ataka, K., Kottke, T. & Heberle, J. Thinner, smaller, faster: IR techniques to probe the functionality of biological and biomimetic systems. Angew. Chem Int. Ed. 49, 5416-5424 (2010).
5. Gupta, S. C. et al. Multitargeting by curcumin as revealed by molecular interaction studies. Natural Product Reports 28, 1937-1955 (2011).
6. Mahmoudi, M. et al. Protein-nanoparticle interactions: opportunities and challenges. Chem. Rev. 111, 5610-5637 (2011).
7. Lasch, P., Haensch, W., Naumann, D. & Diem, M. Imaging of colorectal adenocarcinoma using FT-IR microspectroscopy and cluster analysis. Biochim. Biophys. Acta 1688, 176-186 (2004). (Pubitemid 38264412)
8. Caine, S., Heraud, P., Tobin, M. J., McNaughton, D. & Bernard, C. C. A. The application of Fourier transform infrared microspectroscopy for the study of diseased central nervous system tissue. Neuroimage 59, 3624-3640 (2012).
9. Xia, Z., Yu, X. & Wei, M. Biomimetic collagen/apatite coating formation on Ti6Al4V substrates. J Biomed. Mater. Res.B Appl. Biomater. 100B, 871-881 (2012).
10. Byler, D. M. & Susi, H. Examination of the secondary structure of proteins by deconvolved FTIR spectra. Biopolymers 25, 469-487 (1986).
11. Bouchard, M., Zurdo, J., Nettleton, E. J., Dobson, C. M. & Robinson, C. V. Formation of insulin amyloid fibrils followed by FTIR simultaneously with CD and electron microscopy. Prot. Sci. 9, 1960-1967 (2000).
12. Ritter, C. et al. Correlation of structural elements and infectivity of the HET-s prion. Nature 435, 844-848 (2005). (Pubitemid 40839737)
13. Rodriguez-Perez, J. C., Hamley, I. W., Grasb, S. L. & Squires, A. M. Local orientational disorder in peptide fibrils probed by a combination of residuespecific C-13-O-18 labelling, polarised infrared spectroscopy and molecular combing. Chem. Comm. 48, 11835-11837 (2012).
14. Amarie, S. & Keilmann, F. Broadband-infrared assessment of phonon resonance in scattering-type near-field microscopy. Phys. Rev. B 83, 045404 (2011).
15. Huth, F., Schnell, M., Wittborn, J., Ocelic, N. & Hillenbrand, R. Infraredspectroscopic nanoimaging with a thermal source. Nat. Mater. 10, 352-356 (2011).
16. Amarie, S. et al. Nano-FTIR chemical mapping of minerals in biological materials. Beilstein J. Nanotechnol. 3, 312-323 (2012).
17. Huth, F. et al. Nano-FTIR absorption spectroscopy of molecular fingerprints at 20 nm spatial resolution. Nano Lett. 12, 3973-3978 (2012).
18. Xu, X. J. G., Rang, M., Craig, I. M. & Raschke, M. B. Pushing the sample-size limit of infrared vibrational nanospectroscopy: from monolayer toward single molecule sensitivity. J. Phys. Chem. Lett. 3, 1836-1841 (2012).
19. Govyadinov, A. A., Amenabar, I., Huth, F., Carney, P. S. & Hillenbrand, R. Quantitative measurement of local infrared absorption and dielectric function with tip-enhanced near-field microscopy. J. Phys. Chem. Lett. 4, 1526-1531 (2013).
20. Keilmann, F. & Hillenbrand, R. Nano-Optics and Near-Field Optical Microscopy (Artech House, 2008).
21. Stöckle, R. M., Suh, Y. D., Deckert, V. & Zenobi, R. Nanoscale chemical analysis by tip-enhanced Raman spectroscopy. Chem. Phys. Lett. 318, 131-136 (2000).
22. Hartschuh, A., Sanchez, E. J., Xie, X. S. & Novotny, L. High-resolution nearfield Raman microscopy of single-walled carbon nanotubes. Phys. Rev. Lett. 90, 095503 (2003).
23. Ichimura, T., Hayazawa, N., Hashimoto, M., Inouye, Y. & Kawata, S. Tipenhanced coherent anti-Stokes Raman scattering for vibrational nanoimaging. Phys. Rev. Lett. 92, 220801 (2004).
24. Verma, P., Ichimura, T., Yano, T.-a., Saito, Y. & Kawata, S. Nano-imaging through tip-enhanced Raman spectroscopy: stepping beyond the classical limits. Laser Photonics Rev. 4, 548-561 (2010).
25. Brehm, M., Taubner, T., Hillenbrand, R. & Keilmann, F. Infrared spectroscopic mapping of single nanoparticles and viruses at nanoscale resolution. Nano Lett. 6, 1307-1310 (2006). (Pubitemid 44195300)
26. Wollny, G., Bruendermann, E., Arsov, Z., Quaroni, L. & Havenith, M Nanoscale depth resolution in scanning near-field infrared microscopy. Opt. Express 16, 7453-7459 (2008). (Pubitemid 351697430)
27. Ballout, F. et al. Scanning near-field IR microscopy of proteins in lipid bilayers. Phys. Chem. Chem. Phys. 13, 21432-21436 (2011).
28. Paulite, M. et al. Imaging secondary structure of individual amyloid fibrils of a b2-microglobulin fragment using near-field infrared spectroscopy. J. Am. Chem. Soc. 133, 7376-7383 (2011).
29. Li, J. J. & Yip, C. M. Super-resolved FT-IR spectroscopy: strategies, challenges, and opportunities for membrane biophysics. Biochim. Biophys. Acta 1828, 2272-2282 (2013).
30. Theil, E. C., Behera, R. K. & Tosha, T. Ferritins for chemistry and for life. Coord. Chem. Rev. 257, 579-586 (2013).
31. Ge, P. & Zhou, Z. H. Hydrogen-bonding networks and RNA bases revealed by cryo electron microscopy suggest a triggering mechanism for calcium switches. Proc. Natl Acad. Sci. USA 108, 9637-9642 (2011).
32. Ivanova, M. I., Sievers, S. A., Sawaya, M. R., Wall, J. S. & Eisenberg, D. Molecular basis for insulin fibril assembly. Proc. Natl Acad. Sci. USA 106, 18990-18995 (2009).
33. Henderson, R. & Unwin, P. N. T. Three-dimensional model of purple membrane obtained by electron-microscopy. Nature 257, 28-32 (1975).
34. Ocelic, N., Huber, A. & Hillenbrand, R. Pseudoheterodyne detection for background-free near-field spectroscopy. Appl. Phys. Lett. 89, 101124 (2006).
35. Keilmann, F. & Amarie, S. Mid-infrared frequency comb spanning an octave based on an er fiber laser and difference-frequency generation. J. Infrared Millimeter Terahertz Waves 33, 479-484 (2012).
36. Griffiths, P. R. & de Haseth, J. A. Fourier Transform Infrared Spectrometry (Wiley, 2007).
37. Rothschild, K. J. & Clark, N. A. Polarized infrared spectroscopy of oriented purple membrane. Biophys. J. 25, 473-487 (1979). (Pubitemid 9134819)
38. Jiang, X. et al. Resolving voltage-dependent structural changes of a membrane photoreceptor by surface-enhanced IR difference spectroscopy. Proc. Natl Acad. Sci. USA 105, 12113-12117 (2008).
39. Salzer, R. & Siesler, H. W. Infrared and Raman Spectroscopic Imaging (Wiley. com, 2009).
40. Selivanova, O. M. & Galzitskaya, O. V. Structural polymorphism and possible pathways of amyloid fibril formation on the example of insulin protein. Biochemistry 77, 1237-1247 (2012).
41. Jimenez, J. L. et al. The protofilament structure of insulin amyloid fibrils. Proc. Natl Acad. Sci. USA 99, 9196-9201 (2002). (Pubitemid 34764590)
42. Deckert-Gaudig, T. & Deckert, V. Tip-enhanced Raman scattering (TERS) and high-resolution bio nano-analysis - a comparison. Phys. Chem. Chem. Phys. 12, 12040-12049 (2010).
43. Kurouski, D., Deckert-Gaudig, T., Deckert, V. & Lednev, I. K. Structure and composition of insulin fibril surfaces probed by TERS. J. Am. Chem. Soc. 134, 13323-13329 (2012).
44. Khurana, R. et al. A general model for amyloid fibril assembly based on morphological studies using atomic force microscopy. Biophys. J. 85, 1135-1144 (2003). (Pubitemid 36909675)
45. Guo, S. & Akhremitchev, B. B. Packing density and structural heterogeneity of insulin amyloid fibrils measured by AFM nanoindentation. Biomacromolecules 7, 1630-1636 (2006). (Pubitemid 43811222)
46. Cheatum, C. M., Tokmakoff, A. & Knoester, J. Signatures of beta-sheet secondary structures in linear and two-dimensional infrared spectroscopy. J. Chem. Phys. 120, 8201-8215 (2004).
47. Huth, F. et al. Resonant antenna probes for tip-enhanced infrared near-field microscopy. Nano Lett. 13, 1065-1072 (2013).
48. Fragola, A., Aigouy, L., Mignotte, P. Y., Formanek, F. & De Wilde, Y. Apertureless scanning near-field fluorescence microscopy in liquids. Ultramicroscopy 101, 47-54 (2004). (Pubitemid 39277158)
49. Hoppener, C., Siebrasse, J. P., Peters, R., Kubitscheck, U. & Naber, A. Highresolution near-field optical imaging of single nuclear pore complexes under physiological conditions. Biophys. J. 88, 3681-3688 (2005). (Pubitemid 40586615)
50. Dzwolak, W., Loksztejn, A. & Smirnovas, V. New insights into the selfassembly of insulin amyloid fibrils: an HD exchange FT-IR study. Biochemistry 45, 8143-8151 (2006). (Pubitemid 43993235)
51. Nielsen, L., Frokjaer, S., Carpenter, J. F. & Brange, J. Studies of the structure of insulin fibrils by Fourier transform infrared (FTIR) spectroscopy and electron microscopy. J. Pharm. Sci. 90, 29-37 (2001). (Pubitemid 32050474)
52. Webster, G. T., Dusting, J., Balabani, S. & Blanch, E. W. Detecting the early onset of shear-induced fibril formation of insulin in situ. J. Phys. Chem. B 115, 2617-2626 (2011).
53. Oesterhelt, D. & Stoeckenius, W. Isolation of the cell membrane of Halobacterium halobium and its fractionation into red and purple membrane. Methods Enzymol. 31, 667-678 (1974).