Fourier transform infrared (FTIR) spectroscopy

Ayala I, Range K, York D, Barry BA (2002) Spectroscopic properties of tyrosyl radicals in dipeptides. J Am Chem Soc 124:5496–5505 Barth A (2000) The infrared absorption of amino acid side chains. Prog Biophys Mol Biol 74:141–173 Barth A (2007) Infrared spectroscopy of proteins. Biochim Biophys Acta 1767:1073–1101 Barth A, Corrie JE (2002) Characterization of a new caged proton capable of inducing large pH jumps. Biophys J 83:2864–2871 Barth A, Mantele W, Kreutz W (1990) Molecular changes in the sarcoplasmic reticulum Ca2+ ATPase during catalytic activity: a Fourier transform infrared (FTIR) study using photolysis of caged ATP to trigger the reaction cycle. FEBS Lett 277:147–150 Bauscher M, Nabedryk E, Bagley K, Breton J, Mäntele W (1990) Investigation of models for photosynthetic electron acceptors. Infrared spectroelectrochemistry of ubiquinone and its anions. FEBS Lett 261:191–195 Berthomieu C, Boussac A (1995) FTIR and EPR study of radicals of aromatic amino acids, 4-methylimidazole and phenol generated by UV-irradiation. Biospectroscopy 1:187–206 Berthomieu C, Hienerwadel R (2001) Iron coordination in photosystem II: interaction between bicarbonate and the QB pocket studied by Fourier transform infrared spectroscopy. Biochemistry 40:4044–4052 Berthomieu C, Hienerwadel R (2005) Vibrational spectroscopy to study the properties of redox-active tyrosines in photosystem II and other proteins. Biochim Biophys Acta 1707:51–66 Berthomieu C, Boussac A, Mäntele W, Breton J, Nabedryk E (1992) Molecular changes following oxidoreduction of cytochrome b559 characterized by Fourier transform infrared spectroscopy and electron paramagnetic resonance: photooxidation in photosystem II and electrochemistry of isolated cytochrome b559 and iron protoporphyrin IX- bisimidazole model compounds. Biochemistry 31:11460–11471 Berthomieu C, Boullais C, Neumann JM, Boussac A (1998a) Effect of 13C, 18O, and 2H labeling on the infrared modes of UV-induced phenoxyl radicals. Biochim Biophys Acta 1365:112–116 Berthomieu C, Hienerwadel R, Boussac A, Breton J, Diner BA (1998b) Hydrogen bonding of redox-active tyrosine Z of photosystem II probed by FTIR difference spectroscopy. Biochemistry 37:10547–10554 Berthomieu C, Marboutin L, Dupeyrat F, Bouyer P (2006) Electrochemically-induced FTIR difference spectroscopy in the mid to far infrared (200 μm) domain: a new setup for the analysis of metal-ligands in redox-proteins. Biopolymers 82:363–367 Breton J (2001) Fourier transform infrared spectroscopy of primary electron donors in type I photosynthetic reaction centers. Biochim Biophys Acta 1507:180–193 Breton J, Burie J-R, Berthomieu C, Berger G, Nabedryk E (1994a) The binding sites of quinones in photosynthetic bacterial reaction centers investigated by light-induced FTIR difference spectroscopy: assignment of the QA vibrations in Rhodobacter sphaeroides using 18O- or 13C- labeled ubiquinones and vitamin K1. Biochemistry 33:4953–4965 Breton J, Boullais C, Burie JR, Nabedryk E, Mioskowsky C (1994b) Binding sites of quinones in photosynthetic bacterial reaction centers investigated by light-induced FTIR difference spectroscopy: assignment of the interactions of each carbonyl of QA in Rhodobacter sphaeroides using site-specific 13C-labeled ubiquinone. Biochemistry 33:14378–14386 Breton J, Boullais C, Mioskowski C, Nabedryk E (1995) Binding sites of quinones in photosynthetic bacterial reaction centers investigated by light-induced FTIR difference spectroscopy: symmetry of the carbonyl interactions and close equivalence of the QB vibrations in Rhodopseudomonas sphaeroides and Rhodobacter viridis probed by isotope labeling. Biochemistry 34:11606–11616 Breton J, Xu W, Diner BA, Chitnis PR (2002) The two histidine axial ligands of the primary electron donor chlorophylls (P700) in photosystem I are similarly perturbed upon P700 + formation. Biochemistry 41:11200–11210 Brudler R, de Groot HJM, van Liemt WBS, Steggerda WF, Esmeijer R, Gast P, Hoff AJ, Lugtenburg J, Gerwert K (1994) Asymmetric binding of the 1- and 4-C=O groups of QA in Rhodobacter sphaeroides R26 reaction centers monitored by Fourier transform infra-red spectroscopy using site-specific isotopically labelled ubiquinone-10. EMBO J 13:5523–5530 Brudler R, de Groot HJM, van Liemt WBS, Gast R, Hoff AJ, Lugtenburg J, Gerwert K (1995) FTIR spectroscopy shows weak symmetric hydrogen bonding of the QB carbonyl groups in Rhodobacter sphaeroides R26 reaction centers. FEBS Lett 370:88–92 Buchet R, Jona I, Martonosi A (1991) Ca2+ release from caged-Ca2+ alters the FTIR spectrum of sarcoplasmic reticulum. Biochim Biophys Acta 1069:209–217 Chu HA, Hillier W, Law NA, Babcock GT (2001) Vibrational spectroscopy of the oxygen-evolving complex and of manganese model compounds. Biochim Biophys Acta 1503:69–82 Chu HA, Hillier W, Debus RJ (2004) Evidence that the C-terminus of the D1 polypeptide of photosystem II is ligated to the manganese ion that undergoes oxidation during the S1 to S2 transition: an isotope-edited FTIR study. Biochemistry 43:3152–3166 Colthup NB, Daly LH, Wiberly SE (1975) Introduction to infrared and Raman spectroscopy. Academic Press, New York Deacon GB, Phillips RJ (1980) Relationships between the carbon-oxygen stretching frequencies of carboxylato complexes and the type of carboxylate coordination. Coord Chem Rev 33:227–250 Debus RJ (2008) Protein ligation of the photosynthetic oxygen-evolving center. Coord Chem Rev 252:244–258 Deng H, Callender R (1999) Raman spectroscopic studies of the structures, energetics, and bond distortions of substrates bound to enzymes. Methods Enzymol 308:176–201 Di Donato M, Cohen RO, Diner BA, Breton J, van Grondelle R, Groot ML (2008) Primary charge separation in the photosystem II core from Synechocystis: a comparison of femtosecond visible/midinfrared pump-probe spectra of wild-type and two P680 mutants. Biophys J 94:4783–4795 Dupeyrat F, Vidaud C, Lorphelin A, Berthomieu C (2004) Long distance charge redistribution upon Cu, Zn-superoxide dismutase reduction—significance of dismutase function. J Biol Chem 279:48091–48101 Faller P, Debus RJ, Brettel K, Sugiura M, Rutherford AW, Boussac A (2001) Rapid formation of the stable tyrosyl radical in photosystem II. Proc Natl Acad Sci USA 98:14368–14373 Gourion-Arsiquaud S, Chevance S, Bouyer P, Garnier L, Montillet JL, Bondon A, Berthomieu C (2005) Identification of a Cd2+ and Zn2+ binding site in cytochrome c using FTIR coupled to an ATR micro-dialysis set-up and NMR spectroscopy. Biochemistry 44:8652–8663 Griffith PR, de Haseth JA (1986) Fourier transform infrared spectroscopy. Wiley, New York Hasegawa K, Ono T, Noguchi T (2000) Vibrational spectra and ab initio DFT calculations of 4-methylimidazole and its different protonation forms: infrared and Raman markers of the protonation state of a histidine side chain. J Phys Chem B 104:4253–4265 Hasegawa K, Ono T, Noguchi T (2002) Ab initio DFT calculations and vibrational analysis of zinc-bound 4-methylimidazole as a model of a histidine ligand in metalloenzymes. J Phys Chem A 106:3377–3390 Hastings G, Ramesh VM, Wang R, Sivakumar V, Webber A (2001) Primary donor photo-oxidation in photosystem I: a re-evaluation of (P700(+) - P700) Fourier transform infrared difference spectra. Biochemistry 40:12943–12949 Hauser K, Krejtschi C, Huang R, Wu L, Keiderling TA (2008) Site-specific relaxation kinetics of a tryptophan zipper hairpin peptide using temperature-jump IR spectroscopy and isotopic labeling. J Am Chem Soc 130:2984–2992 Hienerwadel R, Berthomieu C (1995) Bicarbonate binding to the non-heme iron of photosystem II investigated by Fourier transform infrared difference spectroscopy and 13C-labeled bicarbonate. Biochemistry 34:16288–16297 Hienerwadel R, Thibodeau D, Lenz F, Nabedryk E, Breton J, Kreutz W, Mäntele W (1990) Time-resolved infrared spectroscopy of electron transfer in bacterial photosynthetic reaction centers: dynamics of binding and interaction upon QA and QB reduction. Biochemistry 31:5799–5808 Hienerwadel R, Grzybek S, Fogel C, Kreutz W, Okamura MY, Paddock ML, Breton J, Nabedryk E, Mäntele W (1995) Protonation of Glu L212 following Q −B formation in the photosynthetic reaction center of Rhodobacter sphaeroides: evidence from time-resolved infrared spectroscopy. Biochemistry 34:2832–2843 Hienerwadel R, Boussac A, Breton J, Berthomieu C (1996) Fourier transform infrared difference study of tyrosineD oxidation and plastoquinone QA reduction in photosystem II. Biochemistry 35:15447–15460 Hienerwadel R, Boussac A, Breton J, Diner BA, Berthomieu C (1997) Fourier transform infrared difference spectroscopy of photosystem II tyrosine D using site-directed mutagenesis and specific isotope labeling. Biochemistry 36:14712–14723 Hienerwadel R, Diner BA, Berthomieu C (2008) Molecular origin of the pH dependence of tyrosine D oxidation kinetics and radical stability in photosystem II. Biochim Biophys Acta 1777:525–531 Iwaki M, Andrianambinintsoa S, Rich P, Breton J (2002) Attenuated total reflection Fourier transform infrared spectroscopy of redox transitions in photosynthetic reaction centers: comparison of perfusion- and light-induced difference spectra. Spectrochim Acta A Mol Biomol Spectrosc 58:1523–1533 Kandori H (2000) Role of internal water molecules in bacteriorhodopsin. Biochim Biophys Acta 1460:177–191 Karyakin A, Motiejunas D, Wade RC, Jung C (2007) FTIR studies of the redox partner interaction in cytochrome P450: the Pdx-P450cam couple. Biochim Biophys Acta 1770:420–431 Kimura Y, Mizusawa N, Ishii A, Ono T (2005) FTIR detection of structural changes in a histidine ligand during S-State cycling of photosynthetic oxygen-evolving complex. Biochemistry 44:16072–16078 Kötting C, Gerwert K (2005) Proteins in action monitored by time-resolved FTIR spectroscopy. ChemPhysChem 6:881–888 Krimm S, Bandekar J (1986) Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. Adv Prot Chem 38:181–364 Lehmann N, Aradhyam GK, Fahmy K (2002) Suramin affects coupling of rhodopsin to transducin. Biophys J 82:793–802 Leonhard M, Mäntele W (1993) Fourier transform infrared spectroscopy and electrochemistry of the primary electron donor in Rhodobacter sphaeroides and Rhodopseudomonas viridis reaction centers: vibrational modes of the pigments in situ and evidence for protein and water modes affected by P+ formation. Biochemistry 32:4532–4538 Levin IW, Bhargava R (2005) Fourier transform infrared vibrational spectroscopic imaging: integrating microscopy and molecular recognition. Ann Rev Phys Chem 56:429–474 Lorenz-Fonfria VA, Furutani Y, Kandori H (2008) Active internal waters in the bacteriorhodopsin photocycle. A comparative study of the L and M intermediates at room and cryogenic temperatures by infrared spectroscopy. Biochemistry 47:4071–4081 Mäntele W, Wollenweber AM, Nabedryk E, Breton J (1988a) Infrared spectroelectrochemistry of bacteriochlorophylls and bacteriopheophytins: implications for the binding of the pigments in the reaction center from photosynthetic bacteria. Proc Natl Acad Sci USA 85:8468–8472 Mäntele W, Wollenweber AM, Rashwan F, Heinze J, Nabedryk E, Berger G, Breton J (1988b) Fourier transform infrared spectroelectrochemistry of the bacteriochlorophyll a anion radical. Photochem Photobiol 47:451–456 Mayer G, Heckel A (2006) Biologically active molecules with a “light switch”. Angew Chem 45:4900–4921 Mezzetti A, Seo D, Leibl W, Sakurai H, Breton J (2003) Time-resolved step-scan FTIR investigation on the primary donor of the reaction center from the green sulfur bacterium Chlorobium tepidum. Photosynth Res 75:161–169 Moss D, Nabedryk E, Breton J, Mäntele W (1990) Redox-linked conformational changes in proteins detected by a combination of infrared spectroscopy and protein electrochemistry. Evaluation of the technique with cytochrome c. Eur J Biochem 187:565–572 Mukherjee S, Chowdhury P, Bunagan MR, Gai F (2008) Folding kinetics of a naturally occurring helical peptide: implication of the folding speed limit of helical proteins. J Phys Chem B 112:9146–9150 Nabedryk E (1996) Light-induced Fourier transform infrared difference spectroscopy of the primary electron donor in photosynthetic reaction centers. In: Mantsch HH, Chapman D (eds) Infrared spectroscopy of biomolecules. Wiley-Liss, New York, pp 39–81 Nabedryk E, Breton J (2008) Coupling of electron transfer to proton uptake at the QB site of the bacterial reaction center: a perspective from FTIR difference spectroscopy. Biochim Biophys Acta 1777:1229–1248 Nabedryk E, Leonhardt M, Mäntele W, Breton J (1990a) Fourier transform infrared difference spectroscopy shows no evidence for an enolization of chlorophyll a upon cation formation either in vitro or during P700 photooxidation. Biochemistry 29:3242–3247 Nabedryk E, Bagley KA, Thibodeau DL, Bauscher M, Mäntele W, Breton J (1990b) A protein conformational change associated with the photoreduction of the primary and secondary quinones in the bacterial reaction center. FEBS Lett 266:59–62 Nabedryk E, Breton J, Hienerwadel R, Fogel C, Mäntele W, Paddock ML, Okamura MY (1995) Fourier transforms infrared difference spectroscopy of secondary quinone acceptor photoreduction in proton transfer mutants of Rhodobacter sphaeroides. Biochemistry 34:14722–14732 Nakamoto K (1997) Infrared and Raman spectra of inorganic and coordination compounds. Part b, 5th edn. Wiley, New York, pp 59–62 Nie B, Stutzman J, Xie A (2005) A vibrational spectral marker for probing the hydrogen-bonding status of protonated Asp and Glu residues. Biophysical J 88:2833–2847 Noguchi T (2007) Light-induced FTIR difference spectroscopy as a powerful tool toward understanding the molecular mechanism of photosynthetic oxygen evolution. Photosynth Res 91:59–69 Noguchi T (2008) Fourier transform infrared analysis of the photosynthetic oxygen-evolving center. Coord Chem Rev 252:336–346 Noguchi T, Berthomieu C (2005) Molecular analysis by vibrational spectroscopy. In: Wydrzynski T, Satoh K (eds) Photosystem II: the light-drivenwater/plastoquinone oxidoreductase, vol 16. Springer, Dordrecht, The Netherlands, pp 367–387 Noguchi T, Sugiura M (2000) Structure of an active water molecule in the water-oxidising complex of photosystem II as studied by FTIR spectroscopy. Biochemistry 39:10943–10949 Noguchi T, Sugiura M (2002a) Flash-induced FTIR difference spectroscopy of the water oxidizing complex in moderately hydrated photosystem II core films: effect of hydration extent on S-state transitions. Biochemistry 41:2322–2330 Noguchi T, Sugiura M (2002b) FTIR detection of water reactions during the flash-induced S-state cycle of the photosynthetic water-oxidizing complex. Biochemistry 41:15706–15712 Noguchi T, Sugiura M (2003) Analysis of flash-induced FTIR difference spectra of the S-state cycle in the photosynthetic water-oxidizing complex by uniform 15N and 13C isotope labeling. Biochemistry 42:6035–6042 Noguchi T, Mitsuka T, Inoue Y (1994) Fourier transform infrared spectrum of the radical cation of beta-carotene photoinduced in photosystem II. FEBS Lett 356:179–182 Noguchi T, Ono T, Inoue Y (1995) Direct detection of a carboxylate bridge between Mn and Ca2+ in the photosynthetic oxygen-evolving center by means of Fourier transform infrared spectroscopy. Biochim Biophys Acta 1228:189–200 Noguchi T, Inoue Y, Tang X-S (1997) Structural coupling between the oxygen-evolving Mn cluster and a tyrosine residue in photosystem II as revealed by Fourier transform infrared spectroscopy. Biochemistry 36:14705–14711 Noguchi T, Tomo T, Inoue Y (1998) Fourier transform infrared study of the cation radical of P680 in the photosystem II reaction center: evidence for charge delocalization on the chlorophyll dimer. Biochemistry 37:13614–13625 Noguchi T, Inoue Y, Tang X-S (1999) Structure of a histidine ligand in the photosynthetic oxygen-evolving complex as studied by light-induced Fourier transform infrared difference spectroscopy. Biochemistry 38:10187–10195 O’Malley PJ (2002) Density functional calculations modeling tyrosine oxidation in oxygenic photosynthetic electron transfer. Biochim Biophys Acta 1553:212–217 Pantelidou M, Chitnis PR, Breton J (2004) FTIR spectroscopy of Synechocystis 6803 mutants affected on the hydrogen bonds to the carbonyl groups of the PsaA chlorophyll of P700 supports an extensive delocalization of the charge in P700 +. Biochemistry 43:8380–8390 Petibois C, Déléris G (2006) Chemical mapping of tumor progression by FT-IR imaging: towards molecular histopathology. Trends Biotechnol 24:455–462 Rich P, Iwaki M (2007) Methods to probe protein transitions with ATR infrared spectroscopy. Mol BioSyst 3:398–407 Rose S, Minagawa J, Seufferheld M, Padden S, Svensson B, Kolling DRJ, Crofts AR, Govindjee (2008) D1-arginine mutants (R257E, K and Q) of Chlamydomonas reinhardtii have a lowered QB redox potential: analysis of thermoluminescence and fluorescence measurements. Photosynth Res 98:449–468 Rothschild K, Zagaeski M, Cantore WA (1981) Conformational changes of bacteriorhodopsin detected by Fourier transform infrared difference spectroscopy. Biochem Biophys Res Comm 103:483–489 Siebert F, Hildebrandt P (2008) Vibrational spectroscopy in life science. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany Sivakumar V, Wang R, Hastings G (2005) A1 reduction in intact cyanobacterial photosystem I particles studied by time-resolved step-scan Fourier transform infrared difference spectroscopy and isotope labeling. Biochemistry 44:1880–1893 Socrates G (1994) Infrared characteristic group frequencies: tables and charts, 2nd edn. Wiley, Chichester Strickler MA, Hillier W, Debus J (2006) No evidence from FTIR difference spectroscopy that glutamate-189 of the D1 polypeptide ligates a Mn ion that undergoes oxidation during the S0 to S1, S1 to S2, or S2 to S3 transitions in photosystem II. Biochemistry 45:8801–8811 Strickler MA, Walker LM, Hillier W, Britt RD, Debus J (2007) No evidence from FTIR difference spectroscopy that aspartate-342 of the D1 polypeptide ligates a Mn ion that undergoes oxidation during the S0 to S1, S1 to S2, or S2 to S3 transitions in photosystem II. Biochemistry 46:3151–3160 Takahashi R, Noguchi T (2007) Criteria for determining the hydrogen-bond structures of a tyrosine side chain by Fourier transform infrared spectroscopy: density functional theory analyses of model hydrogen-bonded complexes of p-cresol. J Phys Chem B 111:13833–13844 Takahashi R, Sugiura M, Noguchi T (2007) Water molecules coupled to the redox-active tyrosine YD in photosystem II as detected by FTIR spectroscopy. Biochemistry 46:14245–14249 Thibodeau DL, Nabedryk E, Hienerwadel R, Lenz F, Mäntele W, Breton J (1990) Time-resolved FTIR spectroscopy of quinones in the Rb. sphaeroides reaction centers. Biochim Biophys Acta 1020:253–259 Van Rensen JJS, Xu C, Govindjee (1999) Role of bicarbonate in the photosystem II, the water-plastoquinone oxido-reductase of plant photosynthesis. Physiol Plant 105:585–592 Venyaminov SY, Kalnin NN (1990a) Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. I. Spectral parameters of amino acid residue absorption bands. Biopolymers 30:1243–1257 Venyaminov SY, Kalnin NN (1990b) Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. II. Amide absorption bands of polypeptides and fibrous proteins in alpha, beta-, and random coil conformations. Biopolymers 30:1259–1271 Vidaud C, Gourion-Arsiquaud S, Rollin-Genetet F, Albert C, Plantevin S, Pibbe O, Berthomieu C, Quemeneur E (2007) Structural consequences of UO2 2+ binding to apotransferrin: can this protein account for uranium entry into human cells? Biochemistry 46:2215–2226 Weidlich O, Siebert F (1993) Time-resolved step-scan FT-IR investigations of the transition from KL to L in the bacteriorhodopsin photocycle: identification of chromophore twists by assigning hydrogen-out-of-plane (HOOP) bending vibrations. Appl Spectrosc 47:1394–1400 Wolpert M, Hellwig P (2006) Infrared spectra and molar absorption coefficients of the 20 alpha amino acids in aqueous solutions in the spectral range from 1800 to 500 cm−1. Spectrochim Acta A 64:987–1001 Wydrzynski TJ, Satoh S (2005) Photosystem II—the light-driven water: plastoquinone oxidoreductase. Advances in photosynthesis and respiration, vol 22. Springer, Dordrecht Yamanari T, Kimura Y, Mizusawa N, Ishii A, Ono T (2004) Mid to low-frequency Fourier transform infrared spectra of S-state cycle for photosynthetic water oxidation in Synechocystis sp PCC 6803. Biochemistry 43:7479–7490 Yamazaki Y, Hatanaka M, Kandori H, Sasaki J, Karstens WF, Raap J, Lugtemburg J, Bizounok M, Herzfeld J, Needleman R, Lanyi JK, Maeda A (1995) Water structural changes at the proton uptake site (the Thr46-Asp96 domain) in the L intermediate of bacteriorhodopsin. Biochemistry 34:7088–7093