The infrared absorption of amino acid side chains

Alben, 1980, Ligand-dependent heme-protein interactions in human hemoglobin studied by Fourier transform infrared spectroscopy. Effects of quaternary structure on α-chain tertiary structure measured at the α-109(G11) cysteine-SH, J. Biol. Chem., 255, 3892, 10.1016/S0021-9258(19)85609-0

Arrondo, 1999, Structure and dynamics of membrane proteins as studied by infrared spectroscopy, Prog. Biophys. Mol. Biol., 72, 367, 10.1016/S0079-6107(99)00007-3

Arrondo, 1993, Quantitative studies of the structure of proteins in solution by Fourier-transform infrared-spectroscopy, Prog. Biophys. Mol. Biol., 59, 23, 10.1016/0079-6107(93)90006-6

Asher, 1986, UV resonance Raman excitation profiles of the aromatic amino acids, J. Am. Chem. Soc., 108, 3186, 10.1021/ja00272a005

Ashikawa, 1979, Raman spectra of polypeptides containing l-histidine residues and tautomerism of imidazole side chain, Biopolymers, 18, 1859, 10.1002/bip.1979.360180804

Baburina, 1996, Three of four cysteines, including that responsible for substrate activation, are ionized at pH 6.0 in yeast pyruvate decarboxylase, Biochemistry, 35, 10249, 10.1021/bi961141+

Backmann, 1995, Temperature-jump-induced refolding of ribonuclease A, FEBS Lett., 364, 175, 10.1016/0014-5793(95)00387-O

Barth, 2000, Fine-structure enhancement — Assessment of a simple method to resolve overlapping bands in spectra, Spectrochim. Acta A, 56, 1223, 10.1016/S1386-1425(00)00228-6

Barth, 1998, ATP-induced phosphorylation of the sarcoplasmic reticulum calcium ATPase — molecular interpretation of infrared difference spectra, Biophys. J., 75, 538, 10.1016/S0006-3495(98)77543-5

Barth, 1996, Time-resolved infrared spectroscopy of the calcium ATPase. The enzyme at work, J. Biol. Chem., 271, 30637, 10.1074/jbc.271.48.30637

Barth, 2000, Substrate binding and enzyme function investigated by infrared spectroscopy, FEBS Lett., 477, 151, 10.1016/S0014-5793(00)01782-8

Berendzen, 1990, Temperature-derivative spectroscopy, Proc. Natl. Acad. Sci. USA, 87, 1, 10.1073/pnas.87.1.1

Cao, 1993, Proton transfer from Asp-96 to the bacteriorhodopsin Schiff base is caused by a decrease of the pKa of Asp-96 which follows a protein conformational change, Biochemistry, 32, 1981, 10.1021/bi00059a015

Caswell, 1987, Proline signals in ultraviolett resonance Raman spectra of proteins, J. Am. Chem. Soc., 109, 2796, 10.1021/ja00243a037

Chirgadze, 1975, Estimation of amino acid residue side chain absorption in the infrared spectra of protein solutions in heavy water, Biopolymers, 14, 679, 10.1002/bip.1975.360140402

Colthup, 1975

Deacon, 1980, Relationships between the carbon-oxygen stretching frequencies of carboxylate complexes and the type of carboxylate coordination, Coord. Chem. Rev., 33, 227, 10.1016/S0010-8545(00)80455-5

Dhamelincourt, 1993, Polarized micro-Raman and FT-IR spectra of l-glutamine, Appl. Spectrosc., 47, 446, 10.1366/0003702934335083

Dioumaev, 1995, Modeling vibrational spectra of amino acid side chains in proteins, J. Am. Chem. Soc., 117, 10572, 10.1021/ja00147a020

Dollinger, 1986, Fourier transform infrared difference spectroscopy of bacteriorhodopsin and its photoproducts regenerated with deuterated tyrosine, Biochemistry, 25, 6524, 10.1021/bi00369a028

Doyle, 1971, Conformational investigations on the polypeptide and oligopeptides with the repeating sequence l-alanyl-l-prolylglycine, Biochemistry, 10, 3052, 10.1021/bi00792a011

Dyer, 1998, Infrared studies of fast events in protein folding, Acc. Chem. Res., 31, 709, 10.1021/ar970343a

Fabian, 1999, Two-dimensional IR correlation spectroscopy, Proc. Natl. Acad. Sci. USA, 96, 13153, 10.1073/pnas.96.23.13153

Fabian, 1994, Impact of point mutations on the structure and thermal stability of ribonuclease T1 in aqueous solution probed by Fourier transform infrared spectroscopy, Biochemistry, 33, 10725, 10.1021/bi00201a021

Fabian, 1996, Comparative analysis of the amino- and carboxy-terminal domains of calmodulin by Fourier transform infrared spectroscopy, Eur. Biophys. J., 24, 195, 10.1007/BF00205100

Fahmy, 1993, Aspartic acid-212 of bacteriorhodopsin is ionized in the M and N photocycle intermediates, Biochemistry, 32, 5862, 10.1021/bi00073a020

Gerothanassis, 1992, Solvation state of the Tyr side chain in peptides — An FT-IR and O-17 NMR approach, J. Am. Chem. Soc., 114, 9043, 10.1021/ja00049a041

Gerwert, 1999, Molecular reaction mechanisms of proteins monitored by time-resolved FTIR-spectroscopy, Biol. Chem., 380, 931, 10.1515/BC.1999.115

Gerwert, 1990, Proline residues undergo structural changes during proton pumping in bacteriorhodopsin, FEBS Lett., 261, 449, 10.1016/0014-5793(90)80613-N

Goormaghtigh, 1994, Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy, I. Assignments and model compounds. Subcell. Biochem., 23, 329, 10.1007/978-1-4615-1863-1_8

Goormaghtigh, 1994, Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy, III. Secondary structures. Subcell. Biochem., 23, 405

Goormaghtigh, 1994, Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy. II. Experimental aspects, side chain structure, and H/D exchange, Subcell. Biochem., 23, 363, 10.1007/978-1-4615-1863-1_9

Hasegawa, 2000, Vibrational spectra and ab initio DFT calculations of 4-methylimidazole and its different protonation forms, J. Phys. Chem. B, 104, 4253, 10.1021/jp000157d

Heberle, 1999, Time-resolved ATR/FT-IR spectroscopy of membrane proteins, Recent Res. Dev. Appl. Spectrosc., 2, 147

Herlinger, A.W., Long, T.V., 2d., 1970. Laser-Raman and infrared spectra of amino acids and their metal complexes. 3. Proline and bisprolinato complexes. J. Am. Chem. Soc. 92, 6481–6486.

Hienerwadel, 1997, Fourier transform infrared difference spectroscopy of photosystem II tyrosine D using site-directed mutagenesis and specific isotope labelling, Biochemistry, 36, 14712, 10.1021/bi971521a

Jackson, 1995, The use and misuse of FTIR spectroscopy in the determination of protein structure, Crit. Rev. Biochem. Mol. Biol., 30, 95, 10.3109/10409239509085140

Johnston, 1971, An infrared study of unordered poly-l-proline in CaCl2 solutions, Biopolymers, 10, 2597, 10.1002/bip.360101219

Kakihana, 1988, An empirical potential function of α-glycine derived from infrared spectroscopic data of D-, 13C-, 15N-, and 18O-labeled species, Z. Naturforsch., 43a, 774, 10.1515/zna-1988-8-911

Kauppinen, 1981, Fourier self-deconvolution, Appl. Spectrosc., 35, 271, 10.1366/0003702814732634

Kubota, 1975, The β conformation of polypeptides of valine, isoleucine, and threonine in solution and solid-state, Biopolymers, 14, 605, 10.1002/bip.1975.360140314

Lagant, 1983, Raman spectra and normal vibrations of dipeptides. I. Glycylglycine, Biopolymers, 22, 1267, 10.1002/bip.360220503

Lagant, 1998, On the use of ultraviolett resonance Raman intensities to elaborate molecular force fields, Biospectroscopy, 4, 379, 10.1002/(SICI)1520-6343(1998)4:6<379::AID-BSPY3>3.0.CO;2-2

Laulicht, 1966, The infrared absorption spectrum of oxygen-18-labeled glycine, J. Phys. Chem., 70, 2719, 10.1021/j100881a003

Lautié, 1980, Etude par spectrométrie i.r. et Raman de l’indole et de l’indolizine. Liaison hydrogène NH·π*, Spectrochim. Acta A, 36, 85, 10.1016/0584-8539(80)80062-6

Lazarev, 1985, Amide I band of IR spectrum and structure of collagen and related polypeptides, Biopolymers, 24, 1449, 10.1002/bip.360240804

Lewis, 1996, Fourier transform infrared spectroscopy in the study of hydrated lipids and lipid bilayer membranes, 159

Liu, 1995, Site-directed isotope labelling and FTIR spectroscopy, Biophys. Chem., 56, 63, 10.1016/0301-4622(95)00016-Q

Lord, 1970, Laser-excited Raman spectroscopy of biomolecules. I. Native lysozyme and its constituent amino acids, J. Mol. Biol., 50, 509, 10.1016/0022-2836(70)90208-1

Lord, 1970, Laser-excited Raman spectroscopy of biomolecules. II. Native ribonuclease and α-chymotrypsin, J. Mol. Biol., 51, 203, 10.1016/0022-2836(70)90137-3

Madec, 1978, Etude du spectre de vibration de la dl-serine et des ses dérivés deuteries, Can. J. Spectrosc., 23, 166

Maeda, 1995, Application of FTIR spectroscopy to the structural study on the function of bacteriorhodopsin, Israel J. Chem., 35, 387, 10.1002/ijch.199500038

Mäntele, 1993, Reaction-induced infrared difference spectroscopy for the study of protein function and reaction mechanisms, TIBS, 18, 197

Mäntele, 1995, Infrared vibrational spectroscopy of reaction centers, 627

Maes, 1988, Matrix-isolation IR studies on the basic interaction sites in esters and thiolesters towards proton donors, J. Mol. Struct., 173, 349, 10.1016/0022-2860(88)80066-8

Maes, 1983, Matrix isolation infrared spectra of the complexes between methylacetate and water or hydrochloric acid, J. Mol. Struct., 100, 305, 10.1016/0022-2860(83)90098-4

Mantsch, 1988, Fourier transform methods for spectral resolution enhancement, J. Mol. Struct., 173, 285, 10.1016/0022-2860(88)80061-9

Mizuguchi, M., Nara, M., Kawano, K., Nitta, K., 1997a. FT-IR study of the calcium-binding to bovine α-lactalbumin. Relationships between the type of coordination and characteristics of the bands due to the Asp carboxylate groups in the calcium binding site. FEBS Lett. 417, 153–156.

Mizuguchi, M., Nara, M., Ke, Y., Kawano, K., Hiraoki, T., Nitta, K., 1997b. Fourier-transform infrared spectroscopic studies on the coordination of the side-chain carboxylate groups to calcium in equine lysozyme. Eur. J. Biochem. 250, 72–76.

Moh, 1987, Conformational sensitivity of β-93 cysteine SH to ligation of hemoglobin observed by FT-IR spectroscopy, Biochemistry, 26, 6243, 10.1021/bi00393a044

Nara, 1994, Infrared studies of interaction between metal ions and calcium binding proteins. Marker bands for identifying the types of coordination of the side-chain carboxylate groups to metal ions in pike parvalbumin (pI=4.10), FEBS Lett., 349, 84, 10.1016/0014-5793(94)00645-8

Noguchi, 1997, Fourier transform infrared study on the primary donor P798 of Heliobacterium modesticaldum, Biochemistry, 36, 12329, 10.1021/bi970853c

Noguchi, 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, 10.1021/bi990631+

Overman, 1999, Raman markers of nonaromatic side chains in an α-helix assembly, Biochemistry, 38, 4018, 10.1021/bi982901e

Pinchas, 1971

Rahmelow, 1998, Infrared absorbances of protein side chains, Anal. Biochem., 257, 1, 10.1006/abio.1997.2502

Rava, 1985, Resonance enhancement in the ultraviolet Raman spectra of aromatic amino acids, J. Phys. Chem., 89, 1856, 10.1021/j100256a007

Reinstädler, 1999, New structural insights into the refolding of ribonuclease T1 as seen by time-resolved Fourier-transform infrared spectroscopy, Proteins, 34, 303, 10.1002/(SICI)1097-0134(19990215)34:3<303::AID-PROT4>3.0.CO;2-H

Roepe, 1987, Tyrosine and carboxyl protonation changes in the bacteriorhodopsin photocycle. 1. M412 and L550 intermediates, Biochemistry, 26, 6696, 10.1021/bi00395a020

Rothschild, 1992, FTIR difference spectroscopy of bacteriorhodopsin, J. Bioengn. Biomembr., 24, 147, 10.1007/BF00762674

Rothschild, 1989, Fourier transform infrared evidence for proline structural changes during the bacteriorhodopsin photocycle, Proc. Natl. Acad. Sci. USA, 86, 9832, 10.1073/pnas.86.24.9832

Rothschild, 1986, Evidence for a tyrosine protonation change during the primary phototransition of bacteriorhodopsin at low temperature, Proc. Natl. Acad. Sci. USA, 83, 347, 10.1073/pnas.83.2.347

Rudiger, 1995, Chemical reconstitution of a chloride pump inactivated by a single point mutation, EMBO J., 14, 1599, 10.1002/j.1460-2075.1995.tb07148.x

Sasaki, 1994, Complete identification of C=O stretching vibrational bands of protonated aspartic acid residues in the difference infrared spectra of M and N intermediates versus bacteriorhodopsin, Biochemistry, 33, 3178, 10.1021/bi00177a006

Schultz, 2000, Illuminating folding intermediates, Nat. Struct. Biol., 7, 7, 10.1038/71197

Sengupta, 1984, Vibrational analysis of peptides, polypeptides and proteins. XXI β-calcium-poly(l-glutamate), Biopolymers, 23, 1565, 10.1002/bip.360230811

Sengupta, 1985, Vibrational analysis of peptides, polypeptides, and proteins. XXXII. α-poly(l-glutamic acid), Biopolymers, 24, 1479, 10.1002/bip.360240805

Siebert, F., 1995. Infrared spectroscopy applied to biochemical and biological problems. Meth. Enzymol. 246, 501–526.

Sonar, 1994, Site-directed isotope labelling and FTIR spectroscopy of bacteriorhodopsin, Struct. Biol., 1, 512, 10.1038/nsb0894-512

Spudich, 1994, New tool for spectroscopists, Struct. Biol., 1, 495, 10.1038/nsb0894-495

Susi, 1983, Vibrational analysis of amino acids, J. Mol. Struct., 102, 63, 10.1016/0022-2860(83)80007-6

Tackett, 1989, FT-IR characterisation of metal acetates in aqueous solution, Appl. Spectrosc., 43, 483, 10.1366/0003702894202931

Takeuchi, 1986, Normal coordinate analysis of the indole ring, Spectrochim. Acta A, 42, 1069, 10.1016/0584-8539(86)80021-6

Takeuchi, 1988, Vibrational spectra and normal coordinate analysis of p-cresol and its deuterated analogs, Spectrochim. Acta A, 44, 749, 10.1016/0584-8539(88)80138-7

Troullier, 2000, Transient non-native secondary structures during the refolding of α-lactalbumin detected by infrared spectroscopy, Nat. Struct. Biol., 7, 78, 10.1038/71286

Venyaminov, 1990, Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. I. Spectral parameters of amino acid residue absorption bands, Biopolymers, 30, 1243, 10.1002/bip.360301309

Von Germar, 2000, Structural changes of the sarcoplasmic reticulum calcium ATPase upon nucleotide binding studied by Fourier transform infrared spectroscopy, Biophys. J., 78, 1531, 10.1016/S0006-3495(00)76705-1

White, 1995, A stopped-flow apparatus for infrared spectroscopy of aqueous solutions, Biochem. J., 306, 843, 10.1042/bj3060843

Wright, 1997, Use of IR absorption of the carboxyl group of amino acids and their metabolites to determine pKs, to study proteins, and to monitor enzymatic activity, Biospectroscopy, 3, 457, 10.1002/(SICI)1520-6343(1997)3:6<457::AID-BSPY5>3.0.CO;2-Y

Zscherp, C., Barth, A., 2001. Reaction induced infrared difference spectroscopy for the study of protein reaction mechanisms. Biochemistry, in press.

Zscherp, 1999, In situ determination of transient pKa changes of internal amino acids of bacteriorhodopsin by using time-resolved attenuated total reflection Fourier-transform infrared spectroscopy, Proc. Natl. Acad. Sci. USA, 96, 5498, 10.1073/pnas.96.10.5498