Protein chromophore spectroscopy

Bell AF, He X, Wachter RM, Tonge PJ (2000) Probing the ground state structure of the green fluorescent protein chromophore using Raman spectroscopy. Biochemistry 39 4423 1431... 

Spectroscopy measures the interactions of the protein chromophores with light. Information regarding the concentration and conformation of the protein may be obtained through different types of spectroscopy. 

The spirit is to show some of the results, but also to guide users of the approach by pointing to the problems and limitations of the method. The review covers some of the newer applications in the spectroscopy of organic molecules acetone, methylenecyclopropene, biphenyl, bithiophene, the protein chromophores indole and imidazole, and a series of radical cations of conjugated polyenes and polyaromatic hydrocarbons. The applications in transition metal chemistry include carbonyl, nitrosyl, and cyanide complexes, some dihalogens, and the chromium dimer. 

Resonance Raman (RR) spectroscopy provides information about the vibrational characteristics of a chromophore, for example, a metal center, within the complex environment of a protein. In RR spectra, those vibrational transitions are observed selectively that are coupled to electronic transitions. In iron sulfur proteins, this technique has been used to resolve the complex electronic absorption spectra and to identify both vibrational and electronic transitions. 

Vibrational spectroscopy has played a very important role in the development of potential functions for molecular mechanics studies of proteins. Force constants which appear in the energy expressions are heavily parameterized from infrared and Raman studies of small model compounds. One approach to the interpretation of vibrational spectra for biopolymers has been a harmonic analysis whereby spectra are fit by geometry and/or force constant changes. There are a number of reasons for developing other approaches. The consistent force field (CFF) type potentials used in computer simulations are meant to model the motions of the atoms over a large ranee of conformations and, implicitly temperatures, without reparameterization. It is also desirable to develop a formalism for interpreting vibrational spectra which takes into account the variation in the conformations of the chromophore and surroundings which occur due to thermal motions. 

Amide derivatives have proved especially useful sugars for study by c.d. spectroscopy. The amide substituent is the same as the chromophore found in proteins, so that its optical properties have been extensively studied both experimentally and theoretically. 2-Acetamido sugars are found in many glycoproteins. The structure of 2-acetamido-2-deoxy-a-D-glucopyranose is given as an example in formula 7. 

The chromophore of ECFP does not bear the deprotonable phenol that is crucial to the photophysics of most AvGFP variants, and displays a markedly different spectroscopy. It has been quickly recognized that, despite its prominent interest in biological applications, the properties of this variant are suboptimal. Indeed, while the brightness of the protein is relatively low (eM = 32,000 M 1 cm-1, fluorescence emission is both spectrally and kinetically heterogeneous. The fluorescence comprises two major decay times at 3.6 ns and 1.3 ns... 

Litvinenko KL, Webber NM, Meech SR (2001) An ultrafast polarisation spectroscopy study of internal conversion and orientational relaxation of the chromophore of the green fluorescent protein. Chem Phys Lett 346 47-53... 

The CP MAS NMR spectroscopy has been also extensively used for studies of proteins containing retinylidene chromophore like proteorhodopsin or bacteriorhodopsin. Bacteriorhodopsin is a protein component of purple membrane of Halobacterium salinarium.71 7 This protein contains 248 amino acids residues, forming a 7-helix bundle and a retinal chromophore covalently bound to Lys-216 via a Schiff base linkage. It is a light-driven proton pump that translocates protons from the inside to the outside of the cell. After photoisomerization of retinal, the reaction cycle is described by several intermediate states (J, K, L, M, N, O). Between L and M intermediate states, a proton transfer takes place from the protonated Schiff base to the anionic Asp85 at the central part of the protein. In the M and/or N intermediate states, the global conformational changes of the protein backbone take place. 

Muller et al.understand better the role of tyrosine in the structure and biological function of MDH. Resolution of the protein absorption spectrum, using iV-acetylphenylalanine ethyl ester in dioxane and A-acetyltyrosine ethyl ester in dioxane or 0.1 M phosphate buffer to model the effect of the local environments of the chromophoric groups, indicated that both the pig and the... 

S. N. Khrapunov and A. I. Dragan, Spectroscopy of molecular interactions of tyrosine chromophore. III. Classification of the state of tyrosine residues in protein composition according to their electronic spectra, Biofizika 34, 357-363 (1989). 

The Photoactive Yellow Protein (PYP) is the blue-light photoreceptor that presumably mediates negative phototaxis of the purple bacterium Halorhodospira halophila [1]. Its chromophore is the deprotonated trans-p-coumaric acid covalently linked, via a thioester bond, to the unique cystein residue of the protein. Like for rhodopsins, the trans to cis isomerization of the chromophore was shown to be the first overall step of the PYP photocycle, but the reaction path that leads to the formation of the cis isomer is not clear yet (for review see [2]). From time-resolved spectroscopy measurements on native PYP in solution, it came out that the excited-state deactivation involves a series of fast events on the subpicosecond and picosecond timescales correlated to the chromophore reconfiguration [3-7]. On the other hand, chromophore H-bonding to the nearest amino acids was shown to play a key role in the trans excited state decay kinetics [3,8]. In an attempt to evaluate further the role of the mesoscopic environment in the photophysics of PYP, we made a comparative study of the native and denatured PYP. The excited-state relaxation path and kinetics were monitored by subpicosecond time-resolved absorption and gain spectroscopy. 

The transient absorption spectroscopy of the denatured PYP is found to be similar to that of the native protein in the early stages of the excited-state deactivation. This behavior seems to indicate that the intrinsic properties of the chromophore play a determining role in the complex primary photoprocesses of the native PYP. 

The Photoactive Yellow Protein (PYP) is thought to be the photoreceptor responsible for the negative phototaxis of the bacterium Halorhodospira halophila [1]. Its chromophore, the deprotonated 4-hydroxycinnamic (or p-coumaric) acid, is covalently linked to the side chain of the Cys69 residue by a thioester bond. Trans-cis photoisomerization of the chromophore was proved to occur during the early steps of the PYP photocycle. Nevertheless, the reaction pathway leading to the cis isomer is still discussed (for a review, see ref. [2]). Time-resolved spectroscopy showed that it involves subpicosecond and picosecond components [3-7], some of which could correspond to a flipping motion of the chromophore carbonyl group [8,9]. 

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