Proteins chromophores

Martin ME, Negri F, Olivucci M (2004) Origin, nature, and fate of the fluorescent state of the green fluorescent protein chromophore at the CASPT2//CASSCF resolution. J Am Chem Soc 126 5452... 

Mandal D, Tahara T, Meech SR (2004) Excited-state dynamics in the green fluorescence protein chromophore. J Phys Chem B 108 1102-1108... 

He X, Bell AF, Tonge PJ (2002) Synthesis and spectroscopic studies of model red fluorescent protein chromophores. Org Lett 4 1523-1526... 

Barondeau DP, Putnam CD, Kassmann CJ, Tainer JA, Getzoff ED (2003) Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures. Proc Natl Acad Sci USA 100 12111-12116... 

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... 

Voliani V, Bizzarri R, Nifosi R, Abbruzzetti S, Grandi E, Viappiani C, Beltram F (2008) Cis-trans photoisomerization of fluorescent-protein chromophores. J Phys Chem B 112 10714-10722... 

Dong J, Abulwerdi F, Baldridge A, Kowalik J, Solntsev KM, Tolbert LM (2008) Isomerization in fluorescent protein chromophores involves addition/elimination. J Am Chem Soc 130 14096-14098... 

Yang JS, Huang GJ, Liu YH, Peng SM (2008) Photoisomerization of the green fluorescence protein chromophore and the meta- and para-amino analogues. Chem Commun 1344-1346... 

Flelms V, Winstead C, Langhoff PW (2000) Low-lying electronic excitations of the green fluorescent protein chromophore. Theochem-J Mol Struct 506 179-189... 

Webber NM, Litvinenko KL, Meech SR (2001) Radiationless relaxation in a synthetic analogue of the green fluorescent protein chromophore. J Phys Chem B 105 8036-8039... 

Usman A, Mohammed OP, Nibbering ET, Dong J, Solntsev KM, Tolbert LM (2005) Excited-state structure determination of the green fluorescent protein chromophore. J Am Chem Soc 127 11214-11215... 

Altoe P, Bemardi F, Garavelli M, Orlandi G, Negri F (2005) Solvent effects on the vibrational activity and photodynamics of the green fluorescent protein chromophore a quantum-chemical study. J Am Chem Soc 127 3952-3963... 

The general strategy for establishing the sites of protein-chromophore interactions in rhodopsin involves introduction of selective 13 C labels at each position along the length of the retinal chromophore. 

Ultrafast excited state dynamics in the green fluorescent protein chromophore... 

NCS-Chrom = the non-protein chromophore of the antitumor antibiotic neocarzi-nostatin, associated with the generation of a reactive form of formate 117 from C-5 of deoxyribose of the thymidylate residues. 

Leach and Scheraga (1960a) have presented a summary which appears to formally cover most, if not all, of the types of interactions in which protein chromophores may be involved. 

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. 

A similar study by Yamada et al. [13] concluded that the protein prevents the chromophore from adopting a completely planar structure. Based on their calculations they proposed that the efficiency of photoisomerization in PYP is due to the asymmetric protein-chromophore interaction that can serve as the initial accelerant for the light-induced photocycle. They also found that the C4—C7-C8-C9 dihedral always twists counterclockwise. 

Fig. 5.4 The r (N1-C1-C2-C3) and q> (Cl-C2-C3-C4) dihedral angles of the green fluorescent protein chromophore. In the protein R, is Gly67 and R2 is Ser65, and in HBDI, an often used model compound, = R2 = CH3. In r one-bond flips (r-OBF) the dihedral rotation occurs around the r torsional angle, in a (p-OBF it is around the (p dihedral angle, in a hula twist (HT) the (p and r dihedral angles concertedly rotate.

Fig. 5.5 Models of the green fluorescent protein chromophore in the neutral, anionic, and zwitterionic forms used in the quantum chemical calculations, shown in those resonance structures that best represent the calculated bond orders. Rotation by 180° around (p leaves the structure unchanged. The configurations displayed represent r = 0° and are referred to as cis configurations. The upper panels show energy profiles for rotation around the dihedral angles r and (p and for...

In protein systems in particular, a distinction between intrinsic and extrinsic Cotton effects has been made 31). The intrinsic effects are the result of internal dissymmetric interactions of protein chromophores such as the amide transitions in helical arrays. Extrinsic effects relate to non-protein substances which are usually optically inactive but exhibit optical activity when conjugated to a protein or to an... 

Fig. 12.5. Ball and stick representation of the green fluorescent protein chromophore (left side) as an example of molecule which can waste the photon energy and of the visual pigment rhodopsin chromophore (right side) which can efficiently convert the light energy into molecular motion (adapted from Ref. [8]).

Demmig-Adams B and Adams, III WW (1996) The role of xanthophyll cycle carotenoids in the protection of photosynthesis. Trends Plant Sci 1 21-26 DiMagno TJ, Laible PD, Reddy NR, Small GJ, Norris JR, Schiffer M and Hanson DK (1998) Protein chromophore interactions spectral shifts report the consequences ofmutations in the bacterial photosynthetic reaction center. Spectrochimica Acta A 54 1247-1267... 

Assuming a spherical shape for the fluorescent molecule, the degree of change in the rotational Brownian motion is given by Eq. (3.25), where v is the volume of the spherical molecule, r)0 is the solvent viscosity, r is the fluorescence lifetime of the chromophore, and T is the temperature. The values of r0 and r/v can be obtained from a plot of Mr versus T/rj0. Thus, if the fluorescence lifetime of the chromophore is known, it is possible to determine the hydrodynamic volume of the rotating molecule and its rotational diffusion constant D,. This data treatment is known as the Perrin-Weber approximation,25 after the two scientists who first derived the equations in the case of protein chromophores. 

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