Models green fluorescent proteins

He X, Bell AF, Tonge PJ (2002) Isotopic labeling and normal-mode analysis of a model green fluorescent protein chromophore. J Phys Chem B 106 6056-6066... 

Kojima, S., et al. (1998). Fluorescent properties of model chromophores of tyrosine-66 substitute mutants of Aequorea green fluorescent protein (GFP). Tetrahedron Lett. 39 5239-5242. 

R. Hoffman, Green fluorescent protein imaging of tumour growth, metastasis, and angiogenesis in mouse models. Lancet Oncol. 3 (2002) 546-556. 

Fig. 10 Model protocell systems, a An encapsulated polymerase (polynucleotide phos-phorylase) can synthesize RNA from nucleoside diphosphates such as ADP [79,80], b RNA can be synthesized by a template-dependent T7 RNA polymerase [83], c Proteins such as green fluorescent protein (GFP) can be synthesized by an encapsulated translation system [84], If mRNA coding for hemolysin is also present, the hemolysin forms a pore in the lipid bilayer. Amino acids then permeate the bilayer, and protein synthesis can continue for several days [85]...

Araneda et al. tested 90 odorants for activity with the rat receptor 17 (70). They used an adenovirus to increase the level of 17 in the epithelium and to introduce green fluorescent protein (GFP) simultaneously as a way to detect activation. 17 was found to be very selective toward aldehydes and with a preference for eight carbon atoms in the chain. Both saturated and oleflnic aldehydes were found to be active and some tolerance exists for substituents, mostly methyl groups, on the chain. Using models, they could define more precisely the steric constraints on the binding site. 

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...

Fig. 5.6 Model for the photophysical behavior of green fluorescent protein [40]. Excited states are labeled by asterisks. Barriers may exist for processes of types 2 and 3. Excitation arrows have been omitted for simplicity. The relative free energies ofthe ground state forms...

Proton transfer dynamics of photoacids to the solvent have thus, being reversible in nature, been modelled using the Debye-von Smoluchowski equation for diffusion-assisted reaction dynamics in a large body of experimental work on HPTS [84—87] and naphthols [88-92], with additional studies on the temperature dependence [93-98], and the pressure dependence [99-101], as well as the effects of special media such as reverse micelles [102] or chiral environments [103]. Moreover, results modelled with the Debye-von Smoluchowski approach have also been reported for proton acceptors triggered by optical excitation (photobases) [104, 105], and for molecular compounds with both photoacid and photobase functionalities, such as lO-hydroxycamptothecin [106] and coumarin 4 [107]. It can be expected that proton diffusion also plays a role in hydroxyquinoline compounds [108-112]. Finally, proton diffusion has been suggested in the long time dynamics of green fluorescent protein [113], where the chromophore functions as a photoacid [23,114], with an initial proton release on a 3-20 ps time scale [115,116]. 

Most organelles have a characteristic architecture that is important for function, but may serve as an additional impediment to diffusion within the cell compartment. Organelle membranes within the cell can serve as local barriers (Table 4.9), which affect the rate of diffusion of molecules locally. This effect has been estimated for diffusion in the mitochondrial matrix and the endoplasmic reticulum (Figure 4.28a and b). The mitochondrial matrix was modeled as a closed cylinder with multiple barriers occluding the lumen to simulate the mitochondrial cristae the presence of multiple barriers produced a modest decrease in the rate of diffusion down the axis of the cyUnder (Figure 4.28a) this calculation is consistent with recent measurements of green fluorescent protein (GFP) diffusion in the mitochondrial matrix, which was approximately three-fold slower than diffusion in saline. The endoplasmic reticulum was modeled as an array of interconnected cylinders with a continu-... 

---