RPBS: a web resource for structural bioinformatics

RPBS (Ressource Parisienne en Bioinformatique Structurale) is a resource dedicated primarily to structural bioinformatics. It is the result of a joint effort by several teams to set up an interface that offers original and powerful methods in the field. As an illustration, we focus here on three such methods uniquely available at RPBS: AUTOMAT for sequence databank scanning, YAKUSA for structure databank scanning and WLOOP for homology loop modelling. The RPBS server can be accessed at and the specific services at

A density functional theory based analysis of photoinduced electron transfer in a triazacryptand based K+ sensor

The electronic structure and photoinduced electron transfer processes in a K+ fluorescent sensor that comprises a 4-amino-naphthalimide derived fluorophore with a triazacryptand lig- and is investigated using density functional theory (DFT) and time-dependent density functional theory (TDDFT) in order to rationalise the function of the sensor. The absorption and emission energies of the intense electronic excitation localised on the fluorophore are accurately described using a ∆SCF Kohn-Sham DFT approach, which gives excitation energies closer to experiment than TDDFT. Analysis of the molecular orbital diagram arising from DFT calculations for the isolated molecule or with implicit solvent cannot account for the function of the sensor and it is necessary to consider the relative energies of the electronic states formed from the local excitation on the fluorophore and the lowest fluorophore→chelator charge transfer state. The inclusion of solvent in these calculations is critical since the strong interaction of the charge transfer state with the solvent lowers it energy below the local fluorophore excited state making a reductive photoinduced electron transfer possible in the absence of K+, while no such process is possible when the sensor is bound to K+. The rate of electron transfer is quantified using Marcus theory, which gives a rate of electron transfer of k_ET=5.98 x 10^6 s−1

The 12 kDa FK506-binding protein, FKBP12, modulates the Ca(2+)-flux properties of the type-3 ryanodine receptor

9sireservedWe have characterised the functional regulation of the type-3 ryanodine receptor by the 12 kDa FK506-binding protein. Wild-type type-3 ryanodine receptor and mutant type-3 ryanodine receptor in which the critical valine at position 2322 in the central 12 kDa FK506-binding protein binding site was substituted by aspartate, were stably expressed in human embryonic kidney cells. In contrast to the wild-type receptor, the mutant receptor was strongly impaired in binding to immobilised glutathione S-transferase 12 kDa FK506-binding protein. Caffeine-induced 45Ca(2+)-efflux was markedly increased in cells expressing mutant type-3 ryanodine receptor whereas the maximal-releasable Ca2+ was not affected. Confocal Ca2+ imaging provided clear evidence for a much higher sensitivity of the mutant receptor, which showed global Ca2+ release at about 20-fold lower caffeine concentrations than the wild-type receptor. Spontaneous Ca2+ sparks were observed in both wild-type- and mutant-expressing cells but the number of sparking cells was about 1.5-fold higher in the mutant group, suggesting that the degree of FK506 binding controls the stability of the closed state of ryanodine receptor channels. Furthermore, overexpression of 12 kDa FK506-binding protein decreased the number of sparking cells in the wild-type-expressing cells whereas it did not affect the number of sparking cells in cells expressing the mutant receptor. Concerning spark properties, the amplitude and duration of Ca2+ sparks mediated by mutant channels were significantly reduced in comparison to wild-type channels. This suggests that functional coupling between different mutant type-3 ryanodine receptor channels in a cluster is impaired. Our findings show for the first time that the central binding site for the 12 kDa FK506-binding protein of type-3 ryanodine receptor, encompassing the critical valine proline motif, plays a crucial role in the modulation of the Ca2+ release properties of the type-3 ryanodine receptor channel, including the regulation of both global Ca2+ responses and spontaneous Ca2+ sparks.mixedvan Acker, K.; Bultynck, G.; Rossi, D.; Sorrentino, V.; Boens, N.; Missiaen, L.; De Smedt, H.; Parys, J. B. ; Callewaert, G.van Acker, K.; Bultynck, G.; Rossi, D.; Sorrentino, V.; Boens, N.; Missiaen, L.; De Smedt, H.; Parys, J. B.; Callewaert, G

Synthesis and in vitro evaluation of dioxopyrrolopyrroles as potential low-affinity fluorescent Ca2+ indicators

2nd Mediterranean Meeting on Photochemistry -- 2003 -- Giardini Naxos, ITALYWOS: 000222779200003Three new low-affinity fluorescent Ca2+ indicators excitable with visible light, namely 3-phenyl-6-(4-(3-carboxymethoxy-4-(N,N-dicarboxymethylamino) phenyl) phenyl)-2,5-dicarboxymethyl-1,4-dihydropyrrolo[ 3,4- c] pyrrole-1,4-dione (DPP1), 3-phenyl-6-( 5-(3-carboxymethoxy-4-( N, N-dicarboxymethylamino) phenyl) thien-2-yl)-2,5-dicarboxymethyl-1,4- dihydropyrrolo[ 3,4- c] pyrrole-1,4- dione (DPP2) and 3( thien-2-yl)-6-( 5-(3-carboxymethoxy-4-( N, N-dicarboxymethylamino) phenyl) thien-2-yl)-2,5- dicarboxymethyl-1,4- dihydropyrrolo[ 3,4- c] pyrrole-1,4- dione (DPP3) have been synthesized and evaluated for their Ca2+ binding properties via fluorimetric titrations. The in vitro dissociation constant K-d measured at 21degreesC in 100 mM KCl buffered solution, pH 7.05, for the Ca2+ -DPP1 complex is 10 muM; for Ca2+ -DPP2 and Ca2+ - DPP3 a K-d value of 20 muM is found. All three indicators form 1 : 1 complexes with Ca2+. The fluorescence quantum yields of the uncomplexed forms of DPP1, DPP2 and DPP3 are 1.2 x 10(-2), 3.4 x 10(-2) and 3.6 x 10(-2), respectively. After binding to Ca2+ these values increase to 4.8 x 10(-2), 5.0 x 10(-2) and 5.1 x 10(-2), respectively.Italian Grp Photoche