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International audience; The use of generous distance bounds has been the hallmark of NMR structure determination. However, bounds necessitate the estimation of data quality before the calculation, reduce the information content, introduce human bias, and allow for major errors in the structures. Here, we propose a new rapid structure calculation scheme based on Bayesian analysis. The minimization of an extended energy function, including a new type of distance restraint and a term depending on the data quality, results in an estimation of the data quality in addition to coordinates. This allows for the determination of the optimal weight on the experimental information. The resulting structures are of better quality and closer to the X-ray crystal structure of the same molecule. With the new calculation approach, the analysis of discrepancies from the target distances becomes meaningful. The strategy may be useful in other applications-for example, in homology modeling.

International audience; Previous studies on molecular recognition of uranyl-DCP (dicarboxy-phenanthroline chelator) compound by two distinct monoclonal antibodies (Mabs U04S and U08S) clearly showed the presence of a biphasic shape in Bell-Evans' plots and an accentuated difference in slopes at the high loading rates. To further explore the basis in the slope difference, we have performed complementary experiments using antibody PHE03S, raised against uranyl-DCP but, presenting a strong cross-reactivity toward the DCP chelator. This work allowed us to obtain a reallocation of the respective contributions of the metal ion itself and that of the chelator. Results led us to propose a 2D schematic model representing two energy barriers observed in the systems Mabs U04S- and U08S-[UO(2)-DCP] where the outer barrier characterizes the interaction between UO(2) and Mab whereas the inner barrier characterizes the interaction between DCP and Mab. Using dynamic force spectroscopy, it is thus possible to dissect molecular interactions during the unbinding between proteins and ligands.

Energy transfer mechanisms represent the basis for an array of valuable tools to infer interactions in vitro and in vivo , enhance detection or resolve interspecies distances such as with resonance. Based upon our own previously published studies and new results shown here we present a novel framework describing for the first time a model giving a view of the biophysical relationship between Fluorescence by Unbound Excitation from Luminescence (FUEL), a conventional radiative excitation–emission process, and bioluminescence resonance energy transfer. We show here that in homogeneous solutions and in fluorophore-targeted bacteria, FUEL is the dominant mechanism responsible for the production of red-shifted photons. The minor resonance contribution was ascertained by comparing the intensity of the experimental signal to its theoretical resonance counterpart. Distinctive features of the in vitro FUEL signal include a macroscopic depth dependency, a lack of enhancement upon targeting at a constant fluorophore concentration c f and a non-square dependency on c f . Significantly, FUEL is an important, so far overlooked, component of all resonance phenomena which should guide the design of appropriate controls when elucidating interactions. Last, our results highlight the potential for FUEL as a means to enhance in vivo and in vitro detection through complex media while alleviating the need for targeting.

International audience; The non-linear problem of simulating the structural transition between two known forms of a macromolecule still remains a challenge in structural biology. The problem is usually addressed in an approximate way using 'morphing' techniques, which are linear interpolations of either the Cartesian or the internal coordinates between the initial and end states, followed by energy minimization. Here we describe a web tool that implements a new method to calculate the most probable trajectory that is exact for harmonic potentials; as an illustration of the method, the classical Calpha-based Elastic Network Model (ENM) is used both for the initial and the final states but other variants of the ENM are also possible. The Langevin equation under this potential is solved analytically using the Onsager and Machlup action minimization formalism on each side of the transition, thus replacing the original non-linear problem by a pair of linear differential equations joined by a non-linear boundary matching condition. The crossover between the two multidimensional energy curves around each state is found numerically using an iterative approach, producing the most probable trajectory and fully characterizing the transition state and its energy. Jobs calculating such trajectories can be submitted on-line at: http://lorentz.dynstr.pasteur.fr/joel/index.php.

Real-time visualization of calcium (Ca(2+)) dynamics in the whole animal will enable important advances in understanding the complexities of cellular function. The genetically encoded bioluminescent Ca(2+) reporter green fluorescent protein-aequorin (GA) allows noninvasive detection of intracellular Ca(2+) signaling in freely moving mice. However, the emission spectrum of GA is not optimal for detection of activity from deep tissues in the whole animal. To overcome this limitation, two new reporter genes were constructed by fusing the yellow fluorescent protein (Venus) and the monomeric red fluorescent protein (mRFP1) to aequorin. Transfer of aequorin chemiluminescence energy to Venus (VA) is highly efficient and produces a 58 nm red shift in the peak emission spectrum of aequorin. This substantially improves photon transmission through tissue, such as the skin and thoracic cage. Although the Ca(2+)-induced bioluminescence spectrum of mRFP1-aequorin (RA) is similar to that of aequorin, there is also a small peak above 600 nm corresponding to the peak emission of mRFP1. Small amounts of energy transfer between aequorin and mRFP1 yield an emission spectrum with the highest percentage of total light above 600 nm compared with GA and VA. Accordingly, RA is also detected with higher sensitivity from brain areas. VA and RA will therefore improve optical access to Ca(2+) signaling events in deeper tissues, such as the heart and brain, and offer insight for engineering new hybrid molecules.

Sarcoplasmic reticulum (SR) calcium pump function requires a high local ATP/ADP ratio, which can be maintained by direct nucleotide channelling from mitochondria, and by SR-bound creatine kinase (CK)-catalysed phosphate-transfer from phosphocreatine. We hypothesized that SR calcium uptake supported by mitochondrial direct nucleotide channelling, but not bound CK, depends on the juxtaposition of these organelles. To test this, we studied a well-described model of cytoarchitectural disorganization, the muscle LIM protein (MLP)-null mouse heart. Subcellular organization was characterized using electron microscopy, and mitochondrial, SR and myofibrillar function were assessed in saponin-permeabilized fibres by measuring respiration rates and caffeine-induced tension transients. MLP-null hearts had fewer, less-tightly packed intermyofibrillar mitochondria, and more subsarcolemmal mitochondria. The apparent mitochondrial Km for ADP was significantly lower in the MLP-null heart than in control (175 +/- 15 and 270 +/- 33 microM, respectively), indicating greater ADP accessibility, although maximal respiration rate, mitochondrial content and total CK activity were unaltered. Active tension in the myofibres of MLP-null mice was 54% lower than in controls (39 +/- 3 and 18 +/- 1 mN mm(-2), respectively), consistent with cytoarchitectural disorganization. SR calcium loading in the myofibres of MLP-null mice was similar to that in control myofibres when energy support was provided via Bound CK, but approximately 36% lower than controls when energy support was provided by mitochondrial (P < 0.05). Mitochondrial support for SR calcium uptake was also specifically decreased in the desmin-null heart, which is another model of cytoarchitectural perturbation. Thus, despite normal oxidative capacity, direct nucleotide channelling to the SR was impaired in MLP deficiency, concomitant with looser mitochondrial packing and increased nucleotide accessibility to this organelle. Changes in cytoarchitecture may therefore impair subcellular energy transfer and contribute to energetic and contractile dysfunction.

Sarcoplasmic reticulum (SR) calcium pump function requires a high local ATP/ADP ratio, which can be maintained by direct nucleotide channelling from mitochondria, and by SR-bound creatine kinase (CK)-catalysed phosphate-transfer from phosphocreatine. We hypothesized that SR calcium uptake supported by mitochondrial direct nucleotide channelling, but not bound CK, depends on the juxtaposition of these organelles. To test this, we studied a well-described model of cytoarchitectural disorganization, the muscle LIM protein (MLP)-null mouse heart. Subcellular organization was characterized using electron microscopy, and mitochondrial, SR and myofibrillar function were assessed in saponin-permeabilized fibres by measuring respiration rates and caffeine-induced tension transients. MLP-null hearts had fewer, less-tightly packed intermyofibrillar mitochondria, and more subsarcolemmal mitochondria. The apparent mitochondrial Km for ADP was significantly lower in the MLP-null heart than in control (175 +/- 15 and 270 +/- 33 microM, respectively), indicating greater ADP accessibility, although maximal respiration rate, mitochondrial content and total CK activity were unaltered. Active tension in the myofibres of MLP-null mice was 54% lower than in controls (39 +/- 3 and 18 +/- 1 mN mm(-2), respectively), consistent with cytoarchitectural disorganization. SR calcium loading in the myofibres of MLP-null mice was similar to that in control myofibres when energy support was provided via Bound CK, but approximately 36% lower than controls when energy support was provided by mitochondrial (P < 0.05). Mitochondrial support for SR calcium uptake was also specifically decreased in the desmin-null heart, which is another model of cytoarchitectural perturbation. Thus, despite normal oxidative capacity, direct nucleotide channelling to the SR was impaired in MLP deficiency, concomitant with looser mitochondrial packing and increased nucleotide accessibility to this organelle. Changes in cytoarchitecture may therefore impair subcellular energy transfer and contribute to energetic and contractile dysfunction.

This paper aims at characterizing the mechanical behavior of two human anatomical structures, namely the tongue and the cheek. For this, an indentation experiment was provided, by measuring the mechanical response of tongue and cheek tissues removed from the fresh cadaver of a 74 years old woman. Non-linear relationships were observed between the force applied to the tissues and the corresponding displacements. To infer the mechanical constitutive laws from these measurements, a Finite Element (FE) Analysis was provided. This analysis aimed at simulating the indentation experiment. An optimization process was used to determine the FE constitutive laws that provided the non-linear force/displacements observed during the indentation experiments. The tongue constitutive law was used for simulations provided by a 3D FE biomechanical model of the human tongue. This dynamical model was designed to study speech production. Given a set of tongue muscular commands which levels correspond to the force classically measured during speech production, the FE model successfully simulated the main tongue movements observed during speech data.

Under iron-limiting conditions, Pseudomonas aeruginosa secretes a fluorescent siderophore called pyoverdin (PaA), which, after complexing iron, is transported back into the cells via its outer membrane receptor FpvA. The recent finding that all FpvA receptors on the bacterial cell surface are loaded with iron-free PaA under iron limiting conditions has raised questions about the mechanism by which P. aeruginosa transports efficiently iron. We used [(3)H]PaA' [(55)Fe]PaA-Fe, and a kinetically stable chromium-PaA complex to show that iron loading of the receptor occurs through a siderophore displacement mechanism in vivo. Moreover, the fluorescence properties of iron-free PaA revealed that, after PaA-Fe uptake and dissociation, the PaA molecule is recycled into the extracellular medium. We used fluorescence resonance energy transfer (FRET) between the PaA chromophore and the FpvA tryptophans in vivo to monitor the kinetics of PaA displacement by PaA-Fe at the cell surface, the dissociation of iron from the siderophore, and the recycling of PaA back to the receptor on the outer membrane of the bacteria in real time. The loading status of FpvA (PaA versus PaA-Fe) was shown to depend on the relative concentration of the two forms of pyoverdin in the growth medium.

Several G protein-coupled receptors have been shown to exist as homo-and hetero-oligomeric complexes in living cells. However, the link between ligand-induced receptor activation and its oligomerization state as well as the proportion of the total receptor population that can engage in oligomeric complexes remain open questions. Here, the closely related human MT1 and MT2 melatonin receptors (MT1R, MT2R) were used to address these issues. Bioluminescence resonance energy transfer (BRET) experiments in living HEK 293 cells revealed that these receptors form homo- and hetero-oligomers. Constitutive energy transfer was observed for all receptor combinations at physiological expression levels and could be detected in single cell BRET experiments. Inhibition of the energy transfer by dilution of the BRET partners identified MT1R and MT2R dimers as the predominant receptor species, and this oligomerization state did not change upon agonist and antagonist binding. Agonists, neutral antagonists, and inverse agonists all promoted increases in BRET values for MT2R but not for MT1R homodimers in living cells and isolated plasma membranes. This indicates that no correlation could be inferred between the receptor activation state and the dimerization state of the receptor. This also suggests that ligand-promoted BRET increases represent specific ligand-induced conformational changes of pre-existing dimers rather then increased dimerization. The observation that ligands favored the energy transfer within the hetero-oligomer from MT1R to MT2R but not in the reverse orientation, from MT2R to MT1R, supports this view.

International audience; The three-dimensional structures of the two L-peptides, H-CGGIRGERA-OH, called L(A), and H-CGGIRGERG-OH, called L(G), corresponding or close to the IRGERA sequence present in the C-terminal region (residues 130-135) of histone H3, and their retro-inverso analogues HO-mAreGriGGC-NH2, called RI(mA), and HO-mGreGriGGC-NH2, called RI(mG), have been studied by two-dimensional 1H NMR and molecular dynamics calculations in association with a monoclonal antibody generated against L(A). At 25 degrees C, the affinity constants of the monoclonal antibody with respect to RI(mA) and RI(mG) were 75- and 270-fold higher than those measured with the homologous L(A) and L(G) peptides, respectively. Due to the spontaneous epimerization of the mA malonic residue, RI(mA) gave rise to two sets of resonances. With regard to the NH amide region, one set was similar to that for RI(mG) while the second was similar to those for the parent L-peptides L(A) and L(G). The antibody-bound conformations of the two couples of L- and retro-inverso peptides have been analyzed using molecular modeling calculations based on the transferred NOE interproton distances. Folded structures appeared in both cases with a type II' beta-turn in the parent GGIR sequence and a type I' beta-turn in the retro-inverso reGr sequence.

The purpose of this study is to investigate theoretically which intracellular factors may be important for regulation of mitochondrial respiration in working heart cells in vivo. We have developed a model that describes quantitatively the published experimental data on dependence of the rate of oxygen consumption and metabolic state of working isolated perfused rat heart on workload over its physiological range (Williamson JR, Ford G, Illingworth J, Safer B. Circ Res 38, Suppl I, I39–I51, 1976). Analysis of this model shows that for phosphocreatine, creatine, and ATP the equilibrium assumption is an acceptable approximation with respect to their diffusion in the intracellular bulk water phase. However, the ADP concentration changes in the contraction cycle in a nonequilibrium workload-dependent manner, showing the existence of the intracellular concentration gradients. The model shows that workload-dependent alteration of ADP concentration in the compartmentalized creatine kinase system may be taken, together with the changes in Piconcentration, to be among the major components of the metabolic feedback signal for regulation of respiration in muscle cells.

Under iron limitation, Pseudomonas aeruginosa secretes a fluorescent siderophore called pyoverdin, which, after complexing iron, is transported back into the cell via its outer membrane receptor FpvA. Previous studies demonstrated co-purification of FpvA with iron-free PaA and reported similar binding affinities of iron-free pyoverdin and ferric-pyoverdin to purified FpvA. The fluorescence resonance energy transfer between iron-free PaA and the FpvA receptor here reveals the existence of an FpvA-pyoverdin complex in P. aeruginosa in vivo, suggesting that the pyoverdin-loaded FpvA is the normal state of the receptor in the absence of iron. Using tritiated ferric-pyoverdin, it is shown that iron-free PaA binds to the outer membrane but is not taken up into the cell, and that in vitro and, presumably, in vivo ferric-pyoverdin displaces the bound iron-free pyoverdin on FpvA-PaA to form FpvA-PaA-Fe complexes. In vivo, the kinetics of formation of this FpvA-PaA-Fe complex are more than two orders of magnitude faster than in vitro and depend on the presence of TonB. In P. aeruginosa, two tonB genes have been identified (tonB1 and tonB2). TonB1 is directly involved in ferric-pyoverdin uptake, and TonB2 seems to be able partially to replace TonB1 in its role in iron acquisition. However, no effect of TonB1 or TonB2 on the apparent affinity of free pyoverdin to FpvA was observed, and a 17-fold difference was measured between the affinities of the two forms of pyoverdin (PaA and PaA-Fe) to FpvA in the absence of TonB1 or TonB2. The mechanism of iron uptake in P. aeruginosa via the pyoverdin pathway is discussed in view of these new findings.

A recent article in The Journal of Physiology by Gueguen et al. (2005) shows that an efficient metabolic coupling between mitochondrial creatine kinase (mtCK) or adenylate kinase (AK2), and ADP rephosphorylation via mitochondrial respiration is tissue specific: it is functioning in skinned muscle of oxidative type I and type IIa but not in IIx type muscles, and this coupling can be modified by calcium. We would like to add some critical considerations which may contribute to solving some of discrepancies in this paper, and point out some methodological difficulties in studies of the functional coupling phenomenon. Calcium, ADP, AMP and creatine are known to act as important regulators of energy flux in muscle cells. High energy phosphates may be channelled out of mitochondria via direct ATP flux or by mtCK or AK2 via a phosphoryl-creatine (PCr) shuttle (Wallimann et al. 1992; Dzeja & Terzic, 2003; Saks et al. 2004). While all types of isolated mitochondria studied before show apparent Km (ADP) of 5–17 μm, this parameter is tissue specific in permeabilized cells in situ: Gueguen et al. (2005) showed that it is about the same in fast twitch muscle fibres of IIx type, but very high (212 μm) in slow twitch oxidative fibres of the type I and intermediate in the mixed types of fibres IIax and IIb where two apparent Km are observed. These results are in good agreement with earlier data (Veksler et al. 1995; Kuznetsov et al. 1996; Ventura-Clapier et al. 1998; Saks et al. 2004). Since the fibre diameter is usually bigger in fast glycolytic muscles, these data show very clearly the differences in the intracellular organization between different muscle types, and the very high apparent Km values are caused by specific local restrictions of the diffusion of ADP inside the type I oxidative fibres (Abraham et al. 2002; Vendelin et al. 2004). In their studies Gueguen et al. (2005) have made another remarkable observation: when the calcium concentration in the medium was elevated from 0.1 to 0.4 μm, the affinity of respiration for exogenous ADP was increased due to activation of actomyosin MgATPase. The increased affinity for exogenous ADP increased activation of respiration at submaximal ADP concentrations to the extent usually seen in the presence of creatine. Furthermore, calcium-induced activation of actomyosin ATPase also prevented the stimulation of respiration by creatine and AMP. The authors concluded from these results that mtCK and AK2 are no longer functionally coupled with mitochondrial respiration. This is a very surprising conclusion since under high work load, that is under elevated energy demand, the flux through the mtCK reaction was shown in vivo to increase significantly, e.g. during sea urchin sperm activation (Dorsten et al. 1997) and in muscle during increase of contraction frequency when directly assessed by the in vivo18O labelling technique (Pucar et al. 2001; Janssen et al. 2003), or alternatively, to decrease when demand was lowered (Joubert et al. 2002). In addition, calcium has been shown to strengthen the interaction between mtCK and voltage-dependent anion channels (VDAC) (Schlattner et al. 2001), which also would favour the formation of a VDAC–mtCK–adenine nucleotide translocase (ANT) multienzyme channelling complex, and thus facilitate the export of PCr from mitochondria. The experimental conditions described in the paper by Gueguen et al. (2005) are far from physiological conditions in the sense that the activating steady state level of calcium was continuously maintained at a high level and thus no relaxation was possible. Under these conditions, production of ATP by the activated mitochondrial respiration evidently results in hypercontraction of fibres, complete disturbance of myofibrillar architecture. This will also change the diffusion restrictions for ADP and results in a strong decrease of apparent Km for exogenous ADP (Andrienko et al. 2003). The rather artifactual system may explain the observations made under calcium addition. The fact that in the presence of vanadate, where the fibres are prevented from hypercontraction, calcium no longer ablates creatine-stimulated respiration (see Fig. 7) is direct proof that the observed phenomenon is related to supercontraction of the fibres, much more than to calcium itself. Under these conditions, exogenous ADP added already maximally activates respiration, and there will be no way for creatine to increase respiration further even if functional coupling is intact. For exactly the same reason, the very high apparent affinity of type II fibres for ADP makes it impossible to see the functional coupling between mtCK or AK2 and respiration from measurements at the fixed and relatively high ADP concentration of 0.1 mm (Fig. 5). To study functional coupling under these conditions, more sophisticated approach should be used (Moreadith & Jacobus, 1982). Clearly, metabolic microcompartments depend on the structural organization and integrity of the cells, and these considerations can no longer be ignored in studies of metabolic regulation of the muscle cell respiration (Schlattner & Wallimann, 2004).