Here we define the molecular nature of the mitochondrial permeability transition pore (PTP), a key effector of cell death. The PTP is regulated by matrix cyclophilin D (CyPD), which also binds the lateral stalk of the F O F 1 ATP synthase. We show that CyPD binds the oligomycin sensitivity-conferring protein subunit of the enzyme at the same site as the ATP synthase inhibitor benzodiazepine 423 (Bz-423), that Bz-423 sensitizes the PTP to Ca 2+ like CyPD itself, and that decreasing oligomycin sensitivity-conferring protein expression by RNAi increases the sensitivity of the PTP to Ca 2+ . Purified dimers of the ATP synthase, which did not contain voltage-dependent anion channel or adenine nucleotide translocator, were reconstituted into lipid bilayers. In the presence of Ca 2+ , addition of Bz-423 triggered opening of a channel with currents that were typical of the mitochondrial megachannel, which is the PTP electrophysiological equivalent. Channel openings were inhibited by the ATP synthase inhibitor AMP-PNP (γ-imino ATP, a nonhydrolyzable ATP analog) and Mg 2+ /ADP. These results indicate that the PTP forms from dimers of the ATP synthase.

Electrostatics plays a fundamental role in virtually all processes involving biomolecules in solution. The Poisson-Boltzmann equation constitutes one of the most fundamental approaches to treat electrostatic effects in solution. The theoretical basis of the Poisson-Boltzmann equation is reviewed and a wide range of applications is presented, including the computation of the electrostatic potential at the solvent-accessible molecular surface, the computation of encounter rates between molecules in solution, the computation of the free energy of association and its salt dependence, the study of pKa shifts and the combination with classical molecular mechanics and dynamics. Theoretical results may be used for rationalizing or predicting experimental results, or for suggesting working hypotheses. An ever-increasing body of successful applications proves that the Poisson-Boltzmann equation is a useful tool for structural biology and complementary to other established experimental and theoretical methodologies.

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EPAC is a cAMP-dependent guanine nucleotide exchange factor that serves as a prototypical molecular switch for the regulation of essential cellular processes. Although EPAC activation by cAMP has been extensively investigated, the mechanism of EPAC autoinhibition is still not fully understood. The steric clash between the side chains of two conserved residues, L273 and F300 in EPAC1, has been previously shown to oppose the inactive-to-active conformational transition in the absence of cAMP. However, it has also been hypothesized that autoinhibition is assisted by entropic losses caused by quenching of dynamics that occurs if the inactive-to-active transition takes place in the absence of cAMP. Here, we test this hypothesis through the comparative NMR analysis of several EPAC1 mutants that target different allosteric sites of the cAMP-binding domain (CBD). Using what to our knowledge is a novel projection analysis of NMR chemical shifts to probe the effect of the mutations on the autoinhibition equilibrium of the CBD, we find that whenever the apo/active state is stabilized relative to the apo/inactive state, dynamics are consistently quenched in a conserved loop (β2-β3) and helix (α5) of the CBD. Overall, our results point to the presence of conserved and nondegenerate determinants of CBD autoinhibition that extends beyond the originally proposed L273/F300 residue pair, suggesting that complete activation necessitates the simultaneous suppression of multiple autoinhibitory mechanisms, which in turn confers added specificity for the cAMP allosteric effector.

Dialysis-related amyloidosis is characterized by the deposition of insoluble fibrils of ␤ 2 -microglobulin (␤ 2 -m) in the musculoskeletal system. Atomic force microscopy inspection of ex vivo amyloid material reveals the presence of bundles of fibrils often associated to collagen fibrils. Aggregation experiments were undertaken in vitro with the aim of reproducing the physiopathological fibrillation process. To this purpose, atomic force microscopy, fluorescence techniques, and NMR were employed. We found that in temperature and pH conditions similar to those occurring in periarticular tissues in the presence of flogistic processes, ␤ 2 -m fibrillogenesis takes place in the presence of fibrillar collagen, whereas no fibrils are obtained without collagen. Moreover, the morphology of ␤ 2 -m fibrils obtained in vitro in the presence of collagen is extremely similar to that observed in the ex vivo sample. This result indicates that collagen plays a crucial role in ␤ 2 -m amyloid deposition under physiopathological conditions and suggests an explanation for the strict specificity of dialysis-related amyloidosis for the tissues of the skeletal system. We hypothesize that positively charged regions along the collagen fiber could play a direct role in ␤ 2 -m fibrillogenesis. This hypothesis is sustained by aggregation experiments performed by replacing collagen with a poly-L-lysine-coated mica surface. As shown by NMR measurements, no similar process occurs when poly-L-lysine is dissolved in solution with ␤ 2 -m. Overall, the findings are consistent with the estimates resulting from a simplified collagen model whereby electrostatic effects can lead to high local concentrations of oppositely charged species, such as ␤ 2 -m, that decay on moving away from the fiber surface.The deposition of ␤ 2 -microglobulin (␤ 2 -m) 2 into amyloid fibrils is the hallmark of dialysis-related amyloidosis (DRA), a disease arising as a complication of long-term hemodialysis. ␤ 2 -m is a 99-residue protein (molecular mass 11.7 kDa) that represents the light chain of the major histocompatibility complex class I (MHCI), an integral membrane protein involved in the immune response. As a result of normal MHCI catabolism, ␤ 2 -m is released in the serum from the cell surface and carried to the kidney for clearance. In the presence of kidney failure, the concentration of free circulating ␤ 2 -m can increase by up to 50-fold; the persistent increase in ␤ 2 -m concentration results in amyloid deposition, preferentially localized in the musculoskeletal system. The accumulation of ␤ 2 -m deposits has been shown to cause arthralgias, destructive osteoarthropathies, and carpal tunnel syndrome (1). Although a high concentration of ␤ 2 -m is a necessary condition for the onset of the disease, there is not a strict correlation between the disease severity and ␤ 2 -m levels (2), suggesting that other factors might be involved in ␤ 2 -m amyloid deposition.The aggregation process of ␤ 2 -m has been the object of extensive investigation for many years. Severa...