A mechanistic view of mitochondrial death decision pores.

Mitochondria increase their outer and inner membrane permeability to solutes, protons and metabolites in response to a variety of extrinsic and intrinsic signaling events. The maintenance of cellular and intraorganelle ionic homeostasis, particularly for Ca2+, can determine cell survival or death. Mitochondrial death decision is centered on two processes: inner membrane permeabilization, such as that promoted by the mitochondrial permeability transition pore, formed across inner membranes when Ca2+ reaches a critical threshold, and mitochondrial outer membrane permeabilization, in which the pro-apoptotic proteins BID, BAX, and BAK play active roles. Membrane permeabilization leads to the release of apoptogenic proteins: cytochrome c, apoptosis-inducing factor, Smac/Diablo, HtrA2/Omi, and endonuclease G. Cytochrome c initiates the proteolytic activation of caspases, which in turn cleave hundreds of proteins to produce the morphological and biochemical changes of apoptosis. Voltage-dependent anion channel, cyclophilin D, adenine nucleotide translocase, and the pro-apoptotic proteins BID, BAX, and BAK may be part of the molecular composition of membrane pores leading to mitochondrial permeabilization, but this remains a central question to be resolved. Other transporting pores and channels, including the ceramide channel, the mitochondrial apoptosis-induced channel, as well as a non-specific outer membrane rupture may also be potential release pathways for these apoptogenic factors. In this review, we discuss the mechanistic models by which reactive oxygen species and caspases, via structural and conformational changes of membrane lipids and proteins, promote conditions for inner/outer membrane permeabilization, which may be followed by either opening of pores or a rupture of the outer mitochondrial membrane.

A mechanistic view of mitochondrial death decision pores

Mitochondria increase their outer and inner membrane permeability to solutes, protons and metabolites in response to a variety of extrinsic and intrinsic signaling events. The maintenance of cellular and intraorganelle ionic homeostasis, particularly for Ca2+, can determine cell survival or death. Mitochondrial death decision is centered on two processes: inner membrane permeabilization, such as that promoted by the mitochondrial permeability transition pore, formed across inner membranes when Ca2+ reaches a critical threshold, and mitochondrial outer membrane permeabilization, in which the pro-apoptotic proteins BID, BAX, and BAK play active roles. Membrane permeabilization leads to the release of apoptogenic proteins: cytochrome c, apoptosis-inducing factor, Smac/Diablo, HtrA2/Omi, and endonuclease G. Cytochrome c initiates the proteolytic activation of caspases, which in turn cleave hundreds of proteins to produce the morphological and biochemical changes of apoptosis. Voltage-dependent anion channel, cyclophilin D, adenine nucleotide translocase, and the pro-apoptotic proteins BID, BAX, and BAK may be part of the molecular composition of membrane pores leading to mitochondrial permeabilization, but this remains a central question to be resolved. Other transporting pores and channels, including the ceramide channel, the mitochondrial apoptosis-induced channel, as well as a non-specific outer membrane rupture may also be potential release pathways for these apoptogenic factors. In this review, we discuss the mechanistic models by which reactive oxygen species and caspases, via structural and conformational changes of membrane lipids and proteins, promote conditions for inner/outer membrane permeabilization, which may be followed by either opening of pores or a rupture of the outer mitochondrial membrane.

CaSPredictor: a new computer-based tool for caspase substrate prediction.

MOTIVATION: In vitro studies have shown that the most remarkable catalytic features of caspases, a family of cysteineproteases, are their stringent specificity to Asp (D) in the S1 subsite and at least four amino acids to the left of scissile bound. However, there is little information about the substrate recognition patterns in vivo. The prediction and characterization of proteolytic cleavage sites in natural substrates could be useful for uncovering these structural relationships. RESULTS: PEST-like sequences rich in the amino acids Ser (S), Thr (T), Pro (P), Glu or Asp (E/D), including Asn (N) and Gln (Q) are adjacent structural/sequential elements in the majority of cleavage site regions of the natural caspase substrates described in the literature, supporting its possible implication in the substrate selection by caspases. We developed CaSPredictor, a software which incorporated a PEST-like index and the position-dependent amino acid matrices for prediction of caspase cleavage sites in individual proteins and protein datasets. The program predicted successfully 81% (111/137) of the cleavage sites in experimentally verified caspase substrates not annotated in its internal data file. Its accuracy and confidence was estimated as 80% using ROC methodology. The program was much more efficient in predicting caspase substrates when compared with PeptideCutter and PEPS software. Finally, the program detected potential cleavage sites in the primary sequences of 1644 proteins in a dataset containing 9986 protein entries. AVAILABILITY: Requests for software should be made to Dr José E. Belizário SUPPLEMENTARY INFORMATION: Supplementary information is available for academic users at site http://icb.usp.br/~farmaco/Jose/CaSpredictorfiles.