Computational Method to Predict Mitochondrially Imported Proteins and their Targeting Sequences

Abstract

Most of the proteins that are used in mitochondria are imported through the double membrane of the organelle. The information that guides the protein to mitochondria is contained in its sequence and structure, although no direct evidence can be obtained. In this article, discriminant analysis has been performed with 47 parameters and a large set of mitochondrial proteins extracted from the SwissProt database. A computational method that facilitates the analysis and objective prediction of mitochondrially imported proteins has been developed. If only the amino acid sequence is considered, 75-97% of the mitochondrial proteins studied have been predicted to be imported into mitochondria. Moreover, the existence of mitochondrial-targeting sequences is predicted in 76 -94 % of the analyzed mitochondrial precursor proteins. As a practical application, the number of unknown yeast open reading frames that might be mitochondrial proteins has been predicted, which revealed that many of them are clustered.

Duplication and Quadruplication of Arabidopsis thaliana Cysteinyl- and Asparaginyl-tRNA Synthetase Genes of Organellar Origin

“…Prediction programs suggested that this could be an organellar targeting sequence. MitoProt (Claros and Vincens 1996), searching for putative mitochondrial targeting sequences, strongly predicted (score of 0.97) a 53-amino acid N-terminal targeting peptide. ChloroP (Emanuelsson et al 1999), searching for chloroplast targeting sequences, predicted (score of 0.56) a 34-amino acid N-terminal targeting peptide.…”

Regulatory roles of vertebrate Nocturnin: insights and remaining mysteries

“…Mitochondrial localization is predicted for several NOCT orthologs. PSORTII [101,102], TargetP [103], and MitoProt [104] all predict mitochondrial localization of X. tropicalis, R. norvegicus, H. sapiens, M. musculus , and D. rerio NOCTA. TargetP and MitoProt predictions indicate that D. rerio NOCTB is likely to be mitochondrial; however, this conflicts with the nuclear localization predicted by PSORTII.…”

“…TargetP and MitoProt predictions indicate that D. rerio NOCTB is likely to be mitochondrial; however, this conflicts with the nuclear localization predicted by PSORTII. Neither TargetP nor MitoProt identify D. melanogaster or X. laevis NOCT as mitochondrial [103,104]. Although useful in predicting possible NOCT functions, these programs do not account for shuttling among subcellular compartments.…”

Overexpression, purification and assessment of cyclosporin binding of a family of cyclophilins and cyclophilin-like proteins of the human malarial parasite Plasmodium falciparum

“…The putative mitochondrial signal of PfCYP32 was further investigated since mitochondrial proteins of P. falciparum are very different from human mitochondrial proteins, making them attractive potential drug targets [33]. It was scanned for mitochondrial sequences with MitoProt [34], PlasMit [35] and PFM Pred [36]. All algorithms predicted PfCYP32 to be a mitochondrial protein.…”