Computational Method to Predict Mitochondrially Imported Proteins and their Targeting Sequences

Authors

  • Manuel G. Claros,

    Corresponding author
    1. Laboratoire de Génétique Moléculaire, CNRS URA 1302, Ecole Normale Supérieure, Paris, France
    2. Laboratorio de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Málaga, Spain
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  • Pierre Vincens

    1. Departement de Biologie, Ecole Normale Supérieure, Paris, France
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  • Supplementary material. Computational method to predict mitochondrially imported proteins and their targeting sequences. Table S1. Mitochondrial-targeting-sequence prediction of 18 mitochondrial proteins considered as ‘putative’ or ‘certain’. Table S2. Results of the prediction of chromosome III sequences made with two algorithms. Table S3. Mitochondrial ORF clustered along the yeast chromosomes. This information is available, on request, from the Editorial Office. Nine pages are available.

M. G. Claros, Laboratorio de Bioquímica y Biología Molecular, Facultad de Ciencias, Campus de Teatinos, E-29071 Málaga, Spain
Fax:+34 5 213 20 00.
E-mail:claros@uma.es or claros@cica.es

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.

Abbreviations.
DFM

discriminant function for mitochondrial proteins

ECS

Eisenberg's consensus scale

GES

Goldman, Engelman and Steitz scale

GvH1

Gunnar von Heijne scale

KD

Kyte and Doolittle scale

LDF

linear discriminant function

MTSL

mitochondrial-targeting-sequence localization

PCA

principal-component analysis

Ancillary