No abstract is provided for this article.
No abstract is provided for this article.
No abstract is provided for this article.
Since high-resolution structural data are still scarce, different kinds of theoretical structure prediction algorithms are of major importance in membrane protein biochemistry. But how well do the current prediction methods perform? Which structural features can be predicted and which cannot? And what can we expect in the next few years?
No abstract is provided for this article.
This chapter reviews the characteristics of mitochondrial targeting peptides (mTPs) defined by statistical and experimental studies and discusses their use for predicting the presence of mTPs in protein sequences. Most methods for mTP prediction focus on the amino terminus of possible mitochondrial proteins. However, other portions of proteins also contribute to the import process. It is determined that C-terminal features of the small subunit of Rubisco modulate import of its precursor into chloroplasts. Some experimental evidences are provided for the existence of a cotranslational pathway for protein import into mitochondria. It has been demonstrated that the mTP is involved in the regulation of ribosome binding to the mitochondrial outer membrane. This import pathway may require additional, hitherto unknown mTP features. Thus, improved mTP prediction tools may have to account for features of the mature protein, rather than focusing only on the N-terminal parts of the precursor.
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We have analyzed the amino acid distribution in seven nuclearly encoded and five mitochondrially encoded inner membrane proteins with experimentally well characterized topologies. The mitochondrially encoded proteins conform to the ‘positive inside’ rule, i.e. they have many more positively charged residues in their non‐translocated as compared to translocated domains. However, most of the nuclearly encoded proteins do not show such a bias but instead have a surprisingly skewed distribution of Glu residues with an almost ten times higher frequency in the intermembrane space than in the matrix domains. These findings suggest that some, but possibly not all, nuclearly encoded inner membrane proteins may insert into the membrane by a mechanism that does not depend on the distribution of positively charged amino acids.
A comparative study of three kinds of eukaryotic N-terminal topogenic sequences, viz signal peptides, N-terminal transmembrane anchors, and mitochondrial targeting sequences, suggests: (1) that the sign of the N-terminal charge might influence the orientation of an N-terminal hydrophobic segment relative to the membrane and give rise to N-terminally anchored proteins with their main mass exposed either on the cytosolic or extra-cytosolic side of the membrane; and (2) that N-terminal transmembrane segments in mitochondrial targeting sequences have a relatively low overall hydrophobicity, probably in order to avoid being recognized by the endoplasmic reticulum export machinery.
No abstract is provided for this article.
No abstract is provided for this article.
A number of signal sequences, prokaryotic as well as eukaryotic, have been analyzed in terms of gross amino acid composition and hydrophobicity. It is shown that the amino acid composition of the hydrophobic core can be well reproduced in a computer simulation of signal sequence 'evolution' with selection operating on the mean hydrophobicity of the sequence and the non-occurrence of charged residues. The calculated hydrophobicities are interpreted in terms of a model in which the hydrophobic part of the signal sequence partitions directly into the membrane interior, thereby making further translocation of the growing nascent chain possible.
