Signal sequences model

A Model for the Initial Interactions of Signal Sequences with the... 

Wickner (1980) proposed an alternative mechanism of protein secretion, called the membrane trigger hypothesis. This model proposes that the signal sequence influences the precursor protein or a domain of the precursor to fold into a conformation that can spontaneously partition into the hydrophobic part of the bilayer. In prokaryotes, the membrane potential causes the protein to traverse the bilayer. The protein then regains a water-soluble conformation, and is expelled into the medium. Signal peptidase removes the signal sequence during or after this process. Thus, secretory proteins or domains are transported across the membrane posttranslationally without the aid of a proteinaceous secretory apparatus. An energy source, such as the membrane potential, is required for secretion. 

Exported proteins must cross a biological membrane, which is composed largely of lipids and proteins. Is the translocation site made of lipids or protein The membrane trigger hypothesis, the helical hairpin hypothesis, the domain model, and the model of Nesmayanova postulate that protein translocation occurs directly through the lipid bilayer and that no proteinaceous export site is necessary. Other proteins may be needed for recognition, and signal peptidase is required for removal of the signal sequence after export. Evidence for a lipid translocation site comes primarily from experiments in reconstituted export systems in Wickner s laboratory. It has been shown that the precursors of M13... 

Cleavage of the signal sequence in prokaryotes can occur either cotranslationally (Josefsson and Randall, 1981) or posttranslationally (Wu et al., 1983). Cleavage does not appear to be necessary for protein export, as mutants deficient in the cleavage of lipoprotein (Lin etal., 1978), MBP (Ryan et al., 1986a), or the M13 coat protein (Russell and Model, 1981) signal sequences are localized properly. 

All of these synthetic signal peptides, as well as peptides resembling the signal sequences of lysozyme and lipoprotein (Reddy and Nagaraj, 1985), became partially a helical in polyfluorinated alcohols [trifluoroethanol (TFE) and hexafluoroisopropanol (HFIP)], which are more hydrophobic than water and have been used as models for the membrane interior. These solvents promote the formation of intramolecular hydrogen bonds, and consequently induce a-helix formation. In... 

These experiments have not demonstrated that the conformational preferences of signal sequences are important to their ability to export proteins. To address this problem, we synthesized the family of E. coli K-receptor protein wild-type and mutant signal sequences (shown in Fig. 5 and described in Section III,H) and determined their conformations in various polar and apolar environments by CD (Briggs and Gierasch, 1984 Briggs, 1986). The solvents for these experiments included aqueous buffer and TFE, as described above. In addition, sodium dodecyl sulfate (SDS) micelles and phospholipid vesicles were used as membrane model systems. 

Once the synthetic machinery/nascent protein complex has been delivered to the membrane by SRP, it interacts with the membrane to form a translocation-competent species. It is in this process that we envision the signal sequence to play its most active and crucial part. In Section VIII we propose a model for the initial interactions of a signal sequence with the membrane. These interactions bring the signal sequence and nascent protein into the proper orientation for membrane binding and effect the initial entry of the protein into the membrane interior, readying it for the next step, which is translocation. 

In sum, the most active role played by the signal sequence in the export process appears to be in the second step, where the initial encounter of the export-competent assembly with the membrane occurs. In Section VIII we present a model for this encounter based largely on the biophysical studies presented in Section VI. 

Presented below and illustrated in Fig. 11 is a model for the events that occur in vivo when a signal sequence first encounters the membrane. 

A transgenic mouse model expressing a PrP mutant without the N-terminal signal sequence (cytoPrP) conclusively showed that targeting of PrP to the cytosolic compartment can be neurotoxic [49, 68]. Further evidence for a toxic potential of cytosolically localized PrP was provided by additional mouse models [67, 69], by several mammalian cell culture models [49, 70, 71], and by a yeast model [72]. 

There are some other weight functions that are used to search for functional signals, for example, weights can be received by optimization procedures such as perceptrons or neural networks [29, 30]. Also, different position-specific probability distributions p can be considered. One typical generalization is to use position-specific probability distributions pf of k-base oligonucleotides (instead of mononucleotides), another one is to exploit Markov chain models, where the probability to generate a particular nucleotide xt of the signal sequence depends on k0 1 previous bases (i.e. 

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