No abstract is provided for this article.
In this concluding chapter the translocation machineries are compared, which are employed in different membrane systems to highlight their similarities and unique properties, depicting the Sec and Oxa1p translocation systems along with the Tat and peroxisomal pathway. This chapter puts forth a summary note by taking together the preceding chapters that described how proteins are transported across the bacterial plasma membrane, the endoplasmic reticulum (ER) membrane, the chloroplast thylakoid membrane, and how proteins are imported into mitochondria, chloroplasts, peroxisomes, and the nucleus. In chloroplast and bacteria, this is achieved by using the twin arginine translocation (Tat) translocase, comprising the TatA, TatB, TatC and TatE proteins. The Tat system is present in both the bacterial plasma membrane and the chloroplast thylakoid membrane. The Tom complex contains receptors that recognize the signal sequences of mitochondrial imported proteins. The field of protein targeting has come a long way since the pioneering studies by Günter Blobel and collaborators in the early 1970s. Literally, thousands of postdoc-years have gone into figuring out the complex targeting pathways and translocation mechanisms that have evolved to ship proteins within and between cells. And yet, we cannot claim to have a full, atomic-level understanding of even a single translocation process. Finally, this chapter concludes with a positive hope that there is certainly more to come!
No abstract is provided for this article.
No abstract is provided for this article.
No abstract is provided for this article.
We present a neural network based method (ChloroP) for identifying chloroplast transit peptides and their cleavage sites. Using cross‐validation, 88% of the sequences in our homology reduced training set were correctly classified as transit peptides or nontransit peptides. This performance level is well above that of the publicly available chloroplast localization predictor PSORT. Cleavage sites are predicted using a scoring matrix derived by an automatic motif‐finding algorithm. Approximately 60% of the known cleavage sites in our sequence collection were predicted to within 62 residues from the cleavage sites given in SWISS‐PROT. An analysis of 715 Arabidopsis thaliana sequences from SWISS‐PROT suggests that the ChloroP method should be useful for the identification of putative transit peptides in genome‐wide sequence data. The ChloroP predictor is available as a web‐server at http://www.cbs.dtu.dk/services/ChloroP/ .
No abstract is provided for this article.
Voltage-sensitive ion channels open and close in response to changes in transmembrane (TM) potential caused by the motion of the S4 voltage sensors. These sensors are α–helices that include four or more positively charged amino acids, most commonly arginine. The so-called paddle model, based on the high-resolution structure of the KvAP K + channel [Jiang, et al. (2003) Nature 423, 33–41], posits that the S4 sensors move within the membrane bilayer in response to TM voltage changes. Direct exposure of S4 sensors to lipid is contrary to the classical expectation that the dielectric contrast between the membrane hydrocarbon core and water presents an insurmountable energetic penalty to burial of electric charges. Nevertheless, recent experiments have shown that a helix with the sequence of KvAP S4 can be inserted across the endoplasmic reticulum membrane. To reconcile this result with the classical energetics argument, we have carried out a molecular dynamics simulation of an isolated TM S4 helix in a lipid bilayer. The simulation reveals a stabilizing hydrogen-bonded network of water and lipid phosphates around the arginines that reduces the effective thickness of the bilayer hydrocarbon core to ≈10Åinthe vicinity of the helix. It suggests that bilayer phospholipids can adapt locally to strongly perturbing protein elements, causing the phospholipids to become a structural extension of the protein.
No abstract is provided for this article.
Statistical analysis of lipoprotein and non-lipoprotein signal peptides reveals that the two classes differ significantly only in the region close to the signal peptidase cleavage site. This region is apolar and has the consensus sequence LA(G,A) decreases C in the lipoproteins, but is polar and has small, uncharged residues in positions -3 and -1 in the non-lipoproteins. A simple search for matches to the lipoprotein consensus cleavage site suffices to discriminate between the two groups with close to 100% reliability.
Cotranslational folding of small protein domains within the ribosome exit tunnel may be an important cellular strategy to avoid protein misfolding. However, the pathway of cotranslational folding has so far been described only for a few proteins, and therefore, it is unclear whether folding in the ribosome exit tunnel is a common feature for small protein domains. Here, we have analyzed nine small protein domains and determined at which point during translation their folding generates sufficient force on the nascent chain to release translational arrest by the SecM arrest peptide, both in vitro and in live E. coli cells. We find that all nine protein domains initiate folding while still located well within the ribosome exit tunnel.
Research on the targeting of proteins to the cytoplasmic membrane of E. coli has mainly focused on the so-called 'general secretory pathway' (GSP) which involves the Sec-proteins. Recently, evidence has been obtained for an alternative targeting pathway in E. coli which involves the signal recognition particle (SRP). The constituents of this SRP pathway in E. coli are homologous to those of the well-characterized eukaryotic SRP pathway, which is the main targeting pathway for both proteins translocated across and inserted into the endoplasmic reticulum membrane. However, until recently, no clear function could be assigned to the SRP in E. coli. New studies point to an important role of the E. coli SRP in the assembly of inner membrane proteins.
