Hydrophobic moment drives penetration of bacterial membranes by transmembrane peptides

With antimicrobial resistance (AMR) remaining a persistent and growing threat to human health worldwide, membrane-active peptides are gaining traction as an alternative strategy to overcome the issue. Membrane-embedded multi-drug resistant (MDR) efflux pumps are a prime target for membrane-active peptides, as they are a well-established contributor to clinically relevant AMR infections. Here, we describe a series of transmembrane peptides (TMs) to target the oligomerization motif of the AcrB component of the AcrAB-TolC MDR efflux pump from Escherichia coli. These peptides contain an N-terminal acetyl-A-(Sar)3 (sarcosine; N-methylglycine) tag and a C-terminal lysine tag-a design strategy our lab has utilized to improve the solubility and specificity of targeting for TMs previously. While these peptides have proven useful in preventing AcrB-mediated substrate efflux, the mechanisms by which these peptides associate with and penetrate the bacterial membrane remained unknown. In this study, we have shown peptide hydrophobic moment (μH)-the measure of concentrated hydrophobicity on one face of a lipopathic α-helix-drives bacterial membrane permeabilization and depolarization, likely through lateral-phase separation of negatively-charged POPG lipids and the disruption of lipid packing. Our results show peptide μH is an important consideration when designing membrane-active peptides and may be the determining factor in whether a TM will function in a permeabilizing or non-permeabilizing manner when embedded in the bacterial membrane.

Disrupting GPCR Complexes with Smart Drug-like Peptides

G protein-coupled receptors (GPCRs) are a superfamily of proteins classically described as monomeric transmembrane (TM) receptors. However, increasing evidence indicates that many GPCRs form higher-order assemblies made up of monomers pertaining to identical (homo) or to various (hetero) receptors. The formation and structure of these oligomers, their physiological role and possible therapeutic applications raise a variety of issues that are currently being actively explored. In this context, synthetic peptides derived from TM domains stand out as powerful tools that can be predictably targeted to disrupt GPCR oligomers, especially at the interface level, eventually impairing their action. However, despite such potential, TM-derived, GPCR-disrupting peptides often suffer from inadequate pharmacokinetic properties, such as low bioavailability, a short half-life or rapid clearance, which put into question their therapeutic relevance and promise. In this review, we provide a comprehensive overview of GPCR complexes, with an emphasis on current studies using GPCR-disrupting peptides mimicking TM domains involved in multimerization, and we also highlight recent strategies used to achieve drug-like versions of such TM peptide candidates for therapeutic application.

Transmembrane Peptides as Inhibitors of Protein-Protein Interactions: An Efficient Strategy to Target Cancer Cells?

Cellular functions are regulated by extracellular signals such as hormones, neurotransmitters, matrix ligands, and other chemical or physical stimuli. Ligand binding on its transmembrane receptor induced cell signaling and the recruitment of several interacting partners to the plasma membrane. Nowadays, it is well-established that the transmembrane domain is not only an anchor of these receptors to the membrane, but it also plays a key role in receptor dimerization and activation. Indeed, interactions between transmembrane helices are associated with specific biological activity of the proteins as cell migration, proliferation, or differentiation. Overexpression or constitutive dimerization (due notably to mutations) of these transmembrane receptors are involved in several physiopathological contexts as cancers. The transmembrane domain of tyrosine kinase receptors as ErbB family proteins (implicated in several cancers as HER2 in breast cancer) or other receptors as Neuropilins has been described these last years as a target to inhibit their dimerization/activation using several strategies. In this review, we will focus on the strategy which consists in using peptides to disturb in a specific manner the interactions between transmembrane domains and the signaling pathways (induced by ligand binding) of these receptors involved in cancer. This approach can be extended to inhibit other transmembrane protein dimerization as neuraminidase-1 (the catalytic subunit of elastin receptor complex), Discoidin Domain Receptor 1 (a tyrosine kinase receptor activated by type I collagen) or G-protein coupled receptors (GPCRs) which are involved in cancer processes.

High-resolution structures of a heterochiral coiled coil

Interactions between polypeptide chains containing amino acid residues with opposite absolute configurations have long been a source of interest and speculation, but there is very little structural information for such heterochiral associations. The need to address this lacuna has grown in recent years because of increasing interest in the use of peptides generated from d amino acids (d peptides) as specific ligands for natural proteins, e.g., to inhibit deleterious protein-protein interactions. Coiled-coil interactions, between or among α-helices, represent the most common tertiary and quaternary packing motif in proteins. Heterochiral coiled-coil interactions were predicted over 50 years ago by Crick, and limited experimental data obtained in solution suggest that such interactions can indeed occur. To address the dearth of atomic-level structural characterization of heterochiral helix pairings, we report two independent crystal structures that elucidate coiled-coil packing between l- and d-peptide helices. Both structures resulted from racemic crystallization of a peptide corresponding to the transmembrane segment of the influenza M2 protein. Networks of canonical knobs-into-holes side-chain packing interactions are observed at each helical interface. However, the underlying patterns for these heterochiral coiled coils seem to deviate from the heptad sequence repeat that is characteristic of most homochiral analogs, with an apparent preference for a hendecad repeat pattern.

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

Thousands of small Open Reading Frames (smORFs) with the potential to encode small peptides of fewer than 100 amino acids exist in our genomes. However, the number of smORFs actually translated, and their molecular and functional roles are still unclear. In this study, we present a genome-wide assessment of smORF translation by ribosomal profiling of polysomal fractions in Drosophila. We detect two types of smORFs bound by multiple ribosomes and thus undergoing productive translation. The ‘longer’ smORFs of around 80 amino acids resemble canonical proteins in translational metrics and conservation, and display a propensity to contain transmembrane motifs. The ‘dwarf’ smORFs are in general shorter (around 20 amino-acid long), are mostly found in 5′-UTRs and non-coding RNAs, are less well conserved, and have no bioinformatic indicators of peptide function. Our findings indicate that thousands of smORFs are translated in metazoan genomes, reinforcing the idea that smORFs are an abundant and fundamental genome component.

DOI:http://dx.doi.org/10.7554/eLife.03528.001

To produce a protein, a stretch of DNA must first be transcribed to produce a molecule of messenger RNA (mRNA). The genetic information copied from the DNA is then read three letters at a time, in groups called codons. Each codon either encodes a particular amino acid to be added into a protein or provides further instructions: ‘start codons’ mark the beginning of a protein; ‘stop codons’ mark its end. The DNA between these two points is called an open reading frame (or ORF)—however, not all ORFs produce proteins.

Most proteins are made of several hundred amino acids, but the genomes of animals contain thousands of ORFs that would generate much smaller proteins made of fewer than 100 amino acids, if they were translated. It is, however, unclear how many of these small ORFs are converted into mRNA molecules and functional proteins.

Ribosomes are large molecular machines that translate the code in mRNA molecules and join together the appropriate amino acids in the right order to make a protein. Ribosome profiling is a technique that identifies which mRNA molecules are translated into proteins by determining the sequences of all the mRNA molecules bound to ribosomes at a particular moment. The mRNA sequences can then be compared with the sequence of the whole genome to work out which ORFs they correspond to. Ribosome profiling has been used to detect translated small ORFs, but the method yields a relatively high false positive rate as some mRNAs can bind to ribosomes without being translated.

To better detect small protein-producing ORFs, Aspden et al. developed a technique based on ribosome profiling called Poly-Ribo-Seq. The method takes advantage of the fact that during active translation, clusters of multiple ribosomes, called polysomes, bind mRNAs. Poly-Ribo-Seq isolates these polysomes and determines the sequence bound by each of the ribosomes, thereby reducing the number of false positives.

Applying Poly-Ribo-Seq to cells from the fruit fly Drosophila allowed Aspden et al. to identify two types of short ORF. The first type codes for proteins that are around 80 amino acids long and are translated with the same efficiency as larger ORFs. The sequences of these ORFs are found in other species, match at least in part sequences of known functional ORFs, and the proteins produced are found in specific locations inside cells. These small proteins may contribute to membrane integrity or function. Together, these properties suggest that these mRNAs create functional small proteins.

The second pool consists of very small ORFs (‘dwarf smORFs’) that code for around 20 amino acids, which are not translated so often and do not show many similarities with other species.

As the findings of Aspden et al. suggest that a large fraction of Drosophila small ORFs are translated into proteins, the next challenge will be to determine the roles of these small proteins in cells.

DOI:http://dx.doi.org/10.7554/eLife.03528.002