Protein-inspired antibiotics active against vancomycin- and daptomycin-resistant bacteria.

The public health threat posed by a looming 'post-antibiotic' era necessitates new approaches to antibiotic discovery. Drug development has typically avoided exploitation of membrane-binding properties, in contrast to nature's control of biological pathways via modulation of membrane-associated proteins and membrane lipid composition. Here, we describe the rejuvenation of the glycopeptide antibiotic vancomycin via selective targeting of bacterial membranes.

Effects of the oncogenic V(664)E mutation on membrane insertion, structure, and sequence-dependent interactions of the Neu transmembrane domain in micelles and model membranes: an integrated biophysical and simulation study.

Receptor tyrosine kinases bind ligands such as cytokines, hormones, and growth factors and regulate key cellular processes, including cell division. They are also implicated in the development of many types of cancer. One such example is the Neu receptor tyrosine kinase found in rats (homologous to the human ErbB2 protein), which can undergo a valine to glutamic acid (V(664)E) mutation at the center of its α-helical transmembrane domain.

Helical membrane peptides to modulate cell function.

In recent years there has been an abundance of research into the potential of helical peptides to influence cell function. These peptides have been used to achieve a variety of different outcomes from cell repair to cell death, depending upon the peptide sequence and the nature of its interactions with cell membranes and membrane proteins. In this critical review, we summarise several mechanisms by which helical peptides, acting as either transporters, inhibitors, agonists or antibiotics, can have significant effects on cell membranes and can radically affect the internal mechanisms of the cell.

Sequence-dependent oligomerization of the Neu transmembrane domain suggests inhibition of "conformational switching" by an oncogenic mutant.

Membrane-spanning epidermal growth factor receptor ErbB2 is of key importance in cell division, in which a dimeric complex of the protein is responsible for tyrosine kinase activation following ligand binding. The rat homologue of this receptor (Neu) is prone to a valine to glutamic acid mutation in the transmembrane domain (TM), resulting in permanent activation and oncogenesis. In this study, the TM domains of Neu and the corresponding oncogenic mutant Neu*, which contains a V to E mutation at position 664 in the TM domain, have been analyzed to improve our understanding of the structural effects of the oncogenic V(664)E mutation.

Solid-state 17O NMR spectroscopy of a phospholemman transmembrane domain protein: implications for the limits of detecting dilute 17O sites in biomaterials.

The 17O-'diluted' glycine-14 sites in a phospholemman (PLM) transmembrane domain protein are characterized by solid-state 17O NMR spectroscopy. The PLM transmembrane domain is an alpha-helical tetramer unit of four 28-residue peptides and is rigidly embedded in a bilayer where each alpha-helix has an average tilt of 7.3 degrees against the membrane normal.

Transmembrane protein models based on high-throughput molecular dynamics simulations with experimental constraints.

Elucidating the structure of transmembrane proteins domains with high-resolution methods is a difficult and sometimes impossible task. Here, we explain the method of combining a limited amount of experimental data with automated high-throughput molecular dynamics (MD) simulations of alpha-helical transmembrane bundles in an explicit lipid bilayer/water environment. The procedure uses a systematic conformational search of the helix rotation with experimentally constrained MDs simulations.

Phospholemman transmembrane structure reveals potential interactions with Na+/K+-ATPase.

Phospholemman (PLM) is a 72-residue bitopic cardiac transmembrane protein, which acts as a modulator of the Na(+)/K(+)-ATPase and the Na(+)/Ca(2+) exchanger and possibly forms taurine channels in nonheart tissue. This work presents a high resolution structural model obtained from a combination of site-specific infrared spectroscopy and experimentally constrained high throughput molecular dynamics (MD) simulations. Altogether, 37 experimental constraints, including nine long range orientational constraints, have been used during MD simulations in an explicit lipid bilayer/water system.

The transmembrane domain of the oncogenic mutant ErbB-2 receptor: a structure obtained from site-specific infrared dichroism and molecular dynamics.

ErbB-2 is a member of the family of epidermal growth factor receptors, which shows an oncogenic mutation in the rat gene neu, Val664Glu in the transmembrane domain that causes permanent dimerisation and subsequently leads to uncontrollable cell division and tumour formation. We have obtained the alpha-helical structure of the mutant transmembrane domain dimer experimentally with site-specific infrared dichroism (SSID) based on six transmembrane peptides with 13C18O carbonyl group-labelled residues. The derived orientational data indicate a local helix tilt ranging from 28(+/-6) degrees to 22(+/-4) degrees.

Secondary structure, orientation, and oligomerization of phospholemman, a cardiac transmembrane protein.

Human phospholemman (PLM) is a 72-residue protein, which is expressed at high density in the cardiac plasma membrane and in various other tissues. It forms ion channels selective for K+, Cl-, and taurine in lipid bilayers and colocalizes with the Na+/K+-ATPase and the Na+/Ca2+-exchanger, which may suggest a role in the regulation of cell volume. Here we present the first structural data based on synthetic peptides representing the transmembrane domain of PLM.

Systematic molecular dynamics searching in a lipid bilayer: application to the glycophorin A and oncogenic ErbB-2 transmembrane domains.

Molecular dynamics (MD) simulations of proteins in a lipid bilayer environment are usually undertaken with one or a few starting structures. Here we report a search protocol for systematically exploring the possible interactions in helical bundle transmembrane proteins, a frequently occurring structural motif. The search protocol correctly identifies the experimentally known structure of the dimeric human glycophorin A transmembrane domain as the lowest energy structure among five different models without any prior assumptions, whilst an identical in vacuo search fails to identify the correct structure.

Conformational flexibility of the peptide hormone ghrelin in solution and lipid membrane bound: a molecular dynamics study.

Human ghrelin is a peptide hormone of 28 aminoacid residues, in which the Ser3 is modified by an octanoyl group. Ghrelin has a major role in the energy metabolism of the human body stimulating growth hormone release as well as food intake. Here we perform molecular dynamics simulations in explicit water and in a DMPC-lipid bilayer/water system in order to structurally characterize this highly flexible peptide and its lipid binding properties.

NMR and UV studies of 3'-S-phosphorothiolate modified DNA in a DNA : RNA hybrid dodecamer duplex; implications for antisense drug design.

High-resolution NMR spectroscopy has been used to establish the conformational consequences of the introduction of a single 3[prime or minute]-S-phosphorothiolate link in the DNA strand of a DNA : RNA hybrid. These systems are of interest as potential antisense therapeutic agents. Previous studies on similarly modified dinucleotides have shown that the conformation of the sugar to which the sulfur is attached shifts to the north (C(3[prime or minute])-endo/C(2[prime or minute])-exo).

Energy migration in novel pH-triggered self-assembled beta-sheet ribbons.

Energy migration between tryptophan residues has been experimentally demonstrated in self-assembled peptide tapes. Each peptide contains 11 amino acids with a Trp at position 6. The peptide self-assembly is pH-sensitive and forms amphiphilic tapes, which further stack in ribbons (double tapes) and fibrils in water depending on the concentration.

Synthesis and use of a pseudo-cysteine for native chemical ligation.

The process of native chemical ligation (NCL) is well described in the literature. An N-terminal cysteine-containing peptide reacts with a C-terminal thioester-containing peptide to yield a native amide bond after transesterification and acyl transfer. An N-terminal cysteine is required as both the N-terminal amino function and the sidechain thiol participate in the ligation reaction.

Probing the effect of a 3'-S-phosphorothiolate link on the conformation of a DNA:RNA hybrid; implications for antisense drug design.

The effects of a single 3'-S-phosphorothiolate link in the DNA strand of a DNA:RNA dodecamer duplex is described; the sulfur induces a conformational shift in the (attached) sugar pucker, as shown by 1H NMR studies, and increases the thermal stability of the duplex compared to the non-modified system.