We have observed a common sequence motif in membrane proteins, which we call a glycine zipper. Glycine zipper motifs are strongly overrepresented and conserved in membrane protein sequences, and mutations in glycine zipper motifs are deleterious to function in many cases. The glycine zipper has a significant structural impact, engendering a strong driving force for right-handed packing against a neighboring helix. Thus, the presence of a glycine zipper motif leads directly to testable structural hypotheses, particularly for a subclass of glycine zipper proteins that form channels. For example, we suggest that the membrane pores formed by the amyloid-␤ peptide in vitro are constructed by glycine zipper packing and find that mutations in the glycine zipper motif block channel formation. Our findings highlight an important structural motif in a wide variety of normal and pathological processes.amyloid-␤ ͉ membrane channel ͉ membrane protein structure ͉ prion ͉ transmembrane helix M ore than 13 structures a day are currently being deposited in the Protein Data Bank (1), and structural genomics centers have been created to obtain structures even faster [such as the National Institute of General Medical Sciences (NIGMS) Protein Structure Initiative, www.nigms.nih.gov͞psi]. In this assault on protein structure, however, technical challenges have left membrane proteins far behind. Membrane protein structures are currently being solved at Ϸ0.2% of the pace of soluble proteins (2). Thus, membrane protein biochemists are relatively starved for structural insight into these key proteins. In the absence of dramatic technical improvements, alternatives to experimental structure determination are needed.Here, we describe a transmembrane (TM) sequence motif, the glycine zipper, that can lead directly to structural models for many membrane proteins. The most significant glycine zipper sequence patterns are (G,A,S)XXXGXXXG and GXXXGX-XX(G,S,T). These patterns contain a GXXXG motif, which is known to be important in TM helix homodimers where the Gly faces are in direct contact (3-5). The GXXXG sequence pattern is statistically overrepresented in membrane proteins in general, not just in TM homodimers (4). Nevertheless, the structural role of the GXXXG pattern in other types of TM helix packing interactions has not been elucidated. We find that the addition of an appropriately spaced small residue, as found in the glycine zipper, leads to a distinct preference for right-handed packing against a heterologous helix surface. Thus, the presence of a glycine zipper generates a strong helix packing prediction, particularly for homooligomeric channel proteins, providing a structural foundation for hypothesis-driven investigations. MethodsGlycine Zipper Motif Search. We started with Swiss-Prot release 41.15 containing 129,996 proteins (6). All sequences Ͻ50 residues in length were removed, leaving 125,887 proteins. Helical membrane proteins were identified by using the Eisenberg hydrophobicity scale and a window length of 21 residues (7). ...

We have encapsulated free-standing planar lipid membranes in a polymer hydrogel via in situ photopolymerization. These encapsulated membranes were measured to last at least 5 days and provided a stable environment for single-molecule measurements of incorporated alpha-hemolysin channel proteins. The translocation of single-stranded DNA through alpha-hemolysin incorporated into these encapsulated membranes is slowed over 100 times relative to that of the gel-free state. These stabilized membranes, therefore, have application to the single-molecule analysis of DNA as well as broader application to biomolecular sensors, membrane protein biophysical studies, and drug discovery.

Ionic liquids (ILs) are often considered to be green solvents based on their unusual stability, although their toxicity to living organisms has become an emerging issue based on a number of recent studies. We assume that one of the main reasons for this high level of cell toxicity is the molecular interactions between ILs and cell membranes. In this study, we used model cells to demonstrate that ILs can incorporate into lipid membranes, resulting in the perturbation of membrane structure. We employed various methods to elucidate the molecular interactions between cell membranes and ILs. Our results demonstrate that the stability of cell membranes is inversely related to the alkyl chain length and concentration of ILs, providing important information for the design of greener and safer ILs.

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Lipid bilayer membranes have been extensively utilized to examine membrane channel and pore proteins and are the subjects of study in their own right. There has been considerable recent interest in developing technologies to substitute or strengthen lipid bilayer membranes for a number of applications, including sensing or drug delivery. In particular, biomimetic amphiphilic block co-polymers have been shown to have the capacity to form membrane structures and to contain membrane proteins within them. In this work, we describe the creation of biomimetic membranes from a 5.7 nm thick tri-block co-polymer and the investigation of the effects of the polymer environment on incorporated channel proteins (α-haemolysin, OmpG, and alamethicin) with single molecule transport measurements. We found that the polymer membranes consistently have seal resistances of tens of GΩ and greater, and that the conductance of single channels is reduced by approximately 10% from that measured in diphytanoyl phosphatidylcholine lipid membranes, possibly as a result of increased cohesion of the polymer compared to lipid. The voltage gating ability and threshold voltages of voltage gated channels were also found to be very similar in the lipid and polymer environments.