Structure and dynamics of polypeptides and proteins in lipid membranes

Molecularly engineered surfaces for cell biology: from static to dynamic surfaces

Surfaces with a well-defined presentation of ligands for receptors on the cell membrane can serve as models of the extracellular matrix for studying cell adhesion or as model cell surfaces for exploring cell-cell contacts. Because such surfaces can provide exquisite control over, for example, the density of these ligands or when the ligands are presented to the cell, they provide a very precise strategy for understanding the mechanisms by which cells respond to external adhesive cues. In the present feature article, we present an overview of the basic biology of cell adhesion before discussing surfaces that have a static presentation of immobile ligands. We outline the biological information that such surfaces have given us, before progressing to recently developed switchable surfaces and surfaces that mimic the lipid bilayer, having adhesive ligands that can move around the membrane and be remodeled by the cell. Finally, the feature article closes with some of the biological information that these new types of surfaces could provide.

Internal packing of helical membrane proteins

Helix packing is important in the folding, stability, and association of membrane proteins. Packing analysis of the helical portions of 7 integral membrane proteins and 37 soluble proteins show that the helices in membrane proteins have higher packing values (0.431) than in soluble proteins (0.405). The highest packing values in integral membrane proteins originate from small hydrophobic (G and A) and small hydroxyl-containing (S and T) amino acids, whereas in soluble proteins large hydrophobic and aromatic residues have the highest packing values. The highest packing values for membrane proteins are found in the transmembrane helix-helix interfaces. Glycine and alanine have the highest occurrence among the buried amino acids in membrane proteins, whereas leucine and alanine are the most common buried residue in soluble proteins. These observations are consistent with a shorter axial separation between helices in membrane proteins. The tight helix packing revealed in this analysis contributes to membrane protein stability and likely compensates for the lack of the hydrophobic effect as a driving force for helix-helix association in membranes.

Point mutations in bovine opsin can be classified in four groups with respect to their effect on the biosynthetic pathway of opsin

Expression in vitro with the recombinant baculovirus expression system showed correct biosynthesis and post-translational processing of "wild-type' bovine opsin with regard to translocation, glycosylation, palmitoylation and targeting. However, several of these processes were severely affected by point mutations. From the overall results of 16 mutants reported here, four groups were distinguished. One group significantly affected neither biosynthesis nor folding of opsin (D83N, P291A, A299C-V300A-P303G). A second group produced a truncated protein (R69H, Y301F), suggesting that these positions are essential for a correct translational process. A third group affected membrane translocation as well as glycosylation, which can be interpreted as interference with the function of a transfer signal. Substitutions at positions Glu-113, Glu-122, Glu-134, Arg-135 and Lys-248 belong to this category. A fourth group induced structural changes in the protein that led to heterogeneous distribution in the plasma membrane (E113Q/D, W265F, Y268S). Taking any functional consequences of these mutations into consideration, it seems that point mutations can have mosaic effects and therefore should be examined at several levels (folding, targeting, functional parameters).

Design of membrane-inserting peptides: spectroscopic characterization with and without lipid bilayers

This paper reports the spectroscopic characterization of two de novo peptides. The first sequence, Ala peptide = H2N-Ala27-Tyr-Lys6-CONH2, gives circular dichroism (CD) and Fourier transform infrared (FTIR) spectra characteristic of beta structure in solution, binds to lipid bilayer vesicles poorly, and tends to precipitate in buffered 0.1 M salt solutions. In the second sequence, Leu peptide = H2N-Ala2-Leu3-Ala22-Tyr-Lys6-CONH2, three leucines are substituted for three alanine residues. This small sequence change results in CD spectra that are characteristic of helical structures, while the FTIR spectra give evidence for complex equilibria between multiple structures in solution. The Leu peptide does not precipitate in buffered salt solutions and binds to lipid bilayers. The polarized attenuated total reflectance infrared spectra provide evidence of a transmembrane orientation for the helical peptide in lipid bilayers. The collective spectroscopic results are summarized in a tentative model in which the Leu peptide exhibits multiple equilibria between extended unordered, helix, and coiled-coil structures in solution; when lipid vesicles are added, the peptide binds to the lipid surface and then inserts into the lipid in a transmembrane orientation. The slow kinetics exhibited by the peptide suggest multiple conformational changes during the lipid-peptide interactions. The design rationale for the peptides is included in an appendix.

Alpha-helical, but not beta-sheet, propensity of proline is determined by peptide environment

Proline is established as a potent breaker of both alpha-helical and beta-sheet structures in soluble (globular) proteins. Thus, the frequent occurrence of the Pro residue in the putative transmembrane helices of integral membrane proteins, particularly transport proteins, presents a structural dilemma. We propose that this phenomenon results from the fact that the structural propensity of a given amino acid may be altered to conform to changes imposed by molecular environment. To test this hypothesis on proline, we synthesized model peptides of generic sequence H2N-(Ser-LyS)2-Ala- Leu-Z-Ala-Leu-Z-Trp-Ala-Leu-Z-(Lys-Ser)3-OH (Z = Ala and/or Pro). Peptide conformations were analyzed by circular dichroism spectroscopy in aqueous buffer, SDS, lysophosphatidylglycerol micelles, and organic solvents (methanol, trifluoroethanol, and 2-propanol). The helical propensity of Pro was found to be greatly enhanced in the membrane-mimetic environments of both lipid micelles and organic solvents. Proline was found to stabilize the alpha-helical conformation relative to Ala at elevated temperatures in 2-propanol, an observation that argues against the doctrine that Pro is the most potent alpha-helix breaker as established in aqueous media. Parallel studies in deoxycholate micelles of the temperature-induced conformational transitions of the single-spanning membrane bacteriophage IKe major coat protein, in which the Pro-containing wild type was compared with Pro30 --> Ala mutant, Pro was found to protect the helix, but disrupt the beta-sheet structure as effectively as it does to model peptides in water. The intrinsic capacity of Pro to disrupt beta-sheets was further reflected in a survey of porins where Pro was found to be selectively excluded from the core of membrane-spanning beta-sheet barrels. The overall data provide a rationale for predicting and understanding the structural consequences when Pro occurs in the context of a membrane.

Detailed description of an alpha helix-->pi bulge transition detected by molecular dynamics simulations of the p185c-erbB2 V659G transmembrane domain

Molecular dynamics simulations of a 29-residue peptide including the transmembrane domain of the V659G mutant of the c-erbB2 protein demonstrate important dynamical behavior. Although the alpha helix is the structure commonly assumed for transmembrane hydrophobic segments, we found that hydrogen bond rearrangements can occur, giving rise to a structural deformation termed pi bulge stabilized by successive hydrogen bonds of pi helix type. A series of simulations enables us to give a detailed description, at the atomic level, of the alpha helix->pi bulge transition. The major consequence of this deformation covering one and a half turn of helix results in a noticeable shift around the helix axis of the C-Terminal residues relatively to those of the N-terminus. Such a deformation closely related to structural motifs described in the literature, induces a change in the distribution of the residues along the helix faces which could modulate the protein activity mediated by a dimerization process.

Role of hydrophobic and hydrophilic forces in peptide-protein interaction: new advances

A considerable part of important biological processes is governed by the noncovalent association of peptides and proteins. Various types of intermolecular forces may be involved in the formation of these molecular assemblies. This review gives a brief account of the physicochemical bases of interactive forces, with special emphasis on their impact on various peptide-protein interactions; summarizes the newest biochemical and biophysical methods for the study of such interactions; and discusses the role of various hydrophilic and hydrophobic forces in peptide-protein interactions in various fields of life sciences, such as immunology, enzymology, receptor binding, and toxicology.

Sequence analysis of subunits of the membrane-bound nitrate reductase from a denitrifying bacterium: the integral membrane subunit provides a prototype for the dihaem electron-carrying arm of a redox loop

Three genes, narH, narJ and narI, of the membrane-bound nitrate reductase operon of the denitrifying bacterium Thiosphaera pantotropha have been identified and sequenced. The derived gene products show high sequence similarity to the equivalent (beta, putative delta and gamma) subunits of the two membrane-bound nitrate reductases of the enteric bacterium Escherichia coli. All iron-sulphur cluster ligands proposed for the E. coli beta subunits are conserved in T. pantotropha NarH. Secondary structure analysis of NarJ suggests that this protein has a predominantly alpha-helical structure. Comparison of T. pantotropha NarI with the b-haem-binding integral membrane subunits of the E. coli enzymes allows assignment of His-53, His-63, His-186 and His-204 (T. pantotropha NarI numbering) as b-haem axial ligands and the construction of a three-dimensional model of this subunit. This model, in which the two b-haems are in different halves of the membrane bilayer, is consistent with a mechanism of energy conservation whereby electrons are moved from the periplasmic to the cytoplasmic side of the membrane via the haems. Similar movement of electrons is required in the membrane-bound uptake hydrogenases and membrane-bound formate dehydrogenases. We have identified two pairs of conserved histidine residues in the integral membrane subunits of these enzymes that are appropriately positioned to bind one haem towards each side of the membrane bilayer. One subunit of a hydrogenase complex involved in transfer of electrons across the cytoplasmic membrane of sulphate-reducing bacteria has structural resemblance to NarI.

Structure and function of channel-forming peptaibols

Transport of ions through channels is fundamental to a number of physiological processes, especially the electrical properties of excitable cells (Hille, 1992). To understand this process at a molecular level requires atomic resolution structures of channel proteins.

Orientation and aggregation of hydrophobic helical peptides in phospholipid bilayer membrane

Hydrophobic sequential peptides with various chain lengths, Boc-(Ala-Aib)n-OMe (n = 2, 4, 6, 8) and Boc-Ser(CH2Ant)-(Ala-Aib)n-OMe (n = 2, 4, 6, 8, 10, Ant represents O-anthrylmethyl; abbreviated as A2-A10), were synthesized and their orientation and aggregation in a lipid bilayer membrane were investigated. Circular dichroism (CD) measurements revealed that the peptides took a partially helical structure, and that the helix content increased with increasing chain length and upon distribution to phospholipid vesicles. When long-chain peptides, A8 and A10, were incorporated into lipid bilayer membranes, the membrane fluidity was reduced, while 5/6-carboxyfluorescein (CF) leakage through the bilayer membranes was enhanced. Fluorescence quenching of the anthracene group with 12-doxylstearic acid suggested that these peptides took a perpendicular orientation in the membrane. Detection of excimer emission and large fluorescence depolarization of the peptides indicated an aggregation in the membrane. In addition, Boc-(Ala-Aib)n-OMe (n = 4, 8) showed a channel-like activity in a bilayer lipid membrane (BLM). The channel-forming ability of the hexadecapeptide was higher than that of the octapeptide. Taken together, the long-chain hydrophobic helical peptides tend to aggregate in lipid bilayer membranes with a transmembrane orientation.