A simple flexible program for the computational analysis of amino acyl residue distribution in proteins: application to the distribution of aromatic versus aliphatic hydrophobic amino acids in transmembrane alpha-helical spanners of integral membrane transport proteins

Specificity in transmembrane helix-helix interactions mediated by aromatic residues

Aromatic residues have been previously shown to mediate the self-assembly of different soluble proteins through pi-pi interactions (McGaughey, G. B., Gagne, M., and Rappe, A. K. (1998) J. Biol. Chem. 273, 15458-15463). However, their role in transmembrane (TM) assembly is not yet clear. In this study, we performed statistical analysis of the frequency of occurrence of aromatic pairs in a bacterial TM data base that provided an initial indication that the appearance of a specific aromatic pattern, Aromatic-XX-Aromatic, is not coincidental, similar to the well characterized QXXS motif. The QXXS motif was previously shown to be both critical and sufficient for stabilizing TM self-assembly. Using the ToxR system, we monitored the dimerization propensities of TM domains that contain mutations of interacting residues to aromatic amino acids and demonstrated that aromatic residues can adequately stabilize self-association. Importantly, we have provided an example of a natural TM domain, the cholera toxin secretion protein EpsM, whose TM self-assembly is mediated by an aromatic motif (WXXW). This is, in fact, the first evidence that aromatic residues are involved in the dimerization of a wild type TM domain. The association mediated by aromatic residues was found to be sensitive to the TM sequence, suggesting that aromatic residue motifs can provide a general means for specificity in TM assembly. Molecular dynamics provided a structural explanation for this backbone sequence sensitivity.

Intragenic suppression of gain-of-function mutations in the Escherichia coli mechanosensitive channel, MscL

Mechanosensitive channels play an important role in protecting bacterial cells from osmotic downshock by serving as biological 'pressure release valves'. One of these channels, MscL, is found throughout the bacterial kingdom, but has been most studied in Escherichia coli. The E. coli MscL is a 136-amino-acid protein organized as a homopentamer with each subunit containing two transmembrane segments. Previous studies have shown that several residues, including V23 and G26, are essential for normal function of MscL; very severe gain-of-function phenotypes in which cell growth slows or is arrested can result from residue substitutions at these positions. Through random mutagenesis and growth selection, we have generated intragenic suppressors of the V23A and G26S mutations. The suppressor mutants have been characterized by growth phenotype, Western blot and patch clamp. Most of the mutations that render phenotypic suppression are located in the transmembrane domains with additional sites lying in the periplasmic loop. In contrast, only one mutation is found in the amino-terminal S1 domain, and none is found within the carboxyl-terminal domain. Not only have these findings revealed functional domains and subdomains critical for MscL function, but they also predict a pair of residues that interact directly during channel opening.

Cysteine scanning of MscL transmembrane domains reveals residues critical for mechanosensitive channel gating

The mechanosensitive channel of large conductance (MscL), a bacterial channel, is perhaps the best characterized mechanosensitive protein. A structure of the Mycobacterium tuberculosis ortholog has been solved by x-ray crystallography, but details of how the channel gates remain obscure. Here, cysteine scanning was used to identify residues within the transmembrane domains of Escherichia coli MscL that are crucial for normal function. Utilizing genetic screens, we identified several mutations that induced gain-of-function or loss-of-function phenotypes in vivo. Mutants that exhibited the most severe phenotypes were further characterized using electrophysiological techniques and chemical modifications of the substituted cysteines. Our results verify the importance of residues in the putative primary gate in the first transmembrane domain, corroborate other residues previously noted as critical for normal function, and identify new ones. In addition, evaluation of disulfide bridging in native membranes suggests alterations of existing structural models for the "fully closed" state of the channel.

Aromaticity of Tyr-202 in the alpha4-alpha5 loop is essential for toxicity of the Bacillus thuringiensis Cry4A toxin

The current model for the mechanism of action of the Bacillus thuringiensis Cry delta-endotoxins involves the penetration of the alpha4-alpha5 hairpin into the target midgut epithelial cell membranes, followed by pore formation. In this study, PCR-based mutagenesis was employed to identify a critical residue within the alpha4-alpha5 loop of the 130kDa Cry4A mosquito-larvicidal protein. Alanine-substitutions of two charged (Asp-198 and Asp-200) and four polar (Asn-190, Asn-195, Tyr-201 and Tyr-202) residues in the alpha4-alpha5 loop were performed. Like the wild-type, all of the mutant toxins were over-expressed as inclusion bodies in Escherichia coli. When E. coli cells expressing each mutant toxin were bioassayed against Aedes aegypti larvae, larvicidal activity was completely abolished for the substitution of only Tyr-202, while replacements at the other positions still retained a high level of toxicity. Further replacement of Tyr-202 with an aromatic side chain, phenylalanine, did not affect the toxicity. These results revealed a crucial role in toxin activity for the conserved aromatic residue at the 202 position within the alpha4-alpha5 loop of the Cry4A toxin.

Nonclassical transport proteins and peptides: an alternative to classical macromolecule delivery systems

The number of peptides and proteins known to exhibit nonclassical transport activity has increased significantly in recent years. In most cases, these entities have been studied in relation to their ability to deliver high molecular weight compounds, including proteins and DNA, for the ultimate purpose of developing new drug delivery strategies. In this review, an overview of the various types of vectors is presented. The in vitro and in vivo delivery successes of this technology, as well as preliminary therapeutic efforts, are described. Although a comprehensive mechanism of nonclassical transport has not yet been clearly established, we propose a straightforward model based on the cationic nature of the vectors and the need for lack of highly organized structure. In this hypothesis we suggest that the movement of polycations is mediated by a network of extra- and intracellular polyanions while transport across the bilayer is facilitated by cation-pi interactions between the vectors' basic groups and aromatic amino acid side chains in the bilayer spanning helices of membrane proteins.

Methods for studying transmembrane peptides in bicelles: consequences of hydrophobic mismatch and peptide sequence

We have shown that bicelles prepared from dilauryl phosphatidylcholine (DLPC) and dipalmitoyl phosphatidylcholine (DPPC) align in a magnetic field under conditions similar to the more common dimyristoyl phosphatidylcholine (DMPC) bicelles. In addition, a model transmembrane peptide, P16, with a hydrophobic stretch of 24 A, and specific alanine-d(3) labels, was incorporated into all of the different bicelles. The long-chain phospholipid (DLPC, DMPC, or DPPC) remained unperturbed upon incorporation of the peptide while the quadrupolar splitting of the short-chain phospholipid along the bicelle rim increased by varying degrees in the different bicelle systems. The change in quadrupolar splitting of the short-chain phospholipids was attributed to changes in either fluidity of the planar region of the bicelle or differences in overall lipid packing. When the hydrophobic stretch of the bilayer was 22.8 (DMPC) or 26.3 A (DPPC), the peptide tilt was found to be transmembrane (33-35 degrees with respect to the bicelle normal). When the hydrophobic stretch of the bilayer was 19.5 A (DLPC), the peptide quadrupolar splittings suggested a loss of transmembrane orientation. When tryptophan was incorporated in the middle of the transmembrane region, the transmembrane orientation was also lost.

Role of aromatic residues at the lipid-water interface in micelle-bound bacteriophage M13 major coat protein

Analyses of transmembrane domains of proteins have revealed that aromatic residues tend to cluster at or near the lipid-water interface of the membrane. To assess protein-membrane interactions of such residues, a viable mutant library was generated of the major coat protein of bacteriophage M13 (a model single membrane-spanning protein) in which one or the other of its interfacial tyrosine residues (Tyr-21 and Tyr-24) is mutated. Using the interfacial tryptophan (Trp-26) as an intrinsic probe, blue shifts in fluorescence emission spectra and quenching constants indicated that mutants with a polar amino acid substitution (such as Y24D or Y24N) are less buried in a deoxycholate micelle environment than in the wild type protein. These polar mutants also exhibited alpha-helix to beta-structure transition temperatures in incremental-heating circular dichroism studies relatively lower than those of wild type and nonpolar mutants (such as Y21V, Y21I, and Y24A), indicating that specific side chains in the lipid-water interface influence local protein-micelle interactions. Mutant Y21F exhibited the highest transition temperature, suggesting that phenylalanine is ostensibly the most effective interfacial anchoring residue. Using phage viability as the assay in a combination of site-directed and saturation mutagenesis experiments, it was further observed that both Tyr residues could not simultaneously be "knocked out". The overall results support the notion that an interfacial Tyr is a primary recognition element for precise strand positioning in vivo, a function that apparently cannot be performed optimally by residues with simple aliphatic character.

A bacterial model system for understanding multi-drug resistance

Mankind stands at the crossroads, recognizing the need for a radical change in bacterial disease management. The development of several antimicrobial agents in the 1940s and 1950s allowed man to gain the upper hand in controlling these diseases. However, the horizon is now clouded by the activation in bacteria of cryptic multi-drug resistance (MDR) genes and the spread of plasmid- and integron-born MDR genes through bacterial populations. Unless remedial measures are taken, nearly all currently available antimicrobial agents are likely to soon lose their efficacies. We briefly review the bacterial MDR phenomenon and focus on a recently emerging family of small multi-drug resistance (SMR) pumps which may provide an ideal model system for understanding the MDR phenomenon in general.

Flexible programs for the prediction of average amphipathicity of multiply aligned homologous proteins: application to integral membrane transport proteins

Simple flexible programs (TREEMOMENT and PILEUPMOMENT) are described for depicting the average amphipathicity (hydrophobic moment) along multiply aligned sequences of a family of evolutionarily related proteins. The programs are applicable to any number of aligned sequences and can be set for any desired angle corresponding to a residue repeat unit in a protein secondary structural element such as 100 degrees per residue for an alpha-helix or 180 degrees per residue for a beta-strand. These programs can be used to identify amphipathic regions common to the members of a protein family. The use of these programs is exemplified by showing that some families of integral membrane transport proteins (i.e. permeases of the bacterial phosphotransferase system (PTS) and the anion exchangers of animals) exhibit strikingly amphipathic alpha-helical structures immediately preceding the first hydrophobic transmembrane segment of their membrane-embedded domain(s). Other families, such as the major facilitator superfamily of uniporters, symporters and antiporters, do not exhibit this structural feature. The amphipathic structures in PTS permeases have been implicated in membrane insertion during biogenesis.