A photogenerated pore-forming protein

Design and Synthesis of Photochemically Controllable Restriction EndonucleaseBamHI by Manipulating the Salt-Bridge Network in the Dimer Interface

The strategy for the design of photochemically controllable enzymes by manipulating the dimer interface is described. Employing a restriction endonuclease BamHI, the selective incorporation of amino acids having a photoremovable 6-nitroveratryl group into the specific position (Lys132) in the dimer interface of the BamHI mutant (H133A) was performed. The activity of the photofunctionalized BamHI mutant was significantly suppressed, and the following photoirradiation induced the recovery of the activity. In addition, uncaging of the 6-nitroveratryl group introduced to Lys132 did not seriously reduce the catalytic activity and affinity for the substrate. These results indicate that the activity of the enzyme can be effectively regulated by caging and uncaging of the specific amino acid in the dimer interface using the photoremovable group.

Caging proteins through unnatural amino acid mutagenesis

The caging of specific residues of proteins is a powerful tool. This discussion attempts to alert the reader to the considerations that must be made in preparing and analyzing a caged protein through nonsense suppression. Although the suppression methodology is conceptually straightforward, it not possible to provide a failsafe "cook book" method for using caged unnaturals. We have emphasized the preparation of caged receptors expressed in Xenopus oocytes, but these approaches can clearly be adapted to many other systems.

Beta-barrel membrane protein folding and structure viewed through the lens of alpha-hemolysin

The beta-barrel is a transmembrane structural motif commonly encountered in bacterial outer membrane proteins and pore-forming toxins (PFTs). Alpha-hemolysin (alphaHL) is a cytotoxin secreted by Staphylococcus aureus that assembles from a water-soluble monomer to form a membrane-bound heptameric beta-barrel on the surface of susceptible cells, perforating the cell membranes, leading to cell death and lysis. The mechanism of heptamer assembly, which has been studied extensively, occurs in a stepwise manner, and the structures of the initial, monomeric form and final, membrane-embedded pore are known. The toxin's ability to assemble from an aqueous, hydrophilic species to a membrane-inserted oligomer is of interest in understanding the assembly of PFTs in particular and the folding and structure of beta-barrel membrane proteins in general. Here we review the structures of the monomeric and heptamer states of LukF and alphaHL, respectively, the mechanism of toxin assembly, and the relationships between alphaHL and nontoxin beta-barrel membrane proteins.

A caged sperm-activating peptide that has a photocleavable protecting group on the backbone amide

A backbone-caged sperm-activating peptide (caged speract) that has a 2-nitrobenzyl group at a backbone amide and a vastly reduced affinity for its receptor (IC50=950 nM) was synthesized. UV irradiation of caged speract photocleaves the 2-nitrobenzyl group (tau1/2=26 micros), restoring its affinity (IC50=0.67 nM) and ability to increase sperm intracellular pH and Ca2+, as intact speract. Backbone caging of the biological activity was more efficient than side chain caging, which adds a nitrobenzyl group on the peptide side chain. The backbone caging strategy described can be used as a general procedure to cage biologically active peptides, which have no side chain for introduction of a caging group.

Mode of action of beta-barrel pore-forming toxins of the staphylococcal alpha-hemolysin family

Staphylococcal alpha-hemolysin is the prototype of a family of bacterial exotoxins with membrane-damaging function, which share sequence and structure homology. These toxins are secreted in a soluble form which finally converts into a transmembrane pore by assembling an oligomeric beta-barrel, with hydrophobic residues facing the lipids and hydrophilic residues facing the lumen of the channel. Besides alpha-hemolysin the family includes other single chain toxins forming homo-oligomers, e.g. beta-toxin of Clostridium perfringens, hemolysin II and cytotoxin K of Bacillus cereus, but also the staphylococcal bi-component toxins, like gamma-hemolysins and leucocidins, which are only active as the combination of two similar proteins which form hetero-oligomers. The molecular basis of membrane insertion has become clearer after the determination of the crystal structure of both the oligomeric pore and the soluble monomer. Studies on this family of beta-barrel pore-forming toxins are important for many aspects: (i) they are involved in serious pathologies of humans and farmed animals, (ii) they are a good model system to investigate protein-membrane interaction and (iii) they are the basic elements for the construction of nanopores with biotechnological applications in various fields.

Interaction of the noncovalent molecular adapter, beta-cyclodextrin, with the staphylococcal alpha-hemolysin pore

Cyclodextrins act as noncovalent molecular adapters when lodged in the lumen of the alpha-hemolysin (alphaHL) pore. The adapters act as binding sites for channel blockers, thereby offering a basis for the detection of a variety of organic molecules with alphaHL as a biosensor element. To further such studies, it is important to find conditions under which the dwell time of cyclodextrins in the lumen of the pore is extended. Here, we use single-channel recording to explore the pH- and voltage-dependence of the interaction of beta-cyclodextrin (betaCD) with alphaHL. betaCD can access its binding site only from the trans entrance of pores inserted from the cis side of a bilayer. Analysis of the binding kinetics shows that there is a single binding site for betaCD, with an apparent equilibrium dissociation constant that varies by >100-fold under the conditions explored. The dissociation rate constant for the neutral betaCD molecule varies with pH and voltage, a result that is incompatible with two states of the alphaHL pore, one of high and the other of low affinity. Rather, the data suggest that the actual equilibrium dissociation constant for the alphaHL. betaCD complex varies continuously with the transmembrane potential.

Detecting protein analytes that modulate transmembrane movement of a polymer chain within a single protein pore

Here we describe a new type of biosensor element for detecting proteins in solution at nanomolar concentrations. We tethered a 3.4 kDa polyethylene glycol chain at a defined site within the lumen of the transmembrane protein pore formed by staphylococcal alpha-hemolysin. The free end of the polymer was covalently attached to a biotin molecule. On incorporation of the modified pore into a lipid bilayer, the biotinyl group moves from one side of the membrane to the other, and is detected by reversible capture with a mutant streptavidin. The capture events are observed as changes in ionic current passing through single pores in planar bilayers. Accordingly, the modified pore allows detection of a protein analyte at the single-molecule level, facilitating both quantification and identification through a distinctive current signature. The approach has higher time resolution compared with other kinetic measurements, such as those obtained by surface plasmon resonance.

A functional protein pore with a "retro" transmembrane domain

Extended retro (reversed) peptide sequences have not previously been accommodated within functional proteins. Here, we show that the entire transmembrane portion of the beta-barrel of the pore-forming protein alpha-hemolysin can be formed by retrosequences comprising a total of 175 amino acid residues, 25 contributed by the central sequence of each subunit of the heptameric pore. The properties of wild-type and retro heptamers in planar bilayers are similar. The single-channel conductance of the retro pore is 15% less than that of the wild-type heptamer and its current-voltage relationship denotes close to ohmic behavior, while the wild-type pore is weakly rectifying. Both wild-type and retro pores are very weakly anion selective. These results and the examination of molecular models suggest that beta-barrels may be especially accepting of retro sequences compared to other protein folds. Indeed, the ability to form a retro domain could be diagnostic of a beta-barrel, explaining, for example, the activity of the retro forms of many membrane-permeabilizing peptides. By contrast with the wild-type subunits, monomeric retro subunits undergo premature assembly in the absence of membranes, most likely because the altered central sequence fails to interact with the remainder of the subunit, thereby initiating assembly. Despite this difficulty, a technique was devised for obtaining heteromeric pores containing both wild-type and retro subunits. Most probably as a consequence of unfavorable interstrand side-chain interactions, the heteromeric pores are less stable than either the wild-type or retro homoheptamers, as judged by the presence of subconductance states in single-channel recordings. Knowledge about the extraordinary plasticity of the transmembrane beta-barrel of alpha-hemolysin will be very useful in the de novo design of functional membrane proteins based on the beta-barrel motif.

PATIC: a conformationally constrained photoisomerizable amino acid

The synthesis of a conformationally constrained photoisomerizable amino acid, phenylazo-1,2,3,4-tetrahydro-3-isoquinolinecarboxylic acid (PATIC), is described. This amino acid can be incorporated into peptides using standard Fmoc procedures and can be accommodated within alpha-helical structures albeit with some loss of stability of the structure. PATIC can serve as a useful building block for the synthesis of photoregulated peptides and proteins.

Synthesis and applications of heterobifunctional photocleavable cross-linking reagents

This study designed, synthesized, and characterized a number of new heterobifunctional photocleavable cross-linking reagents that may be used to photomodulate the activity of proteins or to prepare caged fluorescent dyes. Biomolecules or fluorophores caged via a thiol group with the BNBASE reagent can be covalently linked to a second protein, ligand, or derivatized surface through the activated carboxyl group. Members of the new class of photocleavable cross-linking reagent can be used to cage amino groups in the molecule of interest, which can then be covalently linked to a second molecule through the thiol-reactive oxirane group. These crosslinking reagents may be used for the following applications: (1) to cage the activity of a protein by masking its active site with a second macromolecule, e.g., aminodextran; (2) to prepare a protein conjugate exhibiting an enhanced or new activity that is lost on irradiation with near-ultraviolet light, e.g., cross-linked actin dimer; (3) to target the caged compound to a specific site by cross linking to a specific antibody; (4) to attach the caged compound to a thiol or amino derivatized surface; and (5) to render the caged compound fluorescent in order to image or to quantify the yield of the photoactivation reaction.

alpha-Hemolysin from Staphylococcus aureus: an archetype of beta-barrel, channel-forming toxins

alpha-Hemolysin, secreted from Staphylococcus aureus as a water-soluble monomer of 33.2 kDa, assembles on cell membranes to form transmembrane, heptameric channels. The structure of the detergent-solubilized heptamer has been determined by X-ray crystallography to 1.9 A resolution. The heptamer has a mushroom-like shape and measures up to 100 A in diameter and 100 A in height. Spanning the length of the molecule and coincident with the molecular sevenfold axis is a water-filled channel that ranges in diameter from approximately 16 to approximately 46 A. A 14 strand antiparallel beta-barrel, in which two strands are contributed by each subunit, defines the transmembrane domain. On the exterior of the beta-barrel there is a hydrophobic belt approximately 30 A in width that provides a surface complementary to the nonpolar portion of the lipid bilayer. The extensive promoter-protomer interfaces are composed of both salt-links and hydrogen bonds, as well as hydrophobic interactions, and these contacts provide a molecular rationalization for the stability of the heptamer in SDS solutions up to 65 degrees C. With the structure of the heptamer in hand, we can better understand the mechanisms by which the assembled protein interacts with the membrane and can postulate mechanisms of assembly.

Self-assembled alpha-hemolysin pores in an S-layer-supported lipid bilayer

The effects of a supporting proteinaceous surface-layer (S-layer) from Bacillus coagulans E38-66 on a 1,2-diphytanoyl-sn-glycero-3-phosphatidylcholine (DPhPC) bilayer were investigated. Comparative voltage clamp studies on plain and S-layer supported DPhPC bilayers revealed no significant difference in the capacitance. The conductance of the composite membrane decreased slightly upon recrystallization of the S-layer. Thus, the attached S-layer lattice did not interpenetrate or rupture the DPhPC bilayer. The self-assembly of a pore-forming protein into the S-layer supported lipid bilayer was examined. Staphylococcal alpha-hemolysin formed lytic pores when added to the lipid-exposed side. The assembly was slow compared to unsupported membranes, perhaps due to an altered fluidity of the lipid bilayer. No assembly could be detected upon adding alpha-hemolysin monomers to the S-layer-faced side of the composite membrane. Therefore, the intrinsic molecular sieving properties of the S-layer lattice do not allow passage of alpha-hemolysin monomers through the S-layer pores to the lipid bilayer. In comparison to plain lipid bilayers, the S-layer supported lipid membrane had a decreased tendency to rupture in the presence of alpha-hemolysin.

Preparation and photoactivation of caged fluorophores and caged proteins using a new class of heterobifunctional, photocleavable cross-linking reagents

The design, synthesis, and spectroscopic and chemical properties of four members of a new class of heterobifunctional photocleavable (caged) cross-linking reagents were described. One of the two reactive groups of the cross-linker reacted with amino groups to form the corresponding photolabile carbamates. Amino group containing compounds or proteins caged with these reagents can be coupled through the thiol reactive oxirane group of the cross-linker to a different biomolecule or to a thiol-derivatized surface. The 3,4-dimethoxy-6-nitrophenyl photoisomerization group of the reagent was physically and chemically isolated from the cross-linking functionality, and the high extinction coefficient and red-shifted action spectrum of this chromophore make it suitable for photoactivation applications of caged compounds on surfaces or in living cells. The bifunctional, photocleavable cross-linking reagents were used to prepare a thiol reactive caged rhodamine 110. The new reagents and conjugation procedures described may be used as part of a general procedure to cage the activity of proteins by physically masking binding sites.

Signaling pathways underlying eosinophil cell motility revealed by using caged peptides

Insights into structure-function relations of many proteins opens the possibility of engineering peptides to selectively interfere with a protein's activity. To facilitate the use of peptides as probes of cellular processes, we have developed caged peptides whose influence on specific proteins can be suddenly and uniformly changed by near-UV light. Two peptides are described which, on photolysis of a caging moiety, block the action of calcium-calmodulin or myosin light chain kinase (MLCK). The efficacy of theses peptides is demonstrated in vitro and in vivo by determining their effect before and after photolysis on activities of isolated enzymes and cellular functions known to depend on calcium-calmodulin and MLCK. These caged peptides each were injected into motile, polarized eosinophils, and when exposed to light promptly blocked cell locomotion in a similar manner. The results indicate that the action of calcium-calmodulin and MLCK, and by inference myosin II, are required for the ameboid locomotion of these cells. This methodology provides a powerful means for assessing the role of these and other proteins in a wide range of spatio-temporally complex functions in intact living cells.

Novel therapeutic strategies to selectively kill cancer cells

Tumor invasion, metastasis, and resistance to chemotherapeutic drugs or radiation are major obstacles for the successful treatment of cancer. To overcome some of these limitations, therapeutic strategies that increase the specificity and efficacy and reduce the toxicity of the anti-cancer drugs or toxins are being explored. Cancer cells overexpress specific protein antigens and carbohydrate structures that may function as cell surface receptors. These cancer cell specific markers can be exploited while designing new cancer therapies. Monoclonal antibodies that have been humanized to reduce immunogenicity and targeted to specific antigens on cancer cells, enzyme-monoclonal antibody/prodrug conjugates that will selectively kill the target cells following drug activation, and recombinant toxins are some of the novel classes of agents in development. Another novel approach being investigated to treat cancers is the use of inactive pore-forming toxins with built-in biological "triggers" that will activate the toxin following a biological stimulus. These pore-forming cytolytic toxins can be rendered active by tumor-specific proteases, that are often overexpressed in cancer cells, thereby targeting the toxic effects. Such pore-forming or membrane-acting toxins may serve as novel cytolytic agents against solid tumors, which, to date, have proved to be more resistant to conventional toxins.

Designed protein pores as components for biosensors

BACKGROUND

There is a pressing need for new sensors that can detect a variety of analytes, ranging from simple ions to complex compounds and even microorganisms. The devices should offer sensitivity, speed, reversibility and selectivity. Given these criteria, protein pores, remodeled so that their transmembrane conductances are modulated by the association of specific analytes, are excellent prospects as components of biosensors.

RESULTS

Structure-based design and a separation method that employs targeted chemical modification have been used to obtain a heteromeric form of the bacterial pore-forming protein staphylococcal alpha-hemolysin, in which one of the seven subunits contains a binding site for a divalent metal ion, M(II), which serves as a prototypic analyte. The single-channel current of the heteromer in planar bilayers is modulated by nanomolar Zn(II). Other M(II)s modulate the current and produce characteristic signatures. In addition, heteromers containing more than one mutant subunit exhibit distinct responses to M(II)s Hence, a large collection of responsive pores can be generated through subunit diversity and combinatorial assembly.

CONCLUSIONS

Engineered pores have several advantages as potential sensor elements: sensitivity is in the nanomolar range; analyte binding is rapid (diffusion limited in some cases) and reversible; strictly selective binding is not required because single-channel recordings are rich in information; and for a particular analyte, the dissociation rate constant, the extent of channel block and the voltage-dependence of these parameters are distinguishing, while the frequency of partial channel block reflects the analyte concentration. A single sensor element might, therefore, be used to quantitate more than one analyte at once. The approach described here can be generalized for additional analytes.

Reversible permeabilization of plasma membranes with an engineered switchable pore

By using an engineered, self-assembling, proteinaceous, 2-nm pore equipped with a metal-actuated switch, a technique to reversibly permeabilize the plasma membrane to small molecules (approximately 1000 Da) has been developed. We have demonstrated the dose-dependent permeabilization of fibroblasts by pores designed to be blocked and unblocked by the addition and removal of microM concentrations of Zn2+. Further, we have shown that the activity of the switch allows permeabilized cells to maintain viability and ultrastructural integrity following the unconstrained flux of small molecules. This ability to control the transmembrane influx and efflux of molecules and thereby vary the intracellular environment yet maintain cell viability will impact an array of biological and medical problems.

Key residues for membrane binding, oligomerization, and pore forming activity of staphylococcal alpha-hemolysin identified by cysteine scanning mutagenesis and targeted chemical modification

The alpha-hemolysin (alpha HL) polypeptide is secreted by Staphylococcus aureus as a water-soluble monomer that assembles into lipid bilayers to form cylindrical heptameric pores 1-2 nm in effective internal diameter. We have individually replaced each charged residue (79 of 293 amino acids) and four neutral residues in alpha HL with cysteine, which is not found in the wild-type protein. The properties of these mutants have been examined before and after modification with the 450-Da dianionic sulfhydryl reagent 4-acetamido-4'-((iodoacetyl)amino)stilbene-2,2'-disulfonate (IASD). This modification was highly informative as 28 of 83 modified polypeptides showed substantially reduced pore forming activity on rabbit erythrocytes (rRBC), while only five of the unmodified cysteine mutants were markedly affected. Through detailed examination of the phenotypes of the mutant and modified hemolysins, we have pinpointed residues and regions in the alpha HL polypeptide chain that are important for binding to rRBC, oligomer formation and pore activity. Residues in both the N-terminal (Arg-66 and Glu-70) and C-terminal (Arg-200, Asp-254, Asp-255, and Asp-276) thirds of the protein are implicated in binding to cells. The His-35 replacement mutant modified with IASD was the only polypeptide in this study that failed to form SDS-resistant oligomers on rRBC. Altered hemolysins that formed oligomers but failed to lyse rRBC represented the most common defect. These alterations were clustered in the central glycine-rich loop, which has previously been implicated as a component of the lumen of the membrane-spanning channel, and in the regions flanking the loop. Alterations in mutant and modified hemolysins with the same defect were also scattered between the N terminus and His-48, in keeping with previous suggestions that an N-terminal segment and the central loop cooperate in the final step of pore assembly.