Toward p-Octiphenyl β-Barrel RNases

Catalytic peptide assemblies

Self-assembly of molecules often results in new emerging properties. Even very short peptides can self-assemble into structures with a variety of physical and structural characteristics. Remarkably, many peptide assemblies show high catalytic activity in model reactions reaching efficiencies comparable to those found in natural enzymes by weight. In this review, we discuss different strategies used to rationally develop self-assembled peptide catalysts with natural and unnatural backbones as well as with metal-containing cofactors.

Sensing, Threading, Orienting, and Cutting Polymers with Rigid-Rod Pores

This short review describes synthetic pores that are made from rigid-rod molecules and can bind oligo-and polymers such as polyacetylenes, p-oligophenyls, terpenoids, polypeptides, polysaccharides, and oligonucleotides. The spotlight is on recent breakthroughs to image the longtime elusive pore-polymer host-guest complexes as single giant pseudorotaxanes.

Receptor for Anionic Pyrene Derivatives Provides the Basis for New Biomembrane Assays

This study describes a new receptor cyclen 1 capable of strong selective binding of pyrene-based anionic dyes under near-physiological conditions. This receptor comprises four naphthylthiourea groups tethered to a cyclen core via an ester linkage. The complexation behavior of cyclen 1 receptor is characterized by a series of (1)H NMR, microcalorimetry, UV-vis, and fluorometry experiments. The relevance of structural features of this receptor to its recognition function is assessed using control compounds that lack some of the groups found in cyclen 1. The specificity of cyclen 1 toward pyrene-based dyes is assessed through experiments using dyes with different molecular organization. The most important finding was the ability of cyclen 1 to bind efficiently to a pH-sensitive dye pyranine, a dye that is commonly used in various biomembrane assays. The high affinity of cyclen 1 to pyranine, its impermeability to the lipid bilayer membrane, fast kinetics of binding, and ability to quench the pyranine's fluorescence were used as a basis for a new membrane leakage assay. This membrane leakage assay is fully compatible with the commonly applied pH-stat transport assay, and therefore it allows for differentiation of the ion transport and nonselective leakage mechanisms within a single set of experiments. The ability of cyclen 1 to quench the fluorescence of pyranine also finds limited applicability to the detection of endovesiculation.

Thermodynamic and Kinetic Stability of Synthetic Multifunctional Rigid-Rod β-Barrel Pores: Evidence for Supramolecular Catalysis

The lessons learned from p-octiphenyl beta-barrel pores are applied to the rational design of synthetic multifunctional pore 1 that is unstable but inert, two characteristics proposed to be ideal for practical applications. Nonlinear dependence on monomer concentration provided direct evidence that pore 1 is tetrameric (n = 4.0), unstable, and "invisible," i.e., incompatible with structural studies by conventional methods. The long lifetime of high-conductance single pores in planar bilayers demonstrated that rigid-rod beta-barrel 1 is inert and large (d approximately 12 A). Multifunctionality of rigid-rod beta-barrel 1 was confirmed by adaptable blockage of pore host 1 with representative guests in planar (8-hydroxy-1,3,6-pyrenetrisulfonate, KD = 190 microM, n = 4.9) and spherical bilayers (poly-L-glutamate, KD < or = 105 nM, n = 1.0; adenosine triphosphate, KD = 240 microM, n = 2.0) and saturation kinetics for the esterolysis of a representative substrate (8-acetoxy-1,3,6-pyrenetrisulfonate, KM = 0.6 microM). The thermodynamic instability of rigid-rod beta-barrel 1 provided unprecedented access to experimental evidence for supramolecular catalysis (n = 3.7). Comparison of the obtained kcat = 0.03 min(-1) with the kcat approximately 0.18 min(-1) for stable analogues gave a global KD approximately 39 microM3 for supramolecular catalyst 1 with a monomer/barrel ratio approximately 20 under experimental conditions. The demonstrated "invisibility" of supramolecular multifunctionality identified molecular modeling as an attractive method to secure otherwise elusive insights into structure. The first molecular mechanics modeling (MacroModel, MMFF94) of multifunctional rigid-rod beta-barrel pore hosts 1 with internal 1,3,6-pyrenetrisulfonate guests is reported.

On selectivity and sensitivity of synthetic multifunctional pores as enzyme sensors: discrimination between ATP and ADP and comparison with biological pores

This report delineates scope and limitation of the selectivity of synthetic multifunctional pores as enzyme sensors using glycolytic enzymes as example (G. Das, P. Talukdar, and S. Matile, Science, 2002, Vol. 298, pp. 1600-1602). Unproblematic detectability of hexokinase and phosphofructokinase demonstrates that the selectivity of synthetic multifunctional pore (SMPs) sensors suffices to sense ATP in mixed analytes containing ADP, whereas detection of the isomerization of glucose 6-phosphate into fructose 6-phosphate by phosphoglucose isomerase is not possible with confidence. The sensitivity of SMP sensors is sufficient for end-point detection of one picomole poly-L-glutamate hydrolyzed by papain in unoptimized assay format; the sensitivity of melittin as representative biological pore of similar charge and aggregation number to detect the same reaction is more than four orders of magnitude inferior.

Outer surface modification of synthetic multifunctional pores

The characteristics of pores formed by p-octiphenyl beta-barrels with LWV triads at the outer surface are reported in comparison with the conventional rigid-rod beta-barrels with all-L outer surface. Maintained multifunctionality of tetrameric pores with external LWV triads (inversion of ion selectivity, molecular recognition and transformation) is implicative for intact barrel interior. Increased pore activity supports dominance of high bilayer affinity for W over low affinity for V. Transmembrane p-octiphenyl orientation (from fluorescence depth quenching) supports barrel-stave (rather than toroidal) pores and dominance of transmembrane preference of rigid rods over interfacial preference of W. Destabilization of beta-barrel pores in membranes (from short single-channel lifetimes) and in the media (from 4th-power dependence on monomer concentration) by LWV triads supports dominance of low beta-propensity for W over high beta-propensity for V. The relation between the stability of supramolecular (pre)pores and dependence of activity on monomer concentration is discussed in a more general context.

Complementary characteristics of homologous p-octiphenyl beta-barrels with ion channel and esterase activity

We report that decreasing beta-sheet length in homologous multifunctional rigid-rod beta-barrels with internal histidines increases ion channel stability by three orders of magnitude, reduces binding activity by four orders of magnitude, and reduces esterase activity up to 22-times. These results are further used to evaluate methods employed to characterize suprastructure and activity of synthetic multifunctional pores formed by p-octiphenyl beta-barrels with emphasis on applicability of the Hille model to determine internal diameters and the Woodhull equation to locate internal active sites.

Synthetic multifunctional pores: lessons from rigid-rod β-barrels

In this account, studies on synthetic multifunctional pores formed by rigid-rod beta-barrels are summarized comprehensively. The first section outlines the evolution of synthetic multifunctional pores from the introduction of rigid-rod molecules in bioorganic chemistry and the discovery of synthetic beta-barrels in comparison with pertinent developments in related areas of research. Design strategies to position active sites at the inner surface of rigid-rod beta-barrel pores are described in the second section. The third section focuses on the characteristics of transmembrane barrel-stave pores, emphasizing the dynamic nature of supramolecular oligomers with the aid of notional phase and energy diagrams. Section four introduces multifunctionality with the use of synthetic pores as hosts of a rich collection of guests, reaching from inorganic cations to organic macromolecules like peptides, oligonucleotides, polysaccharides and polyacetylenes. In section five, practical applicability of molecular recognition by synthetic multifunctional pores is documented with non-invasive fluorometric enzyme sensing. The application of host-guest chemistry within synthetic pores to couple molecular recognition and translocation with molecular transformation is the topic of section six. The last section mentions some perspectives and challenges with synthetic multifunctional pores.