High‐Resolution Structural Characterization of a Helical α/β‐Peptide Foldamer Bound to the Anti‐Apoptotic Protein Bcl‐xL

Get into the groove : The first high‐resolution structure of a foldamer bound to a protein target is described (see picture; foldamer in sticks). The foldamer consists of α‐ and β‐amino acid residues and is bound to the anti‐apoptotic protein Bcl‐x_L. The overall binding mode and key interactions observed in the foldamer/Bcl‐x_L complex mimic those seen in complexes of Bcl‐x_L with natural α‐peptide ligands. Additional contacts in the foldamer/Bcl‐x_L complex involving β‐amino acid residues appear to contribute to binding affinity.

     

Interaction of alcohols and ethers with a-CF(x) films

The surfaces of the magnetic data storage hard disks used in computers are coated with a thin film of amorphous carbon and a layer of perfluoropolyalkyl ether (PFPE) lubricant. Both protect the surface of the magnetic layer from contact with the read-write head flying over the disk surface. Although the most commonly used carbon films are amorphous hydrogenated carbon, a-CH(x), it has been suggested that the thermal properties of amorphous fluorinated carbon films, a-CF(x), might be superior. This work has probed the interaction of small fluorinated ethers and alcohols with the surfaces of a-CF(x) films to understand the effects of carbon film fluorination on the interaction of the lubricant with its surface. Temperature-programmed desorption was used to measure the desorption energies of small fluorocarbons from the a-CF(x) surface and to compare their desorption energies with those from the surfaces of a-CH(x) films. These measurements reveal that, similarly to a-CH(x) films, a-CF(x) films expose a heterogeneous surface on which fluorocarbons adsorb at sites with a range of binding energies. The fluorocarbon ethers all have lower heats of adsorption than their hydrocarbon counterparts, suggesting that the ethers adsorb by donation of electron density from the oxygen lone-pair electrons to sites on the surface. Fluorinated alcohols have roughly the same heats of adsorption as their hydrocarbon counterparts. There is little significant difference between the interactions of fluorinated ethers (or alcohols) with the surfaces of either a-CF(x) or a-CH(x) films.     

Thermodynamic analysis of autonomous parallel beta-sheet formation in water

We report the first thermodynamic analysis of parallel beta-sheet formation in a model system that folds in aqueous solution. NMR chemical shifts were used to determine beta-sheet population, and van't Hoff anaysis provided thermodynamic parameters. Our approach relies upon the d-prolyl-1,1-dimethyl-1,2-diaminoethane unit to promote parallel beta-sheet formation between attached peptide strands. The development of a macrocyclic reference molecule to provide chemical shift data for the fully folded state was crucial to the quantitative anaylsis.     

An antiparallel alpha-helical coiled-coil model system for rapid assessment of side-chain recognition at the hydrophobic interface

Both parallel and antiparallel alpha-helical coiled-coil dimers are common among proteins; however, biophysical scrutiny has focused almost entirely on parallel dimers. We describe the development of a model system that enables efficient and systematic analysis of hydrophobic packing between antiparallel alpha-helices. Our findings reveal significant differences in packing preferences between parallel and antiparallel coiled-coils.     

Tandem facial amphiphiles for membrane protein stabilization

We describe a new type of synthetic amphiphile that is intended to support biochemical characterization of intrinsic membrane proteins. Members of this new family displayed favorable behavior with four of five membrane proteins tested, and these amphiphiles formed relatively small micelles.     

Enantioselective surface chemistry of R-2-bromobutane on Cu(643)R&S and Cu(531)R&S

The enantioselective surface chemistry of chiral R-2-bromobutane was studied on the naturally chiral Cu(643)R&S and Cu(531)R&S surfaces by comparing relative product yields during temperature-programmed reaction spectroscopy. Molecularly adsorbed R-2-bromobutane can desorb molecularly or debrominate to form R-2-butyl groups on the surfaces. The R-2-butyl groups react further by beta-hydride elimination to form 1- or 2-butene or by hydrogenation to form butane. Temperature-programmed reaction spectroscopy was used to quantify the relative yields of the various reaction products. At low coverages of R-2-bromobutane on Cu(643)R&S and Cu(531)R&S, the surface chemistry is not enantioselective. At monolayer coverage, however, the product yields indicate that the R-2-bromobutane decomposition reaction rates are sensitive to the handedness of the two chiral surfaces. The impact of surface structure on enantioselectivity was examined by studying the chemistry of R-2-bromobutane on both Cu(643)R&S and Cu(531)R&S. The selectivity of R-2-bromobutane desorption versus debromination is enantiospecific and differs significantly from Cu(643) to Cu(531). The selectivity of the R-2-butyl reaction by beta-hydride elimination versus hydrogenation is only weakly enantiospecific and is similar on both the Cu(643) and Cu(531) surfaces. These results represent the first quantitative observations of enantioselectivity in reactions with well-known mechanisms probed using a simple adsorbate on naturally chiral metal surfaces.     

Environment-independent 14-helix formation in short beta-peptides: striking a balance between shape control and functional diversity

We report a significant and unanticipated advance in the study of beta-amino acid-based foldamers: a small proportion of highly preorganized residues can impart high stability to a specific helical secondary structure in water. Most of the residues in these beta-peptides (2 and 3) are intrinsically flexible. Flexible beta-amino acids can be readily and enantiospecifically prepared in functionally diverse forms, but preorganized residues with side chains are rare and challenging to synthesize. Our findings demonstrate that interspersing a few copies of an unfunctionalized but rigid residue among a larger number of flexible residues with diverse side chains is a viable strategy for creating beta-peptides that adopt the 14-helix conformation and therefore display side chains in a predictable spatial arrangement. These results are significant because they enhance the prospects of developing beta-peptides with useful activities.     

Secondary structural preferences of 2,2-disubstituted pyrrolidine-4-carboxylic acid oligomers: beta-peptide foldamers that cannot form internal hydrogen bonds

We examine a new class of beta-peptides, 2,2-disubstituted pyrrolidine-4-carboxylic acid oligomers, and show that they manifest discrete conformational preferences despite the impossibility of internal hydrogen bonding. Numerous beta-peptide families have been described that display specific secondary structural preferences, but all of the conformations characterized in detail so far have contained internal hydrogen bonds. Internal hydrogen bonding is observed within the most common secondary structures of conventional peptides as well. Identifying foldamers in which shape control is independent of hydrogen bonding is significant in two ways. At a fundamental level, foldamers in this small but growing class are interesting because their shapes are controlled by distinctive networks of noncovalent forces. At a practical level, non-hydrogen bonded foldamers may be useful in biomedical applications because the low intrinsic polarity of their backbones may promote bioavailability.     

Non-hydrogen-bonded secondary structure in beta-peptides: evidence from circular dichroism of (S)-pyrrolidine-3-carboxylic acid oligomers and (S)-nipecotic acid oligomers

[formula: see text] Homooligomers of beta-amino acids (S)-3-pyrrolidine-3-carboxylic acid (PCA) and (S)-nipecotic acid (Nip) were studied by circular dichroism (CD) in methanol. In each series, a profound change in the far-UV CD spectrum was observed from monomer to tetramer, but little change was observed from tetramer to hexamer. A comparable pattern is observed in the CD spectra of short proline oligomers. We conclude that both PCA and Nip oligomers with > or = four residues adopt a characteristic secondary structure.