Peptide tic-tac-toe: heterotrimeric coiled-coil specificity from steric matching of multiple hydrophobic side chains

Specific coiled-coil heterotrimers result from steric matching of hydrophobic core side chains. A 2:1 heterotrimer is formed by peptides containing alanine or cyclohexylalanine, respectively, at a central core residue. Detailed thermodynamic analysis reveals that the designed complex is considerably more stable than the corresponding alanine homotrimer (deltaT(m) = 25 degrees C, deltadeltaG(unf) = 4.5 kcal/mol), while control complexes with naphthylalanine or cyclopropylalanine peptides are much less stable. However, the cyclohexylalanine homotrimer is of comparable stability to the 2:1 complex, prompting an investigation of multiply substituted peptides. A specific 1:1:1 heterotrimer is formed from three independent peptide strands, each bearing one large (cyclohexylalanine) and two small (alanine) side chains at the same three core positions but in different order. The combined impact of three substitutions improves specificity to the point where each pure peptide and all pairwise equimolar mixtures form significantly less stable complexes (deltaTm = 22-24 degrees C). The capacity for specific complex formation governed by multiple unnatural core side chains should facilitate design of numerous new peptide assemblies.     

The Role of Specific Side Groups and pH in Magnetization Transfer in Polymers

The nature of water–macromolecule interactions in aqueous model polymers has been investigated using quantitative measurements of magnetization transfer. Cross-linked polymer gels composed of 94% water, 3%N,N′-methylene-bis-acrylamide, and 3% functional monomer (acrylamide, methacrylamide, acrylic acid, methacrylic acid, 2-hydroxyethyl-acrylate, or 2-hydroxyethyl-methacrylate) were studied. Water–macromolecule interactions were modified by varying the pH and specific functional group on the monomer. The magnitudes of the interactions were quantified by measuring the rate of proton nuclear spin magnetization exchange between the polymer matrix and the water. This rate was highly sensitive to the presence of carboxyl side groups on the macromolecule. However, the dependence of the rate on pH was not consistent with simple acid/base-catalyzed chemical exchange, and instead, the data suggest that multiequilibria proton exchange, a wide distribution in surface group pKvalues, and/or a macromolecular structural dependence on pH may play a significant role in magnetization transfer in polymer systems. These model polymer gels afford useful insights into the relevance of chemical composition and chemical dynamics on relaxation in tissues.     

Convenient access to glutamic acid side chain homologues compatible with solid phase peptide synthesis

[reaction: see text] Preparation of several side chain length variants of glutamic acid is achieved via olefin cross metathesis of allyl glycine derivatives. The products are suitably protected for direct use in Fmoc solid-phase peptide synthesis, as demonstrated by successful synthesis of test sequences.     

pH-triggered strand exchange in coiled-coil heterotrimers

The capacity for pH-triggered strand exchange in designed coiled-coil heterotrimers is demonstrated. Systems employing both hydrophobic core (steric matching) and hydrophilic interface (electrostatic matching) design principles assemble into specific 1:1:1 heterotrimers. Alteration of pH creates electrostatic mismatches, inducing strand exchange in the presence of a suitable replacement peptide. Complexes with one Lys/Lys interface, favored at neutral to high pH, can be transformed to ones with a Glu/Glu contact by lowering pH and adding an appropriate new binding partner. The need to simultaneously maintain matched core alignments enforces specificity in this exchange, such that only a single specific peptide is replaced. These principles have subsequently been applied to the design of dynamically triggered cross-linked structures, in which a bifunctional disulfide-tethered peptide can cross-link two heterotrimers. Both formation and disruption of the cross-link are under pH control.