Protein design with L- and D-alpha-amino acid structures as the alphabet

Chirality-Mediated Mechanical and Structural Properties of Oligopeptide Hydrogels

The origin and the effects of homochirality in the biological world continuously stimulate numerous hypotheses and much debate. This work attempts to look at the biohomochirality issue from a different angle-the mechanical properties of the bulk biomaterial and their relation to nanoscale structures. Using a pair of oppositely charged peptides that co-assemble into hydrogels, we systematically investigated the effect of chirality on the mechanical properties of these hydrogels through different combinations of syndiotactic and isotactic peptides. It was found that homochirality confers mechanical advantage, resulting in higher elastic modulus and strain yield value. Yet, heterochirality confer kinetic advantage, resulting in faster gelation. Structurally, both homochiral and heterochiral hydrogels are made of fibers interconnected by lappet-like webs, but the homochiral peptide fibers are thicker and denser. The result highlights the possible role of biohomochirality in the evolution and/or natural selection of biomaterials.

Creating novel protein scripts beyond natural alphabets

Natural proteins are concatenated amino acids with definite handedness or chirality, with their spatial orientation being preferentially left handed or L-chiral. This paper discusses the biophysics of stereo-chemical perturbation to proteins using D-(α) amino acid and its utility as an additional design alphabet while scripting novel protein structures.

Zinc-finger hydrolase: Computational selection of a linker and a sequence towards metal activation with a synthetic αββ protein

The zinc-finger protein is targeted for computational redesign as a hydrolase enzyme. Successful in having zinc activated for hydrolase function, the study validates the stepwise approach to having the protein tuned in main-chain structure stereochemically and over side chains chemically. A leucine homopolypeptide, harboring histidines to tri coordinate zinc and d-amino-acid-nucleated α-helix and β-hairpin building blocks of an αββ protein, is taken up for modeling, first with cyana, in a mixed-chirality linker between the building blocks, and then with IDeAS, in a sequence over side chains. The designed mixed-chirality polypeptide structure is proven to order as an intended αββ fold and capture zinc to activate its role as a hydrolase catalyst. The design approach to have protein folds defined stereochemically and receptor and catalysis functions defined chemically is presented, and illustrates L- and D-α-amino-acid structures as the alphabet integrating chemical- and stereochemical-structure variables as its letters.

Modeling of peptides containing D-amino acids: implications on cyclization

Cyclic peptides are therapeutically attractive due to their high bioavailability, potential selectivity, and scaffold novelty. Furthermore, the presence of D-residues induces conformational preferences not followed by peptides consisting of naturally abundant L-residues. Therefore, comprehending how amino acids induce turns in peptides, subsequently facilitating cyclization, is significant in peptide design. Here, we performed 20-ns explicit-solvent molecular dynamics simulations for three diastereomeric peptides with stereochemistries: LLLLL, LLLDL, and LDLDL. Experimentally LLLLL and LDLDL readily cyclize, whereas LLLDL cyclizes in low yield. Simulations at 310 K produced conformations with inter-terminal hydrogen bonds that correlated qualitatively with the experimental cyclization trend. Energies obtained for representative structures from quantum chemical (B3LYP/PCM/cc-pVTZ//HF/6-31G*) calculations predicted pseudo-cyclic and extended conformations as the most stable for LLLLL and LLLDL, respectively, in agreement with the experimental data. In contrast, the most stable conformer predicted for peptide LDLDL was not a pseudo-cyclic structure. Moreover, D-residues preferred the experimentally less populated alpha(L) rotamers even when simulations were performed at a higher temperature and with strategically selected starting conformations. Energies calculated with molecular mechanics were consistent only with peptide LLLLL. Thus, the conformational preferences obtained for the all L: -amino acid peptide were in agreement with the experimental observations. Moreover, refinement of the force field is expected to provide far-reaching conformational sampling of peptides containing D-residues to further develop force field-based conformational-searching methods.

Chemogenomics with protein secondary-structure mimetics

During molecular recognition of proteins in biological systems, helices, reverse turns, and beta-sheets are dominant motifs. Often there are therapeutic reasons for blocking such recognition sites, and significant progress has been made by medicinal chemists in the design and synthesis of semirigid molecular scaffolds on which to display amino acid side chains. The basic premise is that preorganization of the competing ligand enhances the binding affinity and potential selectivity of the inhibitor. In this chapter, current progress in these efforts is reviewed.

Switching the chirality of the metal environment alters the coordination mode in designed peptides

The effects of switching the chirality of a single layer of amino acids in a three stranded coiled coil has been investigated. X-ray crystallography reveals that this modification is well tolerated and does not alter the designed structure. In contrast, spectroscopic studies of cadmium binding to both the L- and D- enantiomers of the penicillamine, provide evidence that this switch dramatically alters the metal binding capability, the resulting coordination environment and the position of binding.