Design of a peptide hairpin containing a central three-residue loop

The construction of a designed beta-hairpin structure, containing a central three-residue loop has been successfully achieved in the synthetic nonapeptide Boc-Leu-Phe-Val-(D)Pro-(L)Pro-(D)Ala-Leu-Phe-Val-OMe (2). The design is based on expanding the two-residue loop established in the peptide beta-hairpin Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (1). Characterization of the registered beta-hairpins in peptides 1 and 2 is based on the observation of key nuclear Overhauser effects (NOEs) in CDCl(3) and CD(3)OH. Solvent titration and temperature dependence of NH chemical shifts establish the identity of NH groups involved in interstrand hydrogen bonding. In peptide 2, the antiparallel registry is maintained, with the formation of a (D)Pro-(L)Pro-(D)Ala loop, stabilized by a 5-->1 hydrogen bond between Val3 CO and Leu7 NH groups (C(13), alpha-turn) and a 3-->1 hydrogen bond between (D)Pro4 CO and (d)Ala6 NH groups (C(7), gamma-turn). NMR derived structures suggest that in peptide 2, (d)Ala(6) adopts an alpha(L) conformation. In peptide 1, the (D)Pro-(L)Pro segment adopts a type II' beta-turn. Replacement of (D)Ala (6) in peptide 2 by (L)Ala in peptide 3 yields a beta-hairpin conformation, with a central (D)Pro-(L)Pro two-residue loop. Strand slippage at the C-terminus results in altered registry of the antiparallel strands.     

Substrate specificity and novel selective inhibitors of TNF-alpha converting enzyme (TACE) from two-dimensional substrate mapping

We report a systematic analysis of the P1' and P2' substrate specificity of TNF-alpha converting enzyme (TACE) using a peptide library and a novel analytical method, and we use the substrate specificity information to design novel reverse hydroxamate inhibitors. Initial truncation studies, using the amino acid sequence around the cleavage site in precursor-TNF-alpha, showed that good turnover was obtained with the peptide DNP-LAQAVRSS-NH2. Based on this result, 1000 different peptide substrates of the form Biotin-LAQA-P1'-P2'-SSK(DNP)-NH2 were prepared, with 50 different natural and unnatural amino acids at P1' in combination with 20 different amino acids at P2'. The peptides were pooled, treated with purified microsomal TACE, and the reaction mixtures were passed over a streptavidin affinity column to remove unreacted substrate and the N-terminal biotinylated product. C-terminal cleavage products not binding to streptavidin were subjected to liquid chromatography/mass spectrometry analysis where individual products were identified and semiquantitated. 25 of the substrates were resynthesized as discrete peptides and assayed with recombinant TACE. The experiments show that recombinant TACE prefers lipophilic amino acids at the P1' position, such as phenylglycine, homophenylalanine, leucine and valine. At the P2' position, TACE can accommodate basic amino acids, such as arginine and lysine, as well as certain non-basic amino acids such as citrulline, methionine sulfoxide and threonine. These substrate preferences were used in the design of novel reverse hydroxamate TACE inhibitors with phenethyl and 5-methyl-thiophene-methyl side-chains at P1', and threonine and nitro-arginine at P2'.     

Substrate specificity of the human proteasome

BACKGROUND: Regulated proteolysis by the proteasome is crucial for a broad array of cellular processes, from control of the cell cycle to production of antigens. RESULTS: The rules governing the N-terminal primary and extended substrate specificity of the human 20S proteasome in the presence or absence of 11S proteasome activators (REGalpha/beta and REGgamma) have been elaborated using activity-based proteomic library tools. CONCLUSIONS: The 11S proteasome activators are shown to be important for both increasing the activity of the 20S proteasome and for altering its cleavage pattern and substrate specificity. These data also establish that the extended substrate specificity is an important factor for proteasomal cleavage. The specificities observed have features in common with major histocompatibility complex (MHC) class I ligands and can be used to improve the prediction of MHC class I restricted cytotoxic T-cell responses.     

Substrate specificity and reaction mechanism of recombinant styrene oxide isomerase from Pseudomonas putida S12

To clarify the substrate specificity of the recombinant styrene oxide isomerase, various epoxides were subjected to the reaction. From the substituent effect on the rate of isomerization, the mechanism of the isomerase catalyzed reaction was estimated.     

Synthesis and complexation of a novel cyclophane

A novel cyclophane, 17, 17, 40, 40-tetramethyl-7, 30-dinitro-1, 10, 24, 33-tetraoxa[2.2.1.2.2.1] metaparaparametaparaparacyclophane, was synthesized by 2:2 cyclization of 3,5-bis(bromomethyl)nitrobenzene, derived from 3,5-dimethylnitrobenzene, and bisphenol A. The cyclophane was found to form 1:1 complex with benzene.     

Asymmetric acyloin condensation catalysed by phenylpyruvate decarboxylase. Part 2: Substrate specificity and purification of the enzyme

Phenylpyruvate decarboxylase from Achromobacter eurydice was used to catalyse the asymmetric acyloin condensation of phenylpyruvate 1 with various aldehydes 2 to produce optically active acyloins PhCH₂COCH(OH)R 3. The specific activity of the phenylpyruvate decarboxylase enzyme was increased by a factor of 332 after its purification. The molecular weight of the purified enzyme was shown to be 150 kDa by gel filtration chromatography, while SDS gel electrophoresis showed two sub-units with molecular weights of 90 and 40 kDa. The acyloin condensation yield decreased with increasing chain length for straight chain aliphatic aldehydes from 76% for acetaldehyde to 24% for valeraldehyde. The e.e.s of the acyloin products were 87–98%. Low yields of acyloin products were obtained with chloroacetaldehyde (13%) and glycoaldehyde (16%). Indole-3-pyruvate was a substrate of the enzyme and provided acyloin condensation product 3-hydroxy-1-(3-indolyl)-2-butanone 5 with acetaldehyde in 19% yield, while benzoylformate was not a substrate for the enzyme.     

Conformational dynamics of a bispyridinium cyclophane

A complete study of the conformational behavior of 4,8-diaza-3(1,4),9(4,1)-dipyridina-1,6(1,4)-dibenzenacyclodecaphan-3(1),9(1)-bis(ilium) bishexafluorophosphate is described. This study allows us to conclude that the process observed by which the different chemical shifts of the pyridinium protons show coalescence at a high-temperature 1H NMR is the rotation around the C-N bond, whereas the conformational equilibrium between the four conformers is produced at low temperature.     

Studies on a forskolin ring C forming reaction

Results are reported that indicate that the rearrangement of hydroxy epoxide 2a to dihydropyran 3 which occurs with retention of configuration at C-8 proceeds either via a carbocation intermediate or by two successive substitution reactions, both with inversion of configuration.     

Ultra-high pressure synthesis of a tetrathiafulvalene-diquat cyclophane

Quaternization of a tetrathiafulvalene (TTF)/2,2′-bipyridine cyclophane under 10 kbar of pressure yields a TTF-diquat donor-acceptor cyclophane revealing distinct charge-transfer interactions.     

Substrate specificity of prostate-specific antigen (PSA)

Background: The serine protease prostate-specific antigen (PSA) is a useful clinical marker for prostatic malignancy. PSA is a member of the kallikrein subgroup of the (chymo)trypsin serine protease family, but differs from the prototypical member of this subgroup, tissue kallikrein, in possessing a specificity more similar to that of chymotrypsin than trypsin. We report the use of two strategies, substrate phage display and iterative optimization of natural cleavage sites, to identify labile sequences for PSA cleavage.Results: Iterative optimization and substrate phage display converged on the amino-acid sequence SS(Y/F)YIS(G/S) as preferred subsite occupancy for PSA. These sequences were cleaved by PSA with catalytic efficiencies as high as 220–3100 M⁻¹ s⁻¹, compared with values of 2–46 M⁻¹ s⁻¹ for peptides containing likely physiological target sequences of PSA from the protein semenogelin. Substrate residues that bind to secondary (non-S1) subsites have a critical role in defining labile substrates and can even cause otherwise disfavored amino acids to bind in the primary specificity (S1) pocket.Conclusions: The importance of secondary subsites in defining both the specificity and efficiency of cleavage suggests that substrate recognition by PSA is mediated by an extended binding site. Elucidation of preferred subsite occupancy allowed refinement of the structural model of PSA and should facilitate the development of more sensitive activity-based assays and the design of potent inhibitors.     

Substrate specificity of yeast invertase in transglycosylation reactions

The substrate specificity of purified yeast invertase isolated fromSaccharomyces cerevisiae in transglycosylation reactions was determined. The enzyme is specific for primary alcohols. The yeast activity is a function of the alkyl length and substrate hydrophobicity (n-butyl, isobutyl, isoamyl alcohols).Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 69–70, January–February, 2000.     

Solid state structure and solution conformation of a macrobicyclic cyclophane

X-ray crystallographic structure determination of the macrobicyclic cyclophane L¹ reveals a compact structure involving close edge-to-face approach of aromatic rings; ¹H nmr shows that this is also the solution conformation.     

Synthesis of large-ring lactams by a carbene-anion bond forming reaction

Treatment of large-ring lactams 1 with potassium t-butoxide results in the formation of bicyclic structures 2 . Evidence was obtained to support the formation of 2 through a carbene-anion coupling. The structures of a series of bicyclic lactams 2 have been rigorously defined.     

Spectroscopic evidence for gas-phase formation of successive beta-turns in a three-residue peptide chain

We report the first gas-phase spectroscopic study of a three-residue model of a peptide chain, Ac-Phe-Gly-Gly-NH2 (Ac = acetyl), using the IR/UV double resonance technique. The existence of at least five different conformers under supersonic expansion conditions is established, most of them exhibiting rather strong intramolecular H-bonds. One of the most populated conformers, however, exhibits a different H-bonding network characterized by two weak H-bonds. Comparison of the amide A and I/II experimental data with density functional theory calculations carried out on a series of selected conformations enables us to assign this conformer to two successive beta-turns along the peptide chain, the two H-bonds being of C10 type, i.e., each of them closing a 10-atom ring in the molecule. The corresponding form is found to be more stable than the 310 helix secondary structure (not observed), presumably because of specific effects due to the glycine residues.     

Spectroscopic properties of cyclophane/anthracene and cyclophane/9-fluorenone complexes in dichloromethane

Host/guest interactions of cyclophane/anthracene (C/A) and cyclophane/9-fluorenone (C/F) complexes in dichloromethane, where the cyclophane molecule is the host, are investigated. The stability constants, log K_a, for the C/A and C/F complexes are determined by absorption and fluorescence spectroscopy. For the C/A system, log K_a is 4.2±0.2 as determined from absorption (at 325 nm) and emission (at 382, 403 and 427 nm) spectroscopic data. The analogous measurements yield 3.6±0.2 from absorption (at 309 nm) and emission (at 505 nm) spectroscopic data for the C/F system. Heats of formation of these complexes were determined by measuring the complex association constants at 25, 29 and 32 °C. These results reveal that binding of the anthracene guest by this cyclophane molecule is thermodynamically favored over that for a 9-fluorenone guest. Excited state lifetimes of these systems are also determined.     

Engineering enzyme specificity using computational design of a defined-sequence library

Engineered biosynthetic pathways have the potential to produce high-value molecules from inexpensive feedstocks, but a key limitation is engineering enzymes with high activity and specificity for new reactions. Here, we developed a method for combining structure-based computational protein design with library-based enzyme screening, in which inter-residue correlations favored by the design are encoded into a defined-sequence library. We validated this approach by engineering a glucose 6-oxidase enzyme for use in a proposed pathway to convert D-glucose into D-glucaric acid. The most active variant, identified after only one round of diversification and screening of only 10,000 wells, is approximately 400-fold more active on glucose than is the wild-type enzyme. We anticipate that this strategy will be broadly applicable to the discovery of new enzymes for engineered biological pathways.