Biomedical subjects
Publications and source records attributed to James S Nowick.
[structure: see text] The widely used internal standard for NMR studies in aqueous solution DSS (sodium 4,4-dimethyl-4-silapentane-1-sulfonate) can interact with cationic peptides, diminishing its value for such studies. This paper introduces DSA (4,4-dimethyl-4-silapentane-1-ammonium trifluoroacetate) as a new internal standard that does not suffer from this problem.
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Previous studies by Gellman and co-workers have elegantly shown that mirror-image beta-turns based upon d-Pro-Gly are especially good at stabilizing beta-hairpins and have demonstrated that peptide 1 [Arg-Trp-Gln-Tyr-Val-d-Pro-Gly-Lys-Phe-Thr-Val-Gln-NH2] folds into a well-defined beta-hairpin [Espinosa, J. F.; Gellman, S. H. Angew. Chem., Int. Ed. 2000, 39, 2330-2333]. The present study establishes that the amino acid ornithine (Orn) also forms a turn structure that is excellent at stabilizing beta-hairpins when linked through the delta-amino group and that this turn is comparable to d-Pro-Gly in ability to induce beta-hairpin formation. Thus, 1H NMR chemical shift and NOE studies establish that Orn-containing analogue 2 [Arg-Trp-Gln-Tyr-Val-deltaOrn-Lys-Phe-Thr-Val-Gln-NH2] is comparable in structure to peptide 1. The present study also establishes that the Orn turn is superior to Asn-Gly turns and that replacement of the deltaOrn with epsilonLys or d-deltaOrn generates structures that do not fold significantly.
The ability to generate RNA molecules that can catalyze complex organic transformations not only facilitates the reconstruction and plausibility of possible prebiotic reaction pathways but is also crucial for elucidating the potential of the application of RNA catalysts in organic syntheses. Iterative RNA selection previously identified a ribozyme that catalyzes the Michael addition of a cysteine thiol to an alpha,beta-unsaturated amide. This reaction is chemically similar to the rate limiting step of the thymidylate synthase reaction, which is the corresponding reaction of a cysteine thiol to the double-bond of the uracil nucleobase. Here we provide a detailed description of the synthesis of the ribozyme substrates and the substrate oligonucleotides used for its characterization and the investigation of the background reaction. We also describe the further characterization of the ribozyme with respect to substrate specificity. We show that the thiol group of the cysteine nucleophile is essential for the reaction to proceed. When substituted for a thiomethyl group, no reaction takes place.
Recent reports by Galeazzi and co-workers demonstrated the susceptibility of Abeta(1-42) to undergo dityrosine formation via peroxidase-catalyzed tyrosine cross-linking. We have formed dityrosine cross-links in Abeta(1-40) using these enzymatic conditions as well as a copper-H(2)O(2) method. The efficiency of dityrosine cross-link formation is strongly influenced by the aggregation state of Abeta; more dityrosine is formed when copper-H(2)O(2) or horseradish peroxidase-catalyzed oxidation is applied to fibrillar Abeta vs soluble Abeta. Once formed, dityrosine cross-links are susceptible to further oxidative processes and it appears that cross-links formed in soluble Abeta react through these pathways more readily than those formed in fibrillar Abeta. Because preorganization of fibrils affects the efficiency of dityrosine formation, we examined the effect of dityrosine formation upon local peptide conformation by assessing the solution structure of a small dityrosine dimer derived from Abeta(8-14). Two-dimensional (1)H NMR studies of the short dityrosine dimer offer no evidence of structure. Thus, the fibrillar structure of Abeta enhances formation of dityrosine cross-links, but dityrosine cross-links do not seem to enhance local secondary structure.
enol-Pyruvaldehyde (ePY or 2-hydroxypropenal, O=C(H)-C(OH)=CH(2)) a transient intermediate in the alkaline decomposition of the triosephosphates to methylglyoxal is now observed by UV and (1)H NMR spectroscopy as the immediate product of the methylglyoxal synthetase (MGS) reaction: dihydroxyacetone-P --> P(i) + ePY --> methylglyoxal (MG). Analysis of ePY formed from 1-(13)C- and (1R, 3S) -[1,3-(2)H]-DHAP establishes the stereochemical course of its formation by MGS. Its rate of ketonization is much too slow to be in the sequence required for the assay of MGS by coupling of the MG produced to glyoxalase I (Glx I): MG + glutathione (GSH) --> (S)-lactylglutathione (D-LG). Instead, ketonization occurs by way of the hemithioacetal (HTA) formed between ePY and GSH, and could be either an enzymatic function of Glx I or occur nonenzymatically at an activated rate. Enzymatic ketonization was ruled out because the methyl group of D-LG formed from specifically labeled ePY is achiral. Chemical ketonization of ePY is activated by general bases, such as acetate, and by thiols such as GSH and 2-mercaptoethanol, which disrupt its stabilizing double bond conjugation as hemithioacetal (HTA) adducts. 2-Mercaptoacetate combines both functions, acting as the HTA adduct of ePY with the appended carboxylate group presumably positioned to promote abstraction of the enol proton and protonation of the enolate carbon at an accelerated rate. In the MGS-Glx I system (dihydroxyacetone-P --> ePY, ePY + GSH --> GS-ePY, GS-ePY --> GS-MG, GS-MG --> D-LG), the nonenzymatic 2nd and 3rd steps describe the catalytic role of GSH in the critical ketonization process and set the stage for its participation in the glyoxalase system.
This paper introduces a unique amino acid that can readily be incorporated into peptides to make them fold into beta-sheetlike structures that dimerize through beta-sheet interactions. This new amino acid, Orn(i-PrCO-Hao), consists of an ornithine residue with the beta-strand-mimicking amino acid Hao [J. Am. Chem. Soc. 2000, 122, 7654-7661] attached to its side chain. When Orn(i-PrCO-Hao) is incorporated into a peptide, or appended to its N-terminus, the Hao group hydrogen bonds to the three subsequent residues to form a beta-sheetlike structure. The amino acid Orn(i-PrCO-Hao) is readily used in peptide synthesis as its Fmoc derivative, Fmoc-Orn(i-PrCO-Hao)-OH (3). Fmoc-Orn(i-PrCO-Hao)-OH behaves like a regular amino acid in peptide synthesis and was uneventfully incorporated into the peptide o-anisoyl-Val-Orn(i-PrCO-Hao)-Phe-Ile-Leu-NHMe (4) through standard automated Fmoc solid-phase peptide synthesis, with DIC and HOAt as the coupling agent for Fmoc-Orn(i-PrCO-Hao)-OH and o-anisic acid and HATU as the coupling agent for all other couplings. A second synthetic strategy was developed to facilitate the preparation of peptides with N-terminal Orn(i-PrCO-Hao) residues, which avoids the need for the preparation of Fmoc-Orn(i-PrCO-Hao)-OH. In this strategy, Boc-Orn(Fmoc)-OH is used as the penultimate amino acid in the peptide synthesis, and i-PrCO-Hao-OH (2) is used as the final amino acid. N-Terminal Orn(i-PrCO-Hao) peptide H-Orn(i-PrCO-Hao)-Phe-Ile-Leu-NHMe.TFA (5) was prepared in a fashion similar to that for 4, using DIC and HOAt as the coupling agent for i-PrCO-Hao-OH and HATU as the coupling agent for all other couplings. 1H NMR transverse-ROESY, coupling constant, and chemical shift studies establish that peptide 4 forms a dimeric beta-sheetlike structure in CDCl3 solution. The 1H NMR studies also suggest that the ornithine unit adopts a well-defined turn conformation. Analogous 1H NMR studies of peptide 5 indicate that this TFA salt folds but does not dimerize in CD3OD solution. Collectively, these synthetic and spectroscopic studies establish that the amino acid Orn(i-PrCO-Hao) induces beta-sheet structure and interactions in peptides in suitable organic solvents. Unlike the Hao amino acid, which acts as a prosthetic to replace three residues of the peptide strand, the Orn(i-PrCO-Hao) amino acid acts as a splint that helps enforce a beta-sheetlike structure without replacing the residues and their side chains. This feature of Orn(i-PrCO-Hao) is important, because it allows the creation of beta-sheet structure with minimal perturbation of the peptide sequence.