An official website of the United States government
Abstract Thioamides represent highly valuable isosteric in the strictest sense “single‐atom substitution” analogues of amides that have found broad applications in chemistry and biology. A long‐standing challenge is the direct transamidation of thioamides, a process which would convert one thioamide bond (R−C(S)−NR1R2) into another (R−C(S)−NR3N4). Herein, we report the first general method for the direct transamidation of thioamides by highly chemoselective N−C(S) transacylation. The method relies on site‐selective N‐tert‐butoxycarbonyl activation of 2° and 1° thioamides, resulting in ground‐state‐destabilization of thioamides, thus enabling to rationally manipulate nucleophilic addition to the thioamide bond. This method showcases a remarkably broad scope including late‐stage functionalization (>100 examples). We further present extensive DFT studies that provide insight into the chemoselectivity and provide guidelines for the development of transamidation methods of the thioamide bond.
more »
« less
Side‐chain thioamides as fluorescence quenching probes
Abstract Thioamides, single atom oxygen‐to‐sulfur substitutions of canonical amide bonds, can be valuable probes for protein folding and protease studies. Here, we investigate the fluorescence quenching properties of thioamides incorporated into the side‐chains of amino acids. We synthesize and incorporate Fmoc‐protected, solid‐phase peptide synthesis building blocks for introducingNε‐thioacetyl‐lysine andγ‐thioasparagine. Using rigid model peptides, we demonstrate the distance‐dependent fluorescence quenching of these thioamides. Furthermore, we describe attempts to incorporate ofNε‐thioacetyl‐lysine into proteins expressed inEscherichia coliusing amber codon suppression.
more »
« less
- PAR ID:
- 10454296
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Biopolymers
- Volume:
- 112
- Issue:
- 1
- ISSN:
- 0006-3525
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Thioamide substitutions in the backbones of proteins can modulate their structure and thermostability, or serve as spectroscopic probes in fluorescence quenching experiments. Using native chemical ligation, we have produced the first examples of a protein (calmodulin) containing two thioamides. Dithioamide variants were made to explore the effects of combining stabilizing, neutral, and destabilizing single thioamide substitutions. One of the dithioamide calmodulin variants exhibited stabilization greater than any monothioamide variant, although the effect could not easily be anticipated from the results of single substitutions. Each of the calmodulin variants retained the ability to bind a target peptide, and the dithioamide proteins exhibited an increase in fluorescence quenching of tryptophan relative to their single thioamide counterparts. These results show that multiply thioamidated proteins can be synthesized, and that properly placed thioamides can be used to increase protein thermostability or enhance fluorecsence quenching in peptide binding experiments.more » « less
-
Estimating the volume of a convex body is a central problem in convex geometry and can be viewed as a continuous version of counting. We present a quantum algorithm that estimates the volume of ann-dimensional convex body within multiplicative error ε usingÕ(n3+ n2.5/ε) queries to a membership oracle andÕ(n5+n4.5/ε)additional arithmetic operations. For comparison, the best known classical algorithm usesÕ(n3.5+n3/ε2)queries andÕ(n5.5+n5/ε2)additional arithmetic operations. To the best of our knowledge, this is the first quantum speedup for volume estimation. Our algorithm is based on a refined framework for speeding up simulated annealing algorithms that might be of independent interest. This framework applies in the setting of “Chebyshev cooling,” where the solution is expressed as a telescoping product of ratios, each having bounded variance. We develop several novel techniques when implementing our framework, including a theory of continuous-space quantum walks with rigorous bounds on discretization error. To complement our quantum algorithms, we also prove that volume estimation requiresΩ (√ n+1/ε)quantum membership queries, which rules out the possibility of exponential quantum speedup innand shows optimality of our algorithm in 1/ε up to poly-logarithmic factors.more » « less
-
Abstract The syntheses are reported of Nϵ‐(2,2,2‐trifluoroethyl)‐D,L‐lysine (tFK) and Nζ‐(2,2,2‐trifluoroethyl)‐D,L‐homolysine (tFK+1) from amino alcohols HO−(CH2)n−NH2. The syntheses involve reductive amination, Appel bromination, and the stereoselective bond formation between Cα of the amino acid and the fluorinated alkyl chain in the Schöllkopf bislactim amino acid synthesis. The methyl esters of the fluorinated amino acids are the relevant substrates for oligopeptide synthesis. With theR‐Schöllkopf reagent, we stereoselectively generated methyl Nϵ‐boc‐Nϵ‐(2,2,2‐trifluoroethyl)‐L‐lysinate and methyl Nζ‐boc‐Nζ‐(2,2,2‐trifluoroethyl)‐L‐homolysinate. Products and intermediates were characterized by 1H NMR, 13C NMR, COSY, HSQC, and LCMS. A variety of N‐functionality may be introduced by reacting hemiacetals with different appendages. This fluorine modification reduces the sidechain N‐basicity by combined ‐I effect of the three fluorines. This effect increases the [amine]/[ammonium ion] ratio of the sidechain amine in lysine to facilitate carbamylation at lower pH conditions.more » « less
-
Abstract Crop N decision support tools are typically based on either empirical relationships that lack mechanistic underpinnings or simulation models that are too complex to use on farms with limited input data. We developed an N mineralization model for corn that lies between these endpoints; it includes a mechanistic model structure reflecting microbial and texture controls on N mineralization but requires just a few simple inputs: soil texture soil C and N concentration and cover crop N content and carbon to nitgrogen ratio (C/N). We evaluated a previous version of the model with an independent dataset to determine the accuracy in predictions of unfertilized corn (Zea maysL.) yield across a wider range of soil texture, cover crop, and growing season precipitation conditions. We tested three assumptions used in the original model: (1) soil C/N is equal to 10, (2) yield does not need to be adjusted for growing season precipitation, and (3) sand content controls humification efficiency (ε). The best new model used measured values for soil C/N, had a summertime precipitation adjustment, and included both sand and clay content as predictors ofε(root mean square error [RMSE] = 1.43 Mg ha−1;r2 = 0.69). In the new model, clay has a stronger influence than sand onε, corresponding to lower predicted mineralization rates on fine‐textured soils. The new model had a reasonable validation fit (RMSE = 1.71 Mg ha−1;r2 = 0.56) using an independent dataset. Our results indicate the new model is an improvement over the previous version because it predicts unfertilized corn yield for a wider range of conditions.more » « less
