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4 article(s) from Kubyshkin, Vladimir

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

Vladimir Kubyshkin,
Rebecca Davis and
Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

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Figure 1: The structures of the fluoroprolines discussed herein.

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Figure 2: The distinction between “the alanine and the proline worlds”. While the polyalanine backbone leads ...

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Figure 3: Molecular volume for 20 coded amino acids and fluoroprolines. The COSMO volume was calculated for a...

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Figure 4: Comparative analysis of the electrostatic potential for proline and fluoroprolines (electrostatic p...

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Figure 5: Experimental logP data for methyl esters of N-acetylamino acids.

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Figure 6: The conformational dependence of the proline ring on the fluorination at position 4.

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Figure 7: Rotation around the peptidyl-prolyl fragments in polypeptide structures is important for correct ov...

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Figure 8: The complex fate of a protein-encoded amino acid in the cell (EF-Tu – elongation factor thermo unst...

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Figure 9: Metabolic routes for proline in E. coli. A) Synthesis of proline and B) degradation of proline.

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Figure 10: A complete flowchart for the proline incorporation into proteins during ribosomal biosynthesis. A) ...

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Figure 11: Amide bond formation capacities of fluoroprolines compared to some coded amino acids measured on ri...

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Figure 12: Ribbon representation of the X-ray crystal structures of proteins containing fluoroprolines. A) Enh...

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Figure 13: Problems and phenomena associated with the production of a protein-containing proline-to-fluoroprol...

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Figure 14: Effects of fluoroprolines on recombinant protein expression using the auxotrophic expression host E...

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Figure 15: A) Experimental setup for the incorporation of fluoroprolines into proteins. B) Adaptive laboratory...

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Review

Published 15 Feb 2021

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Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines

Vladimir Kubyshkin

Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151

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Figure 1: A) Three types of the backbone amino acid structures that are included in protein translation: glyc...

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Figure 2: The set of amino acids examined in this study.

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Figure 3: Design of the model system.

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Figure 4: Propagation of the C⁴-conformation into the values of the J coupling in the C²H–C³H₂ fragments.

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Figure 5: Preferred side-chain conformations according to the multiplicity data.

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Figure 6: A) The basicity reduction from the introduction of the dipoles reflects the preferred conformation ...

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Figure 7: The lipophilicity data of the model compounds.

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Figure 8: The expectations regarding the amide-bond rotation preferences in 1–4.

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Figure 9: The explanation for the difference in the rotation barriers in the diastereomeric (A), 4-(trifluoro...

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Figure 10: A) The structures of difluorinated model compounds 5 and 6, and the fluorine-free reference 7. B) B...

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Full Research Paper

Published 23 Jul 2020

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Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

Vladimir Kubyshkin and
Nediljko Budisa

Beilstein J. Org. Chem. 2017, 13, 2442–2457, doi:10.3762/bjoc.13.241

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Figure 1: A. Dependence of the lipophilicity (logP) on the number of fluorine atoms in a partially fluorinate...

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Scheme 1: Synthesis of the model compounds.

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Figure 2: Kinetics of the C-terminal ester hydrolysis.

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Figure 3: Partitioning of the esters 1–5 between octan-1-ol and water. Insert: comparison with the other part...

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Scheme 2: Amide isomerism in the N-acetylprolyl fragment.

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Figure 4: Enhancement of the trans/cis thermodynamic preferences in the ester models as a function of the sol...

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Scheme 3: A. Four-state conformational equilibrium model used by Siebler et al. [72] for explanations of the elev...

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Scheme 4: Elevation of the trans/cis ratio in derivatives of N-acyl proline may result from the enhanced n→π*...

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Scheme 5: Synthesis of the model peptides.

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Figure 5: Mean residue molar circular dichroism (Δε) of peptides 8–10 in methanol (left) and aqueous phosphat...

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Figure 6: Conformational analysis of the peptides by ¹H DOSY NMR (D₂O, 298 K). The theoretical values were ca...

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Figure 7: Hydrolysis of the C-terminal 2,2-difluoroethyl esters of the oligopeptides in buffered deuterium ox...

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Published 16 Nov 2017

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cis–trans-Amide isomerism of the 3,4-dehydroproline residue, the ‘unpuckered’ proline

Vladimir Kubyshkin and
Nediljko Budisa

Beilstein J. Org. Chem. 2016, 12, 589–593, doi:10.3762/bjoc.12.57

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Scheme 1: s-cis–s-trans Amide bond isomerism in an N-acyl-proline fragment.

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Figure 1: Amino acids that have been compared in this study.

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Figure 2: X-ray crystal structures of compounds 5–9. Carbon- grey, nitrogen – blue, oxygen – red, fluorine – ...

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Scheme 2: The relationship between the pK_a of the ammonium function in the amino acid and the amide rotationa...

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Figure 3: The double bond between C³ and C⁴ atoms in 3,4-dehydroproline residues induces an increase in the a...

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Published 29 Mar 2016

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