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Banaś K, Lenartowicz P, Staś M, Dziuk B, Siodłak D. Insight into the Structure of Victorin, the Host-Selective Toxin from the Oat Pathogen Cochliobolus victoriae. Studies of the Unique Dehydroamino Acid β-Chlorodehydroalanine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37486973 PMCID: PMC10401702 DOI: 10.1021/acs.jafc.3c01387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Victorins, a family of peptide toxins, produced by the fungal pathogen Cochliobolus victoriae and responsible for disease of some oat varieties, contain a β-chlorodehydroalanine residue, ΔAla(βCl). To determine the conformational properties of this unique dehydroamino acid, a series of model compounds was studied using X-ray, NMR, and FT-IR methods, supported by theoretical calculations. The ΔAla(βCl) geometrical isomers differ in conformational profile. The isomer Z prefers the helical conformation α (φ, ψ = -61°, -24°), PPII type conformation β (φ, ψ = -47°, 136°), and semiextended conformation β2 (φ, ψ = -116°, 9°) in weakly and more polar solutions. The isomer E prefers mainly the extended conformation C5 (φ, ψ = -177°, 160°), but with an increase of the environment polarity also conformations β (φ, ψ = -44°, 132°) and α (φ, ψ = -53°, -39°). In the most stable conformations the N-H···Cl hydrogen bond (5γ) occurs, created between the chlorine atom of the side chain and the N-H donor of the flanking amide group. The method of synthesis of the β-chlorodehydroalanine residue is proposed, by chlorination of dehydroalanine and then the photoisomerization from the isomer Z to E. The presented results indicate that the assignment of the geometrical isomer of the ΔAla(βCl) residue in naturally occurring victorins still remains an open question, despite being crucial for biological activity.
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Affiliation(s)
- Karolina Banaś
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Paweł Lenartowicz
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Monika Staś
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Błażej Dziuk
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14, Wroclaw 50-383, Poland
| | - Dawid Siodłak
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
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Staś M, Najgebauer P, Siodłak D. Imidazole-amino acids. Conformational switch under tautomer and pH change. Amino Acids 2023; 55:33-49. [PMID: 36319875 PMCID: PMC9877100 DOI: 10.1007/s00726-022-03201-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/16/2022] [Indexed: 01/26/2023]
Abstract
Replacement of the main chain peptide bond by imidazole ring seems to be a promising tool for the peptide-based drug design, due to the specific prototropic tautomeric as well as amphoteric properties. In this study, we present that both tautomer and pH change can cause a conformational switch of the studied residues of alanine (1-4) and dehydroalanine (5-8) with the C-terminal peptide group replaced by imidazole. The DFT methods are applied and an environment of increasing polarity is simulated. The conformational maps (Ramachandram diagrams) are presented and the stability of possible conformations is discussed. The neutral forms, tautomers τ (1) and π (2), adapt the conformations αRτ (φ, ψ = - 75°, - 114°) and C7eq (φ, ψ = - 75°, 66°), respectively. Their torsion angles ψ differ by about 180°, which results in a considerable impact on the peptide chain conformation. The cation form (3) adapts both these conformations, whereas the anion analogue (4) prefers the conformations C5 (φ, ψ = - 165°, - 178°) and β2 (φ, ψ ~ - 165°, - 3°). Dehydroamino acid analogues, the tautomers τ (5) and π (6) as well as the anion form (8), have a strong tendency toward the conformations β2 (φ, ψ = - 179°, 0°) and C5 (φ, ψ = - 180°, 180°). The preferences of the protonated imidazolium form (7) depend on the environment. The imidazole ring, acting as a donor or acceptor of the hydrogen bonds created within the studied residues, has a profound effect on the type of conformation.
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Affiliation(s)
- Monika Staś
- Faculty of Chemistry, University of Opole, 45-052, Opole, Poland.
| | - Piotr Najgebauer
- Faculty of Chemistry, University of Opole, 45-052, Opole, Poland
| | - Dawid Siodłak
- Faculty of Chemistry, University of Opole, 45-052, Opole, Poland
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Pellegrino R, Blasi F, Angelini P, Ianni F, Alabed HBR, Emiliani C, Venanzoni R, Cossignani L. LC/MS Q-TOF Metabolomic Investigation of Amino Acids and Dipeptides in Pleurotus ostreatus Grown on Different Substrates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10371-10382. [PMID: 35944091 PMCID: PMC9413224 DOI: 10.1021/acs.jafc.2c04197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 05/13/2023]
Abstract
The well-established correlation between diet and health arouses great interest in seeking new health-promoting functional foods that may contribute to improving health and well-being. Herein, the metabolomic investigation of Pleurotus ostreatus samples grown on two different substrates (black poplar wood logs, WS, and lignocellulosic byproducts, LcS) revealed the high potential of such a mushroom as a source of bioactive species. The liquid chromatography/mass spectrometry combined with quadrupole time-of-flight (LC/MS Q-TOF) analysis allowed the identification of essential and nonessential amino acids along with the outstanding presence of dipeptides. Multivariate statistical models highlighted important differences in the expression of both classes of compounds arising from the growth of P. ostreatus strains on WS and LcS. The former, in particular, was correlated to an increased expression of carnitine-based amino acid derivatives and proline-based dipeptides. This finding may represent a potential strategy to drive the expression of bioactive compounds of interest to obtain enriched mushrooms or useful functional ingredients from them.
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Affiliation(s)
| | - Francesca Blasi
- Department
of Pharmaceutical Sciences, University of
Perugia, 06126 Perugia, Italy
| | - Paola Angelini
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06122 Perugia, Italy
| | - Federica Ianni
- Department
of Pharmaceutical Sciences, University of
Perugia, 06126 Perugia, Italy
| | - Husam B. R. Alabed
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06122 Perugia, Italy
| | - Carla Emiliani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06122 Perugia, Italy
| | - Roberto Venanzoni
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06122 Perugia, Italy
| | - Lina Cossignani
- Department
of Pharmaceutical Sciences, University of
Perugia, 06126 Perugia, Italy
- Center
for Perinatal and Reproductive Medicine, Santa Maria della Misericordia University Hospital, University of
Perugia, Sant’Andrea
delle Fratte, 06132 Perugia, Italy
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Staś M, Broda MA, Siodłak D. Thiazole-amino acids: influence of thiazole ring on conformational properties of amino acid residues. Amino Acids 2021; 53:673-686. [PMID: 33837859 PMCID: PMC8128816 DOI: 10.1007/s00726-021-02974-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/29/2021] [Indexed: 12/29/2022]
Abstract
Post-translational modified thiazole-amino acid (Xaa-Tzl) residues have been found in macrocyclic peptides (e.g., thiopeptides and cyanobactins), which mostly inhibit protein synthesis in Gram + bacteria. Conformational study of the series of model compounds containing this structural motif with alanine, dehydroalanine, dehydrobutyrine and dehydrophenylalanine were performed using DFT method in various environments. The solid-state crystal structure conformations of thiazole-amino acid residues retrieved from the Cambridge Structural Database were also analysed. The studied structural units tend to adopt the unique semi-extended β2 conformation; which is stabilised mainly by N-H⋯NTzl hydrogen bond, and for dehydroamino acids also by π-electron conjugation. The conformational preferences of amino acids with a thiazole ring were compared with oxazole analogues and the role of the sulfur atom in stabilising the conformations of studied peptides was discussed.
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Affiliation(s)
- Monika Staś
- Faculty of Chemistry, University of Opole, 45-052, Opole, Poland.
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo Náměstí 2, 166 10, Praha 6, Czech Republic.
| | | | - Dawid Siodłak
- Faculty of Chemistry, University of Opole, 45-052, Opole, Poland.
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Wałęsa R, Broda MA. The influence of solvent on conformational properties of peptides with Aib residue-a DFT study. J Mol Model 2017; 23:349. [PMID: 29164349 PMCID: PMC5698364 DOI: 10.1007/s00894-017-3508-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/24/2017] [Indexed: 12/30/2022]
Abstract
The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results, the available conformations of similar X-ray structures from the Cambridge Crystallographic Data Center (CCDC) were analyzed. The results of the calculations show that both derivatives with the Aib residue in the gas phase prefer structures stabilized by intramolecular N-H⋯O hydrogen bonds, i.e., C5 and C7 conformations, while polar solvent promotes helical conformation with φ, ψ values equal to +/-60°, +/-40°. In addition, in the case of molecule 2, the helical conformation is the only one available in the polar environment. This result is fully consistent with the X-ray data. Graphical abstract Effect of solvent on the Ramachandran maps of the model peptides with Aib residue.
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Affiliation(s)
- Roksana Wałęsa
- Faculty of Chemistry, University of Opole, 48, Oleska St., 45-052 Opole, Poland
| | - Małgorzata A. Broda
- Faculty of Chemistry, University of Opole, 48, Oleska St., 45-052 Opole, Poland
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Wałęsa R, Broda MA. Solvent effects on the conformational preferences of model peptoids. MP2 study. J Pept Sci 2014; 20:203-11. [PMID: 24520015 DOI: 10.1002/psc.2601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/12/2013] [Accepted: 11/22/2013] [Indexed: 01/04/2023]
Abstract
The influence of aqueous environment on the main-chain conformation (ω0 , ϕ, and ψ dihedral angles) of two model peptoids: N-acetyl-N-methylglycine N'-methylamide (Ac-N(Me)-Gly-NHMe) (1) and N-acetyl-N-methylglycine N',N'-dimethylamide (Ac-N(Me)-Gly-NMe₂) (2) was investigated by MP2/6-311++G(d,p) method. The Ramachandran maps of both studied molecules with cis and trans configuration of the N-terminal amide bond in the gas phase and in water environment were obtained and all energy minima localized. The polarizable continuum model was applied to estimate the solvation effect on conformation. Energy minima of the Ac-N(Me)-Gly-NHMe and Ac-N(Me)-Gly-NMe₂ have been analyzed in terms of the possible hydrogen bonds and C = O dipole attraction. To validate the theoretical results obtained, conformations of the similar structures gathered in the Cambridge Crystallographic Data Centre were analyzed. Obtained results indicate that aqueous environment in model peptoids 1 and 2 favors the conformation F (ϕ and ψ = -70º, 180º), and additionally significantly increases the percentage of structures with cis configuration of N-terminal amide bond in studied compounds.
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Buczek A, Wałęsa R, Broda MA. β-turn tendency in N-methylated peptides with dehydrophenylalanine residue: DFT study. Biopolymers 2012; 97:518-28. [DOI: 10.1002/bip.22034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Revised: 02/02/2011] [Accepted: 02/04/2011] [Indexed: 01/10/2023]
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Weinzierl ROJ. The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain. BMC Biol 2010; 8:134. [PMID: 21034443 PMCID: PMC2988716 DOI: 10.1186/1741-7007-8-134] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 10/29/2010] [Indexed: 01/24/2023] Open
Abstract
Background Cellular RNA polymerases (RNAPs) are complex molecular machines that combine catalysis with concerted conformational changes in the active center. Previous work showed that kinking of a hinge region near the C-terminus of the Bridge Helix (BH-HC) plays a critical role in controlling the catalytic rate. Results Here, new evidence for the existence of an additional hinge region in the amino-terminal portion of the Bridge Helix domain (BH-HN) is presented. The nanomechanical properties of BH-HN emerge as a direct consequence of the highly conserved primary amino acid sequence. Mutations that are predicted to influence its flexibility cause corresponding changes in the rate of the nucleotide addition cycle (NAC). BH-HN displays functional properties that are distinct from BH-HC, suggesting that conformational changes in the Bridge Helix control the NAC via two independent mechanisms. Conclusions The properties of two distinct molecular hinges in the Bridge Helix of RNAP determine the functional contribution of this domain to key stages of the NAC by coordinating conformational changes in surrounding domains.
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