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Effect of the Addition of the Fifth Amino Acid to [GADV]-Protein on the Three-Dimensional Structure. LIFE (BASEL, SWITZERLAND) 2023; 13:life13010246. [PMID: 36676195 PMCID: PMC9863117 DOI: 10.3390/life13010246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023]
Abstract
The [GADV]-protein, consisting only of glycine (G), alanine (A), aspartic acid (D), and valine (V), is frequently studied as a candidate for a primitive protein that existed at the beginning of life on Earth. The number of proteogenic amino acids increased during evolution, and glutamic acid may have been added as the fifth amino acid. In this study, we used molecular dynamics simulations to estimate the conformation of random peptides when glutamate is added to G, A, D, and V ([GADVE]), when leucine is added ([GADVL]), and when the frequency of alanine is doubled ([GADVA]). The results showed that the secondary structure contents of the [GADVE]-peptide and [GADVL]-peptide were higher than that of the [GADVA]-peptide. Although the [GADVL]-peptide had a higher secondary structure formation ability than the [GADVE]-peptide, it was less water soluble, suggesting that it may not be a primitive protein. The [GA(D/E)V]-peptide with G:A:D:V:E = 2:2:1:2:1 according to the occurrence ratio in the codon table also increased the secondary structure contents compared to the [GADV]-peptide, indicating that the addition of glutamic acid increased the structure formation ability of the primitive protein candidates.
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2
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Savelieva EM, Zenchenko AA, Drenichev MS, Kozlova AA, Kurochkin NN, Arkhipov DV, Chizhov AO, Oslovsky VE, Romanov GA. In Planta, In Vitro and In Silico Studies of Chiral N6-Benzyladenine Derivatives: Discovery of Receptor-Specific S-Enantiomers with Cytokinin or Anticytokinin Activities. Int J Mol Sci 2022; 23:ijms231911334. [PMID: 36232653 PMCID: PMC9569578 DOI: 10.3390/ijms231911334] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 01/12/2023] Open
Abstract
Cytokinins, classical phytohormones, affect all stages of plant ontogenesis, but their application in agriculture is limited because of the lack of appropriate ligands, including those specific for individual cytokinin receptors. In this work, a series of chiral N6-benzyladenine derivatives were studied as potential cytokinins or anticytokinins. All compounds contained a methyl group at the α-carbon atom of the benzyl moiety, making them R- or S-enantiomers. Four pairs of chiral nucleobases and corresponding ribonucleosides containing various substituents at the C2 position of adenine heterocycle were synthesized. A nucleophilic substitution reaction by secondary optically active amines was used. A strong influence of the chirality of studied compounds on their interaction with individual cytokinin receptors of Arabidopsis thaliana was uncovered in in vivo and in vitro assays. The AHK2 and CRE1/AHK4 receptors were shown to have low affinity for the studied S-nucleobases while the AHK3 receptor exhibited significant affinity for most of them. Thereby, three synthetic AHK3-specific cytokinins were discovered: N6-((S)-α-methylbenzyl)adenine (S-MBA), 2-fluoro,N6-((S)-α-methylbenzyl)adenine (S-FMBA) and 2-chloro,N6-((S)-α-methylbenzyl)adenine (S-CMBA). Interaction patterns between individual receptors and specific enantiomers were rationalized by structure analysis and molecular docking. Two other S-enantiomers (N6-((S)-α-methylbenzyl)adenosine, 2-amino,N6-((S)-α-methylbenzyl)adenosine) were found to exhibit receptor-specific and chirality-dependent anticytokinin properties.
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Affiliation(s)
- Ekaterina M. Savelieva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, 127276 Moscow, Russia
| | - Anastasia A. Zenchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Mikhail S. Drenichev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Anna A. Kozlova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Nikolay N. Kurochkin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Dmitry V. Arkhipov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, 127276 Moscow, Russia
| | - Alexander O. Chizhov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky pr. 47, 119991 Moscow, Russia
| | - Vladimir E. Oslovsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
| | - Georgy A. Romanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, 127276 Moscow, Russia
- Correspondence: or
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Reetz MT, Garcia-Borràs M. The Unexplored Importance of Fleeting Chiral Intermediates in Enzyme-Catalyzed Reactions. J Am Chem Soc 2021; 143:14939-14950. [PMID: 34491742 PMCID: PMC8461649 DOI: 10.1021/jacs.1c04551] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Indexed: 02/07/2023]
Abstract
Decades of extensive research efforts by biochemists, organic chemists, and protein engineers have led to an understanding of the basic mechanisms of essentially all known types of enzymes, but in a formidable number of cases an essential aspect has been overlooked. The occurrence of short-lived chiral intermediates formed by symmetry-breaking of prochiral precursors in enzyme catalyzed reactions has been systematically neglected. We designate these elusive species as fleeting chiral intermediates and analyze such crucial questions as "Do such intermediates occur in homochiral form?" If so, what is the absolute configuration, and why did Nature choose that particular stereoisomeric form, even when the isolable final product may be achiral? Does the absolute configuration of a chiral product depend in any way on the absolute configuration of the fleeting chiral precursor? How does this affect the catalytic proficiency of the enzyme? If these issues continue to be unexplored, then an understanding of the mechanisms of many enzyme types remains incomplete. We have systematized the occurrence of these chiral intermediates according to their structures and enzyme types. This is followed by critical analyses of selected case studies and by final conclusions and perspectives. We hope that the fascinating concept of fleeting chiral intermediates will attract the attention of scientists, thereby opening an exciting new research field.
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Affiliation(s)
- Manfred T. Reetz
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Marc Garcia-Borràs
- Institute
of Computational Chemistry and Catalysis (IQCC) and Departament de
Química, Universitat de Girona, Carrer Maria Aurèlia Capmany
69, 17003 Girona, Spain
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4
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Structural Characterization of EnpA D,L-Endopeptidase from Enterococcus faecalis Prophage Provides Insights into Substrate Specificity of M23 Peptidases. Int J Mol Sci 2021; 22:ijms22137136. [PMID: 34281200 PMCID: PMC8269130 DOI: 10.3390/ijms22137136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/18/2021] [Accepted: 06/29/2021] [Indexed: 01/28/2023] Open
Abstract
The best-characterized members of the M23 family are glycyl-glycine hydrolases, such as lysostaphin (Lss) from Staphylococcus simulans or LytM from Staphylococcus aureus. Recently, enzymes with broad specificities were reported, such as EnpACD from Enterococcus faecalis, that cleaves D,L peptide bond between the stem peptide and a cross-bridge. Previously, the activity of EnpACD was demonstrated only on isolated peptidoglycan fragments. Herein we report conditions in which EnpACD lyses bacterial cells live with very high efficiency demonstrating great bacteriolytic potential, though limited to a low ionic strength environment. We have solved the structure of the EnpACD H109A inactive variant and analyzed it in the context of related peptidoglycan hydrolases structures to reveal the bases for the specificity determination. All M23 structures share a very conserved β-sheet core which constitutes the rigid bottom of the substrate-binding groove and active site, while variable loops create the walls of the deep and narrow binding cleft. A detailed analysis of the binding groove architecture, specificity of M23 enzymes and D,L peptidases demonstrates that the substrate groove, which is particularly deep and narrow, is accessible preferably for peptides composed of amino acids with short side chains or subsequent L and D-isomers. As a result, the bottom of the groove is involved in interactions with the main chain of the substrate while the side chains are protruding in one plane towards the groove opening. We concluded that the selectivity of the substrates is based on their conformations allowed only for polyglycine chains and alternating chirality of the amino acids.
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Bocková J, Jones NC, Meierhenrich UJ, Hoffmann SV, Meinert C. Chiroptical activity of hydroxycarboxylic acids with implications for the origin of biological homochirality. Commun Chem 2021; 4:86. [PMID: 36697718 PMCID: PMC9814692 DOI: 10.1038/s42004-021-00524-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/14/2021] [Indexed: 02/05/2023] Open
Abstract
Circularly polarised light (CPL) interacting with interstellar organic molecules might have imparted chiral bias and hence preluded prebiotic evolution of biomolecular homochirality. The L-enrichment of extra-terrestrial amino acids in meteorites, as opposed to no detectable excess in monocarboxylic acids and amines, has previously been attributed to their intrinsic interaction with stellar CPL revealed by substantial differences in their chiroptical signals. Recent analyses of meteoritic hydroxycarboxylic acids (HCAs) - potential co-building blocks of ancestral proto-peptides - indicated a chiral bias toward the L-enantiomer of lactic acid. Here we report on novel anisotropy spectra of several HCAs using a synchrotron radiation electronic circular dichroism spectrophotometer to support the re-evaluation of chiral biomarkers of extra-terrestrial origin in the context of absolute photochirogenesis. We found that irradiation by CPL which would yield L-excess in amino acids would also yield L-excess in aliphatic chain HCAs, including lactic acid and mandelic acid, in the examined conditions. Only tartaric acid would show "unnatural" D-enrichment, which makes it a suitable target compound for further assessing the relevance of the CPL scenario.
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Affiliation(s)
- Jana Bocková
- grid.460782.f0000 0004 4910 6551University Côte d’Azur, CNRS, Institute de Chimie de Nice, UMR 7272, Nice, France
| | - Nykola C. Jones
- grid.7048.b0000 0001 1956 2722ISA, Department of Physics and Astronomy, Aarhus University, Aarhus C, Denmark
| | - Uwe J. Meierhenrich
- grid.460782.f0000 0004 4910 6551University Côte d’Azur, CNRS, Institute de Chimie de Nice, UMR 7272, Nice, France
| | - Søren V. Hoffmann
- grid.7048.b0000 0001 1956 2722ISA, Department of Physics and Astronomy, Aarhus University, Aarhus C, Denmark
| | - Cornelia Meinert
- grid.460782.f0000 0004 4910 6551University Côte d’Azur, CNRS, Institute de Chimie de Nice, UMR 7272, Nice, France
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Khrustalev VV. Random Coils of Proteins Situated Between a Beta Strand and an Alpha Helix Demonstrate Decreased Solvent Accessibility. Protein J 2020; 39:308-317. [DOI: 10.1007/s10930-020-09905-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Nakayoshi T, Kato K, Kurimoto E, Oda A. Influence of the conformations of αA-crystallin peptides on the isomerization rates of aspartic acid residues. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140480. [PMID: 32599296 DOI: 10.1016/j.bbapap.2020.140480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/08/2020] [Accepted: 06/23/2020] [Indexed: 10/24/2022]
Abstract
The isomerization rate of aspartic acid (Asp) residue is known to be affected by the three-dimensional structures of peptides and proteins. Although the isomerized Asp residues were experimentally observed, structural features which affect the isomerization cannot be elucidated sufficiently because of protein denaturation and aggregation. In this study, molecular dynamics (MD) simulations were conducted on three αA-crystallin peptides (T6, T10, and T18), each containing a single Asp residue with different isomerization rate (T18 > T6 > T10) to clarify the structural factors of Asp isomerization tendency. For MD trajectories, distances between side-chain carboxyl carbon of Asp and main-chain amide nitrogen of (n + 1) residue (Cγ-N distances), root mean square fluctuations (RMSFs), and polar surface areas for main-chain amide nitrogen of (n + 1) residues (PSAN) were calculated, because these structural features are considered to relate to the formations of cyclic imide intermediates. RMSFs and PSAN are indexes of peptide backbone flexibilities and solvent exposure of the amide nitrogen, respectively. The average Cγ-N distances of T10 was longer than those of the other two peptides. In addition, the peptide containing Asp residue with a higher isomerization rate showed higher flexibility of the peptide backbone around the Asp residue. PSAN for amide nitrogen in T18 were much larger than those of other two peptides. The computational results suggest that Asp-residue isomerization rates are affected by these factors.
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Affiliation(s)
- Tomoki Nakayoshi
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
| | - Koichi Kato
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; Department of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan.
| | - Eiji Kurimoto
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan.
| | - Akifumi Oda
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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8
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Kato K, Nakayoshi T, Sato M, Kurimoto E, Oda A. Molecular Dynamics Simulations for Three-Dimensional Structures of Orotate Phosphoribosyltransferases Constructed from a Simplified Amino Acid Set. ACS OMEGA 2020; 5:13069-13076. [PMID: 32548492 PMCID: PMC7288596 DOI: 10.1021/acsomega.0c01012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/19/2020] [Indexed: 05/08/2023]
Abstract
Proteins of modern terrestrial organisms are composed of nearly 20 amino acids; however, the amino acid sets of primitive organisms may have contained fewer than 20 amino acids. Furthermore, the full set of 20 amino acids is not required by some proteins to encode their function. Indeed, simplified variants of Escherichia coli (E. coli) orotate phosphoribosyltransferase (OPRTase) constructed by Akanuma et al. and composed of a limited amino acid set exhibit significant catalytic activity for the growth of E. coli. However, its structural details are currently unclear. Here, we predict the structures of simplified variants of OPRTase using molecular dynamics (MD) simulations and evaluate the accuracy of the MD simulations for simplified proteins. The three-dimensional structure of the wild-type was largely maintained in the simplified variants, but differences in the catalyst loop and C-terminal helix were observed. These results are considered sufficient to elucidate the differences in catalytic activity between the wild-type and simplified OPRTase variants. Thus, using MD simulations to make structural predictions appears to be a useful strategy when investigating non-wild-type proteins composed of reduced amino acid sets.
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Affiliation(s)
- Koichi Kato
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Department
of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Tomoki Nakayoshi
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Mizuha Sato
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Eiji Kurimoto
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Akifumi Oda
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- .
Phone: +81-52-832-1151
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