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Khatri B, Raghunathan S, Chakraborti S, Rahisuddin R, Kumaran S, Tadala R, Wagh P, Priyakumar UD, Chatterjee J. Desolvation of Peptide Bond by O to S Substitution Impacts Protein Stability. Angew Chem Int Ed Engl 2021; 60:24870-24874. [PMID: 34519402 DOI: 10.1002/anie.202110978] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/10/2021] [Indexed: 12/31/2022]
Abstract
Amino acid side chains are key to fine-tuning the microenvironment polarity in proteins composed of polar amide bonds. Here, we report that substituting an oxygen atom of the backbone amide bond with sulfur atom desolvates the thioamide bond, thereby increasing its lipophilicity. The impact of such local desolvation by O to S substitution in proteins was tested by synthesizing thioamidated variants of Pin1 WW domain. We observe that a thioamide acts in synergy with nonpolar amino acid side chains to reduce the microenvironment polarity and increase protein stability by more than 14 °C. Through favorable van der Waals and hydrogen bonding interactions, this single atom substitution significantly stabilizes proteins without altering the amino acid sequence and structure of the native protein.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India.,Present Address: École Centrale School of Engineering, Mahindra University, Hyderabad, 500043, India
| | - Sohini Chakraborti
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - R Rahisuddin
- CSIR- Institute of Microbial Technology, Chandigarh 1, 60036, India
| | - S Kumaran
- CSIR- Institute of Microbial Technology, Chandigarh 1, 60036, India
| | | | | | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
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2
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Khatri B, Raghunathan S, Chakraborti S, Rahisuddin R, Kumaran S, Tadala R, Wagh P, Priyakumar UD, Chatterjee J. Desolvation of Peptide Bond by O to S Substitution Impacts Protein Stability. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit Indian Institute of Science Bangalore 560012 India
| | - Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology Hyderabad 500032 India
- Present Address: École Centrale School of Engineering Mahindra University Hyderabad 500043 India
| | - Sohini Chakraborti
- Molecular Biophysics Unit Indian Institute of Science Bangalore 560012 India
| | - R. Rahisuddin
- CSIR- Institute of Microbial Technology Chandigarh 1 60036 India
| | - S. Kumaran
- CSIR- Institute of Microbial Technology Chandigarh 1 60036 India
| | | | | | - U. Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology Hyderabad 500032 India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit Indian Institute of Science Bangalore 560012 India
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3
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Mahapatra AK, Karmakar P, Roy J, Manna S, Maiti K, Sahoo P, Mandal D. Colorimetric and ratiometric fluorescent chemosensor for fluoride ions based on phenanthroimidazole (PI): spectroscopic, NMR and density functional studies. RSC Adv 2015. [DOI: 10.1039/c5ra05327g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Phenanthro-imidazole conjugate of biscarbanohyrazone, probe PI was designed, synthesized and characterized for selective detection of fluoride ion.
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Affiliation(s)
- Ajit Kumar Mahapatra
- Department of Chemistry
- Indian Institute of Engineering Science and Technology
- Howrah-711103
- India
| | - Parthasarathi Karmakar
- Department of Chemistry
- Indian Institute of Engineering Science and Technology
- Howrah-711103
- India
| | - Jagannath Roy
- Department of Chemistry
- Indian Institute of Engineering Science and Technology
- Howrah-711103
- India
| | - Srimanta Manna
- Department of Chemistry
- Indian Institute of Engineering Science and Technology
- Howrah-711103
- India
| | - Kalipada Maiti
- Department of Chemistry
- Indian Institute of Engineering Science and Technology
- Howrah-711103
- India
| | | | - Debasish Mandal
- Institute of Chemistry
- The Hebrew University of Jerusalem
- 91904 Jerusalem
- Israel
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4
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Nelli YR, Antunes S, Salaün A, Thinon E, Massip S, Kauffmann B, Douat C, Guichard G. Isosteric Substitutions of Urea to Thiourea and Selenourea in Aliphatic Oligourea Foldamers: Site-Specific Perturbation of the Helix Geometry. Chemistry 2014; 21:2870-80. [DOI: 10.1002/chem.201405792] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Indexed: 01/05/2023]
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5
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Huang Y, Jahreis G, Lücke C, Fischer G. Rapid Nitrogen Inversion Pathway in thecis/transIsomerization of Selenoxo Peptide Bonds. Chemistry 2012; 19:1179-83. [DOI: 10.1002/chem.201203721] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Indexed: 01/08/2023]
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Crespo‐Otero R, Mardyukov A, Sanchez‐Garcia E, Barbatti M, Sander W. Photochemistry of
N
‐Methylformamide: Matrix Isolation and Nonadiabatic Dynamics. Chemphyschem 2012; 14:827-36. [DOI: 10.1002/cphc.201200573] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Rachel Crespo‐Otero
- Department of Theory, Max Planck Institute for Coal Research, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) (0)208/306‐2980
| | - Artur Mardyukov
- Lehrstuhl für Organische Chemie II, Ruhr Universität Bochum, Universitätsstraße 150 44801 Bochum (Germany), Fax: (+49) (0)234‐3214353
| | - Elsa Sanchez‐Garcia
- Department of Theory, Max Planck Institute for Coal Research, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) (0)208/306‐2980
| | - Mario Barbatti
- Department of Theory, Max Planck Institute for Coal Research, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) (0)208/306‐2980
| | - Wolfram Sander
- Lehrstuhl für Organische Chemie II, Ruhr Universität Bochum, Universitätsstraße 150 44801 Bochum (Germany), Fax: (+49) (0)234‐3214353
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7
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Abstract
Peptide-bond isosteres can enable a deep interrogation of the structure and function of a peptide or protein by amplifying or attenuating particular chemical properties. In this Minireview, the electronic, structural, and conformational attributes of four such isosteres-thioamides, esters, alkenes, and fluoroalkenes-are examined in detail. In particular, the ability of these isosteres to partake in noncovalent interactions is compared with that of the peptide bond. The consequential perturbations provide a useful tool for chemical biologists to reveal new structure-function relationships, and to endow peptides and proteins with desirable attributes.
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Affiliation(s)
- Amit Choudhary
- Graduate Program in Biophysics, University of Wisconsin–Madison, 1525 Linden Drive, Madison, WI 53706-1534 (USA)
| | - Ronald T. Raines
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706-1544 (USA), Fax: (+1) 608-890-2583
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706-1322 (USA)
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Koeller S, Kadota J, Peruch F, Deffieux A, Pinaud N, Pianet I, Massip S, Léger JM, Desvergne JP, Bibal B. (Thio)Amidoindoles and (Thio)Amidobenzimidazoles: An Investigation of Their Hydrogen-Bonding and Organocatalytic Properties in the Ring-Opening Polymerization of Lactide. Chemistry 2010; 16:4196-205. [DOI: 10.1002/chem.200902912] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Lincke T, Behnken S, Ishida K, Roth M, Hertweck C. Closthioamide: An Unprecedented Polythioamide Antibiotic from the Strictly Anaerobic Bacterium Clostridium cellulolyticum. Angew Chem Int Ed Engl 2010; 49:2011-3. [DOI: 10.1002/anie.200906114] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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10
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Lincke T, Behnken S, Ishida K, Roth M, Hertweck C. Closthioamide: An Unprecedented Polythioamide Antibiotic from the Strictly Anaerobic Bacterium Clostridium cellulolyticum. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906114] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Han F, Bao Y, Yang Z, Fyles TM, Zhao J, Peng X, Fan J, Wu Y, Sun S. Simple bis-thiocarbono-hydrazones as sensitive, selective, colorimetric, and switch-on fluorescent chemosensors for fluoride anions. Chemistry 2007; 13:2880-92. [PMID: 17200934 DOI: 10.1002/chem.200600904] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Bis-thiocarbono-hydrazones are found to be a class of sensitive, selective, ratiometric, and colorimetric chemosensors for anions such as fluoride (F(-)) or acetate (Ac(-)). The sensitivities, or the binding constants of the sensors with anions, were found to be strongly dependent on the substituents appended on the pi-conjugation framework, the delocalization bridge CH==N, the aromatic moiety, and the hetero atom in the C==X group (X=O, S) of the sensors. Single-crystal structures and (1)H NMR titration analysis shows that the --CH==N-- moiety is a hydrogen-bond donor, and it is proposed that an additional CHF hydrogen bond is formed for the sensors in the presence F(-). A sensor bearing anthracenyl groups is demonstrated as a switch-on fluorescent chemosensor for F(-) and Ac(-). The recognition of F(-) in acetonitrile (MeCN) by a sensor with nitrophenyl substituents is tolerant to MeOH (MeCN/MeOH=10:1, v/v) and water (MeCN/H(2)O=30:1, v/v); at these solvent ratios the absorption intensity of the sensor-F(-) complex solution at maximal absorption wavelength was attenuated to half of the original value in pure MeCN.
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Affiliation(s)
- Feng Han
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 158 Zhongshan Road, Dalian 116012, P.R. China
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Wildemann D, Schiene-Fischer C, Aumüller T, Bachmann A, Kiefhaber T, Lücke C, Fischer G. A nearly isosteric photosensitive amide-backbone substitution allows enzyme activity switching in ribonuclease s. J Am Chem Soc 2007; 129:4910-8. [PMID: 17397159 DOI: 10.1021/ja069048o] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
psi[CS-NH]4-RNase S, a site specific modified version of RNase S obtained by thioxylation (O/S exchange) at the Ala4-Ala5- peptide bond, was used to evaluate the impact of protein backbone photoswitching on bioactivity. psi[CS-NH](4)-RNase S was yielded by recombination of the S-protein and the respective chemically synthesized thioxylated S-peptide derivative. Comparison with RNase S revealed similar thermodynamic stability of the complex and an unperturbed enzymatic activity toward cytidine 2',3'-cyclic monophosphate (cCMP). Reversible photoisomerization with a highly increased cis/trans isomer ratio of the thioxopeptide bond of psi[CS-NH](4)-RNase S in the photostationary state occurred under UV irradiation conditions (254 nm). The slow thermal reisomerization (t(1/2) = 180 s) permitted us to determine the enzymatic activity of cis psi[CS-NH](4)-RNase S by measurement of initial rates of cCMP hydrolysis. Despite thermodynamic stability of cis psi[CS-NH](4)-RNase S, its enzymatic activity is completely abolished but recovers after reisomerization. We conclude that the thioxopeptide bond modified polypeptide backbone represents a versatile probe for site-directed photoswitching of proteins.
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Affiliation(s)
- Dirk Wildemann
- Max-Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, D-06120 Halle/Saale, Germany
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Micheau JC, Zhao J. Cis/trans configurations of the peptide CN bonds: isomerization and photoswitching. J PHYS ORG CHEM 2007. [DOI: 10.1002/poc.1216] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abstract
The photoinduced isomerization of azobenzene between the extended (trans) and compact (cis) conformations is reversibly triggered by light of two differing wavelengths. The resulting changes in molecular geometry have been extensively utilized to photoswitch transformations in chemical species reversibly for applications in optoelectronic devises as well as to photocontrol conformational states in (bio)polymers. The high isomerization yield, remarkable photostability and ultrafast kinetics (few ps) of azobenzene are well suited for the design of small, defined model systems that allow detailed folding studies to be carried out both experimentally and theoretically on the same molecules. In our and other laboratories such systems were recently obtained with cyclic peptides of defined conformational preferences as well as with alpha-helical and beta-hairpin peptides. These should, by comparison of simulation and experiment, permit an assessment and improvement of the theoretical description on the one hand and a detailed interpretation of the ultrafast conformational dynamics on the other. The phototriggered changes in conformational states lead to concurrent changes in biophysical properties that can be exploited in the photocontrol of biochemical and biological events, as exemplarily discussed with redox-active cyclic bis-cysteinyl peptides and receptor ligands.
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Affiliation(s)
- Christian Renner
- School of Biomedical and Natural Sciences, Nottingham Trent University, Nottingham, NG11 8NS, UK.
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Zhao J, Micheau JC, Vargas C, Schiene-Fischer C. cis/trans Photoisomerization of Secondary Thiopeptide Bonds. Chemistry 2004; 10:6093-101. [PMID: 15515071 DOI: 10.1002/chem.200400400] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The reversible cis/trans photoisomerization of secondary thiopeptide bonds has been systematically studied with UV-visible absorption, capillary electrophoresis, 1H NMR spectroscopy, and circular dichroism methods. It was found that the concentration of the cis conformers could be increased from less than 1 % in the thermal equilibrated solution to up to 20 % in the photostationary state. The rotational barriers of the thiopeptide bond and the pH dependence of the isomerization rates were also studied. The quantum yields of the trans-->cis and the cis-->trans processes were determined from photokinetic analysis.
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Affiliation(s)
- Jianzhang Zhao
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany.
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