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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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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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De Zotti M, Peggion C, Biondi B, Crisma M, Formaggio F, Toniolo C. Endothioxopeptides: A conformational overview. Biopolymers 2016; 106:697-713. [DOI: 10.1002/bip.22899] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/08/2016] [Accepted: 06/25/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Marta De Zotti
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
| | - Cristina Peggion
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Fernando Formaggio
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Claudio Toniolo
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
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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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Ishida T. [Overview of structural study on conformations and intermolecular interactions of biomolecules]. YAKUGAKU ZASSHI 2012; 132:785-816. [PMID: 22790026 DOI: 10.1248/yakushi.132.785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Information on the conformational feature and specific intermolecular interaction of biomolecules is important to understand the biological function and to develop device for treating disorder caused by the abnormal function. Thus the 3D structures of the biologically active molecules and the specific interactions with their target molecules at the atomic level have been investigated by various physicochemical approaches. Herein, the following five subjects are reviewed: (1) function-linked conformations of biomolecules including natural annular products, opioid peptides and neuropeptides; (2) π-π stacking interactions of tryptophan derivatives with coenzymes and nucleic acid bases; (3) mRNA cap recognition of eukaryotic initiation factor 4E and its regulation by 4E-binding protein; (4) conformational feature of histamine H2 receptor antagonists and design of cathepsin B inhibitors; (5) self-aggregation mechanism of tau protein and its inhibition.
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Affiliation(s)
- Toshimasa Ishida
- Laboratory of Physical Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan.
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Affiliation(s)
- Thomas Hoeg-jensen
- a Chemistry Department , Royal Veterinary and Agricultural University , Thorvaldsensvej 40, DK-1871, Frederiksberg, C, Denmark
- b Thomas Hoeg-Jensen, Ph.D., Insulin Research , Novo Nordisk 6B 2.54, DK-2880, Bagsvaerd, Denmark
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Seebach D, Ko SY, Kessler H, Köck M, Reggelin M, Schmieder P, Walkinshaw MD, Bölsterli JJ, Bevec D. Thiocyclosporins: Preparation, Solution and Crystal Structure, and Immunosuppressive Activity. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19910740833] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Doi M, Asano A, Komura E, Ueda Y. The structure of an endomorphin analogue incorporating 1-aminocyclohexane-1-carboxlylic acid for proline is similar to the beta-turn of Leu-enkephalin. Biochem Biophys Res Commun 2002; 297:138-42. [PMID: 12220521 DOI: 10.1016/s0006-291x(02)02087-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Endomorphin (EM2, Tyr-Pro-Phe-Phe-NH(2)) can assume various conformations related to cis/trans-rotamers of the amide linkage of Tyr-Pro. To control isomerization, restricted or flexible components have been introduced at the Pro position. We focused on [Chx(2)]EM2, an EM2 analogue substituting 1-aminocyclohexane-1-carboxlylic acid (Chx) for Pro. X-ray diffraction analysis revealed that [Chx(2)]EM2 is folded into the trans-form of Tyr-Chx. The manner of folding resembled that seen in D-TIPP, an EM analogue incorporating tetrahydroisoquinoline carboxylic acid, as well as the beta-turn of Leu-enkephalin. Selectivity for the opioid mu-receptor was fairly well conserved by [Chx(2)]EM, suggesting that the folded form is important for mu-selectivity.
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Affiliation(s)
- Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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Abstract
The X-ray diffraction experiments on peptides and related molecules which have been carried out in Western Europe, except Italy, in the last eight years are reviewed. The crystal structures of some bioactive peptides such as Leu-enkephalin (a neurotransmitter), cyclosporin A (an immunomodulator in both the free and protein-bound state), balhimycin (an antibiotic) and octreotide (a somatostatin analogue) are briefly presented. Crystallized N- and C-protected model peptides have given an insight into the folding tendency and folding modes depending on the peptide sequences. The crystal structures of various pseudopeptide molecules reveal how the three-dimensional structure of peptide analogues can be modulated by substituting non-peptide groups for the peptide bond. A few examples of structural mimetics of the beta- and gamma-turns, and of templates for alpha-helix induction are also presented.
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Affiliation(s)
- M Marraud
- LCPM, CNRS-URA 494, ENSIC-INPL, Nancy, France
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Doi M, In Y, Inoue M, Ishida T. Characteristic molecular packing in the crystal structure of tert-butoxycarbonyl-L-phenylalanyl-L-methionine methyl ester. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1994; 44:532-8. [PMID: 7705974 DOI: 10.1111/j.1399-3011.1994.tb01141.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The molecular conformation and association of the peptide Boc-L-Phe-L-Met-OMe have been studied in the solid state by X-ray diffraction. The peptide crystallizes in the orthorhombic system, space group P2(1)2(1)2(1), with cell parameters of a = 9.821(2), b = 25.394(6), c = 28.714(8) A, V = 7161(3) A3. The structure has been solved by direct methods and refined to a final R of 0.079 for 5464 independent reflections with Fo > or = sigma(Fo). The crystal consists of three independent molecular conformations per asymmetric unit. Respective peptide backbones adopt an extended conformation with the side-chains of Phe and Met residues being arranged below and above the backbone chains. Contrary to the sheet structure most frequently observed in the crystal packing of the extended peptide conformations, three independent molecules lie spirally along the c-axis and form a pin-wheel-like crystal packing. The sheet structures formed by two of three independent molecules are almost at right angles to the backbone of the remaining molecule. This molecular packing mode would provide a possible interaction model between the intersecting beta-sheet structure and single-strand structure of polypeptide.
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Affiliation(s)
- M Doi
- Osaka University of Pharmaceutical Sciences, Japan
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Doi M, Ishibe A, Shinozaki H, Urata H, Inoue M, Ishida T. Conserved and novel structural characteristics of enantiomorphic Leu-enkephalin. X-ray crystal analysis of Leu-enkephalin enantiomer, L-Tyr-Gly-Gly-L-Phe-L-Leu and D-Tyr-Gly-Gly-D-Phe-D-Leu. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1994; 43:325-31. [PMID: 8045677 DOI: 10.1111/j.1399-3011.1994.tb00526.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The crystal of the Leu-enkephalin racemate (L-Tyr-Gly-Gly-L-Phe-L-Leu and D-Tyr-Gly-Gly-D-Phe-D-Leu) was obtained as a centrosymmetric space group. Crystal data: C28H37N5O7 x 1.5H2O, Mw = 582.6, triclinic, space group P1, a = 11.176(3), b = 16.115(3), c = 10.204(4) A, alpha = 92.41(3), beta = 104.86(2), gamma = 85.35(2)degrees, V = 1770(1)A3, Z = 2; F(000) = 640, mu(CuK alpha) = 6.50 cm-1, D chi = 1.081 g cm-3. The structure was determined by X-ray diffraction. The conformation of the Leu-enkephalin racemate was classified into the extended form which has been often observed in natural enkephalin. The symmetry-related molecules were connected by hydrogen bonds and arranged in an antiparallel fashion. The molecular packing showed a sheet structure similar to that of natural enkephalin.
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Affiliation(s)
- M Doi
- Osaka University of Pharmaceutical Sciences, Japan
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Marraud M, Dupont V, Grand V, Zerkout S, Lecoq A, Boussard G, Vidal J, Collet A, Aubry A. Modifications of the amide bond and conformational constraints in pseudopeptide analogues. Biopolymers 1993. [DOI: 10.1002/bip.360330715] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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