1
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Samajdar R, Meigooni M, Yang H, Li J, Liu X, Jackson NE, Mosquera MA, Tajkhorshid E, Schroeder CM. Secondary structure determines electron transport in peptides. Proc Natl Acad Sci U S A 2024; 121:e2403324121. [PMID: 39052850 PMCID: PMC11317557 DOI: 10.1073/pnas.2403324121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/14/2024] [Indexed: 07/27/2024] Open
Abstract
Proteins play a key role in biological electron transport, but the structure-function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green's function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 310 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.
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Affiliation(s)
- Rajarshi Samajdar
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Moeen Meigooni
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Hao Yang
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Jialing Li
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Xiaolin Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Nicholas E. Jackson
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Martín A. Mosquera
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Charles M. Schroeder
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
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2
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Tilly DP, Cullen W, Zhong H, Jamagne R, Vitórica-Yrezábal I, Webb SJ. α-Amino-iso-butyric acid foldamers terminated with rhodium(I) N-heterocyclic carbene catalysts. Chemistry 2021; 28:e202104293. [PMID: 34932229 PMCID: PMC9305545 DOI: 10.1002/chem.202104293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Indexed: 12/01/2022]
Abstract
To investigate how remotely induced changes in ligand folding might affect catalysis by organometallic complexes, dynamic α‐amino‐iso‐butyric acid (Aib) peptide foldamers bearing rhodium(I) N‐heterocyclic carbene (NHC) complexes have been synthesized and studied. X‐ray crystallography of a foldamer with an N‐terminal azide and a C‐terminal Rh(NHC)(Cl)(diene) complex showed a racemate with a chiral axis in the Rh(NHC) complex and a distorted 310 helical body. Replacing the azide with either one or two chiral L‐α‐methylvaline (L‐αMeVal) residues gave diastereoisomeric foldamers that each possessed point, helical and axial chirality. NMR spectroscopy revealed an unequal ratio of diastereoisomers for some foldamers, indicating that the chiral conformational preference of the N‐terminal residue(s) was relayed down the 1 nm helical body to the axially chiral Rh(NHC) complex. Although the remote chiral residue(s) did not affect the stereoselectivity of hydrosilylation reactions catalysed by these foldamers, these studies suggest a potential pathway towards remote conformational control of organometallic catalysts.
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Affiliation(s)
- David P Tilly
- The University of Manchester, Department of Chemistry, UNITED KINGDOM
| | - William Cullen
- The University of Manchester, Department of Chemistry, UNITED KINGDOM
| | - Heng Zhong
- The University of Manchester, Department of Chemistry, UNITED KINGDOM
| | - Romain Jamagne
- The University of Manchester, Department of Chemistry, UNITED KINGDOM
| | | | - Simon John Webb
- University of Manchester, School of Chemistry and MIB, 131 Princess St, M1 7DN, Manchester, UNITED KINGDOM
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3
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Bodero L, Guitot K, Lensen N, Lequin O, Brigaud T, Ongeri S, Chaume G. Introducing the Chiral Constrained α-Trifluoromethylalanine in Aib foldamers to Control, Quantify and Assign the Helical Screw-Sense. Chemistry 2021; 28:e202103887. [PMID: 34890083 DOI: 10.1002/chem.202103887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Indexed: 11/11/2022]
Abstract
Oligomers of α-aminoisobutyric acid (Aib) are achiral peptides that adopt 3 10 helical structures with equal population of left- and right-handed conformers. Yet, the screw-sense preference of the helical chain may be controlled by a single chiral residue located at one terminus. 1 H and 19 F NMR, X-ray crystallography and circular dichroism studies on new Aib oligomers show that the incorporation of a chiral quaternary α-trifluoromethylalanine at their N -terminus induces a reversal of the screw-sense preference of the 3 10 -helix compared to that of a non-fluorinated analogue having an l-α-methyl valine residue. This work demonstrates that, among the many particular properties of introducing a trifluoromethyl group into foldamers, its stereo-electronic properties are of major interest to control the helical screw sense. Its use as an easy-to-handle 19 F NMR probe to reliably determine both the magnitude of the screw-sense preference and its sign assignment is also of remarkable interest.
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Affiliation(s)
| | | | | | - Olivier Lequin
- Sorbonne Université Campus Pierre et Marie Curie: Sorbonne Universite Campus Pierre et Marie Curie, chemistry, FRANCE
| | | | | | - Grégory Chaume
- CY Cergy Paris Universite, Chemistry, 5 mail Gay Lussac, 95000, Cergy-Pontoise, FRANCE
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4
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Lizio MG, Campana M, De Poli M, Jefferies DF, Cullen W, Andrushchenko V, Chmel NP, Bouř P, Khalid S, Clayden J, Blanch E, Rodger A, Webb SJ. Insight into the Mechanism of Action and Peptide-Membrane Interactions of Aib-Rich Peptides: Multitechnique Experimental and Theoretical Analysis. Chembiochem 2021; 22:1656-1667. [PMID: 33411956 PMCID: PMC8248331 DOI: 10.1002/cbic.202000834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/06/2021] [Indexed: 12/16/2022]
Abstract
The increase in resistant bacterial strains necessitates the identification of new antimicrobial molecules. Antimicrobial peptides (AMPs) are an attractive option because of evidence that bacteria cannot easily develop resistance to AMPs. The peptaibols, a class of naturally occurring AMPs, have shown particular promise as antimicrobial drugs, but their development has been hindered by their mechanism of action not being clearly understood. To explore how peptaibols might interact with membranes, circular dichroism, vibrational circular dichroism, linear dichroism, Raman spectroscopy, Raman optical activity, neutron reflectivity and molecular dynamics simulations have been used to study a small library of peptaibol mimics, the Aib-rich peptides. All the peptides studied quickly partitioned and oriented in membranes, and we found evidence of chiral interactions between the phospholipids and membrane-embedded peptides. The protocols presented in this paper open new ground by showing how chiro-optical spectroscopies can throw light on the mechanism of action of AMPs.
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Affiliation(s)
| | - Mario Campana
- ISIS Neutron and Muon SourceRutherford Appleton Laboratory Harwell DidcotOxfordOX11 0QXUK
| | - Matteo De Poli
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | | | - William Cullen
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
- Manchester Institute of BiotechnologyUniversity of Manchester131 Princess St.ManchesterM1 7DNUK
| | - Valery Andrushchenko
- Institute of Organic Chemistry and BiochemistryAcademy of SciencesFlemingovo náměstí 216610Prague 6Czech Republic
| | - Nikola P. Chmel
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
| | - Petr Bouř
- Institute of Organic Chemistry and BiochemistryAcademy of SciencesFlemingovo náměstí 216610Prague 6Czech Republic
| | - Syma Khalid
- School of ChemistryUniversity of Southampton HighfieldSouthamptonSO17 1BJUK
| | - Jonathan Clayden
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Ewan Blanch
- School of ScienceRMIT UniversityGPO Box 2476MelbourneVictoria3001Australia
| | - Alison Rodger
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Department of Molecular SciencesMacquarie UniversitySydneyNSW 2109Australia
| | - Simon J. Webb
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
- Manchester Institute of BiotechnologyUniversity of Manchester131 Princess St.ManchesterM1 7DNUK
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5
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Rodríguez R, Suárez‐Picado E, Quiñoá E, Riguera R, Freire F. A Stimuli‐Responsive Macromolecular Gear: Interlocking Dynamic Helical Polymers with Foldamers. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915488] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Rafael Rodríguez
- Centro Singular de investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Esteban Suárez‐Picado
- Centro Singular de investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Emilio Quiñoá
- Centro Singular de investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Ricardo Riguera
- Centro Singular de investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Félix Freire
- Centro Singular de investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
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6
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Rodríguez R, Suárez‐Picado E, Quiñoá E, Riguera R, Freire F. A Stimuli‐Responsive Macromolecular Gear: Interlocking Dynamic Helical Polymers with Foldamers. Angew Chem Int Ed Engl 2020; 59:8616-8622. [DOI: 10.1002/anie.201915488] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/07/2020] [Indexed: 01/11/2023]
Affiliation(s)
- Rafael Rodríguez
- Centro Singular de investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Esteban Suárez‐Picado
- Centro Singular de investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Emilio Quiñoá
- Centro Singular de investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Ricardo Riguera
- Centro Singular de investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Félix Freire
- Centro Singular de investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica Universidade de Santiago de Compostela 15782 Santiago de Compostela Spain
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7
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Eccles N, della Sala F, Le Bailly BAF, Whitehead GFS, Clayden J, Webb SJ. Molecular Recognition by Zn(II)-Capped Dynamic Foldamers. ChemistryOpen 2020; 9:338-345. [PMID: 32195074 PMCID: PMC7080544 DOI: 10.1002/open.201900362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/05/2020] [Indexed: 11/29/2022] Open
Abstract
Two α-aminoisobutyric acid (Aib) foldamers bearing Zn(II)-chelating N-termini have been synthesized and compared with a reported Aib foldamer that has a bis(quinolinyl)/mono(pyridyl) cap (BQPA group). Replacement of the quinolinyl arms of the BQPA-capped foldamer with pyridyl gave a BPPA-capped foldamer, then further replacement of the linking pyridyl with a 1,2,3-triazole gave a BPTA-capped foldamer. Their ability to relay chiral information from carboxylate bound to Zn(II) at the N-terminus to a glycinamide-based NMR reporter of conformational preference at the C-terminus was measured. The importance of the quinolinyl arms became readily apparent, as the foldamers with pyridyl arms were unable to report on the presence of chiral carboxylate in acetonitrile. Low solubility, X-ray crystallography and 1H NMR spectroscopy suggested that interfoldamer interactions inhibited carboxylate binding. However changing solvent to methanol revealed that the end-to-end relay of chiral information could be observed for the Zn(II) complex of the BPTA-capped foldamer at low temperature.
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Affiliation(s)
- Natasha Eccles
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
- Manchester Institute of BiotechnologyUniversity of Manchester131 Princess StManchesterM1 7DNUK
| | - Flavio della Sala
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
- Manchester Institute of BiotechnologyUniversity of Manchester131 Princess StManchesterM1 7DNUK
| | - Bryden A. F. Le Bailly
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | | | - Jonathan Clayden
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Simon J. Webb
- Department of ChemistryUniversity of ManchesterOxford RoadManchesterM13 9PLUK
- Manchester Institute of BiotechnologyUniversity of Manchester131 Princess StManchesterM1 7DNUK
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8
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Misra R, George G, Saseendran A, Raghothama S, Gopi HN. Ambidextrous α,γ-Hybrid Peptide Foldamers. Chem Asian J 2019; 14:4408-4414. [PMID: 31670907 DOI: 10.1002/asia.201901411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/21/2019] [Indexed: 12/12/2022]
Abstract
Molecular chirality is ubiquitous in nature. The natural biopolymers, proteins and DNA, preferred a right-handed helical bias due to the inherent stereochemistry of the monomer building blocks. Here, we are reporting a rare co-existence of left- and right-handed helical conformations and helix-terminating property at the C-terminus within a single molecule of α,γ-hybrid peptide foldamers composed of achiral Aib (α-aminoisobutyric acid) and 3,3-dimethyl-substituted γ-amino acid (Adb; 4-amino-3,3-dimethylbutanoic acid). At the molecular level, the left- and right-handed helical screw sense of α,γ-hybrid peptides are representing a macroscopic tendril perversion. The pronounced helix-terminating behaviour of C-terminal Adb residues was further explored to design helix-Schellman loop mimetics and to study their conformations in solution and single crystals. The stereochemical constraints of dialkyl substitutions on γ-amino acids showed a marked impact on the folding behaviour of α,γ-hybrid peptides.
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Affiliation(s)
- Rajkumar Misra
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Gijo George
- NMR Research Center, Indian Institute of Science, Bangalore, 560012, India
| | - Abhijith Saseendran
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | | | - Hosahudya N Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
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9
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Lizio MG, Andrushchenko V, Pike SJ, Peters AD, Whitehead GFS, Vitórica-Yrezábal IJ, Mutter ST, Clayden J, Bouř P, Blanch EW, Webb SJ. Optically Active Vibrational Spectroscopy of α-Aminoisobutyric Acid Foldamers in Organic Solvents and Phospholipid Bilayers. Chemistry 2018; 24:9399-9408. [PMID: 29745985 DOI: 10.1002/chem.201801121] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Indexed: 12/12/2022]
Abstract
Helical α-aminoisobutyric acid (Aib) foldamers show great potential as devices for the communication of conformational information across phospholipid bilayers, but determining their conformation in bilayers remains a challenge. In the present study, Raman, Raman optical activity (ROA), infrared (IR) and vibrational circular dichroism (VCD) spectroscopies have been used to analyze the conformational preferences of Aib foldamers in solution and when interacting with bilayers. A 310 -helix marker band at 1665-1668 cm-1 in Raman spectra was used to show that net helical content increased strongly with oligomer length. ROA and VCD spectra of chiral Aib foldamers provided the chiroptical signature for both left- and right-handed 310 -helices in organic solvents, with VCD establishing that foldamer screw-sense was preserved when the foldamers became embedded within bilayers. However, the population distribution between different secondary structures was perturbed by the chiral phospholipid. These studies indicate that ROA and VCD spectroscopies are valuable tools for the study of biomimetic structures, such as artificial signal transduction molecules, in phospholipid bilayers.
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Affiliation(s)
- Maria Giovanna Lizio
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Sarah J Pike
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.,Faculty of Life Sciences, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK
| | - Anna D Peters
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - George F S Whitehead
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | | | - Shaun T Mutter
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Ewan W Blanch
- School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria, 3001, Australia
| | - Simon J Webb
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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10
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Eto R, Oba M, Ueda A, Uku T, Doi M, Matsuo Y, Tanaka T, Demizu Y, Kurihara M, Tanaka M. Diastereomeric Right- and Left-Handed Helical Structures with Fourteen (R)-Chiral Centers. Chemistry 2017; 23:18120-18124. [PMID: 29134704 DOI: 10.1002/chem.201705306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Indexed: 12/31/2022]
Abstract
The relationship between chiral centers and the helical-screw control of their peptides has already been reported, but it has yet to be elucidated in detail. A chiral four-membered ring α,α-disubstituted α-amino acid with a (R,R)-butane-2,3-diol acetal moiety at the γ-position, but no α-chiral carbon, was synthesized. X-ray crystallographic analysis unambiguously revealed that its homo-chiral heptapeptide formed right-handed (P) and left-handed (M) 310 -helical structures at a ratio of 1:1. They appeared to be enantiomeric at the peptide backbone, but diastereomeric with fourteen (R)-configuration chiral centers. Conformational analyses of homopeptides in solution also indicated that diastereomeric (P) and (M) helices existed at approximately equal amounts, with a slight preference toward right-handedness, and they quickly interchanged at room temperature. The circumstances of chiral centers are important for the control of their helical-screw direction.
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Affiliation(s)
- Ryo Eto
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Atsushi Ueda
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Tsubasa Uku
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences, Osaka, 569-1094, Japan
| | - Yosuke Matsuo
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Takashi Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Yosuke Demizu
- National Institute of Health Sciences, Tokyo, 158-8501, Japan
| | - Masaaki Kurihara
- Graduate School of Pharmaceutical Sciences, International University of Health and Welfare, Ohtawara, 324-8501, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
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11
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Rudzińska-Szostak E, Berlicki Ł. Sequence Engineering to Control the Helix Handedness of Peptide Foldamers. Chemistry 2017; 23:14980-14986. [DOI: 10.1002/chem.201702730] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Ewa Rudzińska-Szostak
- Department of Bioorganic Chemistry; Faculty of Chemistry; Wrocław University of Science and Technology; Wyb. Wyspiańskiego 27 50-370 Wrocław Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry; Faculty of Chemistry; Wrocław University of Science and Technology; Wyb. Wyspiańskiego 27 50-370 Wrocław Poland
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12
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Liu Z, Hu X, Abramyan AM, Mészáros Á, Csékei M, Kotschy A, Huc I, Pophristic V. Computational Prediction and Rationalization, and Experimental Validation of Handedness Induction in Helical Aromatic Oligoamide Foldamers. Chemistry 2017; 23:3605-3615. [DOI: 10.1002/chem.201605082] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Zhiwei Liu
- Department of Chemistry & Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Xiaobo Hu
- University of Bordeaux, CBMN (UMR 5248) Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248) France
- Bordeaux Institut National Polytechnique CBMN (UMR 5248) France
| | - Ara M. Abramyan
- Department of Chemistry & Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Ádám Mészáros
- Servier Research Institute of Medicinal Chemistry Záhony utca 7. 1031 Budapest Hungary
| | - Márton Csékei
- Servier Research Institute of Medicinal Chemistry Záhony utca 7. 1031 Budapest Hungary
| | - András Kotschy
- Servier Research Institute of Medicinal Chemistry Záhony utca 7. 1031 Budapest Hungary
| | - Ivan Huc
- University of Bordeaux, CBMN (UMR 5248) Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248) France
- Bordeaux Institut National Polytechnique CBMN (UMR 5248) France
| | - Vojislava Pophristic
- Department of Chemistry & Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
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13
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Biswas S, Sarkar S, Pandey PR, Roy S. Transferability of different classical force fields for right and left handed α-helices constructed from enantiomeric amino acids. Phys Chem Chem Phys 2016; 18:5550-63. [PMID: 26863595 DOI: 10.1039/c5cp06715d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amino acids can form d and l enantiomers, of which the l enantiomer is abundant in nature. The naturally occurring l enantiomer has a greater preference for a right handed helical conformation, and the d enantiomer for a left handed helical conformation. The other conformations, that is, left handed helical conformations of the l enantiomers and right handed helical conformations of the d enantiomers, are not common. The energetic differences between left and right handed alpha helical peptide chains constructed from enantiomeric amino acids are investigated using quantum chemical calculations (using the M06/6-311g(d,p) level of theory). Further, the performances of commonly used biomolecular force fields (OPLS/AA, CHARMM27/CMAP and AMBER) to represent the different helical conformations (left and right handed) constructed from enantiomeric (D and L) amino acids are evaluated. 5- and 10-mer chains from d and l enantiomers of alanine, leucine, lysine, and glutamic acid, in right and left handed helical conformations, are considered in the study. Thus, in total, 32 α-helical polypeptides (4 amino acids × 4 conformations of 5-mer and 10-mer) are studied. Conclusions, with regards to the performance of the force fields, are derived keeping the quantum optimized geometry as the benchmark, and on the basis of phi and psi angle calculations, hydrogen bond analysis, and different long range helical order parameters.
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Affiliation(s)
- Santu Biswas
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune - 411008, India.
| | - Sujit Sarkar
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune - 411008, India.
| | - Prithvi Raj Pandey
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune - 411008, India.
| | - Sudip Roy
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune - 411008, India.
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Le Bailly BAF, Byrne L, Clayden J. Refoldable Foldamers: Global Conformational Switching by Deletion or Insertion of a Single Hydrogen Bond. Angew Chem Int Ed Engl 2016; 55:2132-6. [PMID: 26762559 PMCID: PMC4755161 DOI: 10.1002/anie.201510605] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 11/12/2022]
Abstract
Small changes in the structure of a foldamer may lead to gross changes in conformational preference. We show that the simple insertion or deletion of a single hydrogen bond by changes in pH or by photochemical deprotection is sufficient to refold a helical oligomer, interconverting M and P screw-sense preference. As a consequence of the switch, information may be transmitted to a remote catalytic site, selectively directing the formation of either of two enantiomeric products by a reaction involving 1,22-remote intermolecular asymmetric induction.
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Affiliation(s)
- Bryden A F Le Bailly
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.,School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Liam Byrne
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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15
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Le Bailly BAF, Byrne L, Clayden J. Refoldable Foldamers: Global Conformational Switching by Deletion or Insertion of a Single Hydrogen Bond. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510605] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bryden A. F. Le Bailly
- School of Chemistry; University of Bristol; Cantock's Close Bristol BS8 1TS UK
- School of Chemistry; University of Manchester; Oxford Road Manchester M13 9PL UK
| | - Liam Byrne
- School of Chemistry; University of Manchester; Oxford Road Manchester M13 9PL UK
| | - Jonathan Clayden
- School of Chemistry; University of Bristol; Cantock's Close Bristol BS8 1TS UK
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16
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Yamashita H, Oba M, Misawa T, Tanaka M, Hattori T, Naito M, Kurihara M, Demizu Y. A Helix-Stabilized Cell-Penetrating Peptide as an Intracellular Delivery Tool. Chembiochem 2015; 17:137-40. [DOI: 10.1002/cbic.201500468] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Hiroko Yamashita
- National Institute of Health Sciences; Setagaya Tokyo 158-8501 Japan
- Graduate School of Bioscience and Biotechnology; Tokyo Institute of Technology; Yokohama 226-8501 Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences; Nagasaki University; Nagasaki 852-8521 Japan
| | - Takashi Misawa
- National Institute of Health Sciences; Setagaya Tokyo 158-8501 Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences; Nagasaki University; Nagasaki 852-8521 Japan
| | - Takayuki Hattori
- National Institute of Health Sciences; Setagaya Tokyo 158-8501 Japan
| | - Mikihiko Naito
- National Institute of Health Sciences; Setagaya Tokyo 158-8501 Japan
| | - Masaaki Kurihara
- National Institute of Health Sciences; Setagaya Tokyo 158-8501 Japan
- Graduate School of Bioscience and Biotechnology; Tokyo Institute of Technology; Yokohama 226-8501 Japan
| | - Yosuke Demizu
- National Institute of Health Sciences; Setagaya Tokyo 158-8501 Japan
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17
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Memeo MG, Mella M, Montagna V, Quadrelli P. Design, Synthesis, and Conformational Analysis of Proposed β-Turn Mimics from Isoxazoline-Cyclopentane Aminols. Chemistry 2015; 21:16374-8. [PMID: 26418579 DOI: 10.1002/chem.201503062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Indexed: 11/09/2022]
Abstract
Constrained aminols from oxazanorbornene derivatives have the geometrical features to be used as β-turn inducers. Four different stereoisomers were prepared and spectroscopically characterized (MD calculations, NMR-titration and VT-NMR experiments). Temperature coefficients in DMSO are indicative for the existence of an intramolecular hydrogen bond. Chirooptical properties revealed a β-turn arrangement of all the synthesized compounds, where, depending on the absolute configuration of the cyclopentane spacer, they can be labeled as left- or right-handed turns.
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Affiliation(s)
- Misal Giuseppe Memeo
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 - Pavia (Italy)
| | - Mariella Mella
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 - Pavia (Italy)
| | - Valentina Montagna
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 - Pavia (Italy)
| | - Paolo Quadrelli
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 - Pavia (Italy).
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18
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Pike SJ, Diemer V, Raftery J, Webb SJ, Clayden J. Designing foldamer-foldamer interactions in solution: the roles of helix length and terminus functionality in promoting the self-association of aminoisobutyric acid oligomers. Chemistry 2014; 20:15981-90. [PMID: 25280242 DOI: 10.1002/chem.201403626] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 12/11/2022]
Abstract
The biological activity of antibiotic peptaibols has been linked to their ability to aggregate, but the structure-activity relationship for aggregation is not well understood. Herein, we report a systematic study of a class of synthetic helical oligomer (foldamer) composed of aminoisobutyric acid (Aib) residues, which mimic the folding behavior of peptaibols. NMR spectroscopic analysis was used to quantify the dimerization constants in solution, which showed hydrogen-bond donors at the N terminus promoted aggregation more effectively than similar modifications at the C terminus. Elongation of the peptide chain also favored aggregation. The geometry of aggregation in solution was investigated by means of titrations with [D6]DMSO and 2D NOE NMR spectroscopy, which allowed the NH protons most involved in intermolecular hydrogen bonds in solution to be identified. X-ray crystallography studies of two oligomers allowed a comparison of the inter- and intramolecular hydrogen-bonding interactions in the solid state and in solution and gave further insight into the geometry of foldamer-foldamer interactions. These solution-based and solid-state studies indicated that the preferred geometry for aggregation is through head-to-tail interactions between the N and C termini of adjacent Aib oligomers.
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Affiliation(s)
- Sarah J Pike
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL (UK), Fax: (+44) 161-275-4939
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19
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Maity I, Manna MK, Rasale DB, Das AK. Peptide-Nanofiber-Supported Palladium Nanoparticles as an Efficient Catalyst for the Removal of N-Terminus Protecting Groups. Chempluschem 2014; 79:413-420. [PMID: 31986601 DOI: 10.1002/cplu.201300348] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/17/2013] [Indexed: 11/08/2022]
Abstract
Sonication-induced tryptophan- and tyrosine-based peptide bolaamphiphile nanofibers have been used to synthesize and stabilize Pd nanoparticles under physiological conditions. The peptide bolaamphiphile self-assembly process has been thoroughly studied by using several spectroscopic and microscopic techniques. The stiffness of the soft hydrogel matrix was measured by an oscillatory rheological experiment. FTIR and circular dichroism (CD) experiments revealed a hydrogen-bonded β-sheet conformation of peptide bolaamphiphile molecules in a gel-phase medium. The π-π stacking interactions also played a crucial role in the self-assembly process, which was confirmed by fluorescence spectroscopy. Electron (SEM and TEM) and atomic force microscopy (AFM) studies showed that the peptide bolaamphiphile molecules self-assemble into nanofibrillar structures. Pd nanoparticles were synthesized in the hydrogel matrix in which redox-active tryptophan and tyrosine residues reduce the metal ions to metal nanoparticles. The size of the Pd nanoparticles are in the range of 3-9 nm, and are stabilized by peptide nanofibers. The peptide-nanofiber-supported Pd nanoparticles have shown effective catalytic activity for the removal of N-terminus protecting groups of amino acids and peptides.
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Affiliation(s)
- Indrajit Maity
- Department of Chemistry, Indian Institute of Technology Indore, Khandwa Road, Indore (India), Fax: (+91) 731-236-4182
| | - Manoj K Manna
- Department of Chemistry, Indian Institute of Technology Indore, Khandwa Road, Indore (India), Fax: (+91) 731-236-4182
| | - Dnyaneshwar B Rasale
- Department of Chemistry, Indian Institute of Technology Indore, Khandwa Road, Indore (India), Fax: (+91) 731-236-4182
| | - Apurba K Das
- Department of Chemistry, Indian Institute of Technology Indore, Khandwa Road, Indore (India), Fax: (+91) 731-236-4182
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Byrne L, Solà J, Boddaert T, Marcelli T, Adams RW, Morris GA, Clayden J. Foldamer-Mediated Remote Stereocontrol: >1,60 Asymmetric Induction. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308264] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Byrne L, Solà J, Boddaert T, Marcelli T, Adams RW, Morris GA, Clayden J. Foldamer-Mediated Remote Stereocontrol: >1,60 Asymmetric Induction. Angew Chem Int Ed Engl 2013; 53:151-5. [DOI: 10.1002/anie.201308264] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Indexed: 11/11/2022]
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Orcel U, De Poli M, De Zotti M, Clayden J. The N-Terminal Nonapeptide of Cephaibols A and C: A Naturally Occurring Example of Mismatched Helical Screw-Sense Control. Chemistry 2013; 19:16357-65. [DOI: 10.1002/chem.201302648] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Indexed: 12/14/2022]
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Xu H, Ghijsens E, George SJ, Wolffs M, Tomović Ž, Schenning APHJ, De Feyter S. Chiral Induction and Amplification in Supramolecular Systems at the Liquid-Solid Interface. Chemphyschem 2013; 14:1583-90. [DOI: 10.1002/cphc.201300212] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Indexed: 11/12/2022]
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Szolnoki É, Hetényi A, Mándity IM, Fülöp F, Martinek TA. Foldameric β-H18/20PMixed Helix Stabilized by Head-to-Tail Contacts: A Way to Higher-Order Structures. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201633] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Kayamori F, Abe H, Inouye M. Stabilization of Chiral Helices for Saccharide-Linked Ethynylpyridine Oligomers Possessing a Conformationally Well-Defined Linkage. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201376] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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