1
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Liu TH, Okuno M. Characterization of Secondary Structures of Model Polypeptides in Solutions with Hyper-Raman Spectroscopy. J Phys Chem B 2023. [PMID: 37468171 DOI: 10.1021/acs.jpcb.3c02101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Characterization of the secondary structures of two model polypeptides, poly-l-lysine and poly-l-glutamic acid in aqueous solutions has been demonstrated by hyper-Raman (HR) spectroscopy for the first time. Complementary to infrared (IR) and visible Raman spectroscopy, HR spectroscopy gives the amide I, II, and III bands originating from the polypeptide backbones and the CCH3 symmetric bending mode, enabling us to distinguish different conformations. The α-helix gives the broad and weak amide III band, while the β-sheet and the random coil show similar spectral patterns with different relative intensities between the amide I and II bands. HR spectra from aqueous solutions of the α-helix and the random coil of poly-l-ornithine also possess these spectral features. The HR spectra are analogous to UV resonance Raman (UVRR) spectra, indicating the signal enhancement due to the electronic resonance effect via the π-π* transition. In contrast, the vibrational frequencies of the amide I band in the HR spectra are much higher than those in the IR, visible Raman, and UVRR spectra, suggesting the non-coincidence between HR, IR, and Raman bands. Our finding suggests that HR spectroscopy is promising to provide complementary information on the secondary structures of polypeptides in aqueous solutions as a spectral approach differing from existing vibrational spectroscopic methods.
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Affiliation(s)
- Tsung-Han Liu
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
| | - Masanari Okuno
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
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2
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Manouchehri S, Zarrintaj P, Saeb MR, Ramsey JD. Advanced Delivery Systems Based on Lysine or Lysine Polymers. Mol Pharm 2021; 18:3652-3670. [PMID: 34519501 DOI: 10.1021/acs.molpharmaceut.1c00474] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Polylysine and materials that integrate lysine form promising drug delivery platforms. As a cationic macromolecule, a polylysine polymer electrostatically interacts with cells and is efficiently internalized, thereby enabling intracellular delivery. Although polylysine is intrinsically pH-responsive, the conjugation with different functional groups imparts smart, stimuli-responsive traits by adding pH-, temperature-, hypoxia-, redox-, and enzyme-responsive features for enhanced delivery of therapeutic agents. Because of such characteristics, polylysine has been used to deliver various cargos such as small-molecule drugs, genes, proteins, and imaging agents. Furthermore, modifying contrast agents with polylysine has been shown to improve performance, including increasing cellular uptake and stability. In this review, the use of lysine residues, peptides, and polymers in various drug delivery systems has been discussed comprehensively to provide insight into the design and robust manufacturing of lysine-based delivery platforms.
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Affiliation(s)
- Saeed Manouchehri
- School of Chemical Engineering, Oklahoma State University, 420 Engineering North, Stillwater, Oklahoma 74078, United States
| | - Payam Zarrintaj
- School of Chemical Engineering, Oklahoma State University, 420 Engineering North, Stillwater, Oklahoma 74078, United States
| | | | - Joshua D Ramsey
- School of Chemical Engineering, Oklahoma State University, 420 Engineering North, Stillwater, Oklahoma 74078, United States
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3
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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4
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Interaction of Halictine-Related Antimicrobial Peptides with Membrane Models. Int J Mol Sci 2019; 20:ijms20030631. [PMID: 30717183 PMCID: PMC6387077 DOI: 10.3390/ijms20030631] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 01/19/2023] Open
Abstract
We have investigated structural changes of peptides related to antimicrobial peptide Halictine-1 (HAL-1) induced by interaction with various membrane-mimicking models with the aim to identify a mechanism of the peptide mode of action and to find a correlation between changes of primary/secondary structure and biological activity. Modifications in the HAL-1 amino acid sequence at particular positions, causing an increase of amphipathicity (Arg/Lys exchange), restricted mobility (insertion of Pro) and consequent changes in antimicrobial and hemolytic activity, led to different behavior towards model membranes. Secondary structure changes induced by peptide-membrane interaction were studied by circular dichroism, infrared spectroscopy, and fluorescence spectroscopy. The experimental results were complemented by molecular dynamics calculations. An α-helical structure has been found to be necessary but not completely sufficient for the HAL-1 peptides antimicrobial action. The role of alternative conformations (such as β-sheet, PPII or 310-helix) also seems to be important. A mechanism of the peptide mode of action probably involves formation of peptide assemblies (possibly membrane pores), which disrupt bacterial membrane and, consequently, allow membrane penetration.
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5
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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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6
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Kurouski D. Advances of Vibrational Circular Dichroism (VCD) in bioanalytical chemistry. A review. Anal Chim Acta 2017; 990:54-66. [PMID: 29029743 PMCID: PMC10389559 DOI: 10.1016/j.aca.2017.08.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/26/2022]
Abstract
Vibrational Circular Dichroism (VCD) is a unique and relatively new spectroscopic technique that is capable of determining an absolute configuration of chiral molecules. VCD can be also used to determine structure of large macromolecules. This review highlights the most recent advances of VCD in bioanalytical chemistry. It shows that VCD is capable of unraveling supramolecular organization of peptides, proteins, saccharides, glycerophospholipids, polypeptide microcrystals, as well as amyloid fibrils and DNA. This review also demonstrates how VCD can be utilized to explore molecule-molecule interactions that determine mechanisms of chiral separations in chromatography. It aims to attract attention of scientists from all different research areas demonstrating the strength and capability of this very powerful spectroscopic technique.
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Affiliation(s)
- Dmitry Kurouski
- Department Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA.
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7
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Keiderling TA. Sensing site-specific structural characteristics and chirality using vibrational circular dichroism of isotope labeled peptides. Chirality 2017; 29:763-773. [DOI: 10.1002/chir.22749] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 11/07/2022]
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8
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Das D, Pal SK. Liquid Crystal Unveiled Interactions between Melittin and Phospholipids at Aqueous-Liquid Crystal Interface. ChemistrySelect 2017. [DOI: 10.1002/slct.201700604] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dibyendu Das
- Department of Chemical Sciences; Indian Institute of Science Education and Research Mohali (IISERM), Sector-81, SAS Nagar, Knowledge City; Manauli- 140306 India
| | - Santanu Kumar Pal
- Department of Chemical Sciences; Indian Institute of Science Education and Research Mohali (IISERM), Sector-81, SAS Nagar, Knowledge City; Manauli- 140306 India
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9
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Kocourková L, Novotná P, Čujová S, Čeřovský V, Urbanová M, Setnička V. Conformational study of melectin and antapin antimicrobial peptides in model membrane environments. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 170:247-255. [PMID: 27450123 DOI: 10.1016/j.saa.2016.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 07/07/2016] [Indexed: 06/06/2023]
Abstract
Antimicrobial peptides have long been considered as promising compounds against drug-resistant pathogens. In this work, we studied the secondary structure of antimicrobial peptides melectin and antapin using electronic (ECD) and vibrational circular dichroism (VCD) spectroscopies that are sensitive to peptide secondary structures. The results from quantitative ECD spectral evaluation by Dichroweb and CDNN program and from the qualitative evaluation of the VCD spectra were compared. The antimicrobial activity of the selected peptides depends on their ability to adopt an amphipathic α-helical conformation on the surface of the bacterial membrane. Hence, solutions of different zwitterionic and negatively charged liposomes and micelles were used to mimic the eukaryotic and bacterial biological membranes. The results show a significant content of α-helical conformation in the solutions of negatively charged liposomes mimicking the bacterial membrane, thus correlating with the antimicrobial activity of the studied peptides. On the other hand in the solutions of zwitterionic liposomes used as models of the eukaryotic membranes, the fraction of α-helical conformation was lower, which corresponds with their moderate hemolytic activity.
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Affiliation(s)
- Lucie Kocourková
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Pavlína Novotná
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Sabína Čujová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Václav Čeřovský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Marie Urbanová
- Department of Physics and Measurements, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Vladimír Setnička
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic.
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10
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Vibrational and electronic circular dichroism as powerful tools for the conformational analysis of cationic antimicrobial peptides. MONATSHEFTE FUR CHEMIE 2016. [DOI: 10.1007/s00706-016-1807-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Góbi S, Magyarfalvi G, Tarczay G. VCD Robustness of the Amide-I and Amide-II Vibrational Modes of Small Peptide Models. Chirality 2015; 27:625-34. [DOI: 10.1002/chir.22475] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 04/21/2015] [Accepted: 05/08/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Sándor Góbi
- Laboratory of Molecular Spectroscopy; Institute of Chemistry, Eötvös University; Budapest Hungary
| | - Gábor Magyarfalvi
- Laboratory of Molecular Spectroscopy; Institute of Chemistry, Eötvös University; Budapest Hungary
| | - György Tarczay
- Laboratory of Molecular Spectroscopy; Institute of Chemistry, Eötvös University; Budapest Hungary
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12
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D’Hondt M, Bracke N, Taevernier L, Gevaert B, Verbeke F, Wynendaele E, De Spiegeleer B. Related impurities in peptide medicines. J Pharm Biomed Anal 2014; 101:2-30. [DOI: 10.1016/j.jpba.2014.06.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 06/05/2014] [Accepted: 06/08/2014] [Indexed: 12/16/2022]
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13
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Dawson SJ, Mészáros Á, Pethő L, Colombo C, Csékei M, Kotschy A, Huc I. Controlling Helix Handedness in Water-Soluble Quinoline Oligoamide Foldamers. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402247] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Castellucci N, Falini G, Milli L, Monari M, Abbate S, Longhi G, Castiglioni E, Mazzeo G, Tomasini C. Solid-State Properties and Vibrational Circular Dichroism Spectroscopy in Solution of Hybrid Foldamers Stereoisomeric Mixtures. Chempluschem 2013; 79:114-121. [DOI: 10.1002/cplu.201300306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 01/19/2023]
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15
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Schwartz E, Liégeois V, Koepf M, Bodis P, Cornelissen JJLM, Brocorens P, Beljonne D, Nolte RJM, Rowan AE, Woutersen S, Champagne B. Beta Sheets with a Twist: The Conformation of Helical Polyisocyanopeptides Determined by Using Vibrational Circular Dichroism. Chemistry 2013; 19:13168-74. [DOI: 10.1002/chem.201300073] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 05/07/2013] [Indexed: 11/10/2022]
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16
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17
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Mirtič A, Grdadolnik J. The structure of poly-l-lysine in different solvents. Biophys Chem 2013; 175-176:47-53. [DOI: 10.1016/j.bpc.2013.02.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 02/13/2013] [Accepted: 02/13/2013] [Indexed: 10/27/2022]
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18
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Giugliarelli A, Sassi P, Paolantoni M, Morresi A, Dukor R, Nafie L. Vibrational Circular Dichroism Spectra of Lysozyme Solutions: Solvent Effects on Thermal Denaturation Processes. J Phys Chem B 2013; 117:2645-52. [DOI: 10.1021/jp311268x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
| | - Paola Sassi
- Dipartimento
di Chimica, Università di Perugia, Via Elce di sotto 8, 06123 Perugia, Italy
| | - Marco Paolantoni
- Dipartimento
di Chimica, Università di Perugia, Via Elce di sotto 8, 06123 Perugia, Italy
| | - Assunta Morresi
- Dipartimento
di Chimica, Università di Perugia, Via Elce di sotto 8, 06123 Perugia, Italy
| | - Rina Dukor
- BioTools, Inc., 17546
Bee Line Highway, Jupiter, Florida, 33458, United States
| | - Laurence Nafie
- Department of Chemistry, Syracuse University, Syracuse, New York, 13244, United
States
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19
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Deng H. Enzyme active site interactions by Raman/FTIR, NMR, and ab initio calculations. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 93:153-82. [PMID: 24018325 PMCID: PMC5484042 DOI: 10.1016/b978-0-12-416596-0.00005-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and NMR chemical shift measurements of enzyme-bound ligands are often used for such purpose when X-ray structures are not available or when higher resolution active site structures are desired. This review is focused on how ab initio calculations may be integrated with vibrational and NMR chemical shift measurements to quantitatively determine high-resolution ligand structures (up to 0.001 Å for bond length and 0.01 Å for hydrogen bonding distance) and how interaction energies between bound ligand and its surroundings at the active site may be determined. Quantitative characterization of substrate ionic states, bond polarizations, tautomeric forms, conformational changes and its interactions with surroundings in enzyme complexes that mimic ground state or transition state can provide snapshots for visualizing the substrate structural evolution along enzyme-catalyzed reaction pathway. Our results have shown that the integration of spectroscopic studies with theoretical computation greatly enhances our ability to interpret experimental data and significantly increases the reliability of the theoretical analysis.
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Affiliation(s)
- Hua Deng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.
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20
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Dzwolak W, Kalinowski J, Johannessen C, Babenko V, Zhang G, Keiderling TA. On the DMSO-Dissolved State of Insulin: A Vibrational Spectroscopic Study of Structural Disorder. J Phys Chem B 2012; 116:11863-71. [DOI: 10.1021/jp3062674] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wojciech Dzwolak
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093
Warsaw, Poland
| | - Jarosław Kalinowski
- Institute of High
Pressure Physics, Polish Academy of Sciences, Sokolowska 29/37, 01-142 Warsaw, Poland
| | - Christian Johannessen
- Manchester Interdisciplinary
Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Viktoria Babenko
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093
Warsaw, Poland
| | - Ge Zhang
- Department of Chemistry, University of Illinois at Chicago, 845
West Taylor Street (m/c 111), Chicago, Illinois 60607-7061, United
States
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845
West Taylor Street (m/c 111), Chicago, Illinois 60607-7061, United
States
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21
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Xiong K, Asher SA. Impact of ion binding on poly-L-lysine (un)folding energy landscape and kinetics. J Phys Chem B 2012; 116:7102-12. [PMID: 22612556 PMCID: PMC3381074 DOI: 10.1021/jp302007g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We utilize T-jump UV resonance Raman spectroscopy (UVRR) to study the impact of ion binding on the equilibrium energy landscape and on (un)folding kinetics of poly-L-lysine (PLL). We observe that the relaxation rates of the folded conformations (including π-helix (bulge), pure α-helix, and turns) of PLL are slower than those of short alanine-based peptides. The PLL pure α-helix folding time is similar to that of short alanine-based peptides. We for the first time have directly observed that turn conformations are α-helix and π-helix (bulge) unfolding intermediates. ClO(4)(-) binding to the Lys side chain -NH(3)(+) groups and the peptide backbone slows the α-helix unfolding rate compared to that in pure water, but little impacts the folding rate, resulting in an increased α-helix stability. ClO(4)(-) binding significantly increases the PLL unfolding activation barrier but little impacts the folding barrier. Thus, the PLL folding coordinate(s) differs from the unfolding coordinate(s). The-π helix (bulge) unfolding and folding coordinates do not directly go through the α-helix energy well. Our results clearly demonstrate that PLL (un)folding is not a two-state process.
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Affiliation(s)
- Kan Xiong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
| | - Sanford A. Asher
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
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22
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Li X, Hopmann KH, Hudecová J, Stensen W, Novotná J, Urbanová M, Svendsen JS, Bouř P, Ruud K. Absolute Configuration of a Cyclic Dipeptide Reflected in Vibrational Optical Activity: Ab Initio and Experimental Investigation. J Phys Chem A 2012; 116:2554-63. [DOI: 10.1021/jp211454v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaojun Li
- Centre for
Theoretical and Computational
Chemistry (CTCC), Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | | | - Jana Hudecová
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences,
166 10 Prague, Czech Republic
| | - Wenche Stensen
- Lytix Biopharma AS, Tromsø Research
Park, N-9294 Tromsø, Norway
| | - Jana Novotná
- Department of Analytical Chemistry, Institute of Chemical Technology, Prague, 166 28 Prague, Czech
Republic
| | - Marie Urbanová
- Department of
Physics and Measurements, Institute of Chemical Technology, Prague, 166 28 Prague, Czech
Republic
| | | | - Petr Bouř
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences,
166 10 Prague, Czech Republic
| | - Kenneth Ruud
- Centre for
Theoretical and Computational
Chemistry (CTCC), Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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23
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Setnička V, Hlaváček J, Urbanová M. Oligopeptide-porphyrin interactions studied by circular dichroism spectroscopy: the effect of metalloporphyrin axial ligands on peptide matrix conformation. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424608000650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Vibrational (VCD) and electronic circular dichroism (ECD) spectroscopies were used to investigate non-covalent interactions between the cationic tripeptide L-lysyl-L-alanyl-L-alanine (KAA) and the anionic porphyrin meso-tetrakis(4-sulfonatophenyl)porphyrin (TPPS) in aqueous solution. Also studied were the interactions between KAA and the three metal derivatives of TPPS (copper(II), iron(III), and manganese(III)), each of which has a different number of axial ligands. VCD spectra in the amide I' ( C = O stretching vibration) region are extremely sensitive to peptide conformation, and, consequently, provide direct information about the conformational changes of host oligopeptide matrices caused by electrostatic interaction with guest porphyrin molecules. We found that pure KAA adopts a left-handed polyproline II (PPII) helical conformation when dissolved in aqueous solution at near-neutral pH values. When mixed with metal-free TPPS under the same conditions, VCD intensities were markedly reduced in the amide I' region and a new negative band was observed at 1634 cm−1; both findings indicating the transition of the PPII conformation into a less compact structure having similarities to β-sheet, herein termed a β-sheet-like conformation. In the case of the metal derivatives of TPPS studied, only variations in the VCD intensities in the amide I' region were observed. Compared to the results for pure KAA, the binding of Cu (II) TPPS , which has no axial ligand, resulted in the greatest decrease in amide I' VCD intensity. Nevertheless, the shape of a VCD spectrum characteristic for a PPII conformation was maintained, thereby indicating the presence of an “extended” PPII conformation in the Cu (II) TPPS -KAA complex. Conversely, Mn (III) TPPS , which has two axial ligands, did not significantly affect the PPII conformation of KAA in the Mn (III) TPPS -KAA complex. The effects of the metalation and axial ligation of TPPS on the conformation of KAA in peptide-porphyrin complexes are discussed, together with the results of our ECD study.
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Affiliation(s)
- Vladimír Setnička
- Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, Prague 6, 166 28, Czech Republic
| | - Jan Hlaváček
- Department of Natural Products, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, Prague 6, 166 10, Czech Republic
| | - Marie Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Technická 5, Prague 6, 166 28, Czech Republic
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24
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Formation of β-sheets in glutamine and alanine tripeptides. Biochem Biophys Res Commun 2011; 406:348-52. [DOI: 10.1016/j.bbrc.2011.02.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 02/10/2011] [Indexed: 11/20/2022]
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25
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Urbanová M. Bioinspired interactions studied by vibrational circular dichroism. Chirality 2010; 21 Suppl 1:E215-30. [PMID: 19937957 DOI: 10.1002/chir.20803] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Vibrational circular dichroism (VCD) spectra are reliable indicators of the spatial structure of chiral molecules. The specific and characteristic feature of vibrational spectroscopy, and therefore also of VCD, where the energy of some vibrational modes is predominantly focused to a specific part of the molecule, enables monitoring both the structure of the molecule dissolved in different solvents and under different physicochemical conditions and molecular interactions. This minireview deals with recent contributions covering structural information on the bioinspired interactions obtained by means of VCD, especially in the following areas: interaction of DNA with biomolecules and biogenic metals, guanine tetramers and quadruplexes, biointeractions of bile pigments, and polypeptide and protein interactions with other biomolecules.
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Affiliation(s)
- Marie Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Prague, Czech Republic.
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26
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Hatfield MPD, Murphy RF, Lovas S. VCD spectroscopic properties of the beta-hairpin forming miniprotein CLN025 in various solvents. Biopolymers 2010; 93:442-50. [PMID: 19937759 PMCID: PMC4499852 DOI: 10.1002/bip.21356] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Electronic and vibrational circular dichroism are often used to determine the secondary structure of proteins, because each secondary structure has a unique spectrum. Little is known about the vibrational circular dichroic spectroscopic features of the beta-hairpin. In this study, the VCD spectral features of a decapeptide, YYDPETGTWY (CLN025), which forms a stable beta-hairpin that is stabilized by intramolecular weakly polar interactions and hydrogen bonds were determined. Molecular dynamics simulations and ECD spectropolarimetry were used to confirm that CLN025 adopts a beta-hairpin in water, TFE, MeOH, and DMSO and to examine differences in the secondary structure, hydrogen bonds, and weakly polar interactions. CLN025 was synthesized by microwave-assisted solid phase peptide synthesis with N(alpha)-Fmoc protected amino acids. The VCD spectra displayed a (-,+,-) pattern with bands at 1640 to 1656 cm(-1), 1667 to 1687 cm(-1), and 1679 to 1686 cm(-1) formed by the overlap of a lower frequency negative couplet and a higher frequency positive couplet. A maximum IR absorbance was observed at 1647 to 1663 cm(-1) with component bands at 1630 cm(-1), 1646 cm(-1), 1658 cm(-1), and 1675 to 1680 cm(-1) that are indicative of the beta-sheet, random meander, either random meander or loop and turn, respectively. These results are similar to the results of others, who examined the VCD spectra of beta-hairpins formed by (D)Pro-Xxx turns and indicated that observed pattern is typical of beta-hairpins.
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Affiliation(s)
| | - Richard. F. Murphy
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
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27
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Setnička V, Hlaváček J, Urbanová M. Cationic oligopeptides with the repeating sequence L-lysyl-L-alanyl-L-alanine: conformational and thermal stability study using optical spectroscopic methods. J Pept Sci 2009; 15:533-9. [DOI: 10.1002/psc.1154] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Shanmugam G, Polavarapu PL. Structural transition during thermal denaturation of collagen in the solution and film states. Chirality 2009; 21:152-9. [DOI: 10.1002/chir.20598] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Shanmugam G, Polavarapu PL. Concentration- and dehydration-dependent structural transitions in poly-l-lysine. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.04.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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30
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C3-symmetrical self-assembled structures investigated by vibrational circular dichroism. Chirality 2008; 20:1016-22. [DOI: 10.1002/chir.20568] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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31
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Bochicchio B, Pepe A, Tamburro AM. Investigating by CD the molecular mechanism of elasticity of elastomeric proteins. Chirality 2008; 20:985-94. [DOI: 10.1002/chir.20541] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Ashton L, Blanch EW. Investigation of polypeptide conformational transitions with two-dimensional Raman optical activity correlation analysis, applying autocorrelation and moving window approaches. APPLIED SPECTROSCOPY 2008; 62:469-475. [PMID: 18498686 DOI: 10.1366/000370208784344433] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The study of conformational transitions in polypeptides is not only important for the understanding of folding mechanisms responsible for the self-assembly of proteins but also for the investigation of the misfolding of proteins that can result in diseases including cystic fibrosis, Alzheimer's, and Parkinson's diseases. Our recent studies developing two-dimensional Raman optical activity (ROA) correlation analysis have proven to be successful in the investigation of polypeptide conformational transitions. However, the complexity of the ROA spectra, and the 2D correlation synchronous and asynchronous plots, makes data analysis detailed and complex, requiring great care in interpretation of 2D correlation rules. By utilizing the 2D correlation approaches of autocorrelation and moving windows it has been possible to gain further information from the ROA spectral data sets in a simpler and more consistent way. The most significant spectral intensity changes have been easily identified, facilitating appropriate interpretation of synchronous plots, and transition phases have been identified in the moving window plots, directly relating spectral intensity changes to the perturbation.
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Affiliation(s)
- L Ashton
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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33
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Lee KK, Joo C, Yang S, Han H, Cho M. Phosphorylation effect on the GSSS peptide conformation in water: Infrared, vibrational circular dichroism, and circular dichroism experiments and comparisons with molecular dynamics simulations. J Chem Phys 2007; 126:235102. [PMID: 17600445 DOI: 10.1063/1.2738472] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The phosphorylation effect on the small peptide conformation in water has not been clearly understood yet, despite the widely acknowledged notion that control of protein activity by phosphorylation works mainly by inducing conformational change. To elucidate the detailed mechanism, we performed infrared (IR) absorption and vibrational and electronic circular dichroism studies of both unphosphorylated and phosphorylated tetrapeptides, GSSS 1 and GSSpS 2. The solution structure of the tetrapeptide is found to be little dependent on the presence of the neutral or negatively charged phosphoryl group, and to be a mixture of extended structures including polyproline II (PII) and beta-sheet conformations. The additional band at 1598 cm(-1) in the amide I IR spectrum of the phosphorylated peptide GSSpS at neutral pD appears to be clear spectroscopic evidence for direct intramolecular hydrogen-bonding interaction between the side chain dianionic phosphoryl group and the backbone amide proton. On the basis of amide I IR band analyses, the authors found that the probability of finding the phosphoryl group strongly H bonded to the backbone proton in GSSpS is about 43% at pD 7.0 and 37 degrees C. Such a H-bonding interaction in GSSpS has the biological standard enthalpy and entropy of -15.1 kJ/mol and -51.2 J/K mol, respectively. Comparisons between the experimentally measured IR and VCD spectra and the numerically simulated ones suggested that the currently available force field parameters need to be properly modified. The results in this paper may shed light on an unknown mechanism of controlling the peptide conformation by phosphorylation.
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Affiliation(s)
- Kyung-Koo Lee
- Department of Chemistry, Korea University, Seoul 136-701, Korea and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea
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34
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Ma L, Ahmed Z, Mikhonin AV, Asher SA. UV resonance Raman measurements of poly-L-lysine's conformational energy landscapes: dependence on perchlorate concentration and temperature. J Phys Chem B 2007; 111:7675-80. [PMID: 17567063 DOI: 10.1021/jp0703758] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UV resonance Raman spectroscopy has been used to determine the conformational energy landscape of poly-L-lysine (PLL) in the presence of NaClO4 as a function of temperature. At 1 degree C, in the presence of 0.83 M NaClO4, PLL shows an approximately 86% alpha-helix-like content, which contains alpha-helix and pi-bulge/helix conformations. The high alpha-helix-like content of PLL occurs because of charge screening due to strong ion-pair formation between ClO4- and the lysine side chain -NH3+. As the temperature increases from 1 to 60 degrees C, the alpha-helix and pi-bulge/helix conformations melt into extended conformations (PPII and 2.51-helix). We calculate the Psi Ramachandran angle distribution of the PLL peptide bonds from the UV Raman spectra which allows us to calculate the PLL (un)folding energy landscapes along the Psi reaction coordinate. We observe a basin in the Psi angle conformational space associated with alpha-helix and pi-bulge/helix conformations and another basin for the extended PPII and 2.51-helical conformations.
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Affiliation(s)
- Lu Ma
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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35
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Ashton L, Barron LD, Hecht L, Hyde J, Blanch EW. Two-dimensional Raman and Raman optical activity correlation analysis of the alpha-helix-to-disordered transition in poly(L-glutamic acid). Analyst 2007; 132:468-79. [PMID: 17471394 DOI: 10.1039/b700421d] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rich and complex Raman scattering and Raman optical activity (ROA) spectra have been measured monitoring the pH induced alpha-helix-to-disordered conformational transition in poly(L-glutamic acid). Two-dimensional (2D) correlation techniques have been applied to facilitate a comprehensive analysis of these two complementary spectral sets. Synchronous contour plots have identified band assignments of alpha-helical and disordered conformations, and have revealed bands characteristic of changes in the protonation state of the polypeptide. Asynchronous plots, on the other hand, have probed the relative sequential orders of intensity changes indicating a decrease in intensity of alpha-helical bands in the backbone skeletal stretch region, followed by a subsequent decrease in intensity in the extended amide III and amide I regions, underlying the appearance of disordered structure, including poly(L-proline) II (PPII) helix. The application of a 2D correlation 'moving' window has also disclosed two distinct phases during helix unfolding in the alpha-helix-to-disordered transition, occurring at approximately pH 4.9 and approximately pH 5.2, possibly a result of the difference in helical stability between the end and central regions of the alpha-helix. This paper demonstrates the potential value of combining 2D Raman, 2D ROA and moving window correlation techniques for the detailed investigation of complex and subtle changes of secondary structure during the unfolding mechanisms of polypeptides and proteins.
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Affiliation(s)
- Lorna Ashton
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester, UKM1 7DN
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36
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Mikhonin AV, Asher SA, Bykov SV, Murza A. UV Raman spatially resolved melting dynamics of isotopically labeled polyalanyl peptide: slow alpha-helix melting follows 3(10)-helices and pi-bulges premelting. J Phys Chem B 2007; 111:3280-92. [PMID: 17388440 DOI: 10.1021/jp0654009] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We used UV resonance Raman (UVRR) to examine the spatial dependence of the T-jump secondary structure relaxation of an isotopically labeled 21-residue mainly Ala peptide, AdP. The AdP penultimate Ala residues were perdeuterated, leaving the central residues hydrogenated, to allow separate monitoring of melting of the middle versus the end peptide bonds. For 5 to 30 degrees C T-jumps, the central peptide bonds show a approximately 2-fold slower relaxation time (189 +/- 31 ns) than do the exterior peptide bonds (97 +/- 15 ns). In contrast, for a 20 to 40 degrees C T-jump, the central peptide bond relaxation appears to be faster (56 +/- 6 ns) than that of the penultimate peptide bonds (131 +/- 46 ns). We show that, if the data are modeled as a two-state transition, we find that only exterior peptide bonds show anti-Arrhenius folding behavior; the middle peptide bonds show both normal Arrhenius-like folding and unfolding. This anti-Arrhenius behavior results from the involvement of pi-bulges/helices and 3(10)-helix states in the melting. The unusual temperature dependence of the (un)folding rates of the interior and exterior peptide bonds is due to the different relative (un)folding rates of 3(10)-helices, alpha-helices, and pi-bulges/helices. Pure alpha-helix unfolding rates are approximately 12-fold slower (approximately 1 micros) than that of pi-bulges and 3(10)-helices. In addition, we also find that the alpha-helix is most stable at the AdP N-terminus where eight consecutive Ala occur, whereas the three hydrophilic Arg located in the middle and at the C-terminus destabilize the alpha-helix in these regions and induce defects such as pi-bulges and 3(10)-helices.
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Affiliation(s)
- Aleksandr V Mikhonin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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37
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Valík M, Malina J, Palivec L, Foltýnová J, Tkadlecová M, Urbanová M, Brabec V, Král V. Tröger's base scaffold in racemic and chiral fashion as a spacer for bisdistamycin formation. Synthesis and DNA binding study. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.06.056] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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38
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Affiliation(s)
- Zhengshuang Shi
- Department of Chemistry, New York University, 100 Washington Place, New York, New York 10003-5180, USA
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39
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Shanmugam G, Polavarapu PL. Structures of intact glycoproteins from vibrational circular dichroism. Proteins 2006; 63:768-76. [PMID: 16498615 DOI: 10.1002/prot.20884] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Vibrational circular dichroism (VCD) spectra for the glycoproteins alpha1-acid glycoprotein (AGP) and bovine submaxillary mucin (BSM), have been measured in D2O solutions and for the films prepared from aqueous (H2O) buffer solutions in the 1800 to 900 cm(-1) region. The solution VCD results revealed that AGP has beta-sheet structure, along with a significant amount of alpha-helix as evidenced from a W pattern in the amide I region. The VCD of BSM solution suggested a polyproline II type structure, characterized by the appearance of strong negative couplet in the amide I region. The film VCD results on AGP and BSM suggested that the secondary structures of polypeptide fold in the film state are similar to those in the solution. The absence of any significant film VCD in the low frequency region (1200-900 cm(-1)), suggested that the dominant linkage for carbohydrate residues is likely to be a beta linkage. VCD spectroscopy gains importance in the secondary structural analysis of polypeptide fold in glycoproteins due to the absence of interfering VCD from the carbohydrate residues in the conformationally sensitive amide I region. Also, film VCD studies permit measurements in the low wavenumber region (1200-900 cm(-1)) that reveal the dominant type of linkage for carbohydrate residues. Such clear structural information is unlike that from ECD, where ECD bands of acylated amino sugar residues interfere with those of polypeptide backbone in the conformationally sensitive far-UV region.
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Affiliation(s)
- Ganesh Shanmugam
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
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40
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Mahalakshmi R, Shanmugam G, Polavarapu PL, Balaram P. Circular Dichroism of Designed Peptide Helices and β-Hairpins: Analysis of Trp- and Tyr-Rich Peptides. Chembiochem 2005; 6:2152-8. [PMID: 16261550 DOI: 10.1002/cbic.200500152] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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41
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Pizzanelli S, Monti S, Forte C. Conformation and Orientation of Tetraalanine in a Lyotropic Liquid Crystal Studied by Nuclear Magnetic Resonance. J Phys Chem B 2005; 109:21102-9. [PMID: 16853733 DOI: 10.1021/jp051797p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The (1)H NMR spectra of two isotopomers of tetraalanine deuterated on the two external methyl groups and on the two internal ones, respectively, were recorded in the lyotropic solvent cesium pentadecafluorooctanoate (CsPFO)/water. Eight dipolar couplings could be estimated from the spectra. The set of dipolar couplings was fitted assuming that one rigid conformer is present. Of the four major conformers considered, selected on the basis of theoretical calculations, the one characterized by the two couples of internal dihedral angles in the Ramachandran region of PPII resulted to be the only one to fit the set of couplings within experimental error. The data indicate that the molecule is oriented with the long molecular axis tilted with respect to the surface of the micelles formed by CsPFO.
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Affiliation(s)
- Silvia Pizzanelli
- Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Area della Ricerca di Pisa, via G. Moruzzi 1, 56124 Pisa, Italy
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42
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Shanmugam G, Polavarapu PL, Hallgas B, Majer Z. Effect of d-amino acids at Asp23 and Ser26 residues on the conformational preference of Aβ20–29 peptides. Biochem Biophys Res Commun 2005; 335:712-22. [PMID: 16091285 DOI: 10.1016/j.bbrc.2005.07.136] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Accepted: 07/21/2005] [Indexed: 10/25/2022]
Abstract
The effects of d-amino acids at Asp(23) and Ser(26) residues on the conformational preference of beta-amyloid (Abeta) peptide fragment (Abeta(20-29)) have been studied using different spectroscopic techniques, namely vibrational circular dichroism (VCD), vibrational absorption, and electronic circular dichroism. To study the structure of the Abeta(20-29), [d-Asp(23)]Abeta(20-29), and [d-Ser(26)]Abeta(20-29) peptides under different conditions, the spectra were measured in 10mM acetate buffer (pH 3) and in 2,2,2-trifluoroethanol (TFE). The spectroscopic results indicated that at pH 3, Abeta(20-29) peptide takes random coil with beta-turn structure, while [d-Ser(26)]Abeta(20-29) peptide adopts significant amount of polyproline II (PPII) type structure along with beta-turn contribution and d-Asp-substituted peptide ([d-Asp(23)]Abeta(20-29)) adopts predominantly PPII type structure. The increased propensity for PPII conformation upon d-amino acid substitution, in acidic medium, has important biological implications. In TFE, Abeta(20-29), [d-Asp(23)]Abeta(20-29), and [d-Ser(26)]Abeta(20-29) peptides adopt 3(10)-helix, alpha-helix, and random coil with some beta-turn structures, respectively. The VCD data obtained for the Abeta peptide films suggested that the secondary structures for the peptide films are not the same as those for corresponding solution and are also different among the Abeta peptides studied here. This observation suggests that dehydration can have a significant influence on the structural preferences of these peptides.
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Affiliation(s)
- Ganesh Shanmugam
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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43
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Vibrational and electronic circular dichroism and absorption spectral study of the DNA–5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin interaction. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2005.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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44
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Mikhonin AV, Myshakina NS, Bykov SV, Asher SA. UV Resonance Raman Determination of Polyproline II, Extended 2.51-Helix, and β-Sheet Ψ Angle Energy Landscape in Poly-l-Lysine and Poly-l-Glutamic Acid. J Am Chem Soc 2005; 127:7712-20. [PMID: 15913361 DOI: 10.1021/ja044636s] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UV resonance Raman (UVR) spectroscopy was used to examine the solution conformation of poly-l-lysine (PLL) and poly-l-glutamic acid (PGA) in their non-alpha-helical states. UVR measurements indicate that PLL (at pH = 2) and PGA (at pH = 9) exist mainly in a mixture of polyproline II (PPII) and a novel left-handed 2.5(1)-helical conformation, which is an extended beta-strand-like conformation with Psi approximately +170 degrees and Phi approximately -130 degrees . Both of these conformations are highly exposed to water. The energies of these conformations are very similar. We see no evidence of any disordered "random coil" states. In addition, we find that a PLL and PGA mixture at neutral pH is approximately 60% beta-sheet and contains PPII and extended 2.5(1)-helix conformations. The beta-sheet conformation shows little evidence of amide backbone hydrogen bonding to water. We also developed a method to estimate the distribution of Psi Ramachandran angles for these conformations, which we used to estimate a Psi Ramachandran angle energy landscape. We believe that these are the first experimental studies to give direct information on protein and peptide energy landscapes.
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Affiliation(s)
- Aleksandr V Mikhonin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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45
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Bour P, Michalík D, Kapitán J. Empirical solvent correction for multiple amide group vibrational modes. J Chem Phys 2005; 122:144501. [PMID: 15847539 DOI: 10.1063/1.1877272] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Previously proposed solvent correction to the amide I peptide vibration was extended so that it can be applied to a general solvated chromophore. The combined molecular and quantum mechanics (MMQM) method is based on a linear dependence of harmonic force field and intensity tensor components of the solute on solvent electrostatic field. For N-methylacetamide, realistic solvent frequency and intensity changes as well as inhomogeneous band widths were obtained for amide A, I, II , and III modes. A rather anomalous basis set size dependence was observed for the amide A and I vibrations, when bigger basis lead to narrowing of spectral bands and lesser molecular sensibility to the environment. For a model alpha-helical peptide, a W-shape of the vibrational circular dichroism signal observed in deuterated solvent for the amide I band was reproduced correctly, unlike with previous vacuum models.
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Affiliation(s)
- Petr Bour
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Praha 6, Czech Republic.
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46
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Abstract
The fragment A beta(25-35) of the Alzheimer's amyloid beta-peptide, like its full-length peptide A beta(1-42), has shown neurotoxic activities in cultured cells. The conformational preference of this important peptide is examined here in solution, gel, and film states (obtained with organic and aqueous solvents) by vibrational circular dichroism spectroscopy for the first time. For comparative studies, vibrational absorption and electronic circular dichroism measurements were also carried out under identical conditions. The peptide was found to adopt beta-sheet and beta-turn structures, with their relative proportions changing in different environments.
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Affiliation(s)
- Ganesh Shanmugam
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
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47
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Palivec L, Urbanová M, Volka K. Circular dichroism spectroscopic study of non-covalent interactions of poly-L-glutamic acid with a porphyrin derivative in aqueous solutions. J Pept Sci 2005; 11:536-45. [PMID: 15880603 DOI: 10.1002/psc.672] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The interactions of poly-L-glutamic acid and a cationic porphyrin derivative in aqueous solutions were studied by the combination of vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopies. It was found that non-covalent interactions between both agents influence the structure of the polymeric matrix and the guest porphyrins and vice versa, but the physico-chemical properties of the solutions, especially the pH and the relative permittivity of the solvent, play a key role in the structure of the polypeptide part of the formed complexes. It was shown that the interaction with porphyrins prevents the precipitation of poly-L-glutamic acid in aqueous solution at acidic pH. In special conditions, the porphyrins attached to the polypeptide probably possess face-to-face interaction as demonstrated by the enhancement of the characteristic ECD signal and the appearance of sidebands on its short and long wavelength sides.
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Affiliation(s)
- Lukás Palivec
- Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28 Praha 6, Czech Republic
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48
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Asher SA, Mikhonin AV, Bykov S. UV Raman demonstrates that alpha-helical polyalanine peptides melt to polyproline II conformations. J Am Chem Soc 2004; 126:8433-40. [PMID: 15238000 DOI: 10.1021/ja049518j] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We examined the 204-nm UV Raman spectra of the peptide XAO, which was previously found by Shi et al.'s NMR study to occur in aqueous solution in a polyproline II (PPII) conformation. The UV Raman spectra of XAO are essentially identical to the spectra of small peptides such as ala(5) and to the large 21-residue predominantly Ala peptide, AP. We conclude that the non-alpha-helical conformations of these peptides are dominantly PPII. Thus, AP, which is highly alpha-helical at room temperature, melts to a PPII conformation. There is no indication of any population of intermediate disordered conformations. We continued our development of methods to relate the Ramachandran Psi-angle to the amide III band frequency. We describe a new method to estimate the Ramachandran Psi-angular distributions from amide III band line shapes measured in 204-nm UV Raman spectra. We used this method to compare the Psi-distributions in XAO, ala(5), the non-alpha-helical state of AP, and acid-denatured apomyoglobin. In addition, we estimated the Psi-angle distributions of peptide bonds which occur in non-alpha-helix and non-beta-sheet conformations in a small library of proteins.
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Affiliation(s)
- Sanford A Asher
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
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Xu Q, Keiderling TA. Effect of sodium dodecyl sulfate on folding and thermal stability of acid-denatured cytochrome c: a spectroscopic approach. Protein Sci 2004; 13:2949-59. [PMID: 15459332 PMCID: PMC2286590 DOI: 10.1110/ps.04827604] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The molten globule (MG) state can be an intermediate in the protein folding pathway; thus, its detailed description can help understanding protein folding. Sodium dodecyl sulfate (SDS), an anionic surfactant that is commonly used to mimic hydrophobic binding environments such as cell membranes, is known to denature some native state proteins, including horse cytochrome c (cyt c). In this article, refolding of acid denatured cyt c is studied under the influence of SDS to form MG-like states at both low concentration and above the critical micelle concentration using Fourier transform Infrared (FTIR) and ultraviolet and visible absorption as well as fluorescence and circular dichroism (CD). Thermal denaturation monitored with FTIR and CD shows distinct final high temperature states starting from MG-like states formed with different SDS/protein ratios. The results suggest that the SDS/protein ratio as well as the actual SDS (or protein) concentration affects structure and its thermal stability. Thermal denaturation monitored with CD and FTIR for cyt c at neutral pH but denatured with SDS showed that at a high SDS/protein ratio, the thermal behavior of MG-like states formed at low and neutral pH are quite similar. Based on the results obtained, the merits of two models of the protein-surfactant structure are discussed for different SDS concentrations.
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Affiliation(s)
- Qi Xu
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street (m/c 111), Chicago, IL 60607-7061, USA
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Mazaleyrat JP, Wright K, Gaucher A, Toulemonde N, Wakselman M, Oancea S, Peggion C, Formaggio F, Setnicka V, Keiderling TA, Toniolo C. Induced Axial Chirality in the Biphenyl Core of the Cα-Tetrasubstituted α-Amino Acid Residue Bip and Subsequent Propagation of Chirality in (Bip)n/Val Oligopeptides. J Am Chem Soc 2004; 126:12874-9. [PMID: 15469284 DOI: 10.1021/ja040100v] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the dipeptides Boc-Bip-L-Val-OMe and Boc-Bip-D-Val-OMe, an induced axial chirality in the biphenyl core of the Bip residue, a conformationally labile, proatropoisomeric C(alpha,alpha)-disubstituted glycine, was observed by electronic CD and (1)H NMR. Chiral induction is significantly higher when the Val residue is located at the C-terminal position of Bip. An outstanding phenomenon of propagation of chirality was demonstrated to occur in the related 3(10)-helical -(Bip)n-L-Val (n = 2-6) oligopeptides by CD and vibrational CD techniques.
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Affiliation(s)
- Jean-Paul Mazaleyrat
- Contribution from SIRCOB, UMR CNRS 8086, Bâtiment Lavoisier, University of Versailles, F-78035 Versailles, France
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