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Drost DA, Merten C. Vibrational circular dichroism spectra of proline in water at different pH values. Phys Chem Chem Phys 2024; 26:17753-17759. [PMID: 38873734 DOI: 10.1039/d4cp01768d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Recording VCD spectra of aqueous solution poses a particular challenge as water is a strong infrared absorber. Likewise, the computational analysis of VCD spectra by means of DFT-based spectral calculations requires the consideration of explicit solvent molecules, thus posing an even greater challenge. Several studies suggested that by modeling the solvent environment with a few water molecules in a micro-solvation approach would be sufficient to describe experimental spectra. For example, using proline at different pH values, we herein show that a change in the relative spatial orientation of a single water molecule in five-fold solvated structures strongly affects the computed VCD spectral signatures and that Boltzmann-weighted spectra do not correctly reproduce the experiment. We thus explored an approach based on molecular dynamics and subsequent DFT-calculations, in which we considered 30 water molecules (about 1.5 solvation shells). Once again, it was found that the Boltzmann-weighted spectra obtained on the basis of several hundred structures did not correctly reproduce experimental signatures, and a simple averaging scheme resulted in well-matching spectra with comparable bandwidths. The rationale behind the procedure was that sampling the configurational space of the solvent molecules is as equally important as the conformational sampling of the solute. For conformationally more flexible molecules, it is assumed that a much larger set of structures will have to be computed in order to properly sample the conformational space of both solute and solvent.
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Affiliation(s)
- Deborah A Drost
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Organic Chemistry II, Universitätsstraße 150, 44801 Bochum, Germany. www.mertenlab.de
| | - Christian Merten
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Organic Chemistry II, Universitätsstraße 150, 44801 Bochum, Germany. www.mertenlab.de
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2
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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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3
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Novotná P, Urbanová M. A Solid Phase Vibrational Circular Dichroism Study of Polypeptide-Surfactant Interaction. Chirality 2015; 27:965-72. [DOI: 10.1002/chir.22534] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 08/07/2015] [Accepted: 08/27/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Pavlína Novotná
- Department of Analytical Chemistry; University of Chemistry and Technology; Prague Czech Republic
| | - Marie Urbanová
- Department of Physics and Measurements; University of Chemistry and Technology; Prague Czech Republic
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4
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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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5
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Lakhani A, Roy A, De Poli M, Nakaema M, Formaggio F, Toniolo C, Keiderling TA. Experimental and Theoretical Spectroscopic Study of 310-Helical Peptides Using Isotopic Labeling to Evaluate Vibrational Coupling. J Phys Chem B 2011; 115:6252-64. [DOI: 10.1021/jp2003134] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ahmed Lakhani
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607-7061, United States
| | - Anjan Roy
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607-7061, United States
| | - Matteo De Poli
- Institute of Biomolecular Chemistry, Padova Unit, CNR, and Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Marcelo Nakaema
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607-7061, United States
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, and Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNR, and Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607-7061, United States
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6
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Kubelka J, Huang R, Keiderling TA. Solvent Effects on IR and VCD Spectra of Helical Peptides: DFT-Based Static Spectral Simulations with Explicit Water. J Phys Chem B 2005; 109:8231-43. [PMID: 16851962 DOI: 10.1021/jp0506078] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Simulations of IR and VCD spectra are carried out for model alpha-helical, 3(10)-helical, and 3(1)-helical (polyProII-like) oligopeptides, with up to 21 amide groups, and including explicit consideration of effects of directly hydrogen-bonded solvent (water). Parameters used were obtained from ab initio density functional theory (DFT) computations of force field, atomic polar and axial tensors for oligopeptides of 5 to 7 amides, whose structures were constrained in (phi,psi) to target the secondary structure type but otherwise fully optimized. By comparison with experimental data as well as with calculations for identical but isolated (gas phase) peptides, the computed effects of an inner shell of aqueous solvent on the vibrational spectra of helical oligopeptides are illustrated. The interaction with solvent causes significant frequency shifts of the amide bands, but only minor changes in the characteristic IR intensity distributions and splittings and the VCD band shapes. Better agreement with experimental band shapes is achieved for the alpha-helical amide I' (N-deuterated) VCD by inclusion of explicit solvent in the calculations. Some improvements are also observed in theoretical VCD predictions for 13C labeled alpha-helical peptides when solvated models are used. However, the qualitative isotopic splitting patterns are preserved and just shifted in frequency due to consistent, solvent independent interamide coupling constants. The critical match of experiment and theory for relative positions of transitions in peptides with specifically separated 13C=O labels, including and neglecting solvent, confirms the stability of the coupling interactions. Despite these solvation effects, the calculated VCD band shape of the amide I mode is shown to be a reliable conformational probe, since it remains basically insensitive to frequency shifts caused by environment. Thus theoretical VCD simulations, even vacuum calculations, are shown to provide useful spectral predictions for solution-phase peptides.
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Affiliation(s)
- Jan Kubelka
- Department of Chemistry (M/C 111), University of Illinois at Chicago, 845 W. Taylor Street, room 4500 SES, Chicago, Illinois 60607-7061, USA
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7
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Silva RAGD, Yasui SC, Kubelka J, Formaggio F, Crisma M, Toniolo C, Keiderling TA. Discriminating 3(10)- from alpha-helices: vibrational and electronic CD and IR absorption study of related Aib-containing oligopeptides. Biopolymers 2002; 65:229-43. [PMID: 12382284 DOI: 10.1002/bip.10241] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Model peptides based on -(Aib-Ala)(n)-, and (Aib)(n)-Leu-(Aib)(2) sequences, which have varying amounts of 3(10)-helical character, were studied by use of vibrational and electronic circular dichroism (VCD and ECD) and Fourier transform infrared (FTIR) absorption spectroscopies to test the correlation of spectral response and conformation. The data indicate that these peptides, starting from a length of about four to six residues, predominantly adopt a 3(10)-helical conformation at room temperature. The longest model peptides, depending on the series, may evidence some alpha-helical contribution to the spectra, while the shorter ones, with less than six residues, have much less order. The IR absorption spectra (as supported by theory) showed only small frequency changes between 3(10)- and alpha-helices. By contrast, solvent effects are a source of much bigger perturbations. The ECD results show that the intensity ratio for the approximately 222-nm to approximately 208-nm bands, while useful for distinguishing between these two helical types in some sequences, may have a narrower range of application than VCD. However, the VCD data presented here continue to support the proposed discrimination between alpha- and 3(10)-helices based on qualitative amide I and II bandshape differences. The present study shows the intensities of the 3(10)-helical amide I (peak-to-peak) to its amide II VCD to be of the same order and useful for discriminating them from alpha-helices, whose amide I dominates the amide II in intensity. This qualitative result is experimentally independent of the amount of alphaMe-substituted residues in the sequence. These experimental VCD results are consistent in detail with theoretical spectral simulations for Ac-(Ala)(8)-NH(2), Ac-(Aib-Ala)(4)-NH(2), and Ac-(Aib)(8)-NH(2) in 3(10)- and alpha-helical conformations.
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Affiliation(s)
- R A Gangani D Silva
- Department of Chemistry (M/C 111), University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607-7061, USA
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8
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Kubelka J, Silva RAGD, Keiderling TA. Discrimination between peptide 3(10)- and alpha-helices. Theoretical analysis of the impact of alpha-methyl substitution on experimental spectra. J Am Chem Soc 2002; 124:5325-32. [PMID: 11996573 DOI: 10.1021/ja012685o] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Detailed spectral simulations based on ab initio density functional theory computations of the amide I and II infrared (IR) and vibrational circular dichroism (VCD) spectra for Ac-(Ala)(4)-NH(2), Ac-(Aib-Ala)(2)-NH(2), and Ac-(Aib)(4)-NH(2) constrained to 3(10)- and alpha-helical conformations are presented. Parameters from these ab initio calculations are transferred onto corresponding larger oligopeptides to simulate the spectra for dodecamers. The differences between conformations and for different Aib substitution patterns within a conformation are reflected in observable spectral patterns where data are available. Simulated IR spectra show small frequency shifts in the amide I maxima between 3(10)- and alpha-helices, but the same magnitude shifts occur within one conformation upon Aib substitution. Thus, from a computational basis, the frequency of the amide I maximum does not discriminate between the 3(10)- or alpha-helical conformations. Calculated VCD band shapes for 3(10)-helices showed more significant changes in amplitude, with change in the fraction of Aib, than those for alpha-helices. Generally, with increasing Aib content, the overall amide I VCD intensity becomes weaker and the amide I couplet becomes more conservative, while the amide II VCD is less affected. Although the detailed band shape is shown to be sensitive to alpha-Me substitution, the basic pattern of amide I and II relative VCD intensities still differs between alpha- and 3(10)-helices and, as a consequence, successfully discriminates between them. These predictions are all borne out in experimental spectra of Aib, mixed Aib-Ala, and Ala-based helical peptides, where available.
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Affiliation(s)
- Jan Kubelka
- Department of Chemistry (M/C 111), University of Illinois at Chicago, 60607-7061, USA
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9
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Keiderling TA, Silva RA, Yoder G, Dukor RK. Vibrational circular dichroism spectroscopy of selected oligopeptide conformations. Bioorg Med Chem 1999; 7:133-41. [PMID: 10199663 DOI: 10.1016/s0968-0896(98)00217-x] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Vibrational circular dichroism (VCD) has been shown to be a useful technique for characterization of the qualitative secondary structure type for linear polypeptides and oligopeptides. A brief review of characteristic spectral responses and applications is given. Since VCD is dependent on relatively short range interactions, it detects residual structure in such oligomers even if long range order is lost. VCD studies presented here for Lys oligomers as well as Lys and Glu polymers as a function of length, salt added and temperature, confirm residual local order in these 'random coils'. Comparison to results with Pro oligomers, supports an interpretation that these extended structures have a left handed twist conformation. The 'coil' VCD is shown to be significantly reduced in intensity by temperature increase and by decrease in peptide length. By contrast, for partially alpha-helical Ac-(AAKAA)3GY-NH2 oligomers, the spectrum changes to the high temperature Lys(n) shape on heating, first losing then gaining intensity, indicating an equilibrium shift between structured states, from helix to coil (locally ordered) forms. VCD is shown to be a useful technique for monitoring local order in otherwise random coil structures.
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Affiliation(s)
- T A Keiderling
- Department of Chemistry, University of Illinois at Chicago, 60607-7061, USA.
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10
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Dukor RK, Keiderling TA. Mutarotation studies of poly-L-proline using FTIR, electronic and vibrational circular dichroism. ACTA ACUST UNITED AC 1998. [DOI: 10.1002/(sici)1520-6343(1996)2:2<83::aid-bspy2>3.0.co;2-t] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Yoder G, Polese A, Silva RAGD, Formaggio F, Crisma M, Broxterman QB, Kamphuis J, Toniolo C, Keiderling TA. Conformational Characterization of Terminally Blocked l-(αMe)Val Homopeptides Using Vibrational and Electronic Circular Dichroism. 310-Helical Stabilization by Peptide−Peptide Interaction. J Am Chem Soc 1997. [DOI: 10.1021/ja971392l] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gorm Yoder
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Alessandra Polese
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - R. A. G. D. Silva
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Fernando Formaggio
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Marco Crisma
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Quirinus B. Broxterman
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Johan Kamphuis
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Claudio Toniolo
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Timothy A. Keiderling
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
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12
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Bou? P, Sopkov� J, Bedn�rov� L, Malo? P, Keiderling TA. Transfer of molecular property tensors in cartesian coordinates: A new algorithm for simulation of vibrational spectra. J Comput Chem 1997. [DOI: 10.1002/(sici)1096-987x(19970415)18:5<646::aid-jcc6>3.0.co;2-n] [Citation(s) in RCA: 202] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Bou? P, Sopkov� J, Bedn�rov� L, Malo? P, Keiderling TA. Transfer of molecular property tensors in cartesian coordinates: A new algorithm for simulation of vibrational spectra. J Comput Chem 1997. [DOI: 10.1002/(sici)1096-987x(19970415)18:5%3c646::aid-jcc6%3e3.0.co%3b2-n] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Helical screw sense of homo-oligopeptides of Cα-methylated α-amino acids as determined with vibrational circular dichroism. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/0957-4166(95)00062-t] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Bloemendal M, Johnson WC. Structural information on proteins from circular dichroism spectroscopy possibilities and limitations. PHARMACEUTICAL BIOTECHNOLOGY 1995; 7:65-100. [PMID: 8564023 DOI: 10.1007/978-1-4899-1079-0_2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- M Bloemendal
- Department of Protein and Molecular Biology, Royal Free Hospital School of Medicine, London, England
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16
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Yoder G, Keiderling TA, Formaggio F, Crisma M, Toniolo C. Characterization of beta-bend ribbon spiral forming peptides using electronic and vibrational CD. Biopolymers 1995; 35:103-11. [PMID: 7696550 DOI: 10.1002/bip.360350111] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Terminally blocked (L-Pro-Aib)n and Aib-(L-Pro-Aib)n sequential oligopeptides are known to form right-handed beta-bend ribbon spirals under a variety of experimental conditions. Here we describe the results of a complete CD and ir characterization of this subtype of 3(10)-helical structure. The electronic CD spectra were obtained in solvents of different polarity in the 260-180 nm region. The vibrational CD and Fourier transform ir (FTIR) spectra were measured in deuterochloroform solution in the amide I and amide II (1750-1500 cm-1) regions. The critical chain length for full development of the beta-bend ribbon spiral structure is found to be five to six residues. Spectral effects related to concentration-induced stabilization of the structures of the longer peptides were seen in the resolution-enhanced FTIR spectra. Comparison to previous studies of (Aib)n and (Pro)n oligomers indicate that the low frequency of the amide I mode is due to the interaction of secondary and tertiary amide bonds and not to a strong difference in conformation from a regular 3(10)-helix.
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Affiliation(s)
- G Yoder
- Department of Chemistry, University of Illinois at Chicago 60607-7061
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17
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Abstract
Vibrational optical activity (VOA) is a relatively new spectroscopic technique, which has two principal manifestations, ir vibrational CD and vibrational Raman optical activity. Progress in the study of oligopeptides using both of these forms of VOA is reviewed from the perspective of theoretical and instrumental techniques, spectral results, and structural interpretations.
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Affiliation(s)
- T B Freedman
- Department of Chemistry, Syracuse University, New York 13244-4100, USA
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18
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Baumruk V, Huo D, Dukor RK, Keiderling TA, Lelievre D, Brack A. Conformational study of sequential Lys and Leu based polymers and oligomers using vibrational and electronic CD spectra. Biopolymers 1994; 34:1115-21. [PMID: 8075391 DOI: 10.1002/bip.360340815] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Vibrational CD (VCD) and electronic CD (ECD) spectra of some sequential Lys and Leu based oligo- and polypeptides were studied as a function of added salt and (for ECD) as a function of concentration in aqueous solution. For these samples, the VCD spectra can only be measured at relatively high concentrations under which the well-known salt-induced transition to a beta-sheet form can be observed for the KL based species, but only the end-state alpha-helical conformation is obvious for the LKKL based samples. ECD concentration dependence demonstrates that, at high concentration with no added or with added salt, LKKL based oligomers and polymers give alpha-helical spectra. These data provide evidence of aggregation induced secondary structure formation in an exceptionally simple peptide system. Similarly, the KL based oligomers and polymers give beta-sheet like spectra at high concentration or at high salt. These systems further provide model systems under "normal" aqueous conditions that yield VCD band shapes that correlate to the major secondary structural types of polypeptides. They are in substantial agreement with those spectra obtained on homopolypeptides and on proteins, confirming the relative independence of the VCD technique from side-chain and solvent effects.
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Affiliation(s)
- V Baumruk
- Department of Chemistry, University of Illinois at Chicago 60607
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19
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Ito H, I’Haya YJ. Linear Response Polarizability Tensor Theory for Vibrational Circular Dichroism: VCD and IR Absorption Bandshape Calculations ofα-Helical andβ-Sheet Polypeptides. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1994. [DOI: 10.1246/bcsj.67.1238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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20
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Gupta VP, Keiderling TA. Vibrational CD of the amide II band in some model polypeptides and proteins. Biopolymers 1992; 32:239-48. [PMID: 1374654 DOI: 10.1002/bip.360320305] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The amide II vibrational CD (VCD) spectra of poly (L-glutamic acid) and poly (L-lysine) in various conformational forms and those of several proteins in H2O have been measured. Characteristic VCD patterns have been observed in the amide II region due to helix, beta-sheet, and coil conformations in polypeptides. Based on their x-ray crystal structures, the proteins studied have been assigned to six categories. Proteins in the same category give rise to similar amide II VCD. While the protein conformational type is indicated using the amide II VCD, discrimination between types is less characteristic than with the previously studied amide I' VCD in D2O.
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Affiliation(s)
- V P Gupta
- Department of Chemistry, University of Illinois, Chicago 60680
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21
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Dukor RK, Keiderling TA. Reassessment of the random coil conformation: vibrational CD study of proline oligopeptides and related polypeptides. Biopolymers 1991; 31:1747-61. [PMID: 1793813 DOI: 10.1002/bip.360311409] [Citation(s) in RCA: 206] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The "random coil" conformational problem is examined by comparison of vibrational CD (VCD) spectra of various polypeptide model systems with that of proline oligomers [(Pro)n] and poly(L-proline). VCD, ir and uv CD spectra of blocked L-proline oligopeptides [(Pro)n, n = 2-12] in different solvents are reported and compared to the spectra of poly(L-proline) II, poly(L-glutamic acid), and unblocked proline oligomers. Based on the chain-length dependence of the VCD and electronic CD (ECD) spectra of proline oligomers, it is established that VCD spectra are dominated by short-range interactions. The VCD of random coil model polypeptides is shown to be identical in shape but smaller in magnitude than poly(L-proline) II and of similar magnitude to that of (Pro)n (n = 3, 4). Based on the spectral evidence, it is concluded that the "random coil" conformation has a large fraction of helical regions, conformationally similar to the left-handed, 3(1) polyproline II helix, as was previously suggested by Krimm and co-workers. This conclusion is further supported by studies of effects of salt (CaCl2, LiBr, LiClO4), temperature (5-75 degrees C), and pH on the VCD spectra of L-proline oligomers, poly(L-proline) II, and poly(L-glutamic acid). These show that, after each of these perturbations, a significant local ordering remains in the oligomers and polymers studied, and that charged polypeptides such as poly(L-glutamic acid) are more flexible than are polyproline or even L-proline oligomers.
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Affiliation(s)
- R K Dukor
- Department of Chemistry, University of Illinois, Chicago 60680
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Urbanova M, Dukor RK, Pancoska P, Gupta VP, Keiderling TA. Comparison of alpha-lactalbumin and lysozyme using vibrational circular dichroism. Evidence for a difference in crystal and solution structures. Biochemistry 1991; 30:10479-85. [PMID: 1931971 DOI: 10.1021/bi00107a016] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The conformation of the milk protein alpha-lactalbumin has been studied using vibrational circular dichroism (VCD) and compared to parallel studies on lysozyme. These proteins have been shown by Acharya et al. [(1989) J. Mol. Biol. 208, 99-127] to have very similar three-dimensional crystal structures. However, their VCD spectra in D2O solution are quite different. The VCD of lysozyme in D2O more resembles that of alpha-lactalbumin in 33% propanol/D2O, under which conditions alpha-lactalbumin has conformationally transformed to a structure with increased helical fraction. These results can be seen to be consistent with UVCD and resolution-enhanced FTIR spectra of alpha-lactalbumin and lysozyme in both D2O and H2O environments. The solvent sensitivity of the alpha-lactalbumin spectra and hence of its conformation contrasted with the lack of such sensitivity for lysozyme suggest that the alpha-lactalbumin crystal structure represents a conformation different from that which is dominant in aqueous solution.
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Affiliation(s)
- M Urbanova
- Department of Chemistry, University of Illinois, Chicago 60680
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23
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Conformational studies of proteins using vibrational circular dichroism. Proteins 1991. [DOI: 10.1007/978-94-010-9063-6_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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24
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Gulotta M, Goss DJ, Diem M. IR vibrational CD in model deoxyoligonucleotides: observation of the B----Z phase transition and extended coupled oscillator intensity calculations. Biopolymers 1989; 28:2047-58. [PMID: 2605309 DOI: 10.1002/bip.360281202] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The first observation of ir vibrational CD (VCD) in small model DNA molecules is reported. The VCD signals in the 1550-1750-cm-1 spectral region, which originate from coupling of carbonyl stretching modes of the nucleic acid bases, are found to be sensitive to the handedness of the polymer helix. The formalism to calculate VCD intensities of polymers is developed from the exciton model derived earlier by Tinoco [(1963) Radiation Res. 20, 133; (1960) J. Chem. Phys. 33, 1332; (1964) J. Am. Chem. Soc. 86, 297] and Schellman and co-workers [(1975) Biopolymers 14, 173; (1969) J. Phys. Chem. 73, 28]. The resulting equations, which are a direct extension of the dimeric case known as the "coupled oscillator," are used in model calculations of the helical polymers.
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Lee O, Roberts GM, Diem M. IR vibrational CD in alanyl tripeptide: indication of a stable solution conformer. Biopolymers 1989; 28:1759-70. [PMID: 2597729 DOI: 10.1002/bip.360281009] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Infrared vibrational CD (VCD) of a small peptide, L-alanyl-L-alanyl-L-alanine (Ala3), and a peptide model, N-acetyl-L-alanine-N'-methyl-amide (AAMA), in the 1550-1750-cm-1 region has been observed. The "coupled oscillator" VCD feature observed for Ala3 in the amide I region is interpreted in terms of a solution structure stabilized by the electrostatic interaction of the zwitterionic groups. No such interactions are possible in basic aqueous solution of Ala3 nor in AAMA in neutral solution. Thus, the coupled oscillator features are lost in the latter two cases, indicating the absence of a simple stabilized conformation.
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26
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Malon P, Kobrinskaya R, Keiderling TA. Vibrational CD of polypeptides. XII. Reevaluation of the Fourier transform vibrational CD of poly(gamma-benzyl-L-glutamate). Biopolymers 1988; 27:733-46. [PMID: 2454680 DOI: 10.1002/bip.360270503] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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