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Sato H, Inoué S, Yoshida J, Kawamura I, Koshoubu J, Yamagishi A. Microscopic vibrational circular dichroism on the forewings of a European hornet: heterogenous sequences of protein domains with different secondary structures. Phys Chem Chem Phys 2024; 26:17918-17922. [PMID: 38888259 DOI: 10.1039/d4cp01827c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
We developed a microscopic scanning for vibrational circular dichroism (VCD) spectroscopy in which a quantum cascade laser is equipped with a highly focused infrared light source to attain a spatial resolution of 100 μm. This system was applied to the forewing of a European hornet to reveal how the protein domains are organised. Two-dimensional patterns were obtained from the VCD signals with steps of 100 μm. We scanned the 1500-1740 cm-1 wavenumber range, which covers amide I and II absorptions. Zone sequenced α-helical and β-sheet domains within an area of 200 μm2 in membranes close to where two veins cross. The sign of the VCD signal at 1650 cm-1 changed from positive to negative when probed along the zone axis, intermediated by the absence of VCD activity. The significance of this zone is discussed from the viewpoint of the mechanical properties required for flying motion. These features are unattainable using conventional FTIR (Fourier transform infrared) or FT-VCD methods with a spatial resolution of ∼10 mm2.
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Affiliation(s)
- Hisako Sato
- Faculty of Science, Ehime University, 1 2-5, Bunkyo-cho, Matsuyama, 790-8577, Japan.
| | - Sayako Inoué
- Geodynamics Research Center, Ehime University, Matsuyama 790-8577, Japan
| | - Jun Yoshida
- Department of Chemistry, College of Humanities & Sciences, Nihon University, Setagaya-ku, Tokyo 156-8550, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University Yokohama, 240-8501, Japan
| | - Jun Koshoubu
- JASCO Corporation, Ishikawa 2967-5, Hachioji Tokyo, 192-8537, Japan
| | - Akihiko Yamagishi
- Faculty of Medicine, Toho University, 2 5-21-16 Oomori-nishi, Ota-ku, Tokyo, 143-8540, Japan
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2
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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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3
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Cheeseman JR, Frisch MJ, Keiderling TA. Increased accuracy of vibrational circular dichroism calculations for isotopically labeled helical peptides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124097. [PMID: 38457873 DOI: 10.1016/j.saa.2024.124097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/11/2024] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
Vibrational circular dichroism (VCD) spectra have been computed with qualitatively correct sign patterns for α-helical peptides using various methods, ranging from empirical models to ab initio quantum mechanical computations. However, some details, such as deuteration effects and isotope substitution shifts and sign patterns for the resultant amide I' band shape, have remained a predictive challenge. Fully optimized computations for a 25-residue Ala-rich peptide, including implicit solvent corrections and explicit side chains that experimentally stabilize these model helical peptides in water, have been carried out using density functional theory (DFT). These fully minimized structures show minor changes in the (ϕ,ψ) torsions at the termini and yield an extra negative band to the low energy side of the characteristic amide I' couplet VCD, in agreement with experiments. Additionally, these calculations give the right sign and relative intensity patterns, as compared to experimental results, for several 13C=O substituted variants. The differences from previously reported computations that used ideal helical structures and vacuum conditions imply that inclusion of distorted termini and solvent effects can have an impact on the final detailed spectral patterns. Inclusion of side chains in these calculations had very little effect on the computed amide I' IR and VCD. Tests of constrained geometries, varying dielectric, and different functionals indicate that each can affect the band shapes, particularly for the 12C=O components, but these aspects do not fully explain the difference from previous spectral simulations. Inclusion of long-range amide coupling, as obtained from DFT computation of the full structure, or transfer of parameters from a somewhat longer peptide model, rather than shorter model, seems to be more important for the final detailed band shape under isotopic substitution. However, these corrections can also induce other changes, suggesting that previously reported, limited calculations may have been qualitatively useful due to a balance of errors. This may also explain the success of simple empirical IR models.
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Affiliation(s)
- James R Cheeseman
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, CT 06492, USA
| | - Michael J Frisch
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, CT 06492, USA
| | - Timothy A Keiderling
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA.
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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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5
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Okabe H, Miyata D, Nakabayashi T, Hiramatsu H. Evaluation of Dihedral Angles of Peptides Using IR Bands of Two Successive Isotope Labeled Residues. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hitomi Okabe
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Daisuke Miyata
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Takakazu Nakabayashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Hirotsugu Hiramatsu
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
- Center for Emergent Functional Matter Science, National Chiao Tung University, Hsinchu 30010, Taiwan
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6
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Berbeć S, Dec R, Molodenskiy D, Wielgus-Kutrowska B, Johannessen C, Hernik-Magoń A, Tobias F, Bzowska A, Ścibisz G, Keiderling TA, Svergun D, Dzwolak W. β2-Type Amyloidlike Fibrils of Poly-l-glutamic Acid Convert into Long, Highly Ordered Helices upon Dissolution in Dimethyl Sulfoxide. J Phys Chem B 2018; 122:11895-11905. [DOI: 10.1021/acs.jpcb.8b08308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sylwia Berbeć
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Dmitry Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg 22607, Germany
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-093, Poland
| | | | - Agnieszka Hernik-Magoń
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Fernando Tobias
- Department of Chemistry, University of Illinois at Chicago, Chicago 60607-7061, United States
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-093, Poland
| | - Grzegorz Ścibisz
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, Chicago 60607-7061, United States
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg 22607, Germany
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
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7
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Instrumentation for Vibrational Circular Dichroism Spectroscopy: Method Comparison and Newer Developments. Molecules 2018; 23:molecules23092404. [PMID: 30235902 PMCID: PMC6225159 DOI: 10.3390/molecules23092404] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 08/25/2018] [Accepted: 09/07/2018] [Indexed: 01/10/2023] Open
Abstract
Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolute stereochemistry, and somewhat less so for biomolecule characterization and following dynamic processes. Over the last few decades, different VCD instrument designs have developed for various purposes, and reliable commercial instrumentation is now available. This review will briefly survey historical and currently used instrument designs and describe some aspects of more recently reported developments. An important factor in applying VCD to conformational studies is theoretical modeling of spectra for various structures, techniques for which are briefly surveyed.
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Hamley IW, Castelletto V, Dehsorkhi A, Torras J, Aleman C, Portnaya I, Danino D. The Conformation and Aggregation of Proline-Rich Surfactant-Like Peptides. J Phys Chem B 2018; 122:1826-1835. [PMID: 29357666 DOI: 10.1021/acs.jpcb.7b11463] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The secondary structure of proline-rich surfactant-like peptides is examined for the first time and is found to be influenced by charged end groups in peptides P6K, P6E, and KP6E and an equimolar mixture of P6K and P6E. The peptides exhibit a conformational transition from unordered to polyproline II (PPII) above a critical concentration, detected from circular dichroism (CD) measurements and unexpectedly from fluorescence dye probe measurements. Isothermal titration calorimetry (ITC) measurements provided the Gibbs energies of hydration of P6K and P6E, which correspond essentially to the hydration energies of the terminal charged residues. A detailed analysis of peptide conformation for these peptides was performed using density functional theory calculations, and this was used as a basis for hybrid quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) simulations. Quantum mechanics simulations in implicit water show both peptides (and their 1:1 mixture) exhibit PPII conformations. However, hybrid QM/MM MD simulations suggest that some deviations from this conformation are present for P6K and P6E in peptide bonds close to the charged residue, whereas in the 1:1 mixture a PPII structure is observed. Finally, aggregation of the peptides was investigated using replica exchange molecular dynamics simulations. These reveal a tendency for the average aggregate size (as measured by the radius of gyration) to increase with increasing temperature, which is especially marked for P6K, although the fraction of the most populated clusters is larger for P6E.
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Affiliation(s)
- Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights , Reading RG6 6AD, U.K
| | - Valeria Castelletto
- Department of Chemistry, University of Reading, Whiteknights , Reading RG6 6AD, U.K
| | - Ashkan Dehsorkhi
- Department of Chemistry, University of Reading, Whiteknights , Reading RG6 6AD, U.K
| | - Juan Torras
- Departament d'Enginyeria Química (EEBE) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2, 08019, Barcelona, Spain
| | - Carlos Aleman
- Departament d'Enginyeria Química (EEBE) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2, 08019, Barcelona, Spain
| | - Irina Portnaya
- Department of Biotechnology and Food Engineering and the Russell Berrie Nanotechnology Institute, Technion , Haifa, Israel 32000
| | - Dganit Danino
- Department of Biotechnology and Food Engineering and the Russell Berrie Nanotechnology Institute, Technion , Haifa, Israel 32000
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9
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Keiderling TA, Lakhani A. Mini review: Instrumentation for vibrational circular dichroism spectroscopy, still a role for dispersive instruments. Chirality 2018; 30:238-253. [PMID: 29293282 DOI: 10.1002/chir.22799] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 11/07/2017] [Accepted: 11/16/2017] [Indexed: 01/30/2023]
Abstract
Vibrational circular dichroism (VCD) has become a standard method for determination of absolute stereochemistry, particularly now that reliable commercial instrumentation has become available. These instruments use a now well-documented Fourier transform infrared-based approach to measure VCD that has virtually displaced initial dispersive infrared-based designs. Nonetheless, many papers have appeared reporting dispersive VCD data, especially for biopolymers. Instrumentation designed with these original methods, particularly after more recent updates optimizing performance in selected spectral regions, has been shown still to have advantages for specific applications. This article presents a mini-review of dispersive VCD instrument designs and includes sample spectra obtained for various biopolymer (particularly peptide) samples. Complementary reviews of Fourier transform-VCD designs are broadly available.
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Affiliation(s)
- Timothy A Keiderling
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ahmed Lakhani
- Department of Biophysical Chemistry and Mathematics, Calumet College of St. Joseph, Whiting, Indiana, USA
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10
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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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11
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Reppert M, Tokmakoff A. Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics. Annu Rev Phys Chem 2016; 67:359-86. [DOI: 10.1146/annurev-physchem-040215-112055] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mike Reppert
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637;
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637;
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12
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Tobias F, Keiderling TA. Role of Side Chains in β-Sheet Self-Assembly into Peptide Fibrils. IR and VCD Spectroscopic Studies of Glutamic Acid-Containing Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:4653-61. [PMID: 27099990 DOI: 10.1021/acs.langmuir.6b00077] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Poly(glutamic acid) at low pH self-assembles after incubation at higher temperature into fibrils composed of antiparallel sheets that are stacked in a β2-type structure whose amide carbonyls have bifurcated H-bonds involving the side chains from the next sheet. Oligomers of Glu can also form such structures, and isotope labeling has provided insight into their out-of-register antiparallel structure [ Biomacromolecules 2013 , 14 , 3880 - 3891 ]. In this paper we report IR and VCD spectra and transmission electron micrograph (TEM) images for a series of alternately sequenced oligomers, Lys-(Aaa-Glu)5-Lys-NH2, where Aaa was varied over a variety of polar, aliphatic, or aromatic residues. Their spectral and TEM data show that these oligopeptides self-assemble into different structures, both local and morphological, that are dependent on both the nature of the Aaa side chains and growth conditions employed. Such alternate peptides substituted with small or polar residues, Ala and Thr, do not yield fibrils; but with β-branched aliphatic residues, Val and Ile, that could potentially pack with Glu side chains, these oligopeptides do show evidence of β2-stacking. By contrast, for Leu, with longer side chains, only β1-stacking is seen while with even larger Phe side chains, either β-form can be detected separately, depending on preparation conditions. These structures are dependent on high temperature incubation after reducing the pH and in some cases after sonication of initial fibril forms and reincubation. Some of these fibrillar peptides, but not all, show enhanced VCD, which can offer evidence for formation of long, multistrand, often twisted structures. Substitution of Glu with residues having selected side chains yields a variety of morphologies, leading to both β1- and β2-structures, that overall suggests two different packing modes for the hydrophobic side chains depending on size and type.
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Affiliation(s)
- Fernando Tobias
- Department of Chemistry, University of Illinois at Chicago , 845 W. Taylor Street (m/c111), Chicago, Illinois 60607-7061, United States
| | - Timothy A Keiderling
- Department of Chemistry, University of Illinois at Chicago , 845 W. Taylor Street (m/c111), Chicago, Illinois 60607-7061, United States
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13
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Zhang G, Babenko V, Dzwolak W, Keiderling TA. Dimethyl Sulfoxide Induced Destabilization and Disassembly of Various Structural Variants of Insulin Fibrils Monitored by Vibrational Circular Dichroism. Biochemistry 2015; 54:7193-202. [DOI: 10.1021/acs.biochem.5b00809] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ge Zhang
- Department
of Chemistry, University of Illinois at Chicago, 845 West Taylor
Street (m/c 111), Chicago, Illinois 60607-7061, United States
| | - Viktoria Babenko
- Department
of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Wojciech Dzwolak
- Department
of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - 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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14
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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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15
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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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16
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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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17
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Shanmugam G, Polavarapu PL. Isotope-assisted vibrational circular dichroism investigations of amyloid β peptide fragment, Aβ(16-22). J Struct Biol 2011; 176:212-9. [PMID: 21855637 DOI: 10.1016/j.jsb.2011.08.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 07/26/2011] [Accepted: 08/04/2011] [Indexed: 10/17/2022]
Abstract
Isotope-assisted vibrational circular dichroism (VCD) investigations have been used to probe the site specific local structure of an amyloid peptide for the first time. A seven residue peptide, NH(2)-KLVFFAE-COOH, which represents the Aβ(16-22) fragment of the Alzheimer's amyloid β peptide, was used for these investigations. (13)C labels were introduced separately at the carbonyl group of leucine (residue 17), alanine (residue 21) and also at both sites together. Since VCD spectra provide structure dependent signs, band shapes and frequencies, the isotope-assisted VCD spectroscopy revealed information on site specific secondary structure of the polypeptide. Isotope dilution VCD experiments provided a means to distinguish between parallel and anti-parallel nature of the β-sheet structure formed by the Aβ(16-22) fragment. The current results establish the usefulness of isotope-assisted VCD analysis in determining the site specific secondary structure of amyloid peptides.
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Affiliation(s)
- Ganesh Shanmugam
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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18
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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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