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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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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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Baronio CM, Barth A. The Amide I Spectrum of Proteins-Optimization of Transition Dipole Coupling Parameters Using Density Functional Theory Calculations. J Phys Chem B 2020; 124:1703-1714. [PMID: 32040320 PMCID: PMC7307917 DOI: 10.1021/acs.jpcb.9b11793] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
The
amide I region of the infrared spectrum is related to the protein
backbone conformation and can provide important structural information.
However, the interpretation of the experimental results is hampered
because the theoretical description of the amide I spectrum is still
under development. Quantum mechanical calculations, for example, using
density functional theory (DFT), can be used to study the amide I
spectrum of small systems, but the high computational cost makes them
inapplicable to proteins. Other approaches that solve the eigenvalues
of the coupled amide I oscillator system are used instead. An important
interaction to be considered is transition dipole coupling (TDC).
Its calculation depends on the parameters of the transition dipole
moment. This work aims to find the optimal parameters for TDC in three
major secondary structures: α-helices, antiparallel β-sheets,
and parallel β-sheets. The parameters were suggested through
a comparison between DFT and TDC calculations. The comparison showed
a good agreement for the spectral shape and for the wavenumbers of
the normal modes for all secondary structures. The matching between
the two methods improved when hydrogen bonding to the amide oxygen
was considered. Optimal parameters for individual secondary structures
were also suggested.
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Affiliation(s)
- Cesare M Baronio
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 106 91, Sweden
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 106 91, Sweden
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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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5
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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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6
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Parchaňský V, Kapitán J, Bouř P. Inspecting chiral molecules by Raman optical activity spectroscopy. RSC Adv 2014. [DOI: 10.1039/c4ra10416a] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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7
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Hammami F, Ghalla H, Chebaane A, Nasr S. Structural and spectroscopic investigation of the N-methylformamide–water (NMF···3H2O) complex. Mol Phys 2014. [DOI: 10.1080/00268976.2014.949891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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8
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dos Santos MVP, Proenza YG, Longo RL. PICVib: an accurate, fast and simple procedure to investigate selected vibrational modes and evaluate infrared intensities. Phys Chem Chem Phys 2014; 16:17670-80. [DOI: 10.1039/c4cp02279c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The generalization of the PICVib approach for calculating selected infrared intensities is shown to be successful and to preserves its easiness of implementation and parallelization, flexibility and treatment of large systems and/or at high theoretical levels.
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Affiliation(s)
- Marcus V. P. dos Santos
- Departamento de Química Fundamental
- Universidade Federal de Pernambuco
- Cidade Universitária
- Recife-PE, Brazil
| | - Yaicel G. Proenza
- Departamento de Química Fundamental
- Universidade Federal de Pernambuco
- Cidade Universitária
- Recife-PE, Brazil
| | - Ricardo L. Longo
- Departamento de Química Fundamental
- Universidade Federal de Pernambuco
- Cidade Universitária
- Recife-PE, Brazil
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Zeko T, Hannigan SF, Jacisin T, Guberman-Pfeffer MJ, Falcone ER, Guildford MJ, Szabo C, Cole KE, Placido J, Daly E, Kubasik MA. FT-IR Spectroscopy and Density Functional Theory Calculations of 13C Isotopologues of the Helical Peptide Z-Aib6-OtBu. J Phys Chem B 2013; 118:58-68. [DOI: 10.1021/jp408818g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Timothy Zeko
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Steven F. Hannigan
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Timothy Jacisin
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | | | - Eric R. Falcone
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Melissa J. Guildford
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Christopher Szabo
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Kathryn E. Cole
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Jessica Placido
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Erin Daly
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Matthew A. Kubasik
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
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Welch WRW, Kubelka J, Keiderling TA. Infrared, vibrational circular dichroism, and Raman spectral simulations for β-sheet structures with various isotopic labels, interstrand, and stacking arrangements using density functional theory. J Phys Chem B 2013; 117:10343-58. [PMID: 23924300 DOI: 10.1021/jp4056126] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Infrared (IR), Raman, and vibrational circular dichroism (VCD) spectral variations for different β-sheet structures were studied using simulations based on density functional theory (DFT) force field and intensity computations. The DFT vibrational parameters were obtained for β-sheet fragments containing nine-amides and constrained to a variety of conformations and strand arrangements. These were subsequently transferred onto corresponding larger β-sheet models, normally consisting of five strands with ten amides each, for spectral simulations. Further extension to fibril models composed of multiple stacked β-sheets was achieved by combining the transfer of DFT parameters for each sheet with dipole coupling methods for interactions between sheets. IR spectra of the amide I show different splitting patterns for parallel and antiparallel β-sheets, and their VCD, in the absence of intersheet stacking, have distinct sign variations. Isotopic labeling by (13)C of selected residues yields spectral shifts and intensity changes uniquely sensitive to relative alignment of strands (registry) for antiparallel sheets. Stacking of multiple planar sheets maintains the qualitative spectral character of the single sheet but evidences some reduction in the exciton splitting of the amide I mode. Rotating sheets with respect to each other leads to a significant VCD enhancement, whose sign pattern and intensity is dependent on the handedness and degree of rotation. For twisted β-sheets, a significant VCD enhancement is computed even for sheets stacked with either the same or opposite alignments and the inter-sheet rotation, depending on the sense, can either further increase or weaken the enhanced VCD intensity. In twisted, stacked structures (without rotation), similar VCD amide I patterns (positive couplets) are predicted for both parallel and antiparallel sheets, but different IR intensity distributions still enable their differentiation. Our simulation results prove useful for interpreting experimental vibrational spectra in terms of β-sheet and fibril structure, as illustrated in the accompanying paper.
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Affiliation(s)
- William R W Welch
- Department of Chemistry, University of Wyoming , Laramie, Wyoming 82071, United States
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Shanmugam G, Polavarapu PL. Site-specific structure of Aβ(25-35) peptide: isotope-assisted vibrational circular dichroism study. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:308-16. [PMID: 22910376 DOI: 10.1016/j.bbapap.2012.08.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 08/02/2012] [Accepted: 08/07/2012] [Indexed: 11/17/2022]
Abstract
We investigated the site-specific local structure of an amyloid peptide, NH(2)-GSNKGAIIGLM-COOH [Aβ(25-35)], one of the active fragments of amyloid β peptide that is known to be responsible for Alzheimer's disease, in the fibrillar aggregated state. Isotope-assisted infrared vibrational circular dichroism (VCD) and absorption (VA) spectroscopy were used for the parent Aβ(25-35) peptide, along with doubly (13)C labeled peptides at the carbonyl groups of residues 29 (Gly) and 30 (Ala) [Aβ(25-35:(13)C-29/30)] and at the carbonyl groups of residues 33 (Gly) and 34 (Leu) [Aβ(25-35:(13)C-33/34)]. The present results confirm that Aβ(25-35) peptide fibrils adopt a β-sheet structure and isotopic dilution experiments suggest a parallel β-sheet structure. The isotopic shifts suggest that the microenvironment of residues 29 (Gly) and 30 (Ala) could be different from that of residues 33 (Gly) and 34 (Leu). An unusual enhancement for the amide II' VCD intensities of Aβ(25-35:(13)C-29/30) and Aβ(25-35:(13)C-33/34) peptide fibrils, considered to originate from inter-strand coupling, was found for the first time. The structural information reported in this manuscript has important implications in understanding the role of this peptide in the development of Alzheimer's disease.
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Affiliation(s)
- Ganesh Shanmugam
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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12
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Impact ofβ-Turn Sequence onβ-Hairpin Dynamics Studied with Infrared-Detected Temperature Jump. ACTA ACUST UNITED AC 2012. [DOI: 10.1155/2012/102423] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Folding dynamics forβ-structure loss and disordered structure gain were studied in a modelβ-hairpin peptide based on Cochran’s tryptophan zipper peptide Trpzip2, but with an altered Thr-Gly (TG) turn sequence, that is, SWTWETGKWTWK, using laser-induced temperature-jump (T-jump) kinetics with IR detection. As has been shown previously, the TG turn sequence reduces the thermodynamicβ-hairpin stability as compared to the Asn-Gly sequence used in Trpzip2 (TZ2-NG). In this study, we found that the TG-turn slows down the overall relaxation dynamics as compared to TZ2-NG, which were studied at higher temperatures where the time constants show little difference between relaxation of theβ-strand and the disordered conformation. These time constants become equivalent at lower temperatures for TZ2-TG than was seen for TZ2-NG. The correlation of thermodynamic stability and rates of relaxation suggests that the change from NG to TG turn results in a slowing of folding, lowerkf, with less change of the unfolding rate,ku, assuming two state behavior at higher temperatures.
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13
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Wu L, McElheny D, Setnicka V, Hilario J, Keiderling TA. Role of different β-turns in β-hairpin conformation and stability studied by optical spectroscopy. Proteins 2011; 80:44-60. [DOI: 10.1002/prot.23140] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/28/2011] [Accepted: 07/21/2011] [Indexed: 12/28/2022]
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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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15
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Bieler NS, Haag MP, Jacob CR, Reiher M. Analysis of the Cartesian Tensor Transfer Method for Calculating Vibrational Spectra of Polypeptides. J Chem Theory Comput 2011; 7:1867-81. [DOI: 10.1021/ct2001478] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Noah S. Bieler
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Moritz P. Haag
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Christoph R. Jacob
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures, Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe, Germany
| | - Markus Reiher
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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16
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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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Magyarfalvi G, Tarczay G, Vass E. Vibrational circular dichroism. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.39] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Andrushchenko V, Bouř P. Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides. Chirality 2011; 22 Suppl 1:E96-E114. [PMID: 21038400 DOI: 10.1002/chir.20872] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The application of the Cartesian coordinate tensor transfer (CCT) technique for simulations of the IR absorption and vibrational circular dichroism (VCD) spectra of relatively large nucleic acid fragments is demonstrated on several case studies. The approach is based on direct ab initio calculations of atomic tensors, determining molecular properties, for relatively small fragments, and subsequent transfer of these tensors to the larger systems in Cartesian coordinates. This procedure enables precise computations of vibrational spectra for large biomolecular systems, currently with up to several thousands of atoms. The versatile ability of the CCT methods is emphasized on the examples of VCD and IR absorption spectra calculations for B- and Z-forms of DNA, single-, double-, and triple-stranded RNA helices and DNA structures with different base content and sequences. The development and recent improvements of the methodology are followed, including utilization of the constrained normal mode optimization (NMO) strategy and combined quantum mechanics and molecular dynamics simulations. Advantages, drawbacks, and recommendations for future improvements of the CCT method as applied to nucleic acid spectra calculations are discussed.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic.
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Jiang N, Tan RX, Ma J. Simulations of Solid-State Vibrational Circular Dichroism Spectroscopy of (S)-Alternarlactam by Using Fragmentation Quantum Chemical Calculations. J Phys Chem B 2011; 115:2801-13. [DOI: 10.1021/jp110152q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nan Jiang
- School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing, Jiangsu, 210093, People’s Republic of China
| | - Ren Xiang Tan
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu 210093, People’s Republic of China
| | - Jing Ma
- School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing, Jiangsu, 210093, People’s Republic of China
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20
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Chi H, Lakhani A, Roy A, Nakaema M, Keiderling TA. Inter-residue Coupling and Equilibrium Unfolding of PPII Helical Peptides. Vibrational Spectra Enhanced with 13C Isotopic Labeling. J Phys Chem B 2010; 114:12744-53. [DOI: 10.1021/jp106095q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Heng Chi
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St. (m/c111), Chicago, Illinois 60607-7061
| | - Ahmed Lakhani
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St. (m/c111), Chicago, Illinois 60607-7061
| | - Anjan Roy
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St. (m/c111), Chicago, Illinois 60607-7061
| | - Marcelo Nakaema
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St. (m/c111), Chicago, Illinois 60607-7061
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St. (m/c111), Chicago, Illinois 60607-7061
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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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22
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Petrovic AG, Polavarapu PL, Mahalakshmi R, Balaram P. Characterization of folded conformations in a tetrapeptide containing two tryptophan residues by vibrational circular dichroism. Chirality 2009; 21 Suppl 1:E76-85. [DOI: 10.1002/chir.20779] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Viswanathan R, Dannenberg JJ. A density functional theory study of vibrational coupling in the amide I band of beta-sheet models. J Phys Chem B 2008; 112:5199-208. [PMID: 18386875 DOI: 10.1021/jp8001004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the first molecular orbital/density functional theory (DFT) calculations on the vibrational frequencies involved in the amide I band of completely geometrically optimized models for beta-sheet peptides based upon (up to 16) glycine residues. These calculations use the B3LYP/D95** level of DFT. The primary means of vibrational coupling occurs through H bond, rather than through space, interactions, which is consistent with a previous report on alpha-helical polyalanines and H-bonding chains of both formamides and 4-pyridones. We decoupled the C=O stretching vibrations using selected 14C substitutions to probe the coupling mechanism and to determine "natural" frequencies for individual 14C=Os. The intermolecular H-bonding interactions affect the geometries of the amide groups. Those near the center of H-bonding chains have long C=O bonds. The C=O bond lengths correlate with these "natural" frequencies, The frequencies obtained from the DFT calculations are generally more coupled, and the most intense are more red shifted than those calculated by transition dipole coupling (TDC). TDC inverts the order of the shifted frequencies compared to DFT in several cases.
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Affiliation(s)
- Raji Viswanathan
- Department of Chemistry, Yeshiva College, 500 West 185th Street, New York, New York 10033, USA
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Affiliation(s)
- Minhaeng Cho
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea.
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25
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Wieczorek R, Dannenberg JJ. Amide I Vibrational Frequencies of α-Helical Peptides Based upon ONIOM and Density Functional Theory (DFT) Studies. J Phys Chem B 2008; 112:1320-8. [DOI: 10.1021/jp077527j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert Wieczorek
- Department of Chemistry, City University of New YorkHunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, and Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, Wroclaw, Poland
| | - J. J. Dannenberg
- Department of Chemistry, City University of New YorkHunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, and Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, Wroclaw, Poland
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26
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Bour P, Andrushchenko V, Kabelác M, Maharaj V, Wieser H. Simulations of structure and vibrational spectra of deoxyoctanucleotides. J Phys Chem B 2007; 109:20579-87. [PMID: 16853664 DOI: 10.1021/jp051218g] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Combined molecular dynamics and ab initio computations were applied for analysis of infrared absorption and vibrational circular dichroism spectra of deoxyoctanucleotides. Unlike for previous idealized models, molecular geometries of these shorter DNA fragments in solutions were obtained as dynamic averages from simulations in a periodic water box. Vibrational spectra for the whole octamers including hydrogen-bonded solvent molecules were simulated on the basis of density-functional calculations on small fragments and subsequent transfer of molecular property tensors. Explicit and continuum solvent models were compared. Apparently, the DNA segments retain an approximate B-conformation in the aqueous solutions, but the terminal base pairs significantly deviate from the planar arrangement and the vibrational circular dichroism spectrum for (CG)(2) nucleotide indicates a larger average helical twist. Sodium counterions moved freely around the molecule during the simulation and do not influence spectral intensities. Simulated absorption spectra faithfully reproduced the experimental signal of principal functional groups, while only qualitative agreement was obtained for the dependence on the basis sequence.
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Affiliation(s)
- Petr Bour
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.
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27
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Andrushchenko V, Wieser H, Bour P. DNA oligonucleotide-cis-platin binding: Ab initio interpretation of the vibrational spectra. J Phys Chem A 2007; 111:9714-23. [PMID: 17784739 DOI: 10.1021/jp074572i] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cis-platin binding to the d(CCTGGTCC)*d(GGACCAGG) model DNA octamer was monitored with infrared absorption (IR) and vibrational circular dichroism (VCD) spectroscopies. The spectra were modeled with the aid of density functional computations and a Cartesian coordinate-based transfer of molecular property tensors from smaller DNA fragments. Because of the fragmentation, the tensors could be calculated with a higher precision. Environmental effects, such as the presence of the solvent or the cis-platin ligand, could be included in the modeling. The solvent was modeled by an explicit inclusion of hydrogen-bound water molecules, positions of which were estimated from a molecular dynamics simulation, or by the polarized continuum COSMO model. The B3LYP and BPW91 functionals used for the calculations of the spectral parameters were combined with the relativistic LANL2DZ platinum pseudo-potentials. The simulations reproduced the main IR and VCD DNA spectral features and explained most of the changes observed experimentally upon metal binding. The results confirmed that the influence of the ligand on DNA vibrational properties is quite complex; it originates in the geometry deformation and normal mode coupling pattern changes of the platinated octamer, as well as in local perturbations of the electronic structure and force field of the GC base pairs to which the platinum is bound. Many of the local effects could be accounted for by a point charge used in place of the metal in the GC complex.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nAm. 2, 16610, Praha 6, Czech Republic
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28
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Chen YF, Viswanathan R, Dannenberg JJ. Through Hydrogen-Bond Vibrational Coupling in Hydrogen-Bonding Chains of 4-Pyridones with Implications for Peptide Amide I Absorptions: Density Functional Theory Compared with Transition Dipole Coupling. J Phys Chem B 2007; 111:8329-34. [PMID: 17585803 DOI: 10.1021/jp072624y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present B3LYP/D95** calculations on the C=O and N-H couplings in H-bonded chains of 4-pyridones. 14C-substitutions are used to decouple various vibrations for purposes of illustration. The coupled C=O vibrations bear analogy to the amide I bands of proteins and peptides. The coupling of the C=O's occurs primarily via the cooperative H-bonds rather than transition dipole coupling (TDC), as demonstrated by the fact that (1) the couplings are greater than previously reported for similar studies on formamides despite the larger distance between the C=O's in the pyridone chains (TDC coupling decreases with distance) and (2) the red shifts (also greater than for formamides) can be attributed to the changes in the geometries (particularly the C=O bond lengths) of the individual 4-pyridones in the H-bonding chains induced by the H-bonds and resulting polarization of the monomers.
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Affiliation(s)
- Yung-Fou Chen
- Department of Chemistry and Biochemistry, City University of New York- Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10021, USA
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29
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Lanza G, Salvi AM, Tamburro AM. Molecular properties of a representative glycine-rich sequence of elastin – BocVGGVGOEt: A combined FTIR experimental and quantum chemical investigation. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.02.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Borics A, Murphy RF, Lovas S. Optical spectroscopic elucidation of beta-turns in disulfide bridged cyclic tetrapeptides. Biopolymers 2007; 85:1-11. [PMID: 16948119 DOI: 10.1002/bip.20593] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Vibrational circular dichroism (VCD) spectroscopic features of type II beta-turns were characterized previously, but, criteria for differentiation between beta-turn types had not been established yet. Model tetrapeptides, cyclized through a disulfide bridge, were designed on the basis of previous experimental results and the observed incidence of amino acid residues in the i + 1 and i + 2 positions in beta-turns, to determine the features of VCD spectra of type I and II beta-turns. The results were correlated with electronic circular dichroism (ECD) spectra and VCD spectra calculated from conformational data obtained by molecular dynamics (MD) simulations. All cyclic tetrapeptides yielded VCD signals with a higher frequency negative and a lower frequency positive couplet with negative lobes overlapping. MD simulations confirmed the conformational homogeneity of these peptides in solution. Comparison with ECD spectroscopy, MD, and quantum chemical calculation results suggested that the low frequency component of VCD spectra originating from the tertiary amide vibrations could be used to distinguish between types of beta-turn structures. On the basis of this observation, VCD spectroscopic features of type II and VIII beta-turns and ECD spectroscopic properties of a type VIII beta-turn were suggested. The need for independent experimental as well as theoretical investigations to obtain decisive conformational information was recognized.
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Affiliation(s)
- Attila Borics
- Department of Biomedical Sciences, Creighton University Medical Center, Omaha, NE 68178, USA
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31
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Herrmann C, Neugebauer J, Reiher M. Finding a needle in a haystack: direct determination of vibrational signatures in complex systems. NEW J CHEM 2007. [DOI: 10.1039/b618769m] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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32
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Tight β-turns in peptides. DFT-based study of infrared absorption and vibrational circular dichroism for various conformers including solvent effects. Theor Chem Acc 2006. [DOI: 10.1007/s00214-006-0183-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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33
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Decatur SM. Elucidation of residue-level structure and dynamics of polypeptides via isotope-edited infrared spectroscopy. Acc Chem Res 2006; 39:169-75. [PMID: 16548505 DOI: 10.1021/ar050135f] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Infrared spectroscopy is a powerful tool for analyzing the structure of proteins and peptides. The amide I band is particularly sensitive to the strength and position of the hydrogen bonds that define secondary structure as well as dipole-dipole interactions that are affected by the geometry of the peptide backbone. The introduction of a single (13)C-labeled carbonyl into a peptide backbone results in a resolvable shoulder to the main amide I band, which can be analyzed as a separate peak. Thus, site-specific structural information can be obtained by sequential, systematic labeling of the backbone. This method of isotope-edited infrared spectroscopy is a tool for obtaining medium-resolution information about the backbone conformation and dynamics. This tool has been used to dissect the conformation and dynamics of alpha helices and amyloid aggregates, where the versatility of possible sampling with infrared spectroscopy is well-suited for studies of large-protein aggregates.
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Affiliation(s)
- Sean M Decatur
- Department of Chemistry, Mount Holyoke College, S. Hadley, MA 01075, USA.
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34
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Bour P, Keiderling TA. Vibrational Spectral Simulation for Peptides of Mixed Secondary Structure: Method Comparisons with the Trpzip Model Hairpin. J Phys Chem B 2005; 109:23687-97. [PMID: 16375349 DOI: 10.1021/jp054107q] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infrared absorption and vibrational circular dichroism (IR and VCD) spectra of model fragments of TrpZip-style beta-hairpin structures are simulated using density functional theory (DFT) methods to estimate the influence of fragment size, end effects, conformational irregularities, peptide side chains, and solvent. Different fragmentation schemes, computing the strands and turn segments separately, were tested by varying the sizes of each and their respective overlaps. For suitably overlapping fragments, atomic property tensors were found to be reliably transferable, as tested by their ability to generate simulated spectra in good agreement with results from ab initio DFT computations for the entire peptide. This fragment approach significantly reduces computational times and opens up a wider range of systems that can be studied with a DFT-based approach as compared to previous methods based on uniform repeating sequences. However, vacuum calculations do not adequately represent the frequency dispersion of solvated molecules, and thus, some alternate strategies for solvation correction are explored for improving the simulation accuracy. Unlike for regular periodic secondary structure, the solvent significantly impacts the spectral shapes of hairpins, due to the different degrees of hydration of individual amide groups, which can be exposed to or shielded from water due to external vs internal hydrogen bonding. This is amplified by the shielding of selected amides from the solvent due to bulky side chains. The peptide plus solvent was structurally modeled with molecular dynamics methods, and then an electrostatic field-based parametrization correction was added to the force field and intensity tensors to compensate for the solvent dipolar field. The effect of the shielding and subsequent reordering of modes has a larger impact on VCD than IR band shapes.
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Affiliation(s)
- Petr Bour
- Institute for Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo námestí 2, 16610 Praha 6, Czech Republic.
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35
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Choi JH, Kim JS, Cho M. Amide I vibrational circular dichroism of polypeptides: Generalized fragmentation approximation method. J Chem Phys 2005; 122:174903. [PMID: 15910065 DOI: 10.1063/1.1888390] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Fragment analyses of vibrational circular dichroic response of dipeptides were carried out recently [Choi and Cho, J. Chem. Phys. 120, 4383 (2004)]. In the present paper, by using a minimal size unit peptide containing two chiral carbons covalently bonded to the peptide group, a generalized fragmentation approximation method is discussed and applied to the calculations of infrared-absorption and vibrational circular dichroism (VCD) intensities of amide I vibrations in various secondary structure polypeptides. Unlike the dipole strength determining IR-absorption intensity, the rotational strength is largely determined by the cross terms that are given by the inner product between the transition electric dipole and the transition magnetic dipole of two different peptides. This explains why the signs and magnitudes of VCD peaks are far more sensitive to the relative orientation and distance between different peptide bonds in a given protein. In order to test the validity of fragmentation approximation, three different segments in a globular protein ubiquitin, i.e., right-handed alpha-helix, beta-sheet, and beta-turn regions, were chosen for density-functional theory (DFT) calculations of amide I vibrational properties and the numerically simulated IR-absorption and VCD spectra by using the fragmentation method are directly compared with DFT results. It is believed that the fragmentation approximation method will be of use in numerically simulating vibrational spectra of proteins in solutions.
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Affiliation(s)
- Jun-Ho Choi
- Department of Chemistry, Division of Chemistry and Molecular Engineering, Korea University, Seoul
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36
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Abramavicius D, Mukamel S. Coherent third-order spectroscopic probes of molecular chirality. J Chem Phys 2005; 122:134305. [PMID: 15847463 DOI: 10.1063/1.1869495] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The third-order optical response of a system of coupled localized anharmonic vibrations is studied using a Green's function solution of the nonlinear exciton equations for bosonized excitons, which are treated as interacting quasiparticles. The explicit calculation of two-exciton states is avoided and the scattering of quasiparticles provides the mechanism of optical nonlinearities. To first-order in the optical wave vector we find several rotationally invariant tensor components for isotropic ensembles which are induced by chirality. The nonlocal nonlinear susceptibility tensor is calculated for infinitely large periodic structures in momentum space, where the problem size reduces to the exciton interaction radius. Applications are made to alpha and 3(10) helical infinite peptides.
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37
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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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38
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Bour P, Keiderling TA. Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of 13C Isotopic Labeling on Infrared Spectra. J Phys Chem B 2005; 109:5348-57. [PMID: 16863201 DOI: 10.1021/jp0446837] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isotopic substitution with 13C on the amide C=O has become an important means of determining localized structural information about peptide conformations with vibrational spectroscopy. Various approaches to the modeling of the interactions between labeled amide sites, specifically for antiparallel two-stranded, beta-forming peptides, were investigated, including different force fields [dipole-dipole interaction vs density functional theory (DFT) treatments], basis sets, and sizes of model peptides used for ab initio calculations, as well as employing models of solvation. For these beta-sheet systems the effect of the relative positions of the 13C isotopic labels in each strand on their infrared spectra was investigated. The results suggest that the interaction between labeled amide groups in different strands can be used as an indicator of local beta-structure formation, because coupling between close-lying C=O groups on opposing chains leads to the largest frequency shifts, yet some alternate placements can lead to intensity enhancements. The basic character of the coupling interaction between labeled modes on opposing strands is independent of changes in peptide length, water solvent environment, twisting of the sheet structure, and basis set used in the calculations, although the absolute frequencies and detailed coupling magnitudes change under each of these perturbations. In particular, two strands of three amides each contain the basic interactions needed to simulate larger sheets, with the only exception that the C=O groups forming H-bonded rings at the termini can yield different coupling values than central ones of the same structure. Spectral frequencies and intensities were modeled ab initio by DFT primarily at the BPW91/6-31G** level for pairs of three, four, and six amide strands. Comparison to predictions of a classical coupled oscillator model show qualitative but not quantitative agreement with these DFT results.
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Affiliation(s)
- Petr Bour
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610, Praha 6, Czech Republic.
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39
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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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40
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Ham S, Hahn S, Lee C, Kim TK, Kwak K, Cho M. Amide I Modes of α-Helical Polypeptide in Liquid Water: Conformational Fluctuation, Phase Correlation, and Linear and Nonlinear Vibrational Spectra. J Phys Chem B 2004. [DOI: 10.1021/jp048678e] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Sihyun Ham
- Department of Chemistry, Sookmyung Women's University, Seoul 140-742, Korea, and Department of Chemistry and Center for Multidimensional Spectroscopy, Division of Chemistry and Molecular Engineering, Korea University, Seoul 136-701, Korea
| | - Seungsoo Hahn
- Department of Chemistry, Sookmyung Women's University, Seoul 140-742, Korea, and Department of Chemistry and Center for Multidimensional Spectroscopy, Division of Chemistry and Molecular Engineering, Korea University, Seoul 136-701, Korea
| | - Chewook Lee
- Department of Chemistry, Sookmyung Women's University, Seoul 140-742, Korea, and Department of Chemistry and Center for Multidimensional Spectroscopy, Division of Chemistry and Molecular Engineering, Korea University, Seoul 136-701, Korea
| | - Tae-Kyung Kim
- Department of Chemistry, Sookmyung Women's University, Seoul 140-742, Korea, and Department of Chemistry and Center for Multidimensional Spectroscopy, Division of Chemistry and Molecular Engineering, Korea University, Seoul 136-701, Korea
| | - Kyungwon Kwak
- Department of Chemistry, Sookmyung Women's University, Seoul 140-742, Korea, and Department of Chemistry and Center for Multidimensional Spectroscopy, Division of Chemistry and Molecular Engineering, Korea University, Seoul 136-701, Korea
| | - Minhaeng Cho
- Department of Chemistry, Sookmyung Women's University, Seoul 140-742, Korea, and Department of Chemistry and Center for Multidimensional Spectroscopy, Division of Chemistry and Molecular Engineering, Korea University, Seoul 136-701, Korea
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41
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Bour P, Keiderling TA. Structure, spectra and the effects of twisting of β-sheet peptides. A density functional theory study. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2003.12.046] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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42
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Huang R, Kubelka J, Barber-Armstrong W, Silva RAGD, Decatur SM, Keiderling TA. Nature of Vibrational Coupling in Helical Peptides: An Isotopic Labeling Study. J Am Chem Soc 2004; 126:2346-54. [PMID: 14982438 DOI: 10.1021/ja037998t] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infrared (IR) and vibrational circular dichroism (VCD) spectra were measured for a series of isotopically ((13)C on two or more amide Cdouble bond]O) labeled, 25 residue, alpha-helical peptides of the sequence Ac-(AAAAK)(4)AAAAY-NH(2) that were also studied in the previous paper. Theoretical IR and VCD simulations were performed for correspondingly isotopically labeled Ac-A(24)-NHCH(3) constrained to an alpha-helical conformation by use of property tensor transfer from density functional theory (DFT) calculations on Ac-A(10)-NHCH(3). The simulations predicted and experiments confirmed that the vibrational coupling constants between i, i + 1 and i, i + 2 residues differ in sign, thus leading to a reversal of the (13)C VCD pattern and explaining the large shift in the (13)C amide I frequency as reported in the previous paper. The sign of the coupling constant remained consistent for larger label separation (with the exception of i, i + 4) and for more labels with uniform separation. Such effects confirm that the isotopically labeled group vibrations are essentially only coupled to each other and are effectively uncoupled from those of the unlabeled groups. This development confirms the utility of isotopic labels for site-specific structural studies with vibrational spectra. Observed spectral effects cannot be explained by considering only transition dipole coupling (TDC) between amide oscillators, particularly for smaller label separations, but the TDC and ab initio predicted couplings roughly converge at large separation.
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Affiliation(s)
- Rong Huang
- Department of Chemistry, University of Illinois at Chicago, m/c 111, 845 W. Taylor Street, Chicago, Illinois 60607, USA
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43
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Choi JH, Cho M. Amide I vibrational circular dichroism of dipeptide: Conformation dependence and fragment analysis. J Chem Phys 2004; 120:4383-92. [PMID: 15268607 DOI: 10.1063/1.1644100] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The amide I vibrational circular dichroic response of alanine dipeptide analog (ADA) was theoretically investigated and the density functional theory calculation and fragment analysis results are presented. A variety of vibrational spectroscopic properties, local and normal mode frequencies, coupling constant, dipole, and rotational strengths, are calculated by varying two dihedral angles determining the three-dimensional ADA conformation. Considering two monopeptide fragments separately, we show that the amide I vibrational circular dichroism of the ADA can be quantitatively predicted. For several representative conformations of the model ADA, vibrational circular dichroism spectra are calculated by using both the density functional theory calculation and fragment analysis methods.
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Affiliation(s)
- Jun-Ho Choi
- Department of Chemistry and Center for Multidimensional Spectroscopy, Division of Chemistry and Molecular Engineering, Korea University, Seoul 136-701, Korea
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44
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Andrushchenko V, Wieser H, Bouř P. RNA Structural Forms Studied by Vibrational Circular Dichroism: Ab Initio Interpretation of the Spectra. J Phys Chem B 2004. [DOI: 10.1021/jp037106b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Valery Andrushchenko
- Department of Chemistry, University of Calgary, 2500 University Drive, Calgary AB, T2N 1N4, Canada, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic
| | - Hal Wieser
- Department of Chemistry, University of Calgary, 2500 University Drive, Calgary AB, T2N 1N4, Canada, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic
| | - Petr Bouř
- Department of Chemistry, University of Calgary, 2500 University Drive, Calgary AB, T2N 1N4, Canada, and 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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45
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Keiderling TA, Xu Q. Unfolded peptides and proteins studied with infrared absorption and vibrational circular dichroism spectra. ADVANCES IN PROTEIN CHEMISTRY 2004; 62:111-61. [PMID: 12418103 DOI: 10.1016/s0065-3233(02)62007-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Timothy A Keiderling
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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46
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Kobko N, Dannenberg JJ. Cooperativity in Amide Hydrogen Bonding Chains. A Comparison between Vibrational Coupling through Hydrogen Bonds and Covalent Bonds. Implications for Peptide Vibrational Spectra. J Phys Chem A 2003. [DOI: 10.1021/jp0345497] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nadya Kobko
- Department of Chemistry, City University of New York, Hunter College and the Graduate School, 695 Park Avenue, New York New York 10021
| | - J. J. Dannenberg
- Department of Chemistry, City University of New York, Hunter College and the Graduate School, 695 Park Avenue, New York New York 10021
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47
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Ham S, Cha S, Choi JH, Cho M. Amide I modes of tripeptides: Hessian matrix reconstruction and isotope effects. J Chem Phys 2003. [DOI: 10.1063/1.1581855] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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48
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Hilario J, Kubelka J, Keiderling TA. Optical spectroscopic investigations of model beta-sheet hairpins in aqueous solution. J Am Chem Soc 2003; 125:7562-74. [PMID: 12812496 DOI: 10.1021/ja030039e] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this contribution we report optical spectroscopic data on a series of designed beta hairpins previously shown by NMR to contain a substantial population of beta-sheet structure. These models contain a designed hydrophobic cluster and a (D)Pro-Gly sequence to promote formation of a turn geometry. FTIR, electronic and vibrational CD (ECD and VCD) spectra for these small peptides are comparable to expected bandshapes for peptides of high beta-sheet content. The (D)Pro-Gly sequence provides a better turn motif than Asn-Gly as measured by its beta-sheet spectral characteristics. IR and VCD spectra are in qualitative agreement with theoretical simulations based on transfer of parameters from ab initio quantum mechanical force field and intensity computations for the turn and strands. These calculations provide assignments for some distinguishing modes in both IR and VCD spectra. Increased sheet structure can be induced in these hairpins by use of mixed solvent conditions. Thermal denaturation studies reveal that these hairpins undergo very broad unfolding transitions. Guanidine hydrochloride unfolding transitions for the selected hairpin models are similarly broad. However, the "end-states" of temperature and chaotropic denaturation are spectroscopically differentiable.
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Affiliation(s)
- Jovencio Hilario
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607-7061, USA
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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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Andrushchenko V, Wieser H, Bouř P. B−Z Conformational Transition of DNA Monitored by Vibrational Circular Dichroism. Ab Initio Interpretation of the Experiment. J Phys Chem B 2002. [DOI: 10.1021/jp0262721] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Valery Andrushchenko
- Department of Chemistry, University of Calgary, 2500 University Dr., Calgary AB, T2N 1N4, Canada and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic
| | - Helmut Wieser
- Department of Chemistry, University of Calgary, 2500 University Dr., Calgary AB, T2N 1N4, Canada and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Praha 6, Czech Republic
| | - Petr Bouř
- Department of Chemistry, University of Calgary, 2500 University Dr., Calgary AB, T2N 1N4, Canada and 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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