1
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Yamamoto S, Ishiro S, Kessler J, Bouř P. Intense chiral signal from α-helical poly-L-alanine observed in low-frequency Raman optical activity. Phys Chem Chem Phys 2021; 23:26501-26509. [PMID: 34806737 DOI: 10.1039/d1cp04401j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman optical activity (ROA) spectral features reliably indicate the structure of peptides and proteins, but the signal is often weak. However, we observed significantly enhanced low-frequency bands for α-helical poly-L-alanine (PLA) in solution. The biggest ROA signal at ∼100 cm-1 is about 10 times stronger than higher-frequency bands described previously, which facilitates the detection. The low-frequency bands of PLA were compared to those of α-helical proteins. For PLA, density functional simulations well reproduced the experimental spectra and revealed that about 12 alanine residues within two turns of the α-helix generate the strong ROA band. Averaging based on molecular dynamics (MD) provided an even more realistic spectrum compared to the static model. The low-frequency bands could be largely related to a collective motion of the α-helical backbone, partially modulated by the solvent. Helical and intermolecular vibrational coordinates have been introduced and the helical unwinding modes were assigned to the strongest ROA signal at 101-128 cm-1. Further analysis indicated that the helically arranged amide and methyl groups are important for the strong chiral signal of PLA, while the local chiral centers CαH contribute in a minor way only. The strong low-frequency ROA can thus provide precious information about the motions of the peptide backbone and facilitate future protein studies.
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Affiliation(s)
- Shigeki Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
| | - Shota Ishiro
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
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2
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Torii H, Sato H. Intermediate length-scale chirality related to the vibrational circular dichroism intensity enhancement upon fibril formation in a gelation process. Phys Chem Chem Phys 2018; 20:14992-14996. [DOI: 10.1039/c8cp02121j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The VCD intensity enhancement occurring upon fibril formation arises from the second out of the three hierarchical tiers of chirality.
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Affiliation(s)
- Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering
- Faculty of Engineering, and Department of Optoelectronics and Nanostructure Science
- Graduate School of Science and Technology
- Shizuoka University
- Hamamatsu 432-8561
| | - Hisako Sato
- Graduate School of Science and Engineering
- Ehime University
- 2-5 Bunkyo-cho
- Matsuyama
- Japan
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3
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Andrushchenko V, Benda L, Páv O, Dračínský M, Bouř P. Vibrational Properties of the Phosphate Group Investigated by Molecular Dynamics and Density Functional Theory. J Phys Chem B 2015; 119:10682-92. [PMID: 26193890 DOI: 10.1021/acs.jpcb.5b05124] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The phosphate group (PO2(-)) is an important building block occurring in many components of living matter including nucleic acids. It provides distinct features in vibrational spectra and is useful as a local probe of NA conformation and interactions with the environment. For this purpose, it is desirable to explore in detail various factors influencing spectral shapes of characteristic phosphate vibrations. In the present study, effects of the solvent and conformational averaging are analyzed for simple model molecules, dimethylphosphate, ethylmethylphosphate, and ethylmethylthiophosphate. Infrared absorption (IR) and Raman spectra were measured and calculated using a combination of molecular dynamics (MD) and density functional theory (DFT). To fully understand the link between the structure and the spectra, the solvent has to be explicitly included in the computational modeling. The results indicate that vibrational properties of the phosphate moiety are very sensitive to its conformation and interactions with the aqueous environment indeed. Polarizable continuum solvent models without explicit water molecules provided significantly worse agreement with the experiment. The combined MD/DFT approach captures well spectral characteristics for the model systems and constitutes the most reliable basis for exploration of phosphate vibrational properties in biomolecular structural studies.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Ladislav Benda
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Flemingovo náměstí 2, 16610, Prague, Czech Republic
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4
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Štěpánek P, Bouř P. Origin-independent sum over states simulations of magnetic and electronic circular dichroism spectra via the localized orbital/local origin method. J Comput Chem 2015; 36:723-30. [DOI: 10.1002/jcc.23845] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/05/2015] [Accepted: 01/09/2015] [Indexed: 01/19/2023]
Affiliation(s)
- Petr Štěpánek
- Group of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences; Flemingovo nám. 2 16610 Prague Czech Republic
- Institute of Physics, Faculty of Mathematics and Physics; Charles University; Ke Karlovu 5 121 16 Prague Czech Republic
| | - Petr Bouř
- Group of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences; Flemingovo nám. 2 16610 Prague Czech Republic
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5
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Tubbs J, Condon DE, Kennedy S, Hauser M, Bevilacqua P, Turner DH. The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics. Biochemistry 2013; 52:996-1010. [PMID: 23286901 PMCID: PMC3571207 DOI: 10.1021/bi3010347] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/27/2012] [Indexed: 12/29/2022]
Abstract
The sequence dependence of RNA energetics is important for predicting RNA structure. Hairpins with C(n) loops are consistently less stable than hairpins with other loops, which suggests the structure of C(n) regions could be unusual in the "unfolded" state. For example, previous nuclear magnetic resonance (NMR) evidence suggested that polycytidylic acid forms a left-handed helix. In this study, UV melting experiments show that the hairpin formed by r(5'GGACCCCCGUCC) is less stable than r(5'GGACUUUUGUCC). NMR spectra for single-stranded C(4) oligonucleotide, mimicking the unfolded hairpin loop, are consistent with a right-handed A-form-like helix. Comparisons between NMR spectra and molecular dynamics (MD) simulations suggest that recent reparametrizations, parm99χ_YIL and parm99TOR, of the AMBER parm99 force field improve the agreement between structural features for C(4) determined by NMR and predicted by MD. Evidently, the force field revisions to parm99 improve the modeling of RNA energetics and therefore structure.
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Affiliation(s)
- Jason
D. Tubbs
- Department
of Chemistry, University of Rochester,
Rochester, New York 14627,
United States
- Center for
RNA Biology, University of Rochester, Rochester,
New York 14642,
United States
| | - David E. Condon
- Department
of Chemistry, University of Rochester,
Rochester, New York 14627,
United States
- Center for
RNA Biology, University of Rochester, Rochester,
New York 14642,
United States
| | - Scott
D. Kennedy
- Center for
RNA Biology, University of Rochester, Rochester,
New York 14642,
United States
- Department
of Biochemistry and
Biophysics, University of Rochester, Rochester,
New York 14642, United States
| | - Melanie Hauser
- Department of Chemistry, Buena Vista University, Storm Lake, Iowa 50588, United
States
- Department of Chemistry
and
Center for RNA Molecular Biology, The Pennsylvania State
University, University Park, Pennsylvania 16802, United
States
| | - Philip
C. Bevilacqua
- Department of Chemistry
and
Center for RNA Molecular Biology, The Pennsylvania State
University, University Park, Pennsylvania 16802, United
States
| | - Douglas H. Turner
- Department
of Chemistry, University of Rochester,
Rochester, New York 14627,
United States
- Center for
RNA Biology, University of Rochester, Rochester,
New York 14642,
United States
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6
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Domingos SR, Roeters SJ, Amirjalayer S, Yu Z, Hecht S, Woutersen S. Elucidating the backbone conformation of photoswitchable foldamers using vibrational circular dichroism. Phys Chem Chem Phys 2013; 15:17263-7. [DOI: 10.1039/c3cp53243g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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7
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Andrushchenko V, Tsankov D, Krasteva M, Wieser H, Bour P. Spectroscopic detection of DNA quadruplexes by vibrational circular dichroism. J Am Chem Soc 2011; 133:15055-64. [PMID: 21823674 DOI: 10.1021/ja204630k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The four-stranded G-quadruplex motif is a conformation frequently adopted by guanine-rich nucleic acids that plays an important role in biology, medicine, and nanotechnology. Although vibrational spectroscopy has been widely used to investigate nucleic acid structure, association of particular spectral features with the quadruplex structure has to date been ambiguous. In this work, experimental IR absorption and vibrational circular dichroism (VCD) spectra of the model quadruplex systems d(G)(8) and deoxyguanosine-5'-monophosphate (5'-dGMP) were analyzed using molecular dynamics (MD) and quantum-chemical modeling. The experimental spectra were unambiguously assigned to the quadruplex DNA arrangement, and several IR and VCD bands related to this structural motif were determined. Involvement of MD in the modeling was essential for realistic simulation of the spectra. The VCD signal was found to be more sensitive to dynamical structural variations than the IR signal. The combination of the spectroscopic techniques with multiscale simulations provides extended information about nucleic acid conformations and their dynamics.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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8
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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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9
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Schwartz E, Domingos SR, Vdovin A, Koepf M, Buma WJ, Cornelissen JJLM, Rowan AE, Nolte RJM, Woutersen S. Direct Access to Polyisocyanide Screw Sense Using Vibrational Circular Dichroism. Macromolecules 2010. [DOI: 10.1021/ma101601e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Erik Schwartz
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Sérgio R. Domingos
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Alexander Vdovin
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Matthieu Koepf
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wybren Jan Buma
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
| | - Jeroen J. L. M. Cornelissen
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Alan E. Rowan
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Roeland J. M. Nolte
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Sander Woutersen
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
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10
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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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11
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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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12
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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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13
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The a Priori Calculation of Vibrational Circular Dichroism Intensities. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125847.ch6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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14
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Krummel AT, Zanni MT. Interpreting DNA Vibrational Circular Dichroism Spectra Using a Coupling Model from Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2006; 110:24720-7. [PMID: 17134235 DOI: 10.1021/jp063227a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two-dimensional infrared spectroscopy was recently used to measure the vibrational couplings between carbonyl bonds located on DNA nucleobases (Krummel, A. T.; Mukherjee, P.; Zanni, M. T. J. Phys. Chem. B 2003, 107, 9165 and Krummel, A. T.; Zanni, M. T. J. Phys. Chem. B 2006, 110, 13991). Here, we extend the coupling model derived from these 2D IR experiments to simulate the vibrational absorption and vibrational circular dichroism (VCD) spectra of three double-stranded DNA oligomers: poly(dG)-poly(dC), poly(dG-dC), and dGGCC. Using this model, we determine that the VCD spectrum of A-form poly(dG)-poly(dC) is dominated by interactions between stacked bases, whereas the coupling between base pairs and stacked bases carries equal importance in the VCD spectrum of B-form poly(dG-dC). We also simulate the absorption and VCD spectra of dGGCC, which is a combination of A- and B-form configurations. These simulations give insight into the structural interpretation of VCD and absorption spectroscopies that have long been used to monitor DNA secondary structure and kinetics.
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Affiliation(s)
- Amber T Krummel
- Department of Chemistry, University of Wisconsin at Madison, Madison, Wisconsin 53706-1396, USA
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15
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Sebek J, Kejík Z, Bour P. Geometry and Solvent Dependence of the Electronic Spectra of the Amide Group and Consequences for Peptide Circular Dichroism. J Phys Chem A 2006; 110:4702-11. [PMID: 16599437 DOI: 10.1021/jp060813v] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of geometry variations and solvent environment of N-methylacetamide on its energies and absorption intensities was systematically analyzed with the aid of the time-dependent density functional theory (TD DFT). Selective and often complicated reactions of individual electronic levels on the perturbations were found important for the resultant spectral profile. For example, the n-pi band position varied by tens of nanometers due to the C=O bond length oscillations, while it was rather unaffected by surrounding water. On the contrary, pi-pi type transition energies and intensities were broadly dispersed by the aqueous environment but exhibited a modest coordinate dependence. A simple electrostatic model used previously for absorption in the IR region (J. Chem. Phys. 2005, 122, 144501) explained these changes only partially. Additionally, electronic transfer between the solute and the solvent had to be considered for faithful modeling of the ultraviolet light absorption. The inclusion of the environment and dynamics in the modeling then provided more accurate positions, intensities, and realistic inhomogeneous widths of spectral lines. These factors were found important for absorption and circular dichroism spectra of larger peptides and proteins. This was demonstrated with a combined DFT/coupled oscillator model providing principal features observed in electronic circular dichroism spectra of standard peptide conformations.
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Affiliation(s)
- Jirí Sebek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10
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16
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Simulation of amide I′ band profiles of trans polyproline based on an excitonic coupling model. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.04.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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17
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Mohlenhoff B, Romeo M, Diem M, Wood BR. Mie-type scattering and non-Beer-Lambert absorption behavior of human cells in infrared microspectroscopy. Biophys J 2005; 88:3635-40. [PMID: 15749767 PMCID: PMC1305510 DOI: 10.1529/biophysj.104.057950] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report infrared microspectral features of nuclei in a completely inactive and contracted (pyknotic) state, and of nuclei of actively dividing cells. For pyknotic nuclei, the very high local concentration of DNA leads to opaqueness of the chromatin and, consequently, the absence of DNA signals in the IR spectra of very small nuclei. However, these nuclei can be detected by their scattering properties, which can be described by the Mie theory of scattering from dielectric spheres. This scattering depends on the size of the nucleus; consequently, quite different scattering cross-sections are calculated and observed for pyknotic and mitotic nuclei.
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Affiliation(s)
- Brian Mohlenhoff
- Department of Chemistry and Biochemistry, City University of New York, Hunter College, New York, New York 10021, USA
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18
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Wieczorek R, Dannenberg JJ. Hydrogen-Bond Cooperativity, Vibrational Coupling, and Dependence of Helix Stability on Changes in Amino Acid Sequence in Small 310-Helical Peptides. A Density Functional Theory Study. J Am Chem Soc 2003; 125:14065-71. [PMID: 14611243 DOI: 10.1021/ja034034t] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Five pentapeptides, GGGGG, GAGGG, GVGGG, GLGGG, and GIGGG, have been completely optimized in the 3(10)-helical and open beta-strand conformations at the B3LYP/D95 level. The energies of the helices relative to the beta-strands vary from -2.1 to -3.6 kcal and depend on the amino acid residue sequence. The energies of substituting A, V, L, or I for G in the second position are also presented. Vibrational analyses were performed on the optimized structures. Vibrational coupling through the individual H-bond chains of the helices is confirmed to be stronger than that through space or through the covalent bonds. The cooperative interactions of the H-bonds are evident from both the structures and the coupling of the amide I, amide II, and N-H vibrations.
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Affiliation(s)
- Robert Wieczorek
- Department of Chemistry, City University of New York, Hunter College and the Graduate School, 695 Park Avenue, New York, NY 10021, USA
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19
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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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21
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Self BD, Moore DS. Nucleic acid vibrational circular dichroism, absorption, and linear dichroism spectra. II. A DeVoe theory approach. Biophys J 1998; 74:2249-58. [PMID: 9591652 PMCID: PMC1299568 DOI: 10.1016/s0006-3495(98)77934-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The DeVoe polarizability theory is used to calculate vibrational circular dichroism (VCD) and infrared (IR) absorption spectra of four polyribonucleotides: poly(rA) x poly(rU), poly(rU) x poly(rA) x poly(rU), poly(rG) x poly(rC), and poly(rC+) x poly(rI) x poly(rC). This is the first report on the use of the DeVoe theory to calculate VCD, oriented VCD, IR absorption, and IR linear dichroism (LD) spectra of double- and triple-stranded polyribonucleotides. Results are reported for DeVoe theory calculations--within the base-stretching 1750-1550 cm(-1) spectral region--on several proposed multistranded polyribonucleotide geometries. The calculated spectra obtained from these proposed geometries are compared with previously reported measured and calculated VCD and IR spectral results. Base-base hydrogen-bonding effects on the frequencies and magnitudes of the base carbonyl stretching modes are explicitly considered. The good agreements found between calculated and measured spectra are proposed to be further evidence of the usefulness of the DeVoe theory in drawing three-dimensional structural conclusions from measured polyribonucleotide VCD and IR spectra.
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Affiliation(s)
- B D Self
- Department of Chemistry, Howard University, Washington, DC 20059, USA
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22
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Abstract
Advances in the field of vibrational optical activity (VOA) are reviewed over the past decade. Topics are surveyed with an emphasis on the theoretical and instrumental progress in both vibrational circular dichroism (VCD) and Raman optical activity (ROA). Applications of VOA to stereochemical and biological problems are reviewed, with a bias toward new kinds of experiments made possible by theoretical and instrumental advances. In the field of VCD, the most notable advances have taken place in the quality and size of ab initio calculations of VOA intensities and in the quality of step-scan Fourier transform instrumentation. For ROA, the most dramatic progress has occurred in the areas of theoretical formulation and high-throughput instrumentation. Applications of VOA now include all major classes of biological and pharmaceutical molecules. VOA's importance as a diagnostic tool will likely grow as the control of molecular chirality increases in research and industrial areas.
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Affiliation(s)
- L A Nafie
- Department of Chemistry, Syracuse University, New York 13244-4100, USA.
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23
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Self BD, Moore DS. Nucleic acid vibrational circular dichroism, absorption, and linear dichroism spectra. I. A DeVoe theory approach. Biophys J 1997; 73:339-47. [PMID: 9199798 PMCID: PMC1180935 DOI: 10.1016/s0006-3495(97)78074-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Infrared (IR) vibrational circular dichroism (VCD), absorption, and linear dichroism (LD) spectra of four homopolyribonucleotides, poly(rA), poly(rG), poly(rC), and poly(rU), have been calculated, in the 1750-1550 cm-1 spectral region, using the DeVoe polarizability theory. A newly derived algorithm, which approximates the Hilbert transform of imaginaries to reals, was used in the calculations to obtain real parts of oscillator polarizabilities associated with each normal mode. The calculated spectra of the polynucleotides were compared with previously measured solution spectra. The good agreement between calculated and measured polynucleotide spectra indicates, for the first time, that the DeVoe theory is a useful means of calculating the VCD and IR absorption spectra of polynucleotides. For the first time, calculated DeVoe theory VCD and IR absorption spectra of oriented polynucleotides are presented. The calculated VCD spectra for the oriented polynucleotides are used to predict the spectra for such measurements made in the future. The calculated IR spectra for the oriented polynucleotides are useful in interpreting the linear dichroism of the polynucleotides.
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Affiliation(s)
- B D Self
- Department of Chemistry, Howard University, Washington, DC 20059, USA
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24
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Simard C, Gaudreau E, Savoie R. A vibrational spectroscopic study of the metastable form of associated polyinosinic acid. Biopolymers 1996; 38:329-38. [PMID: 8906969 DOI: 10.1002/(sici)1097-0282(199603)38:3%3c329::aid-bip6%3e3.0.co;2-w] [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: 02/03/2023]
Abstract
We have studied by Raman and ir spectroscopy the metastable complex formed by the self-association of polyinosinic acid in aqueous solution. The complex is easily prepared by quickly cooling to ca. 0 degrees C a warm solution of the polyribonucleotide to which a small amount of rubidium salt has been added. Upon heating, this metastable form melts cooperatively near 13 degrees C, well below the dissociation temperature of a stable four-stranded complex, which occurs at 47 degrees C in the same conditions. The presence of several components in the stretching-mode region of the carbonyl groups in the vibrational spectra of the metastable complex suggests that it also has a parallel four-stranded structure. The difference in structure between the two forms is believed to be caused by the presence of fewer metal ions in the central channel of the metastable complex, in agreement with conclusions reached in previous investigations. The Raman spectra further show that the ribose units in the metastable form have a C3'-endo conformation, in contrast with the stable form, for which we have previously suggested a mixed C2'-endo/C3'-endo conformation.
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Affiliation(s)
- C Simard
- Departement de chimie, Universite Laval Quebec, Canada
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25
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Birke SS, Diem M. Conformational studies of the smallest structural motifs of DNA detectable via vibrational circular dichroism: cytidylyl-(3'-5')-guanosine and guanylyl-(3'-5')-cytidine. Biophys J 1995; 68:1045-9. [PMID: 7756524 PMCID: PMC1281827 DOI: 10.1016/s0006-3495(95)80279-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The infrared absorption and vibrational circular dichroism (VCD) spectra of buffered aqueous solutions of cytidylyl-(3'-5')-guanosine (5'(CG)3') and guanylyl-(3'-5')-cytidine (5'(GC)3') are reported. Under low ionic strength conditions, these dinucleotides exhibit VCD features that can be predicted qualitatively from structural data of (CG)2 and (GC)2 sequences of poly(dG-dC).poly(dG-dC), using the exciton model for infrared VCD intensities.
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Affiliation(s)
- S S Birke
- Department of Chemistry, City University of New York, Hunter College, New York 10021, USA
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