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Schrenková V, Para Kkadan MS, Kessler J, Kapitán J, Bouř P. Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution. Phys Chem Chem Phys 2023; 25:8198-8208. [PMID: 36880812 DOI: 10.1039/d2cp05756e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Nucleotide conformational flexibility affects their biological functions. Although the spectroscopy of Raman optical activity (ROA) is well suited to structural analyses in aqueous solutions, the link between the spectral shape and the nucleotide geometry is not fully understood. We recorded the Raman and ROA spectra of model nucleotides (rAMP, rGMP, rCMP, and dTMP) and interpreted them on the basis of molecular dynamics (MD) combined with density functional theory (DFT). The relation between the sugar puckering, base conformation and spectral intensities is discussed. Hydrogen bonds between the sugar's C3' hydroxyl and the phosphate groups were found to be important for the sugar puckering. The simulated spectra correlated well with the experimental data and provided an understanding of the dependence of the spectral shapes on conformational dynamics. Most of the strongest spectral bands could be assigned to vibrational molecular motions. Decomposition of the experimental spectra into calculated subspectra based on arbitrary maps of free energies provided experimental conformer populations, which could be used to verify and improve the MD predictions. The analyses indicate some flaws of common MD force fields, such as being unable to describe the fine conformer distribution. Also the accuracy of conformer populations obtained from the spectroscopic data depends on the simulations, improvement of which is desirable for gaining a more detailed insight in the future. Improvement of the spectroscopic and computational methodology for nucleotides also provides opportunities for its application to larger nucleic acids.
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Affiliation(s)
- Věra Schrenková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic. .,Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
| | - Mohammed Siddhique Para Kkadan
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic. .,Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague, Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic. .,Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
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2
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Hudecová J, Kapitán J, Dračínský M, Michal P, Profant V, Bouř P. Structure of Zinc and Nickel Histidine Complexes in Solution Revealed by Molecular Dynamics and Raman Optical Activity. Chemistry 2022; 28:e202202045. [DOI: 10.1002/chem.202202045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Jana Hudecová
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16000 Prague Czech Republic
- Department of Optics Palacký University 17. listopadu 12 771 46 Olomouc Czech Republic
| | - Josef Kapitán
- Department of Optics Palacký University 17. listopadu 12 771 46 Olomouc Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16000 Prague Czech Republic
| | - Pavel Michal
- Department of Optics Palacký University 17. listopadu 12 771 46 Olomouc Czech Republic
| | - Václav Profant
- Faculty of Mathematics and Physics Charles University Ke Karlovu 5 121 16 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16000 Prague Czech Republic
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3
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Monitoring peptide tyrosine nitration by spectroscopic methods. Amino Acids 2020; 53:517-532. [PMID: 33205301 DOI: 10.1007/s00726-020-02911-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022]
Abstract
Oxidative stress can lead to various derivatives of the tyrosine residue in peptides and proteins. A typical product is 3-nitro-L-tyrosine residue (Nit), which can affect protein behavior during neurodegenerative processes, such as those associated with Alzheimer's and Parkinson's diseases. Surface enhanced Raman spectroscopy (SERS) is a technique with potential for detecting peptides and their metabolic products at very low concentrations. To explore the applicability to Nit, we use SERS to monitor tyrosine nitration in Met-Enkephalin, rev-Prion protein, and α-synuclein models. Useful nitration indicators were the intensity ratio of two tyrosine marker bands at 825 and 870 cm-1 and a bending vibration of the nitro group. During the SERS measurement, a conversion of nitrotyrosine to azobenzene containing peptides was observed. The interpretation of the spectra has been based on density functional theory (DFT) simulations. The CAM-B3LYP and ωB97XD functionals were found to be most suitable for modeling the measured data. The secondary structure of the α-synuclein models was monitored by electronic and vibrational circular dichroism (ECD and VCD) spectroscopies and modeled by molecular dynamics (MD) simulations. The results suggest that the nitration in these peptides has a limited effect on the secondary structure, but may trigger their aggregation.
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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5
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The Influence of the Amino Acid Side Chains on the Raman Optical Activity Spectra of Proteins. Chemphyschem 2018; 20:42-54. [DOI: 10.1002/cphc.201800924] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 10/19/2018] [Indexed: 11/07/2022]
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6
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Mensch C, Johannessen C. Is Raman Optical Activity Spectroscopy Sensitive to β-Turns in Proteins? Secondary Structure and Side-Chain Dependence. Chemphyschem 2018; 19:3134-3143. [DOI: 10.1002/cphc.201800678] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Carl Mensch
- Department of Chemistry; University of Antwerp; Groenenborgerlaan 171 2020 Antwerp Belgium)
- Department of Chemistry; Ghent University; Krijgslaan 281 (S3) 9000 Ghent Belgium
| | - Christian Johannessen
- Department of Chemistry; University of Antwerp; Groenenborgerlaan 171 2020 Antwerp Belgium)
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7
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Luber S. Localized molecular orbitals for calculation and analysis of vibrational Raman optical activity. Phys Chem Chem Phys 2018; 20:28751-28758. [DOI: 10.1039/c8cp05880f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
First calculations of vibrational Raman optical activity based on localized molecular orbitals are presented, which pave the way for novel insight into spectroscopic signatures of chiral systems.
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Affiliation(s)
- Sandra Luber
- Department of Chemistry
- University of Zurich
- Zurich
- Switzerland
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8
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Kessler J, Yamamoto S, Bouř P. Establishing the link between fibril formation and Raman optical activity spectra of insulin. Phys Chem Chem Phys 2017; 19:13614-13621. [DOI: 10.1039/c7cp01556a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Molecular dynamics and density functional simulations are used to explain changes in Raman optical activity accompanying the formation of insulin fibrils.
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Affiliation(s)
- Jiří Kessler
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences
- 16610 Prague
- Czech Republic
- Department of Physical and Macromolecular Chemistry
| | - Shigeki Yamamoto
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Osaka 560-0043
- Japan
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences
- 16610 Prague
- Czech Republic
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9
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Mukherjee D, Gai F. Exciton circular dichroism couplet arising from nitrile-derivatized aromatic residues as a structural probe of proteins. Anal Biochem 2016; 507:74-8. [PMID: 27251434 DOI: 10.1016/j.ab.2016.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/14/2016] [Accepted: 05/19/2016] [Indexed: 12/19/2022]
Abstract
Exciton coupling between two chromophores can produce a circular dichroism (CD) couplet that depends on their separation distance, among other factors. Therefore, exciton CD signals arising from aromatic sidechains, especially those of tryptophan (Trp), have been used in various protein conformational studies. However, the long-wavelength component of the commonly used CD couplet produced by a pair of Trp residues is typically located around 230 nm, thereby overlapping significantly with the protein backbone CD signal. This overlap often prevents a direct and quantitative assessment of the Trp CD couplet in question without further spectral analysis. Here, we show that this inconvenience can be alleviated by using a derivative of Trp, 5-cyanotryptophan (TrpCN), as the chromophore. Specifically, through studying a series of peptides that fold into either α-helical or ß-hairpin conformations, we demonstrate that in comparison with the Trp CD couplet, that arising from two TrpCN residues not only is significantly red-shifted but also becomes more intense due to the larger extinction coefficient of the underlying electronic transition. In addition, we show that a pair of p-cyanophenylalanines (PheCN) or a PheCN-TrpCN pair can also produce a distinct exciton CD couplet that can be useful in monitoring conformational changes in proteins.
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Affiliation(s)
- Debopreeti Mukherjee
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Sato H, Yajima T, Yamagishi A. Chiroptical Studies on Supramolecular Chirality of Molecular Aggregates. Chirality 2015; 27:659-66. [DOI: 10.1002/chir.22482] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 06/04/2015] [Accepted: 06/08/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Hisako Sato
- Graduated of Science and Engineering; Ehime University; Matsuyama Japan
| | - Tomoko Yajima
- Department of Chemistry; Ochanomizu University; Tokyo Japan
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11
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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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12
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Merten C, Li F, Bravo-Rodriguez K, Sanchez-Garcia E, Xu Y, Sander W. Solvent-induced conformational changes in cyclic peptides: a vibrational circular dichroism study. Phys Chem Chem Phys 2014; 16:5627-33. [PMID: 24513908 DOI: 10.1039/c3cp55018d] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The three-dimensional structure of a peptide is strongly influenced by its solvent environment. In the present study, we study three cyclic tetrapeptides which serve as model peptides for β-turns. They are of the general structure cyclo(Boc-Cys-Pro-X-Cys-OMe) with the amino acid X being either glycine (1), or L- or D-leucine (L- or D-2). Using vibrational circular dichroism (VCD) spectroscopy, we confirm previous NMR results which showed that D-2 adopts predominantly a βII turn structure in apolar and polar solvents. Our results for L-2 indicate a preference for a βI structure over βII. With increasing solvent polarity, the preference for 1 is shifted from βII towards βI. This conformational change goes along with the breaking of an intramolecular hydrogen bond which stabilizes the βII conformation. Instead, a hydrogen bond with a solvent molecule can stabilize the βI turn conformation.
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Affiliation(s)
- Christian Merten
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G2G2, Canada.
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Karabencheva-Christova TG, Carlsson U, Balali-Mood K, Black GW, Christov CZ. Conformational effects on the circular dichroism of Human Carbonic Anhydrase II: a multilevel computational study. PLoS One 2013; 8:e56874. [PMID: 23526922 PMCID: PMC3582176 DOI: 10.1371/journal.pone.0056874] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 01/15/2013] [Indexed: 11/25/2022] Open
Abstract
Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII), with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory) were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD) could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions.
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Affiliation(s)
- Tatyana G Karabencheva-Christova
- Department of Applied Sciences, School of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.
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Li X, Hopmann KH, Hudecová J, Isaksson J, Novotná J, Stensen W, Andrushchenko V, Urbanová M, Svendsen JS, Bouř P, Ruud K. Determination of absolute configuration and conformation of a cyclic dipeptide by NMR and chiral spectroscopic methods. J Phys Chem A 2013; 117:1721-36. [PMID: 23347158 DOI: 10.1021/jp311151h] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Increasing precision of contemporary computational methods makes spectroscopies such as vibrational (VCD) and electronic (ECD) circular dichroism attractive for determination of absolute configurations (AC) of organic compounds. This is, however, difficult for polar, flexible molecules with multiple chiral centers. Typically, a combination of several methods provides the best picture of molecular behavior. As a test case, all possible stereoisomers with known AC (RS, SR, SS, and RR) of the cyclic dipeptide cyclo(Arg-Trp) (CAT) were synthesized, and the performances of the ECD, infrared (IR), VCD, Raman, Raman optical activity (ROA), and nuclear magnetic resonance (NMR) techniques for AC determination were investigated. The spectra were interpreted with the aid of density functional theory (DFT) calculations. Folded geometries stabilized by van der Waals and electrostatic interactions between the diketopiperazine (DKP) ring and the indole group are predicted to be preferred for CAT, with more pronounced folding due to Arg-Trp stacking in the case of SS/RR-CAT. The RS/SR isomers prefer a twist-boat puckering of the DKP ring, which is relatively independent of the orientation of the side chains. Calculated conformer-averaged VCD and ECD spectra explain most of the experimentally observed bands and allow for AC determination of the tryptophan side-chain, whereas the stereochemical configuration of the arginine side-chain is visible only in VCD. NMR studies provide characteristic long-range (2)J(C,H) and (3)J(C,H) coupling constants, and nuclear Overhauser effect (NOE) correlations, which in combination with either ECD or VCD also allow for complete AC determination of CAT.
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Affiliation(s)
- Xiaojun Li
- Centre for Theoretical and Computational Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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