Raman Optical Activity of the Central Part of Hinge Peptide

Kapitán, Josef; Baumruk, Vladimı́r; Gut, V.; Hlaváček, Jan; Dlouhá, Helena; Urbanová, Marie; Wünsch, Erich; Maloň, Petr

doi:10.1135/cccc20050403

Cited by 21 publications

(33 citation statements)

References 11 publications

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“…45 The spectral manipulations were done with the Opus software (Bruker Optics, Inc.). Raman spectrum of free dGMP (not shown) was acquired using analogous conditions as for IR with a multipurpose spectrometer 46 located at the Charles University, Prague. By comparison of computed and experimental Raman intensities, IR assignments of vibrational transitions could be independently verified.…”

Section: Methodsmentioning

confidence: 99%

Infrared Absorption Detection of Metal Ion-Deoxyguanosine Monophosphate Binding: Experimental and Theoretical Study

Andrushchenko

Bouř

2008

J. Phys. Chem. B

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Metal ion interactions with nucleic acids attract attention because of the environmental and biological consequences. The formation of the complex is often monitored by the vibrational spectroscopy. To identify characteristic binding patterns and marker bands on a model DNA component, infrared absorption spectra of the deoxyguanosine monophosphate complexes with Na + , Mg 2+ , Ca 2+ , Ni 2+ , Cu 2+ , Zn 2+ , and Cd 2+ cations were recorded and interpreted on the basis of density-functional computations. The aqueous environment was simulated by continuum and combined continuum-explicit solvent models. For the binding to the N7 position of the guanine base, the computation predicted a characteristic frequency upshift and splitting of the 1578 cm -1 band, which is in accord with available experimental data. Contrary to the expectation, the modeling suggests that the binding to the carbonyl group might not be detectable, as the metal causes smaller spectral changes if compared to the hydrogen-bound water molecules. The binding to the phosphate group causes significant spectral changes in the sugar-phosphate vibrating region (∼800-1200 cm -1 ), but also notable frequency shifts of the carbonyl vibrations. The Cu 2+ and Zn 2+ ions induced the largest alterations in observed vibrational absorption, which corresponds to the calculated strong interaction energies in the N7-complexes and to previous experimental experience. Additional changes in the vibrational spectra of the copper complexes were observed under high metal concentration, corresponding to the simultaneous binding to the phosphate residue. The two-step Cu 2+ binding process was also confirmed by the microcalorimetry titration curve. The computations and combination of more techniques thus help us to assign and localize spectral changes caused by the metal ion binding to nucleic acids. IntroductionComplexes of metal ions with nucleic acids participate in various biological processes, such as DNA replication and transcription, enzymatic cleavages, mutagenesis, carcinogenesis, and DNA packing in a living cell and also stabilize particular nucleic acid secondary structures. 1-6 A vast number of experimental and theoretical studies have been dedicated to metal interactions with nucleic acids and their components. [5][6][7][8][9][10] In the present work we systematically investigate interactions of some common metal ions with deoxyguanosine monophosphate (dGMP) as a model system, in order to better explain previously observed changes in infrared absorption (IR) spectra of nucleic acids upon the interaction with the metals.Being relatively simple and widely available, infrared spectroscopy provided precious information about the interaction of metal ions with nucleic acids (e.g., see refs 11-23). Detailed structural information could be obtained from the IR spectra when observed bands were assigned to particular bonds or DNA functional groups. [24][25][26][27] In practice, however, the assignment is complicated by solvent interference, overlapped and naturally bro...

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Section: Methodsmentioning

confidence: 99%

Infrared Absorption Detection of Metal Ion-Deoxyguanosine Monophosphate Binding: Experimental and Theoretical Study

Andrushchenko

Bouř

2008

J. Phys. Chem. B

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“…Calculations showed that structural changes could be in principle seen by ECD but the correct interpretation is rather difficult and without combination with VOA data, molecular modeling and supporting theoretical calculations may be even impossible. Our theoretical results promoted by preliminary experimental data 23,24 suggest a possibility to study conformation of the SÀ ÀS bridge using methods of VOA. Because of the fact that peptide protein samples usually involve aqueous solutions and disulphide vibrations occur below 1000 cm 21 -difficult to study by the infrared spectroscopy-the Raman spectroscopy and its chiral variant-ROA seem good candidates to solve this problem.…”

Section: Discussionmentioning

confidence: 74%

“…In the study of rigid proline-rich peptides related to immunoglobin core, we already observed nonzero ROA signal in the region of SÀ ÀS (540 cm 21 ) and CÀ ÀS stretching vibrations (655 cm 21 ). 23,24 The latter was indicative of specific conformation of the HÀ ÀCÀ ÀCÀ ÀS bond. However, until now an analogous, dedicated study of vibrational spectra with particular emphasis to VOA that would evaluate its potential possibilities for the disulphide group has yet to be reported.…”

Section: 0mentioning

confidence: 99%

Vibrational and electronic optical activity of the chiral disulphide group: Implications for disulphide bridge conformation

2009

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Using dihydrogendisulphide (H(2)S(2)), dimethyl- ((CH(3))(2)S(2)), and diethyldisulphide ((CH(3)CH(2))(2)S(2))as model molecules, theoretical ECD, VCD, and ROA spectra of nonplanar disulphides were calculated by DFT methods. Most of the calculated electronic and vibrational chiroptical features suffer an equivocal relation between calculatedsigns of ECD, VCD, or ROA and the sense of disulphide nonplanarity as noted earlier for low-lying ECD bands. This is a consequence of local C(2) symmetry of a disulphide group causing most electronic and vibrational transitions to occur as pairs falling to alternative A, B symmetry species, which become degenerate and switch their succession (and consequently the observed chiroptical sign pattern) at the energetically most favorable perpendicular conformation. According to present calculations, the key to resolving this ambiguity may involve the S-S stretching vibrational mode at approximately 500 cm(-1). The relation of signs of the relevant VCD and ROA features to sense of disulphide chirality seems simpler and less ambiguous. The right-handed arrangement of the S-S group (0 < chi(S-S) < 180 degrees) results in mostly negative VCD signals. Although relation to ROA still suffers some ambiguity, it gets clearer along the series H(2)S(2)-(CH(3))(2)S(2)-(CH(3)CH(2))(2)S(2). ROA is also attractive for the analysis of disulphide-containing peptides and proteins, because applying it to aqueous solutions is not problematic.

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“…The Raman techniques for determination of peptide structures were used several times in the past, 10,14,15 but to the best of our knowledge this is the first time when the analysis of the ROA intensities reproduces the NMR data and the conformer ratios with such accuracy.…”

Section: Resultsmentioning

confidence: 99%

Comparison of Quantitative Conformer Analyses by Nuclear Magnetic Resonance and Raman Optical Activity Spectra for Model Dipeptides

et al. 2008

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Interpretation of the Raman optical activity (ROA) of peptides is difficult because of molecular flexibility and interaction with the solvent. Typically, simulations and experiments are compared in terms of a qualitative agreement between the spectra. However, on a series of the Pro-Gly, Gly-Pro, Pro-Ala, and Ala-Pro dipeptides more precise conformer ratios could be obtained with the aid of the density functional computations and numerical decomposition of the spectral shapes. All observed transitions were assigned, and the computed transition frequencies were scaled accordingly. Then the populations predicted by the optical spectroscopy agreed within a few percent with an analysis of the spin-spin coupling constants based on the Karplus equations, which was confirmed also by a comparison of calculated and experimental NMR couplings. The results are supported by molecular dynamics simulations and related to the previous conformational studies of similar molecules.

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Raman Optical Activity of the Central Part of Hinge Peptide

Cited by 21 publications

References 11 publications

Infrared Absorption Detection of Metal Ion-Deoxyguanosine Monophosphate Binding: Experimental and Theoretical Study

Infrared Absorption Detection of Metal Ion-Deoxyguanosine Monophosphate Binding: Experimental and Theoretical Study

Vibrational and electronic optical activity of the chiral disulphide group: Implications for disulphide bridge conformation

Comparison of Quantitative Conformer Analyses by Nuclear Magnetic Resonance and Raman Optical Activity Spectra for Model Dipeptides

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