Structural organization of DNA–protein complexes of chromatin studied by vibrational and electronic circular dichroism

Polyanichko, A. M.; Wieser, H.

doi:10.1155/2010/658374

Cited by 11 publications

(5 citation statements)

References 15 publications

(18 reference statements)

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“…Example studies of high aromatic content proteins and model protein folds have appeared that utilize this property . In some cases, selective protein–DNA interaction studies or protein ligation studies are possible with VCD using the relative intensity and frequency resolution aspects of the IR to separate spectral contributions. − Complex protein systems, for example, keratin, have also been studied with VCD to sort out separate contributions to secondary structure . Glyco proteins can be studied to understand and isolate the peptide contributions since the carbohydrate contribution to VCD is weak. ,,, Little effort has been made to measure protein VCD beyond the amide I and II bands whose stronger transition dipoles can couple along the peptide chain and evidence secondary structure sensitivity.…”

Section: Protein Applicationsmentioning

confidence: 99%

Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques

Keiderling

2020

Chem. Rev.

104

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Peptides and proteins are naturally chiral molecular systems so that sensing their structure and conformation with chirality-based spectral methods is an obvious and long-used diagnostic application. Extending chiroptical techniques to measurement of vibrational transitions, in the form of vibrational circular dichroism (VCD) and Raman optical activity (ROA), expands the number and types of excitations available that might provide structural insight and can provide an alternate and, in some cases, a more distinctive conformational probe. Since the dominant repeating structural element in peptides is the locally achiral amide group, VCD senses the polymeric structure through amide coupling, which is directly dependent on secondary structure. Determination of the type and relative contribution of these structural components through empirical correlation with spectral character has been the main application of VCD for peptides and proteins, although this is now reinforced by extensive theoretical modeling. Monitoring structural and conformational change induced by environmental perturbations provides another important application. More recently, VCD has been used to detect morphological variations in fibril states of aggregated peptides and proteins. ROA has parallel secondary structural sensitivities, with more applications for proteins than peptides, and has more sensitivity to local configuration and side chains. This review covers the range of peptide studies done with VCD and extends them to compare with example protein and ROA applications.

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Section: Protein Applicationsmentioning

confidence: 99%

Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques

Keiderling

2020

Chem. Rev.

104

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“…It is rather sensitive to the mutual orientation of distinct groups in the molecule, thus providing valuable three-dimensional structural information for determination of the absolute configuration. VCD and ROA have been widely applied to determine the ACs of chiral structures of small molecules, ,− as well as to structural studies of proteins, ,, viruses, , and drugs. , The two techniques have also been successfully used for the determination of the ACs of chiral molecules with multiple stereocenters, ,,− although cases have been reported in which, e.g., VCD has failed to resolve the configuration of all stereocenters …”

Section: Introductionmentioning

confidence: 99%

Determination of Absolute Configuration and Conformation of a Cyclic Dipeptide by NMR and Chiral Spectroscopic Methods

Hopmann²,

Hudecová

et al. 2013

J. Phys. Chem. A

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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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“…They exploit differential scattering (ROA) or absorption (VCD) of right- and left-circularly polarized incident light by chiral molecules. Both techniques have been successfully applied to determine the structure and absolute configuration (AC) of a wide range of molecules ranging from small isolated molecules − to oligopeptides, − proteins, − viruses, , and drugs. , The vibrational spectra contain many bands sensitive to particular structural features. ROA and VCD are established techniques for determining the AC of molecules with multiple stereocenters; − however, these methods have rarely studied all stereoisomers of a compound, and sometimes the VCD technique also fails to resolve all stereocenters .…”

Section: Introductionmentioning

confidence: 99%

Absolute Configuration of a Cyclic Dipeptide Reflected in Vibrational Optical Activity: Ab Initio and Experimental Investigation

Hopmann

Hudecová

et al. 2012

J. Phys. Chem. A

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The ability of Raman optical activity (ROA) and vibrational circular dichroism (VCD) experiments to determine the absolute configuration of chiral molecules with multiple stereogenic centers was explored for four diastereoisomers of a conformationally flexible cyclic dipeptide, cyclo(Arg-Tyr(OMe)). The reliability of the interpretation depended on the correct description of the molecular conformation, which was found to be strongly affected by intramolecular interactions. In particular, when dispersion corrections were included in the density functional theory calculations, the simulated spectra matched the experimental observations well. Experimental and theoretical ROA and VCD spectra were well correlated for all the absolute configurations (RS, SR, SS, and RR) of protonated cyclo(Arg-Tyr(OMe)). These spectroscopies thus appear useful not only for reliable determination of the absolute configuration and conformation but also in revealing the role of hydrogen bonds and C-H···π interactions in the structure stabilization, which can potentially be used when designing enzyme inhibitors and supramolecular architectures.

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Structural organization of DNA–protein complexes of chromatin studied by vibrational and electronic circular dichroism

Cited by 11 publications

References 15 publications

Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques

Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques

Determination of Absolute Configuration and Conformation of a Cyclic Dipeptide by NMR and Chiral Spectroscopic Methods

Absolute Configuration of a Cyclic Dipeptide Reflected in Vibrational Optical Activity: Ab Initio and Experimental Investigation

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