Two-dimensional correlation analysis of Raman optical activity – Basic rules and data treatment

Pazderka, Tomáš; Kopecký, Vladimı́r

doi:10.1016/j.vibspec.2011.10.002

Cited by 27 publications

(16 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2D correlation analysis is a cross‐correlation technique that is applied to a previously measured set of perturbation‐induced spectra as a function of two‐independent wavenumber positions . This results in data matrices, including synchronous and asynchronous spectra and moving windows which have the advantage of directly comparing significant spectral variations without having to examine numerous plots of single intensities as a function of concentration.…”

Section: Resultsmentioning

confidence: 99%

“…Despite the structural sensitivity of ROA, which measures a small difference in the intensity of vibrational Raman scattering from chiral molecules in right‐ and left‐circularly polarized incident light, scattered light, or both, a detailed spectral analysis can become complicated when conformational transitions are involved due to the wealth of structural data measured and the complexity of vibrational modes explored. One way of getting around this problem is to use two‐dimensional correlation spectroscopy (2DCOS), which aims to improve visualization and analysis of complex data by spreading a previously measured set of perturbation‐induced spectra as a function of two independent wavenumber positions over a second dimension . This approach has been demonstrated to be very successful in investigating polypeptide conformational transitions .…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Investigation of DMSO‐Induced Conformational Transitions in Human Serum Albumin Using Two‐Dimensional Raman Optical Activity Spectroscopy

Batista

Ashton

et al. 2014

Chirality

View full text Add to dashboard Cite

Recent Raman and Raman optical activity (ROA) results have demonstrated that dimethyl sulfoxide (DMSO) induces the selective conversion of α-helix motifs into the poly(L-proline) II (PPII) helix conformation in an array of proteins, while β-sheets remain mostly unaffected. Human serum albumin (HSA), a highly α-helical protein, underwent the most dramatic changes and, therefore, was selected as a model for further investigations into the mechanism of this conformational change. Herein we report the use of two-dimensional ROA correlation analysis applying synchronous, autocorrelation, and moving windows approaches in order to understand the conformational transitions in HSA as a function of DMSO concentration. Our results indicate that the destabilization of native α-helix starts at DMSO concentrations as little as 20% in water (v/v), with the transition to PPII helix being complete at ~80% DMSO. These results clearly indicate that any protein preparation containing relatively low concentrations of DMSO should consider possible disruptions in α-helical domains.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Investigation of DMSO‐Induced Conformational Transitions in Human Serum Albumin Using Two‐Dimensional Raman Optical Activity Spectroscopy

Batista

Ashton

et al. 2014

Chirality

View full text Add to dashboard Cite

show abstract

“…they analysed the details of the interaction between avidin, a glycoprotein isolated from egg-white, with biotin (vitamin h) [184]. Even though the 2d vCd technique is still rarely used [185,186] in our opinion it certainly will be, along with two-dimensional Raman optical activity spectroscopy (2d RoA) [187,188], an indispensable method for analysing the conformational complexity of biosystems by vibrational spectroscopy methods. the ma et al study in 2006 is an extraordinary example of the potency of 2d vCd spectroscopy in examining the structure of L-alanine in water as a function of ph [176].…”

Section: Vibrational Chiroptical Studies Onmentioning

confidence: 99%

α-Amino Acids In Water: A Review Of VCD And ROA Spectra

Dobrowolski

Lipiński

Rode

et al. 2013

Challenges and Advances in Computational Chemistry and Physics

View full text Add to dashboard Cite

An up-to-date perspective on the capability of vibrational Circular dichroism (vCd) and Raman optical Activity (RoA) spectroscopy of the 20 encoded α-amino acids to solve the structural problems appearing in water is provided in this review. VCD and ROA spectroscopy of the α-amino acid molecules reviewed in this chapter refer only to free and single amino acids in water at various ph levels. to well understand the implications of such studies for biology and medicine, we devote one subchapter to the role of free amino acids in an organism's metabolism and physiology. A variety of side chains that modify the α-amino acids character from acidic to basic and from hydrophilic to hydrophobic makes the possible dissociation equilibria in water very complex and dependent on several factors. therefore, information on dissociation constants, isoelectric points, and hydrophobicity parameters of α-amino acids is summarised in the next subchapter. The conformational variety, complexity of interactions, and entanglement of equilibria makes considering the influence of these factors on vCd and RoA spectra with quantum chemical analysis absolutely necessary. the elements of the theory of chiroptical vibrational spectra and methods enabling solvent simulations are provided in the subsequent subchapter. We report on experimental methods, techniques and tricks for measuring and simulating the vCd and RoA spectra in water at different ph levels. the review is concluded by listing the not-yet-measured amino acids, a presentation of the main challenges for computational methods, and suggestions for the most promising experimental techniques that may be used in future studies. Keywords

show abstract

“…Raman spectra, but the bisignate nature of RoA spectra needs to be taken into account in order to correctly identify the direction of intensity change. Recently, Pazderka and Kopecky have combined 2dCos with principal components analysis (PCA) in order to reduce noise and baseline distortions prior to generation of the 2d contour maps [94]. the ability of 2dCos RoA to reveal new structural information was shown by Ashton et al in their study on α-helix unfolding in the model homopolypeptide poly-L-glutamic acid [95], which distinguished between fraying of the ends of helices and unfolding of the core helical structure.…”

Section: Two-dimensional Correlation Analysismentioning

confidence: 99%