Raman spectroscopy of uncomplexed valinomycin. I. The solid state

Im, Asher; Kj, Rothschild; Anastassakis, E.; He, Stanley

doi:10.1021/ja00449a002

Cited by 22 publications

(9 citation statements)

References 10 publications

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“…3) and normal mode displacements, we could assign most of the observed Raman and ROA bands (Tables S1 in the ESI)w, which mostly corresponds to earlier assignments. 17,18 The region below 400 cm À1 , for example is dominated by soft modes, such as methyl torsions, skeletal deformations, and breathing of the peptide. The sharp ROA peak at 879 cm À1 (Raman at 874 cm À1 ) of free valinomycin which becomes weaker in the complex stems from delocalized CC stretch and carbonyl carbon out of plane deviation.…”

Section: Resultsmentioning

confidence: 99%

“…For smaller dipeptides, the conformer populations obtained by ROA were shown to be equivalent to those obtained by NMR spectroscopy. 14 The valinomycin structure including its complexes was also studied by other methods, including, for example, unpolarized Raman spectroscopy, [15][16][17] infrared absorption (IR), 18 optical rotatory dispersion (ORD), 7 and electronic and vibrational circular dichroism (ECD, VCD). 3,19 In particular, the VCD technique provides important knowledge about the peptide backbone, but the side chain VCD signal is too weak.…”

Section: Introductionmentioning

confidence: 99%

“…3,19 In particular, the VCD technique provides important knowledge about the peptide backbone, but the side chain VCD signal is too weak. 17 The valinomycin molecule can adopt different shapes. If crystallized from non-polar solvents, all six NH groups of the amide bonds are involved in intermolecular hydrogen bonding.…”

Section: Introductionmentioning

confidence: 99%

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Formation and structure of the potassium complex of valinomycin in solution studied by Raman optical activity spectroscopy

Yamamoto

Straka

Watarai

et al. 2010

Phys. Chem. Chem. Phys.

100

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The formation and structure of the potassium complex with valinomycin in solution were studied by means of Raman and Raman optical activity (ROA) spectroscopy. The complexation caused significant spectral changes, particularly in the region 1200-1400 cm(-1). The experimental spectra were interpreted using first principles computations. A complete computational conformational search combined with the spectral analysis revealed the arrangement of the isopropyl side chains in the complex. From a total of 6579 unique conformers two predominant ones were confirmed in the solution by ROA. A third one was predicted theoretically, but its population in the experiment could be estimated only roughly. The most populated conformer does not exhibit C(3) symmetry, and is different from that present in the crystal and the NMR-derived structure. Molecular dynamics techniques were used to estimate the molecular flexibility and its effect on the spectra. Density functional computations and Cartesian coordinate transfer (CCT) techniques provided the ROA and Raman spectral shapes and intensities well comparable with the experiment. The polar solvent (methanol) environment modeled with a polarizable continuum model (PCM) leads to rather minor changes in the conformer populations and vibrational properties as compared to vacuum computations, due to the hydrophobic character of the complex. Additional computational experiments suggest that the vibrational interactions determining the ROA spectra are quite local, which contributes to the good spatial resolution of the method. A reduction of the noise in the experimental spectra as well as increased precision of the simulations is desirable for the further exploration of the potential of the ROA spectroscopy for biomolecular studies in the future.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Formation and structure of the potassium complex of valinomycin in solution studied by Raman optical activity spectroscopy

Yamamoto

Straka

Watarai

et al. 2010

Phys. Chem. Chem. Phys.

100

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“…Therefore, attempts were made to determine the structure of valinomycin in solution phase using different experimental techniques such as infrared vibrational absorption, 6 -9 electronic circular dichroism (ECD), 8 NMR, 6 -10 Raman spectroscopy, [11][12][13][14] and ultrasonic absorption. 8,9 Most of these techniques, unlike x-ray diffraction, however, do not yield structural information at atomic resolution and instead provide evidence for one or more conformations that are dominant in solution.…”

Section: Introductionmentioning

confidence: 99%

A study of the conformations of valinomycin in solution phase

2004

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Vibrational absorption and vibrational circular dichroism (VCD) spectra of valinomycin are measured, in different solvents, in the ester and amide carbonyl stretching regions. The influence of cations, namely Li(+), Na(+), K(+), and Cs(+), in methanol-d(4) solvent is also investigated. Ab initio quantum mechanical calculations using density functional theory and 6-31G* basis set are used to predict the absorption and VCD spectra. A bracelet-type structure for valinomycin that reproduces the experimental absorption and VCD spectra in inert solvents is identified. For the structure of valinomycin in polar solvents, a propeller-type structure was optimized, but further investigations are required to confirm this structure. A symmetric octahedral environment for the ester carbonyl groups in the valinomycin-K(+) complex is supported by the experimental VCD spectra. The results obtained in the present study demonstrate that even for large macrocyclic peptides, such as valinomycin, VCD can be used as an independent structural tool for the study of conformations in solution.

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“…In a series of experiments that also involved Irv Asher, then a postdoctoral research at MIT, the amide I and ester carbonyl frequencies of uncomplexed and cation complexed VM under different conditions was studied [8,9,195,196,212]. We deduced from these measurements that there existed two conformations, closed and open, of VM depending on whether the molecule was in a hydrophobic or hydrophilic environments, helping to explain the mechanism of cation release when VM was located at the membrane surface.…”

Section: Initial Studies Of Model Ion Carriers and Channelsmentioning

confidence: 99%

The early development and application of FTIR difference spectroscopy to membrane proteins: A personal perspective

Rothschild

2016

BSI

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Abstract. Membrane proteins facilitate some of the most important cellular processes including energy conversion, ion transport and signal transduction. While conventional infrared absorption provides information about membrane protein secondary structure, a major challenge is to develop a dynamic picture of the functioning of membrane proteins at the molecular level. The introduction of FTIR difference spectroscopy around 1980 to study structural changes in membrane proteins along with a number of associated techniques including protein isotope labeling, site-directed mutagenesis, polarization dichroism, attenuated total reflection and time-resolved spectroscopy have led to significant progress towards this goal. It is now possible to routinely detect conformational changes of individual amino acid residues, backbone peptides, binding ligands, chromophores and even internal water molecules under physiological conditions with time-resolution down to nanoseconds. The advent of ultrafast pulsed-IR lasers has pushed this time-resolution down to femtoseconds. The early development of FTIR difference spectroscopy as applied to membrane proteins with special focus on bacteriorhodopsin is reviewed from a personal perspective.

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Raman spectroscopy of uncomplexed valinomycin. I. The solid state

Cited by 22 publications

References 10 publications

Formation and structure of the potassium complex of valinomycin in solution studied by Raman optical activity spectroscopy

Formation and structure of the potassium complex of valinomycin in solution studied by Raman optical activity spectroscopy

A study of the conformations of valinomycin in solution phase

The early development and application of FTIR difference spectroscopy to membrane proteins: A personal perspective

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