Structural Details of a Fowl Feather Elucidated by Using Polarized Raman Microspectroscopy

Yokote, Yoshiko; Kubo, Yoshiko; Takahashi, R.; Ikeda, Teruki; Akahane, Kiso; Tsuboi, Masamichi

doi:10.1246/bcsj.80.1148

Cited by 10 publications

(10 citation statements)

References 40 publications

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“…The calculated α bb /α cc value (0.59) is similar to the widely used value reported by Tsuboi et al. of 0.54 70. In general, the above calculated A and E 1 mode Raman polarizability tensors of an α-helix closely match the experimentally measured values reported in the literature, which were determined with polarized Raman experiments on well-aligned α-helical samples.…”

Section: Orientation Determination Of An α-Helixsupporting

confidence: 89%

Orientation Determination of Protein Helical Secondary Structures Using Linear and Nonlinear Vibrational Spectroscopy

et al. 2009

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In this paper, we systematically presented the orientation determination of protein helical secondary structures using vibrational spectroscopic methods, particularly the nonlinear Sum Frequency Generation (SFG) vibrational spectroscopy, along with linear vibrational spectroscopic techniques such as infrared spectroscopy and Raman scattering. SFG amide I signals can be collected using different polarization combinations of the input laser beams and output signal beam to measure the second order nonlinear optical susceptibility components of the helical amide I modes, which are related to their molecular hyperpolarizability elements through the orientation distribution of these helices. The molecular hyperpolarizability elements of amide I modes of a helix can be calculated based on the infrared transition dipole moment and Raman polarizability tensor of the helix; these quantities are determined by using the bond additivity model to sum over the individual infrared dipole transition moments and Raman polarizability tensors, respectively, of the peptide units (or the amino acid residues). The computed overall infrared transition dipole moment and Raman polarizability tensor of a helix can be validated by experimental data using polarized infrared and polarized Raman spectroscopy on samples with well-aligned helical structures. From the deduced SFG hyperpolarizability elements and measured SFG second order nonlinear susceptibility components, orientation information regarding helical structures can be determined. Even though such orientation information can also be measured using polarized infrared or polarized Raman amide I signals, SFG has a much lower detection limit, which can be used to study the orientation of a helix when its surface coverage is much lower than a monolayer. In addition, the combination of different vibrational spectroscopic techniques, e.g., SFG and Attenuated Total Reflectance – Fourier Transform Infrared spectroscopy, provides more measured parameters for orientation determination, aiding in the deduction of more complicated orientation distributions. In this paper, we discussed two types of helices: the α-helix and 3–10 helix. However, the orientation determination method presented here is general, and thus can be applied to study other helices as well. The calculations of SFG amide I hyperpolarizability components for α-helical and 3–10 helical structures with different chain lengths have also been performed. It was found that when the helices reach a certain length, the number of peptide units in the helix should not alter the data analysis substantially. It was shown in the calculation, however, that when the helix chain is short, the SFG hyperpolarizability component ratios can vary substantially when the chain length is changed. Because 3–10 helical structures can be quite short in proteins, the orientation determination for a short 3–10 helix needs to take into account the number of peptide units in the helix.

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Section: Orientation Determination Of An α-Helixsupporting

confidence: 89%

Orientation Determination of Protein Helical Secondary Structures Using Linear and Nonlinear Vibrational Spectroscopy

et al. 2009

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“…In this case, the Raman spectrum www.interscience.wiley.com/journal/jrs exhibits bands in the regions 3100-2600 cm −1 (NH 2 stretch), [29 -33] 1665-1585 cm −1 (C O stretch, Amide I), [44 -52] 1605-1555 cm −1 (NH 3 + asymmetrical deformation, Amide II), [44] 1530-1490 cm −1 (CH 2 torsion and bending, NH 3 + symmetrical deformation), [32 -46] and 1340-1315 cm −1 (CH deformation). [15,32] In the zwitterionic form, contributions from both the ionised (carboxylate) and the non-ionised carboxylic group are expected.…”

Section: Solid State Raman Spectra Of E951mentioning

confidence: 99%

“…The position of the Raman bands for N-H and C O functions served to indicate the degree of intramolecular hydrogen bonding between the terminal carboxyl and amino groups, and the peptide bond and aliphatic carbon chain. The band at 3339 cm −1 , assigned to the symmetrical NH 2 and N-H stretching vibrations and the medium peak at 1666 cm −1 , attributed to the Amide I (C O) mode are characteristic of a peptide bond exhibiting only intramolecular [41] ;δ(C2H 2 ) [29,32,45,46,50] ;Amide I [67] 1666 m 1673 B,C 1658 1655 1651 1663 ms 1667 m υ as (CC Ph ,C4O) [33,41] ;δ(N20H);Amide I [29,42 -50] ;δ as (NH 3 + ) [32] 1652 sh 1603 m/s 1649 C 1645 1648 1644 1604 s 1603 ms υ(C C) [41,44,48,67] ;υ as (COO − ) [47,50,67] ;υ(Phe) [42] ;δ(NH 3 + ) [32] 1584 w/m 1555 1638 1633 1624 1585 m 1586 w δ(N20H,C5H,C6H 2 );Amide II [15,32,42,45 -47] 1549 vw 1535 C 1545 1545 1540 1563 w 1558 sh τ (CH 2 ) [32] ;δ(NH) [44,67] ;NH 2 sciss [44,67] [42,47,48,67] ;δ(C-O-H) [44] 1427 w δ(CH 2 ) [ [42,43,67] 1265 sh ω(C2H 2 ,C6H 2 ,C5H) [32] ;Amide III [42,43,67] C 1230 w υ(C-N) [32] 1216 sh 1217 B 1216 1221 1215 1210 sh 1217 sh υ(C-O) [32] 1205 sh Amide III …”

Section: Solid State Raman Spectra Of E951mentioning

confidence: 99%

Identification and characterisation of the E951 artificial food sweetener by vibrational spectroscopy and theoretical modelling

Peica¹

2009

J Raman Spectroscopy

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Aspartame (E951), a very well-known dipeptide sweetener, approximately 150-200 times sweeter than sugar, is widely used in a variety of applications, especially in soft drinks. A drawback of E951 is its relatively low stability at high pH values and at high temperatures, thereby limiting its use. The changes observed in the very strong bands from the 1600-1300 cm −1 spectral region, characteristic to the υ(CO) mode coupled with the NH bending mode, allows to establish the species present in the Raman and SERS solutions at different concentrations and pH values. More exactly, a molecule protonation at the amino group was detected on going from basic to acidic pH values. The DFT calculated geometry, harmonic vibrational modes and Raman scattering activities of E951 were in good agreement with the experimental data and helped establish its SERS behaviour on silver surfaces. According to the DFT calculations performed, E951 can give rise to an intramolecular hydrogen bonding network, with lengths in the same range as the hydrogen bonds in the peptide unit moieties.

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“…10) contain complex amide I and amide III features. 41) In addition to the main peaks at 1664 and 1243 cm −1 , satellite bands are observed at 1672, 1651 and 1258 cm −1 . The satellite bands are assignable to unordered polypeptide chains and β -turns.…”

Section: Raman Tensors In Structural Studies Of Biomaterialsmentioning

confidence: 93%

“…The tensor components r 1 = α xx / α zz and r 2 = α yy / α zz are denoted by blue and red numerals, respectively. References to the original literature, where details of the tensor calculations are described, are as follows: (A) Ueda et al ; 9) (B) Benevides et al ; 16) (C) Tsuboi et al ; 3),47) (D1) Benevides et al ; 44) (D2) Thomas et al ; 10) (E1) Ushizawa et al ; 14) (E2) Benevides et al ; 44) (F1) Tsuboi et al ; 3) (F2) Tsuboi et al ; 3) (G1) Overman et al ; 25) (G2) Tsuboi et al ; 57) (G3) Yokote et al ; 41) (G4) Yokote et al ; 41) (H1)(H2)(H3) Tsuboi et al ; 8) (I1)(I2)(I3) Tsuboi et al ; 15) (J1) Thomas et al ; 10) (J2) Benevides et al ; 16) (K1)(K2) Benevides et al ; 44) (L1) Thomas et al ; 10) (L2)(L3) Tsuboi et al ; 12) (L4) Kumakura et al ; 49) (M1) Thomas et al ; 10) (M2) Benevides et al ; 44) (M3) Ushizawa et al ; 46) (N1) Ueda et al ; 51) (N2) Benevides et al ; 44) (N3) Ushizawa et al ; 55) (O1) Thomas et al ; 10) (O2)(O3)(O4) Benevides et al ; 16) (O5)(O6) Benevides et al 44) …”

Section: A Catalog Of Raman Tensorsunclassified

Raman Tensors and their application in structural studies of biological systems

Tsuboi

Benevides

Thomas

2009

Proc. Jpn. Acad., Ser. B

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The Raman scattering of a molecule is generated by interactions of its electrons with incident light. The electric vector of the Raman scattered light is related to the electric vector of the incident light through a characteristic Raman tensor. A unique Raman tensor exists for each Raman-active molecular vibrational mode. In the case of biologically important macromolecules Raman tensors have been determined for a few hundred vibrational Raman bands. These include proteins and their amino acid constituents, as well as nucleic acids (DNA and RNA) and their nucleotide constituents. In this review Raman tensors for 39 representative vibrational Raman bands of biological molecules are considered. We present details of the Raman tensor determinations and discuss their application in structural studies of filamentous bacteriophages (fd, Pf1, Pf3 and PH75), fowl feather rachis and eyespots of the protists, Chlamydomonas and Euglena.

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Structural Details of a Fowl Feather Elucidated by Using Polarized Raman Microspectroscopy

Cited by 10 publications

References 40 publications

Orientation Determination of Protein Helical Secondary Structures Using Linear and Nonlinear Vibrational Spectroscopy

Orientation Determination of Protein Helical Secondary Structures Using Linear and Nonlinear Vibrational Spectroscopy

Identification and characterisation of the E951 artificial food sweetener by vibrational spectroscopy and theoretical modelling

Raman Tensors and their application in structural studies of biological systems

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