Determination of peptide conformation via vibrational coupling: Application to diastereoisomeric alanyl dipeptides

Abstract

SynopsisSolution-phase Raman spectra of diastereomeric alanyl dipeptides, BAla-L-Ala and L-Ala-L-Ala, and various mono-and dideuterated isotopomers in H, O and D,O, are reported. Spectral differences between the diastereomeric forms are interpreted, using the Raman analog of the coupled oscillator model, in terms of geometric differences between certain vibrations in the diastereomeric forms. Application of the coupledoscillator formalism allows the determination of a dihedral angle between the coupling vibrations. The results are compared with vibrational coupling employed by other workers in the determination of the vibrational spectra of peptides.

Vibrational Circular Dichroism Spectra of Proteins in the Amide III Region: Measurement and Correlation of Bandshape to Secondary Structure

“…We have used the typical average secondary structure composition (FC) for this initial test and have not tried to address segment prediction (44). There are good physical reasons to think that amide III is a relatively local probe of stereochemistry, due to its very low dipole strength limiting the magnitude of long-range coupling effects and to its established mixing with C-H modes (37). Thus, extension of amide III data to questions beyond secondary structure seems premature at this time.…”

“…Furthermore, Diem and co-workers have shown that, for model pep-described in detail elsewhere (40, 41). In distinction from our usual optical setup, a grating blazed at 9 mm tides, the amide III vibrational coordinate is mixed with at least the C a -H deformations (37). Such mixing with 100 grooves/mm, a slit width of 8 mm (Ç12 cm 01 resolution at 1250 cm 01 ), and an appropriate long will disperse the dipole and rotational strength originating from the true amide III mode over a broader wavelength pass optical filter were used to optimize throughput in the amide III region.…”

Transfer of molecular property tensors in cartesian coordinates: A new algorithm for simulation of vibrational spectra

“…This affects the apparent splitting and intensity distribution in the VCD, in particular, for what would be the amide I and II bands. More severely affected is the amide III region which is known to be affected by 31 NH C H mixing. Because these model calcu-␣ lations are effectively for glycyl oligomers having two ␣ Hs per residue, it is difficult to relate such calculations to experimental observations.…”

“…As a consequence, the ␣ CH groups give rise to scissoring modes 2 at ; 1450 cm y1 that affect amide II yet would not normally be seen in typical peptides, and also to CH rocking and wagging modes that are consid-2 erably different from the normal proteinic amino acid tertiary C H deformations known to inter-␣ act with the amide III modes. 31 As a last example of parameter transfer the best heptapeptide force field was also used to generate a ''complete set'' of the most common vibrational Ž spectra, including ROA and Raman Fig. 6a and b, .…”

Vibrational analysis of various isotopomers of L‐Alanyl‐L‐Alanine in aqueous solution: Vibrational absorption, vibrational circular dichroism, Raman, and Raman optical activity spectra

“…[13] and Figures 1 and 2 of Ref. [12]. Here, again the isotopic data is available, and one can observe experimentally the couplings between the amide mode and methine modes by isotopically changing the masses and hence the couplings.…”