Abstract
Using low-wavenumber Raman spectroscopy in combination with theoretical calculations via solid-state density functional theory (DFT)-D3, we studied the vibrational structures and interaction with solvent of poly-l-proline and the oligoproline P12 series. The P12 series includes P12, the positively charged amino acid residue (arginine and lysine) N-terminus proline oligomers RP11 and KP11, and the C-terminus P11R and P11K. We assigned the spring-type phonon mode to 74–76 cm−1 bands for the PPI and PPII conformers and the carbonyl group ring-opening mode 122 cm−1 in the PPI conformer of poly-l-proline. Amide I and II were assigned based on the results of mode analysis for O, N, and C atom displacements. The broad band feature of the H-bond transverse mode in the Raman spectra indicates that the positively charged proline oligomers PPII form H-bonds with water in the solid phase, whereas P12 is relatively more hydrophobic. In propanol, the PPI conformer of the P12 series forms less H-bond network with the solvent. The PPII conformer exhibits a distinct Raman band at 310 cm−1, whereas the PPI has bands at 365, 660, and 960 cm−1 with reasonable intensity that can be used to quantitatively determine these two conformational forms. The 365 cm−1 mode comprising the motion of a C Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> O group turning to the helix axis was used to monitor the isomerization reaction PPI ↔ PPII. In pure propanol, RP11 and KP11 were found to have mostly PPI present, but P11R and P11K preferred PPII. After adding 20% water, the PPI in P11R and P11K was completely converted to PPII, whereas a small fraction of PPI remained in RP11 and KP11. The substituted positively charged amino acid affected the balance of the PPI/PPII population ratio.
Highlights
Proline is the only cyclic proteinogenic amino acid with a secondary amine forming the peptide bond, and the cyclic side chain provides proline with exceptional rigidity
We obtained one kind of polyproline II (PPII) solid having broad powder X-ray diffraction (PXRD) peaks centered at 2q 1⁄4 12.6, 17.5, and 21.9 (Fig. 1e)
Our results show that the intensity of the Raman 365 cmÀ1 band provides a convenient means to identify the trans and cis conformers of polyprolines and to study the isomerization reaction
Summary
PPII is a dominant conformation in collagen and in elements of the folded and unfolded proteins. Collision cross section distributions of P13 [M + 2H]2+ ions obtained at different transition times indicated the presence of two major conformers, identi ed as the PPI and PPII helices, and six conformers that appeared as subpopulations of polyproline They suggested that prolines sequentially ip from cis to trans starting from the N-terminus.[1,29,30]. Water bridges are networks of water molecules that link nearby hydrogen bond acceptors and/or donors on proteins.[3,31,32,33,34,35] The characteristic ring of polyproline precludes the nitrogen atom of the prolyl bond from engaging in hydrogen bonding This feature affects the structure of the helices and the interaction with solvents. The low-wavenumber Raman spectra reveal the H-bond information in both solid crystalline packing and solutions
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