In proteins, proline-aromatic sequences exhibit increased frequencies of cis-proline amide bonds, via proposed C–H/π interactions between the aromatic ring and either the proline ring or the backbone C–Hα of the residue prior to proline. These interactions would be expected to result in tryptophan, as the most electron-rich aromatic residue, exhibiting the highest frequency of cis-proline. However, prior results from bioinformatics studies on proteins and experiments on proline-aromatic sequences in peptides have not revealed a clear correlation between the properties of the aromatic ring and the population of cis-proline. An investigation of the effects of aromatic residue (aromatic ring properties) on the conformation of proline-aromatic sequences was conducted using three distinct approaches: (1) NMR spectroscopy in model peptides of the sequence Ac-TGPAr-NH2 (Ar = encoded and unnatural aromatic amino acids); (2) bioinformatics analysis of structures in proline-aromatic sequences in the PDB; and (3) computational investigation using DFT and MP2 methods on models of proline-aromatic sequences and interactions. C–H/π and hydrophobic interactions were observed to stabilize local structures in both the trans-proline and cis-proline conformations, with both proline amide conformations exhibiting C–H/π interactions between the aromatic ring and Hα of the residue prior to proline (Hα-trans-Pro-aromatic and Hα-cis-Pro-aromatic interactions) and/or with the proline ring (trans-ProH-aromatic and cis-ProH-aromatic interactions). These C–H/π interactions were strongest with tryptophan (Trp) and weakest with cationic histidine (HisH+). Aromatic interactions with histidine were modulated in strength by His ionization state. Proline-aromatic sequences were associated with specific conformational poses, including type I and type VI β-turns. C–H/π interactions at the pre-proline Hα, which were stronger than interactions at Pro, stabilize normally less favorable conformations, including the ζ or αL conformations at the pre-proline residue, cis-proline, and/or the g+ χ1 rotamer or αL conformation at the aromatic residue. These results indicate that proline-aromatic sequences, especially Pro-Trp sequences, are loci to nucleate turns, helices, loops, and other local structures in proteins. These results also suggest that mutations that introduce proline-aromatic sequences, such as the R406W mutation that is associated with protein misfolding and aggregation in the microtubule-binding protein tau, might result in substantial induced structure, particularly in intrinsically disordered regions of proteins.
This content will become publicly available on May 7, 2025
- PAR ID:
- 10566253
- Publisher / Repository:
- ACS
- Date Published:
- Journal Name:
- Biochemistry
- Volume:
- 63
- Issue:
- 9
- ISSN:
- 0006-2960
- Page Range / eLocation ID:
- 1131 to 1146
- Subject(s) / Keyword(s):
- proline cis-trans isomerism NMR spectroscopy 19F NMR polyproline II helix
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Tau misfolding, oligomerization, and aggregation are central to the pathology of Alzheimer's disease (AD), chronic traumatic encephalopathy (CTE), frontotemporal dementia, and other tauopathies. Increased phosphorylation of tau is associated with conformational changes that are not fully understood. Moreover, tau oligomerization and aggregation are associated with proline cis-trans isomerism, with the phosphorylation-dependent prolyl isomerase Pin1 reducing tau hyperphosphorylation and aggregation. The FTDP-17 tau mutation R406W is frequently used in animal models of Alzheimer's disease, due to earlier onset of the AD phenotype. Despite its extensive application, the mechanisms by which tau-R406W leads to enhanced aggregation and neurotoxicity are poorly understood. Peptides derived from the tau C-terminal domain were examined by NMR spectroscopy as a function of residue 406 identity (Arg versus Trp) and Ser404 phosphorylation state. The R406W modification led to an increased population of Pro405 cis amide bond, which is stabilized by cis-proline-aromatic C–H/π interactions. Ser404 phosphorylation also resulted in an increase in cis amide bond, via a proposed C–H/O interaction between the Pro Hα and the phosphate that stabilizes the cis conformation. An analogous C–H/O interaction was observed in Glu-cis-Pro sequences in the PDB, and is proposed to be the basis of the increased propensity for cis amide bonds in Glu-Pro sequences. The higher activation barriers for proline cis-trans isomerization observed at pSer-Pro and pThr-Pro sequences are proposed to be due to both (a) an intraresidue phosphate-amide bond that stabilizes the trans-proline conformation and (b) the cis-stabilizing proline-phosphate C–H/O interaction identified herein. The combination of both pSer404 and R406W resulted in a further increase in the population of cis amide bond. In contrast to expectations, the R406W modification led to increased dephosphorylation of either pSer404 or pSer409 by PP2A, and had no effect on phosphorylation of Ser404 by cdk5, suggesting that R406W does not inherently increase Ser404 phosphorylation via changes in the actions of these enzymes. Modestly increased phosphorylation of Ser404 was observed by GSK-3β in tau R406W. Collectively, these data suggest a potential role for conformational change to a cis amide bond at Pro405, via Ser404 phosphorylation and/or R406W modification, as a possible mechanism involved in protein misfolding in AD, CTE, and FTDP-17. Alternatively, both Ser404 phosphorylation and the R406W modification lead to increased order, including induced turn formation, in both the trans-proline and cis-proline conformations.
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n→π* interactions between consecutive carbonyls stabilize the α-helix and polyproline II helix (PPII) conformations in proteins. n→π* interactions have been suggested to provide significant conformational biases to the disordered states of proteins. To understand the roles of solvation on the strength of n→π* interactions, computational investigations were conducted on a model n→π* interaction, the twisted-parallel-offset formaldehyde dimer, as a function of explicit solvation of the donor and acceptor carbonyls, using water and HF. In addition, the effects of urea, thiourea, guanidinium, and monovalent cations on n→π* interaction strength were examined. Solvation of the acceptor carbonyl significantly strengthens the n→π* interaction, while solvation of the donor carbonyl only modestly weakens the n→π* interaction. The n→π* interaction strength was maximized with two solvent molecules on the acceptor carbonyl. Urea stabilized the n→π* interaction via simultaneous engagement of both oxygen lone pairs on the acceptor carbonyl. Solvent effects were further investigated in the model peptides Ac-Pro-NMe 2 , Ac-Ala-NMe 2 , and Ac-Pro 2 -NMe 2 . Solvent effects in peptides were similar to those in the formaldehyde dimer, with solvation of the acceptor carbonyl increasing n→π* interaction strength and resulting in more compact conformations, in both the proline endo and exo ring puckers, as well as a reduction in the energy difference between these ring puckers. Carbonyl solvation leads to an energetic preference for PPII over both the α-helix and β/extended conformations, consistent with experimental data that protic solvents and protein denaturants both promote PPII. Solvation of the acceptor carbonyl weakens the intraresidue C5 hydrogen bond that stabilizes the β conformation.more » « less
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