Enhanced stability of <i>cis</i> Pro‐Pro peptide bond in Pro‐Pro‐Phe sequence motif

DasGupta, Bhaskar; Chakrabarti, Pinak; Basu, Gautam

doi:10.1016/j.febslet.2007.08.039

Cited by 30 publications

(54 citation statements)

References 27 publications

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“…1,6–8,20 Studies by Creighton and Basu indicated that cis-Pro-Aromatic interactions, primarily with H α ( i −2) of Gly or Pro two residues prior to Tyr/Trp/Phe, are enthalpically favorable and dependent on electronics of the aromatic residue. 10,11,20,22,23 Aromatic-Pro-aromatic sequences also exhibit a high propensity for cis amide bonds, with aromatic rings able to stack against both faces of the proline ring. 8 Interestingly, Dyson and Wright found that in SYPXDV peptides, the highest population of cis amide bonds was observed with Phe, rather than Tyr or Trp, at the X position.…”

Section: Local Aromatic-proline Interactionsmentioning

confidence: 99%

Aromatic–Proline Interactions: Electronically Tunable CH/π Interactions

2012

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CONSPECTUS Proline residues have unique roles in protein folding, structure, and function. Proline combined with the aromatic amino acids comprise the encoded cyclic protein residues. Aromatic protein side chains are defined by their negatively charged π faces, while the faces of the proline ring are partially positively charged. This polarity results from their two-point connection of the side chain to the electron-withdrawing protein backbone, and the lower electronegativity of hydrogen compared to carbon, nitrogen, and oxygen. The hydrogens adjacent to the carbonyl and amide nitrogen, Ha and Hδ, respectively, are the most partially positive. Proline’s side chain is also conformationally restricted, allowing for interaction with aromatic residues with minimal entropic or steric penalty. Proline and aromatic residues can interact favorably with each other, due to both the hydrophobic effect and the interaction between the π aromatic face and the polarized C-H bonds, called a CH/π interaction. Aromatic-proline interactions can occur locally, for example to stabilize cis-amide bonds, and over larger distances, in the tertiary structures of proteins, and intermolecularly in protein-protein interactions. In peptides and proteins, aromatic-proline sequences more readily adopt cis-prolyl amide bonds, where the aromatic ring interacts with the proline ring in the cis conformation. In aromatic-proline sequences, Trp and Tyr are more likely to induce cis-amide bonds than Phe, suggesting an aromatic electronic effect. This result would be expected for a CH/π interaction, in which a more electron-rich aromatic would have a stronger (more cis-stabilizing) interaction with partial positive charges on prolyl hydrogens. In this Account, we describe our investigations into the nature of local aromatic-proline interactions, using peptide models. We synthesized a series of 26 peptides, TXPN, varying X from electron-rich to electron poor aromatic amino acids, and found that the population of cis-amide bond (Ktrans/cis) is tunable by aromatic electronics. With 4-substituted phenylalanines, we observed a Hammett correlation between aromatic electronics and Ktrans/cis, with cis-trans isomerism electronically controllable by 1.0 kcal/mol. All aromatic residues exhibit a higher cis population than Ala or cyclohexylalanine, with Trp showing the strongest aromatic-proline interaction. In addition, proline stereoelectronic effects can modulate cis-trans isomerism by an additional 1.0 kcal/mol. The aromatic-proline interaction is enthalpic, consistent with its description as a CH/π interaction. Proline-aromatic sequences can also promote cis-prolyl bonds, either through interactions of the aromatic ring with the preceding cis-proline, or with the Hα prior to cis-proline. Within proline-rich peptides, sequences commonly found in natively disordered proteins, aromatic residues promote multiple cis-amide bonds due to multiple favorable aromatic-proline interactions. Collectively, we found aromatic-proline interactions to be significantly CH/...

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Section: Local Aromatic-proline Interactionsmentioning

confidence: 99%

Aromatic–Proline Interactions: Electronically Tunable CH/π Interactions

2012

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“…Moreover, the four cis-trans states also gave rise to multiple spin systems for the aliphatic protons of the proline residues. Although the peaks' assignment result was intricate, we could observe a proline Hα proton highly upfielded (3.77 ppm), likely due to the close proximity of the P3-F5 side chains, as found in some proteins and peptide containing the segment P-P-F, 12 which gives rise to the ring current effect on Hα protons of the first proline. Closely interacting P3-F5 side chains are supposed to be at the basis of the observed stability of the proline-proline cis conformers in the segment P-P-F, when present in a short peptide, devoid of any tertiary interaction.…”

Section: Resultsmentioning

confidence: 99%

“…Specifically, besides the consensus sequence Pro-Phe (P-F) present in common PPIase substrates, a second P was inserted before the P-F segment, as suggested by several other studies. 12 Moreover, a lysine (K6 in PP peptide or K8 in EPP peptide) was introduced in both sequences to improve the peptide solubility. A glutamic acid was inserted at the N-terminus of the EPP peptide (E1) to potentially stabilize the cis conformation of the X-Pro bond through a salt bridge with the K8 at the C-terminus.…”

Section: Resultsmentioning

confidence: 99%

FRET-Protease-Coupled Peptidyl-Prolyl cis-trans Isomerase Assay

et al. 2016

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In this work, a sensitive and convenient protease-based fluorimetric high-throughput screening (HTS) assay for determining peptidyl-prolyl cis-trans isomerase activity was developed. The assay was based on a new intramolecularly quenched substrate, whose fluorescence and structural properties were examined together with kinetic constants and the effects of solvents on its isomerization process. Pilot screens performed using the Library of Pharmacologically Active Compounds (LOPAC) and cyclophilin A (CypA), as isomerase model enzyme, indicated that the assay was robust for HTS, and that comparable results were obtained with a CypA inhibitor tested both manually and automatically. Moreover, a new compound that inhibits CypA activity with an IC 50 in the low micromolar range was identified. Molecular docking studies revealed that the molecule shows a notable shape complementarity with the catalytic pocket confirming the experimental observations. Due to its simplicity and precision in the determination of extent of inhibition and reaction rates required for kinetic analysis, this assay offers many advantages over other commonly used assays.

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“…The population of the cis-conformation was estimated to be 16.3% (from Phe beta protons; see inset to Figure 4A) and 17.2% (from Pro delta protons; data not shown). The two 3 J ab values for Phe were nonidentical (5.8 and 10.1 Hz) in the cis-Pro conformation (inset to Figure 4A) indicating restricted ring rotation, [21][22][23] as opposed to similar values of 3 J ab for the trans-Pro conformation (7.0 and 8.0 Hz) indicating free rotation of the Phe side chain.…”

Section: Nmr Studies On Designed Peptides With [Glu/gln]-pro-aro-xamentioning

confidence: 96%

“…Previous NMR studies from our laboratory, performed on a series of three‐residue peptides with the general sequence Xaa‐Pro‐Tyr showed that the cis Pro conformation is stabilized in the motif through CH ⋅⋅⋅ π interaction when Xaa = Ala, Gly, Pro, Tyr, Phe and Trp. Although the experimental result correlated well with trends observed in protein structural database, Xaa = Glu was an exception.…”

Section: Introductionmentioning

confidence: 98%

Type VIa β‐turn‐fused helix N‐termini: A novel helix N‐cap motif containing cis proline

et al. 2017

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Helix N-capping motifs often form hydrogen bonds with terminal amide groups which otherwise would be free. Also, without an amide hydrogen, proline (trans) is over-represented at helix N-termini (N1 position) because this naturally removes the need to hydrogen bond one terminal amide. However, the preference of cisPro, vis-à-vis helix N-termini, is not known. We show that cisPro (α or PP ) often appears at the N-cap position (N0) of helices. The N-cap cisPro(α ) is associated with a six-residue sequence motif - X -X -cisPro-X -X -X - with preference for Glu/Gln at X , Phe/Tyr/Trp at X and Ser/Thr at X . The motif, formed by the fusion of a helix and a type VIa β-turn, contains a hydrogen bond between the side chain of X and the side chain/backbone of X , a α-helical hydrogen bond between X and X and stacking interaction between cisPro and an aromatic residue at X . NMR experiments on peptides containing the motif and its variants showed that local interactions associated with the motif, as found in folded proteins, were not enough to significantly tilt the cis/trans equilibrium towards cisPro. This suggests that some other evolutionary pressure must select the cisPro motif (over transPro) at helix N-termini. Database analysis showed that >C = O of the pre-cisPro(α ) residue at the helix N-cap, directed opposite to the N→C helical axis, participates in long-range interactions. We hypothesize that the cisPro(α ) motif is preferred at helix N-termini because it allows the helix to participate in long-range interactions that may be structurally and functionally important.

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Enhanced stability of cis Pro‐Pro peptide bond in Pro‐Pro‐Phe sequence motif

Cited by 30 publications

References 27 publications

Aromatic–Proline Interactions: Electronically Tunable CH/π Interactions

Aromatic–Proline Interactions: Electronically Tunable CH/π Interactions

FRET-Protease-Coupled Peptidyl-Prolyl cis-trans Isomerase Assay

Type VIa β‐turn‐fused helix N‐termini: A novel helix N‐cap motif containing cis proline

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