Local Control of <i>cis</i>-Peptidyl–Prolyl Bonds Mediated by CH···π Interactions: The Xaa-Pro-Tyr Motif

Ganguly, Himal K.; Kaur, Hundeep; Basu, Gautam

doi:10.1021/bi4007918

Cited by 13 publications

(25 citation statements)

References 39 publications

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“…Immunoscreening of Peptides-Peptides corresponding to predicted B-cell epitopes were either chemically synthesized using an Endeavor 90-II peptide synthesizer (AAPTec, Louisville, KY) as described (44) or purchased from GL Biochem (Shanghai, China). For ELISA, 5 M each of synthetic peptides (P1-P5), rRhi o 1, HSA, and a random irrelevant oligopeptide were reconstituted in binding buffer (40 mM Na 2 CO 3 , 60 mM NaHCO 3 , 10 mM CaCl 2 , 10 mM DTT, pH 9.6) and separately coated on polystyrene plates.…”

Section: Methodsmentioning

confidence: 99%

Epitope Mapping of Rhi o 1 and Generation of a Hypoallergenic Variant

Sircar

Jana

Dasgupta³

et al. 2016

Journal of Biological Chemistry

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Section: Methodsmentioning

confidence: 99%

Epitope Mapping of Rhi o 1 and Generation of a Hypoallergenic Variant

Sircar

Jana

Dasgupta³

et al. 2016

Journal of Biological Chemistry

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“…Hα ( i – 2)- cis -proline–aromatic interactions may occur with the Hα of any residue two residues prior to ( i – 2 to) the aromatic residue but are most favorable with proline. 20 (c) Conformational heterogeneity in proline-rich sequences (PPFPP) due to multiple aromatic–proline interactions. Additional cis – trans isomerism is possible at other X-Pro sequences.…”

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confidence: 99%

Tunable Control of Polyproline Helix (PPII) Structure via Aromatic Electronic Effects: An Electronic Switch of Polyproline Helix

et al. 2014

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Aromatic rings exhibit defined interactions via the unique aromatic π face. Aromatic amino acids interact favorably with proline residues via both the hydrophobic effect and aromatic–proline interactions, C−H/π interactions between the aromatic π face and proline ring C–H bonds. The canonical aromatic amino acids Trp, Tyr, and Phe strongly disfavor a polyproline helix (PPII) when they are present in proline-rich sequences because of the large populations of cis amide bonds induced by favorable aromatic–proline interactions (aromatic–cis-proline and proline–cis-proline–aromatic interactions). We demonstrate the ability to tune polyproline helix conformation and cis–trans isomerism in proline-rich sequences using aromatic electronic effects. Electron-rich aromatic residues strongly disfavor polyproline helix and exhibit large populations of cis amide bonds, while electron-poor aromatic residues exhibit small populations of cis amide bonds and favor polyproline helix. 4-Aminophenylalanine is a pH-dependent electronic switch of polyproline helix, with cis amide bonds favored as the electron-donating amine, but trans amide bonds and polyproline helix preferred as the electron-withdrawing ammonium. Peptides with block proline–aromatic PPXPPXPPXPP sequences exhibited electronically switchable pH-dependent structures. Electron-poor aromatic amino acids provide special capabilities to integrate aromatic residues into polyproline helices and to serve as the basis of aromatic electronic switches to change structure.

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“…In this work we have focused on cis Pro present at helix N‐termini. As elaborated earlier, the origin of the work was laid out in a previous study on short peptides …”

Section: Discussionmentioning

confidence: 99%

“…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%

“…The motif Glu‐ cis Pro‐Aro, where Aro is an aromatic residue, appeared in proteins more than expected when compared with results obtained from the NMR‐derived cis / trans population of the isolated peptide. Preliminary analysis of protein structures showed that in some instances a helical segment followed the Glu‐ cis Pro motif where the Glu side chain formed a H‐bond with the side chain of Ser at (Glu + 4) position . Therefore, the discrepancy might have been caused by the use of short peptides, incapable of capturing medium range interactions observed in folded proteins.…”

Section: Introductionmentioning

confidence: 99%

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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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Local Control of cis-Peptidyl–Prolyl Bonds Mediated by CH···π Interactions: The Xaa-Pro-Tyr Motif

Cited by 13 publications

References 39 publications

Epitope Mapping of Rhi o 1 and Generation of a Hypoallergenic Variant

Epitope Mapping of Rhi o 1 and Generation of a Hypoallergenic Variant

Tunable Control of Polyproline Helix (PPII) Structure via Aromatic Electronic Effects: An Electronic Switch of Polyproline Helix

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

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