Raghuvansh Kishore

Intramolecular CH···O Hydrogen-bond mediated stabilization of a Cis-DPro imide-bond in a stereocontrolled heterochiral model peptide†

The X-ray diffraction analysis of a stereocontrolled heterochiral designed model peptide Boc-(D) Pro-Thr-OMe (1) revealed the existence of an unusual folded molecular structure, stabilized via an effective unconventional C---H…O type intramolecular hydrogen-bond, encompassing a noncovalent 12-membered ring-motif. Together with an uncommon type a disposition of the urethane moiety, the tightly folded topology is compounded with a cis-(D) Pro imide-bond. The overall conformation is suggested to be the reminiscent of specific type VI β-turn structures, hitherto, characterized across the Aaa-cis-Pro peptide-bonds in globular proteins and polypeptides. The (13) C NMR spectrum of 1 in an apolar CDCl(3) environment revealed the presence of approximately an equal population of cis and trans isomers unexpectedly, analogous to Pro side-chain, the (13) C NMR chemical-shifts of Thr C(β) -resonance is observed to be sensitive toward cis-trans isomerization. In conjunction with solid-state FT-IR spectral data, we established that a network of complex intermolecular hydrogen-bonds stabilize a self-complementary noncovalent helical hexagonal self-assembly and crystallographic supramolecular aggregate. The results incline us to highlight that the stabilization of cis-(D) Pro peptide-bond in crystalline state may be driven by the favorable energy of formation of an unconventional weak C---H…O intramolecular hydrogen-bond.

Isostructural unbranched alkyl-chains as tools for stabilizing β-turn structure

To investigate the structural role played by isostructural unbranched alkyl-chains on the conformational ensemble and stability of β-turn structures, the conformational properties of a designed model peptide: Plm-Pro-Gly-Pda (1, Plm: H3 C-(CH2)14-CONH-; Pda: -CONH- (CH2 )14 -CH3) have been examined and compared with the parent peptide: Boc-Pro-Gly-NHMe (2, Boc: tert-butoxycarbonyl; NHMe: N-methylamide). The characteristic (13)C NMR chemical-shifts of the Pro C(β) and C(γ) resonances ascertained the incidence of an all-trans peptide-bond in low polarity deuterochloroform solution. Using FTIR and (1) H NMR spectroscopy, we establish that apolar alkyl-chains flanking a β-turn promoting Pro-Gly sequence impart definite incremental stability to the well-defined hydrogen-bonded structure. The assessment of (1)H NMR derived thermodynamic parameters of the hydrogen-bonded amide-NHs via variable temperature indicate that much weaker hydrophobic interactions do contribute to the stability of folded reverse turn structures. The far-UV CD spectral patterns of 1 and 2 in 2,2,2-trifluoroethanol are consistent with Pro-Gly specific type II β-turn structure, concomitantly substantiate that the flanking alkyl-chains induce substantial bias in enhanced β-turn populations. In view of structural as well as functional importance of the Pro-Gly mediated secondary structures, besides biochemical and biological significance of proteins lipidation via myristoylation or palmytoilation, we highlight potential convenience of the unbranched Plm and Pda moieities not only as main-chain N- and C-terminal protecting groups but also to mimic and stabilize specific isolated secondary and supersecondary structural components frequently observed in proteins and polypeptides.

ω-Turn: a novel β-turn mimic in globular proteins stabilized by main-chain to side-chain C−H···O interaction.

Mimicry of structural motifs is a common feature in proteins. The 10‐membered hydrogen‐bonded ring involving the main‐chain CO in a β‐turn can be formed using a side‐chain carbonyl group leading to Asx‐turn. We show that the NH component of hydrogen bond can be replaced by a Cγ‐H group in the side chain, culminating in a nonconventional CH···O interaction. Because of its shape this β‐turn mimic is designated as ω‐turn, which is found to occur ∼three times per 100 residues. Three residues (i to i + 2) constitute the turn with the CH···O interaction occurring between the terminal residues, constraining the torsion angles ϕi + 1, ψi + 1, ϕi + 2 and χ′1(i + 2) (using the interacting Cγ atom). Based on these angles there are two types of ω‐turns, each of which can be further divided into two groups. Cβ‐branched side‐chains, and Met and Gln have high propensities to occur at i + 2; for the last two residues the carbonyl oxygen may participate in an additional interaction involving the S and amino group, respectively. With Cys occupying the i + 1 position, such turns are found in the metal‐binding sites. N‐linked glycosylation occurs at the consensus pattern Asn‐Xaa‐Ser/Thr; with Thr at i + 2, the sequence can adopt the secondary structure of a ω‐turn, which may be the recognition site for protein modification. Location between two β‐strands is the most common occurrence in protein tertiary structure, and being generally exposed ω‐turn may constitute the antigenic determinant site. It is a stable scaffold and may be used in protein engineering and peptide design. Proteins 2015; 83:203–214.

A novel secondary structure based on fused five-membered rings motif

An analysis of protein structures indicates the existence of a novel, fused five-membered rings motif, comprising of two residues (i and i + 1), stabilized by interresidue Ni+1–H∙∙∙Ni and intraresidue Ni+1–H∙∙∙O=Ci+1 hydrogen bonds. Fused-rings geometry is the common thread running through many commonly occurring motifs, such as β-turn, β-bulge, Asx-turn, Ser/Thr-turn, Schellman motif, and points to its structural robustness. A location close to the beginning of a β-strand is rather common for the motif. Devoid of side chain, Gly seems to be a key player in this motif, occurring at i, for which the backbone torsion angles cluster at ~(−90°, −10°) and (70°, 20°). The fused-rings structures, distant from each other in sequence, can hydrogen bond with each other, and the two segments aligned to each other in a parallel fashion, give rise to a novel secondary structure, topi, which is quite common in proteins, distinct from two major secondary structures, α-helix and β-sheet. Majority of the peptide segments making topi are identified as aggregation-prone and the residues tend to be conserved among homologous proteins.

Determination of an unusual secondary structural element in the immunostimulating tetrapeptide rigin in aqueous environments: insights via MD simulations, 1H NMR and CD spectroscopic studies

An immunomodulating tetrapeptide, rigin (H‐Gly‐Gln‐Pro‐Arg‐OH), has been examined for its secondary structure preferences through combined use of high‐temperature unrestrained MD simulations in implicit water and 1D and 2D 1H NMR spectroscopy. The distribution of backbone torsion angles revealed the predominance of trans conformers across the Xaa‐Pro peptide bond. The results of MD simulations revealed that of the five predicted families A–E, the predominant families, family A (92 structures), family C (63 structures) and family D (31 structures), could be complemented by extensive 1D and 2D 1H NMR parameters acquired in aqueous PBS solution. A survey of specific inter‐ and intraresidue NOEs substantiated the predominance of an unusual type VII β‐turn structure, defined by two torsion angles, i.e. ψGln ∼ 155° and ϕPro ∼ − 65° across the Gln‐Pro segment. The proposed semi‐folded kinked topology precluded formation of any intramolecular interaction, i.e. hydrogen bond or electrostatic interaction. Far‐UV CD spectral characteristics of rigin in aqueous PBS solution and non‐aqueous structure‐promoting organic solvents, TFE and TMP, revealed its strong solvent dependence. However, in aqueous PBS solution, the presence of a weak negative shoulder at

Unusual Folding Propensity of an Unsubstituted β,γ‐Hybrid Model Peptide: Importance of the CH⋅⋅⋅O Intramolecular Hydrogen Bond

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Collateral Existence of Folded and Extended Conformations of the β-Ala Moiety in a Model Peptide

nm could be ascribed to a small population with ordered, semi‐folded topology. We propose that the plausible structural attributes may be exploited for design and rigidification of the bioactive conformation of this immunomodulator toward improved immunopharmacological properties. Copyright