title: Envisaging Structural Insight of a Terminally Protected Proline Dipeptide by Raman Spectroscopy and Density Functional Theory Analyses.
abstract: The proline residue in a protein sequence generates constraints to its secondary structure as the associated torsion angles become a part of the heterocyclic ring. It becomes more significant when two consecutive proline residues link via amide linkage and produce additional configurational constraint to a protein's folding and stability. In the current manuscript we have illustrated conformation preference of a novel dipeptide, (R)-tert-butyl 2-((S)-2-(methoxycarbonyl)pyrrolidine-1-carbonyl)pyrrolidine-1-carboxylate. The dipeptide crystallized in the orthorhombic crystalline state and produced rod-shaped macroscopic material. The analysis of the crystal coordinates showed dihedral angles (φ, ψ) of the interlinked amide groups as (+72°, -147°) and the dihedral angles (φ, ψ) produced with the next carbonyl were (-68°, +151°), indicating polyglycine II (PGII) and polyproline II (PPII)-like helix states at the N- and C-terminals, respectively. These two states, PGII and PPII, are mirror image configurations and are expected to produce similar vibration bands from the associated carbonyl groups. However, the unique atomic arrangement in the molecule produces three carbonyl groups and one of them was very specific, being part of the main peptide linkage that connects both the pyrrolidine rings. The carbonyl group in the peptide bond exhibited a Raman vibration frequency at ∼1642 cm-1and is considered a signatory Raman marker band for the peptide bond linking two heterochiral proline residues. The carbonyl group (t-Boc) at the N-terminal of the peptide showed a characteristic vibration at ∼1685 cm-1and the C-terminal carbonyl group as a part of the ester showed a vibration signature at a significantly high frequency (1746 cm-1). Conformation analyses performed with density functional theory (DFT) calculations depicted that the dipeptide was stabilized in vacuum with dihedral angles (+72°, -154°) and (-72°, +151°) at the N- and C-terminals, respectively. Molecular dynamics (MD) simulation also showed that the peptide conformation having dihedral angles around (+75°, -150°) and (-75°, +150°) at the N- and C-terminals, respectively, was reasonably stable in water. Due to unique absence of the amide N-H, the peptide was ineffective in forming any intramolecular hydrogen bonding. MD investigation, however, revealed an intermolecular hydrogen bonding interaction with the water molecules, leading to its stability in aqueous solution. Metadynamics simulation analysis of the dipeptide in water also supported the PGII-PPII-like conformation at the N- and C-terminals, respectively, as the energetically stable conformation among the other possible combinations of conformations. The possible electronic transitions along with the HOMO-LUMO analysis further depicted the stability of the dipeptide in water and their possible absorption pattern. Time-dependent density functional theory (TDDFT) analysis showed strong negative rotatory strength of the dipeptide around 210 nm in water and acetonitrile, and it could be the source of experimentally observed high-amplitude negative absorption in the circular dichroism (CD) spectra around 200-203 nm. The very weak positive band (signature) in the region at ∼228 nm in CD spectra could also be correlated to the positive rotatory strength at 228 nm observed in ECD. To test the effect of such a dipeptide on a living cell, an MTT assay was performed and the result indicated no cytotoxic effect toward human hepatocellular carcinoma Hep G2 cancer cell lines.
authors.affiliation: Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology ; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India.
authors.forename: Supriya
authors.identifier: http://orcid.org/0000-0001-7800-6048
authors.initials: S
authors.lastname: Das
authors.affiliation: Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology ; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India.
authors.forename: Uttam
authors.identifier: http://orcid.org/0000-0003-2110-4610
authors.initials: U
authors.lastname: Pal
authors.affiliation: Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology ; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India.
authors.forename: Moumita
authors.initials: M
authors.lastname: Chatterjee
authors.affiliation: Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology ; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India.
authors.forename: Sumit Kumar
authors.initials: SK
authors.lastname: Pramanik
authors.affiliation: Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology ; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India.
authors.forename: Biswadip
authors.initials: B
authors.lastname: Banerji
authors.affiliation: Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology ; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India.
authors.forename: Nakul C
authors.identifier: http://orcid.org/0000-0002-8498-6502
authors.initials: NC
authors.lastname: Maiti
mesh_terms: D004151:Dipeptides / Q000737:chemistry*; D011392:Proline / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory; D013059:Spectrum Analysis, Raman
chemical_list: D004151:Dipeptides; D011392:Proline