Nonionic and zwitterionic forms of glycylglycylarginine as a part of spider silk protein: Spectroscopic and theoretical study

• IR & Raman spectra of glycylglycylarginine (GGR) part of spider silk were measured.
• Conformational analyses were made for neutral and zwitterion forms of GGR.
• The most stable conformers of gas & aqueous phases were determined for both forms.
• Vibrational, NBO, HOMO–LUMO and H-bonding analyses were performed.
• 310-helix structures of nonionic & zwitterionic GGR were optimized and compared.

Glycylglycylarginine as a part of GGX motif of spider silk spidroin in nonionic (non-GGR) and zwitterionic (zwt-GGR) forms have been examined from theoretical and spectroscopic aspects. The most stable conformational isomers of non-GGR and zwt-GGR were obtained through relaxed scan using the DFT/B3LYP with 6-31G(d) basis set. Nonionic and zwitterionic forms of 310-helix structures of GGR have also been calculated and compared with the most stable conformers obtained as a result of conformer analysis of isolated three peptide structures. This comparison should give an idea about the stability contribution of intermolecular interactions between the 310-helix structured peptide chains. O3LYP and B3PW91 hybrid functionals beside B3LYP have also been used for further calculations of geometry optimization, vibrational analysis, Natural Bond Orbital (NBO) analysis, HOMO–LUMO analysis and hydrogen bonding analysis. Normal Mode Analysis was carried through Potential Energy Distribution (PED) calculations by means of VEDA4 program package. IR and Raman spectra of GGR have also been used to relate the spectroscopic data obtained to electronic and structural features.

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