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

Abstract

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 beta-turn structure, defined by two torsion angles, i.e. psiGln approximately 155 degrees and psiPro approximately -65 degrees 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 approximately 234 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.

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

“…To our knowledge, there is no specific size threshold at which an oligopeptide sequence gains the capacity to be a bona fide protein, and reference annotation projects do not have minimal size criteria for protein sequences. Protein secondary structure is thought to be possible at approximately 14 amino acids (Imura et al, 2014) for alpha helices and potentially even less for other secondary structure formations (Kumar and Kishore, 2010), although it is known that some protein sequences are unstructured (Dyson et al, 2005). Even before the advent of Ribo-seq, small proteins had been well characterized in numerous organisms.…”