Conformation of a residue substituted fragment (349-364) of human lactoferrin protein in DMSO-d₆ by ¹H NMR and restrained molecular dynamics

Abstract

The 16mer peptide AVGEQELRGCNQWSGL is the Lys9Gly substitution analogue of 349-364 fragment of human lactoferrin (HLf). Interestingly, this HLf (349-364) fragment shows 68.75% sequence identity with the corresponding sequence in porcine lactoferrin (PLf), 50% with camel lactoferrin (ULf) and other lactoferrins coming in between the above two. From the available crystal structure data, the 349-364 sequence stretch was found to adopt a right-handed ⍺-helical structure. The three-dimensional structure of the analogue in dimethyl sulphoxide-d₆ (DMSO-d₆) at 25°C was determined using two-dimensional (2D) nuclear magnetic resonance (NMR) spectroscopy. 2D correlation experiments (DQF-COSY, TOCSY and NOESY) enabled the complete sequence-specific assignment of all the 1H resonances. The solution structure derived from the combined use of NMR data and restrained molecular dynamics indicated that the sequence stretch from Gln5 to Gln12 formed a right-handed ⍺-helix. Experimental structure showed good superposition with the reported local structure of the complete protein, excepting the terminal residues. This observation led to the conclusion that while designing active peptides with strong structural implication from larger proteins, importance may be given to the flanking regions of the relevant sequence