Computational Insights into the Charge Relaying Properties of β‐Turn Peptides in Protein Charge Transfers

Abstract

Density functional theory calculations suggest that β-turn peptide segments can act as a novel dual-relay elements to facilitate long-range charge hopping transport in proteins, with the N terminus relaying electron hopping transfer and the C terminus relaying hole hopping migration. The electron- or hole-binding ability of such a β-turn is subject to the conformations of oligopeptides and lengths of its linking strands. On the one hand, strand extension at the C-terminal end of a β-turn considerably enhances the electron-binding of the β-turn N terminus, due to its unique electropositivity in the macro-dipole, but does not enhance hole-forming of the β-turn C terminus because of competition from other sites within the β-strand. On the other hand, strand extension at the N terminal end of the β-turn greatly enhances hole-binding of the β-turn C terminus, due to its distinct electronegativity in the macro-dipole, but does not considerably enhance electron-binding ability of the N terminus because of the shared responsibility of other sites in the β-strand. Thus, in the β-hairpin structures, electron- or hole-binding abilities of both termini of the β-turn motif degenerate compared with those of the two hook structures, due to the decreased macro-dipole polarity caused by the extending the two terminal strands. In general, the high polarity of a macro-dipole always plays a principal role in determining charge-relay properties through modifying the components and energies of the highest occupied and lowest unoccupied molecular orbitals of the β-turn motif, whereas local dipoles with low polarity only play a cooperative assisting role. Further exploration is needed to identify other factors that influence relay properties in these protein motifs.

An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain

“…Like the 53 SGGS 56 motif, 53 TGGT 56 in COVA2-39 takes part in a type I b-turn along with V H Y52, which is the first residue (i) in the turn (YTGG). The partial positive dipole from the aligned, up-pointing amides on one face of the b-turn (Sheridan and Allen, 1980;Zhang et al, 2015) forms an electrostatic interaction with the side-chain carboxyl of RBD E484. In addition, V H R71 hydrogen bonds to the 53 TGGT 56 motif and may have a role in stabilizing the interaction between the 53 TGGT 56 motif and RBD E484 (Figure 3D).…”

Electronic Structure of Hole-Conducting States in Polyprolines

“…The efficiency of the first group to serve as stepping stones is due to their low oxidation or reduction potentials, respectively. − Methionine on the other hand can only serve as a hole stepping stone if the oxidized sulfur lone pair is stabilized by a nearby aromatic or amide moiety. − It was also shown that, even in the absence of the above-mentioned side groups, the backbones of α- and 3 10 -helices or β-turns can serve as relay stations. In the case of these structures, a large dipole moment decreases the oxidation potential especially at the C-termini of such structures. ,− …”

Solvated electrons in the complex media: a review

“…Figure27 The schematic plot of dual relay function of β-turn peptide (a) and the dynamics changes of relevant properties (b)[95,96] (color online).…”