Variation of protein backbone amide resonance by electrostatic field (1512.05488v6)

Abstract: Amide resonance is found to be sensitive to electrostatic field with component parallel or antiparallel to the amide C-N bond, an effect we refer to here as EVPR-CN. EVPR-CN is linear and without threshold in the biologically plausible electrostatic field range -0.005 to 0.005 au. Variation of amide resonance varies Resonance-Assisted Hydrogen Bonding such as occurs in the hydrogen bonded chains of backbone amides of protein secondary structures such as beta sheets and alpha helices, varying the stability of these structures. The electrostatic properties including permittivity of amino acid residue sidegroups influence the electrostatic field component parallel or antiparallel to the C-N bond of each amide, giving a novel relationship between residue sequence and protein structure. Additionally, a backbone-based theory of protein folding which includes this effect is presented in Section 8.4. The significance of EVPR-CN relative to other factors in protein folding depends on field C-N component at each backbone amide at a given time. Calculation indicates that backbone amides do not occupy an intrinsically electrostatically-protected niche. We propose that EVPR-CN warrants investigation in any study of stable protein structure or protein folding pathway. EVPR-CN is somewhat associated with hydrophobia, since hydrophobia creates low permittivity environments. EVPR-CN is more directionally and hence structurally specific than hydrophobia. Hypotheses concerning the stability of beta sheets and amyloid fibrils and of protein complexation and molecular chaperone function are offered. An analogous effect in nitrogenous base pairing is proposed. EVPR-CN is energetically significant in biologically plausible electrostatic fields even without considering a hydrogen bonding context, and a hypothesis concerning the stability of polyproline helices types I and II is offered.