Energetic contribution to both acidity and conformational stability in peptide models. (18th April 2016)

• Record Type: Journal Article
• Authors: Kubyshkin, Vladimir; Durkin, Patrick; Budisa, Nediljko
• Is Part Of: New journal of chemistry. Volume 40:Number 6(2016:Jun.)
• Page Start: 5209
• Page End: 5220
• Publication Date: 2016-04-18
• Subjects: Chemistry -- Periodicals; Chimie -- Périodiques; 540
• DOI: 10.1039/c5nj03611a
• Languages: English
• ISSNs: 1144-0546

Abstract

Abstract : The acidity difference of the amide rotamers has been revised for a large set of N -acetyl amino acids. Abstract : The acidity of N -acyl amino acids is dependent upon the rotameric state of the amide bond. In this work we systematically investigated the acidity difference of the rotamers (Δp K a ) in the frames of various acetylated amino acids. Our results indicated a mutual interaction of two carbonyl groups of an attractive type. We observed conservative Δp K a s for acyclic amino acids (2.2–3.0 kJ mol −1 ), whereas in the case of alicyclic amino acids, the experimental values revealed a strong dependency on the structural context (1.5–4.4 kJ mol −1 ). In homologous amino acids (α-, β-, γ-, etc. ), the strength of the attraction decays in an exponential fashion. Furthermore, the interaction can accumulate through a chain of amide bonds in a cascade fashion, as demonstrated by an Ac-Pro-Pro dipeptide. As a result, we demonstrate that Δp K a is an experimental parameter to estimate increments in the carbonyl–carbonyl alignment, as determined by the amino acid or peptidyl context. This parameter is also important in understanding the roles of amino acids in both protein folding and translation in biological systems as well as their evolutionary appearance in the genetic code.