A structural role for tryptophan in proteins, and the ubiquitous Trp C^δ1—H...O=C (backbone) hydrogen bond

Abstract

Tryptophan is the most prominent amino acid found in proteins, with multiple functional roles. Its side chain is made up of the hydrophobic indole moiety, with two groups that act as donors in hydrogen bonds: the Nɛ—H group, which is a potent donor in canonical hydrogen bonds, and a polarized Cδ1—H group, which is capable of forming weaker, noncanonical hydrogen bonds. Due to adjacent electron-withdrawing moieties, C—H...O hydrogen bonds are ubiquitous in macromolecules, albeit contingent on the polarization of the donor C—H group. Consequently, Cα—H groups (adjacent to the carbonyl and amino groups of flanking peptide bonds), as well as the Cɛ1—H and Cδ2—H groups of histidines (adjacent to imidazole N atoms), are known to serve as donors in hydrogen bonds, for example stabilizing parallel and antiparallel β-sheets. However, the nature and the functional role of interactions involving the Cδ1—H group of the indole ring of tryptophan are not well characterized. Here, data mining of high-resolution (r ≤ 1.5 Å) crystal structures from the Protein Data Bank was performed and ubiquitous close contacts between the Cδ1—H groups of tryptophan and a range of electronegative acceptors were identified, specifically main-chain carbonyl O atoms immediately upstream and downstream in the polypeptide chain. The stereochemical analysis shows that most of the interactions bear all of the hallmarks of proper hydrogen bonds. At the same time, their cohesive nature is confirmed by quantum-chemical calculations, which reveal interaction energies of 1.5–3.0 kcal mol−1, depending on the specific stereochemistry.

Differing Effects of Nonlinearity around the Proton Acceptor on CH··O and NH··O H-Bond Strength within Proteins

“…Examples include serine hydrolases, where the active site His is anchored via Cε1-H group to a main-chain carbonyl group 36 and various secondary structure motifs formed by Trp residues. 37 There is a generally held view that a AH••O�C H-bond has a natural preference for a particular geometric configuration. Specifically, the AH••O atoms tend toward a fully linear alignment, commonly referred to as a linear H-bond.…”

“…Stabilization of specific conformers often involves side-chain to main-chain H-bonds, in which peptide carbonyl atoms serve as acceptor groups. Examples include serine hydrolases, where the active site His is anchored via Cε1-H group to a main-chain carbonyl group and various secondary structure motifs formed by Trp residues …”