Amino Acid Propensities for the Collagen Triple-Helix

Abstract

Determination of the tendencies of amino acids to form alpha-helical and beta-sheet structures has been important in clarifying stabilizing interactions, protein design, and the protein folding problem. In this study, we have determined for the first time a complete scale of amino acid propensities for another important protein motif: the collagen triple-helix conformation with its Gly-X-Y repeating sequence. Guest triplets of the form Gly-X-Hyp and Gly-Pro-Y are used to quantitate the conformational propensities of all 20 amino acids for the X and Y positions in the context of a (Gly-Pro-Hyp)(8) host peptide. The rankings for both the X and Y positions show the highly stabilizing nature of imino acids and the destabilizing effects of Gly and aromatic residues. Many residues show differing propensities in the X versus Y position, related to the nonequivalence of these positions in terms of interchain interactions and solvent exposure. The propensity of amino acids to adopt a polyproline II-like conformation plays a role in their triple-helix rankings, as shown by a moderate correlation of triple-helix propensity with frequency of occurrence in polyproline II-like regions. The high propensity of ionizable residues in the X position suggests the importance of interchain hydrogen bonding directly or through water to backbone carbonyls or hydroxyprolines. The low propensity of side chains with branching at the C(delta) in the Y position supports models suggesting these groups block solvent access to backbone C=O groups. These data provide a first step in defining sequence-dependent variations in local triple-helix stability and binding, and are important for a general understanding of side chain interactions in all proteins.

Novel amino acid substitution in the Y‐position of collagen type II causes spondyloepimetaphyseal dysplasia congenita

“…The studies of the triple helix indicate that the most stable residues in the Y-position are hydroxyproline and arginine, followed by methionine. The least stable groups include glycine, leucine, asparagine, tyrosine, phenylalanine, and tryptophan [Persikov et al, 2000]. The arginine to glycine replacement detected in our patients has an effect on intermolecular interactions in the triple-helix and may destabilize the folding.…”

“…The arginine to glycine replacement detected in our patients has an effect on intermolecular interactions in the triple-helix and may destabilize the folding. The unfavorable nature of glycine in the X and Ypositions contrasts with the requirement for glycine as every third residue in the collagen triple helix, where the unfavorable entropy must be overcome by hydrogen bonding and van der Waals interactions [Persikov et al, 2000].…”

How sequence defines structure: A crystallographic map of DNA structure and conformation

“…The question of how sequence determines structure has been attacked by nearly every conceivable experimental and theoretical approach. The effect of sequence on the structure-stability relationship in T4 lysozyme has been extensively studied by crystallographic and thermodynamic analyses (2), whereas the propensity of single amino acids to effect formation of isolated ␣-helices have been studied by using host-guest peptides (3,4). However, if the structures of all possible sequence combinations of a macromolecule are determined, then this problem is solved explicitly.…”

The Peptides Acetyl-(Gly-3(S)Hyp-4(R)Hyp)10-NH2 and Acetyl-(Gly-Pro-3(S)Hyp)10-NH2 Do Not Form a Collagen Triple Helix

“…We therefore synthesized the Gly-3(S)Hyp-4(R)Hyp as the guest peptide in the host-guest peptide system of Brodsky and colleagues (42). The guest tripeptide unit was inserted in the host sequence to produce the acetyl-(Gly-Pro-4(R)Hyp) 3 -(Gly-3(S)Hyp-4(R)Hyp)-(Gly-Pro-4(R)Hyp) 4 -Gly-Gly-NH 2 peptide.…”

“…The CD signal was monitored at 225 nm, and the fraction folded was calculated according to a reference (42). f, Ac-(Gly-Pro-4(R)Hyp) 3 -Gly-3(S)Hyp-4(R)Hyp-(Gly-Pro-4(R)Hyp) 4 -Gly-Gly-NH 2 ; OE, Ac-(Gly-Pro-4(R)Hyp) 3 -Gly-Pro-4(R)Hyp-(Gly-Pro-4(R)Hyp) 4 -Gly-Gly-NH 2 ; ᭜, Ac-(Gly-Pro-4(R)Hyp) 3 -Gly-Pro-3(S)Hyp-(Gly-Pro-4(R)Hyp) 4 -Gly-Gly-NH 2 ; q, Ac-(GlyPro-4(R)Hyp) 3 -Gly-Pro-Pro-(Gly-Pro-4(R)Hyp) 4 -Gly-Gly-NH 2 ; and , and Ac-(Gly-Pro-4(R)Hyp) 3 -Gly-4(R)Hyp-Pro-(Gly-Pro-4(R)Hyp) 4 Gly-Gly-NH 2 .…”