The Role of Aromatic-Aromatic Interactions in Strand-Strand Stabilization of β-Sheets

Abstract

Aromatic-aromatic interactions have long been believed to play key roles in protein structure, folding, and binding functions. However, we still lack full understanding of the contributions of aromatic-aromatic interactions to protein stability and the timing of their formation during folding. Here, using an aromatic ladder in the β-barrel protein, cellular retinoic acid-binding protein 1 (CRABP1), as a case study, we find that aromatic π stacking plays a greater role in the Phe65-Phe71 cross-strand pair, while in another pair, Phe50-Phe65, hydrophobic interactions are dominant. The Phe65-Phe71 pair spans β-strands 4 and 5 in the β-barrel, which lack interstrand hydrogen bonding, and we speculate that it compensates energetically for the absence of strand-strand backbone interactions. Using perturbation analysis, we find that both aromatic-aromatic pairs form after the transition state for folding of CRABP1, thus playing a role in the final stabilization of the β-sheet rather than in its nucleation as had been earlier proposed. The aromatic interaction between strands 4 and 5 in CRABP1 is highly conserved in the intracellular lipid-binding protein (iLBP) family, and several lines of evidence combine to support a model wherein it acts to maintain barrel structure while allowing the dynamic opening that is necessary for ligand entry. Lastly, we carried out a bioinformatics analysis and found 51 examples of aromatic-aromatic interactions across non-hydrogen-bonded β-strands outside the iLBPs, arguing for the generality of the role played by this structural motif.

Keywords: ASA; COM; CRABP1; FABP; H-bond; HSQC; IFABP; ILBP; MD; MSA; PDB; Protein Data Bank; TS; WT; accessible surface area; cellular retinoic acid-binding protein 1; center of mass; dynamics; fatty acid-binding protein; folding; heteronuclear single quantum coherence; hydrogen bond; iLBP; ileal lipid-binding protein; intestinal fatty acid-binding protein; intracellular lipid-binding protein; molecular dynamics; multiple sequence alignment; transition state; wild type; β-barrel; π stacking.