Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL

Abstract

Protein–carbohydrate interactions are very often mediated by the stacking CH–π interactions involving the side chains of aromatic amino acids such as tryptophan (Trp), tyrosine (Tyr) or phenylalanine (Phe). Especially suitable for stacking is the Trp residue. Analysis of the PDB database shows Trp stacking for 265 carbohydrate or carbohydrate like ligands in 5 208 Trp containing motives. An appropriate model system to study such an interaction is the AAL lectin family where the stacking interactions play a crucial role and are thought to be a driving force for carbohydrate binding. In this study we present data showing a novel finding in the stacking interaction of the AAL Trp side chain with the carbohydrate. High resolution X-ray structure of the AAL lectin from Aleuria aurantia with α-methyl-l-fucoside ligand shows two possible Trp side chain conformations with the same occupation in electron density. The in silico data shows that the conformation of the Trp side chain does not influence the interaction energy despite the fact that each conformation creates interactions with different carbohydrate CH groups. Moreover, the PDB data search shows that the conformations are almost equally distributed across all Trp–carbohydrate complexes, which would suggest no substantial preference for one conformation over another.

The CH–π Interaction in Protein–Carbohydrate Binding: Bioinformatics and In Vitro Quantification

“…Whereas, with the Tyr and Phe residues, the majority of the complexes occupy quite a narrow area where the distance and angle range between 3.8–4.1 Å and 10–20° or 3.8–4.1 Å and 15–25° for Tyr and Phe, respectively, the Trp and His stacking complexes can be found in a wider area which ranges between 3.7–4.2 Å and 10–45°. The quite broad area of Trp stacking interaction also supports the previous observation of the possibility of the Trp side chain flipping in the stacking complex and the energetic equality of the flipped complexes …”

“…We attempt to understand in depth the role of stacking residues in each of the binding sites by modeling the mutants of each of them, replacing the stacking residue with either alanine, phenylalanine, or valine. The electrostatic interaction between the ligand and other polar residues remains the same as that of the wild type and has been discussed in our earlier paper . The main residues which participate in stabilizing the ligand in the binding pocket through H‐bonds are R24, E36, and W97 in site 1.…”

“…As was mentioned earlier, site 1 and site 4 of AAL contain tyrosine as a stacking residue whereas site 2, site 3, and site 5 have tryptophan in the crystal structure. The other interesting point to be noted in the AAL crystal structure is the presence of two flipped conformations of tryptophan stacking residues at sites 2, 3, and 5 . In addition to the polar moiety of αMeFuc, which participates in electrostatic interaction, a non‐polar face is created by the CH groups on the C3, C4, C5, and C6 carbon atoms (as labeled in Figure ) of the fucoside ring.…”

N-Linked Glycan Branching and Fucosylation Are Increased Directly in Hcc Tissue As Determined through in Situ Glycan Imaging

“…After incubation, slides were washed with TBS (pH 7.6) for 5 minutes in room temperature and repeated three times. Data on this lectin can be found in [36–38]. Finally, the slides were counterstained with Harris-modified hematoxylin (Fisher Scientific, Hampton, NH) for increased visualization.…”

Pick’s Tau Fibril Shows Multiple Distinct PET Probe Binding Sites: Insights from Computational Modelling

“…For example, in sites S7 and S8, PET probes bind to hydrophobic patches formed by sidechains of K347 and R349, respectively, via stacking interactions between hydrogen atoms of the amino-acid side chain and π electrons in the PET tracers ( Figure 3 ). The CH/π stacking interactions are a strong attractive molecular force occurring between a soft acid and a soft base and are frequently seen in protein–glycan complexes [ 32 , 33 , 34 ].…”