Binding properties of cucurbit[7]uril to neutral and protonated amino acids: A theoretical study

We systematically investigate the binding nature of cucurbit[7] (CB[7]) toward 20 amino acids in both neutral (AAs) and protonated (AAs(+)) states using quantum chemistry methods. The result indicates that, among AAs, Arg and Asn show the largest binding strength to CB[7], and for AAs(+), Gln(+)and Asn(+)bind to CB[7] the strongest. The binding strength of protonated CB[7]/AA(+)is much stronger than that of neutral CB[7]/AA counterpart due to the introduction of ion-dipole interaction and the increase in number and strength of hydrogen bonds. Energy decomposition analysis indicates that electrostatic interactions play major roles in both CB[7]/AAs and CB[7]/AAs(+)complexes. Moreover, we analyzed the dependence of binding strength on single AA volume and dipole moment. This study is beneficial for providing valuable information in predicting the recognition sites for a sequence-based peptide or protein by CB[7] and rationally designing a synthetic host molecule for specific peptide or protein recognition.

Automated summary

Through quantum chemistry methods, this study systematically investigates the binding nature of CB[7] with 20 amino acids in different states, revealing that protonated CB[7]/AA(+) has stronger binding strength than neutral CB[7]/AA due to the introduction of ion-dipole interaction. Electrostatic interactions play a significant role in both CB[7] / AAs and CB[7] / AAs(+) complexes. Additionally, the study analyzes the dependence of binding strength on the volume and dipole moment of single amino acids, providing valuable information for predicting recognition sites and designing synthetic host molecules for specific peptide or protein recognition.