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Published on: December 19, 2020
Principles of Inter-Amino-Acid Recognition Revealed by Binding Energies between Homogeneous Oligopeptides
Huiwen Du1,2, Xiaoyu Hu3, Hongyang Duan1,2
1Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), National Center for Nanoscience and Technology, Beijing 100190, P. R. China.
Abstract:
We have determined the interaction strengths of the common naturally occurring amino acids using a complete binding affinity matrix of 20 × 20 pairs of homo-octapeptides consisting of the 20 common amino acids between stationary and mobile states. We used a bead-based fluorescence assay for these measurements. The results provide a basis for analyzing specificity, polymorphisms, and selectivity of inter-amino-acid interactions. Comparative analyses of the binding energies, i.e., the free energies of association (ΔG A), reveal contributions assignable to both main-chain-related and side-chain-related interactions originating from the chemical structures of these 20 common amino acids. Side-chain-side-chain and side-chain-main-chain interactions are found to be pronounced in an identified set of amino acid pairs that determine the basis of inter-amino-acid recognition.
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