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ACS Cent Sci. 2019 Jan 23;5(1):97-108. doi: 10.1021/acscentsci.8b00723. Epub 2019 Jan 14.

Principles of Inter-Amino-Acid Recognition Revealed by Binding Energies between Homogeneous Oligopeptides.

Du H1,2, Hu X3, Duan H1,2, Yu L1,2, Qu F1,2, Huang Q1,2, Zheng W1,2, Xie H1,2, Peng J1,2, Tuo R4, Yu D4, Lin Y1,2, Li W1,2, Zheng Y1,2, Fang X1,2, Zou Y1,2, Wang H1,2, Wang M1,2, Weiss PS5, Yang Y1,2, Wang C1,6,2.

Author information

Key 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.
University of Chinese Academy of Sciences, Beijing 100049, P. R. China.
College of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China.
Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, P. R. China.
California NanoSystems Institute, Department of Chemistry and Biochemistry, and Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095-7227, United States.
CAS Center for Excellence in Brain Science, Chinese Academy of Sciences, Beijing 100101, P. R. China.


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.

Conflict of interest statement

The authors declare no competing financial interest.

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