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Evaluation of non-covalent interaction between Seryl-Histidine dipeptide and cyclophilin A using NMR and molecular modeling

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Abstract

Seryl-Histidine dipeptide (Ser-His) has been previously reported to be capable of cleaving DNAs and carboxyl esters, as well as proteins. The protein cleavage mechanism has not been addressed yet. As an initial step of protein cleavage activity, the non-covalent binding affinity of Ser-His for proteins is a crucial prerequisite. In this work, we took cyclophilin A (CyPA) as a substrate protein, and evaluated the non-covalent interaction between CyPA and Ser-His using a combination of NMR spectroscopy and molecular modeling approach. Two independent Ser-His binding sites on CyPA were detected using 15N-1H heteronuclear single-quantum coherence (HSQC) spectra. Each binding site binds one Ser-His molecule. Dissociation constants, K d1 and K d2, were estimated to be 2.07 and 6.66 mmol/L, respectively, indicative of the weak non-covalent interaction between Ser-His and CyPA. Based on molecular modeling results, we suggest that both the α-amino and the side chain hydroxyl group of Ser-His are crucial for the non-covalent interaction between Ser-His and CyPA. This work sheds light on the molecular mechanism of Ser-His and its analogues cleaving proteins.

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Authors and Affiliations

  1. Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China

    Yan Liu, XiaoXia Liu, MingKun Lin, DongHai Lin & YuFen Zhao

  2. Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 201203, China

    YanHong Shi & DongHai Lin

  3. Key Laboratory for Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, School of Life Sciences and Engineering, Tsinghua University, Beijing, 100084, China

    YuFen Zhao

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  1. Yan Liu
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  2. YanHong Shi
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  3. XiaoXia Liu
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  5. DongHai Lin
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Correspondence to DongHai Lin or YuFen Zhao.

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Liu, Y., Shi, Y., Liu, X. et al. Evaluation of non-covalent interaction between Seryl-Histidine dipeptide and cyclophilin A using NMR and molecular modeling. Sci. China Chem. 53, 1987–1993 (2010). https://doi.org/10.1007/s11426-010-3192-z

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  • DOI: https://doi.org/10.1007/s11426-010-3192-z

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