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Integrated In Silico-In Vitro Identification and Optimization of Bone Morphogenic Protein-2 Armpit Epitope as Its Antagonist Binding Site

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Abstract

Bone morphogenic protein-2 (BMP-2) is the most documented member of BMP family and plays a crucial role in bone formation and growth. In this study, we systematically analyze and compare the complex crystal structures and interaction properties of BMP-2 with its cognate receptors BMPR-I/BMPR-II and with its natural antagonist crossveinless-2 (CV-2) using an integrated in silico-in vitro strategy. It is found that the antagonist-binding site is not fully overlapped with the two receptor-binding sites on BMP-2 surface; the antagonist can competitively disrupt BMP-2–BMPR-II interaction using a blocking-out-of-site manner, but has no substantial influence on BMP-2–BMPR-I interaction. Here, the antagonist-binding site is assigned as a new functional epitope armpit to differ from the traditional conformational epitope wrist and linear epitope knuckle at receptor-binding sites. Structural analysis reveals that the armpit comprises three sequentially discontinuous, structurally vicinal peptide segments, separately corresponding to a loop region and two β-strands crawling on the protein surface. The three segments cannot work independently when splitting from the protein context, but can restore binding capability to CV-2 if they are connected to a single peptide. A systematic combination of different-length polyglycine linkers between these segments obtains a series of designed single peptides, from which several peptides that can potently interact with the armpit-recognition site of CV-2 with high affinity and specificity are identified using energetic analysis and fluorescence assay; they are expected to target BMP-2–CV-2 interaction in a self-inhibitory manner.

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Acknowledgements

This work was supported by the YCH funds.

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Author notes

  1. Yan** Wu and Guanghong Jia contributed equally to this work.

Authors and Affiliations

  1. Department of Joint and Traumatic Orthopedics, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China

    Yan** Wu, Zhaode Jiao & Yinghua Sun

  2. Department of Pediatrics, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China

    Guanghong Jia & Haiyan Chi

Authors
  1. Yan** Wu
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  2. Guanghong Jia
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  3. Haiyan Chi
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  4. Zhaode Jiao
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  5. Yinghua Sun
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Correspondence to Yinghua Sun.

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Wu, Y., Jia, G., Chi, H. et al. Integrated In Silico-In Vitro Identification and Optimization of Bone Morphogenic Protein-2 Armpit Epitope as Its Antagonist Binding Site. Protein J 39, 703–710 (2020). https://doi.org/10.1007/s10930-020-09937-6

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  • DOI: https://doi.org/10.1007/s10930-020-09937-6

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