Advertisement

Grafting, Stripping and Stapling of Helical Peptides from the Dimerization Interface of ONFH-Related Bone Morphogenetic Protein-2

  • Wenqi Song
  • Kunzheng WangEmail author
  • Wei Wang
  • Pei Yang
  • Xiaoqian Dang
Article
  • 31 Downloads

Abstract

Transforming growth factor-β/bone morphogenetic protein (TGF-β/BMP) signaling plays a fundamental role in embryonic skeletal development and postnatal bone homeostasis. The signaling pivot protein BMP-2 belongs to the TGF-β superfamily and has been implicated in the pathogenesis of osteonecrosis of femoral head (ONFH). The biologically functional BMP-2 is a homodimer that has two tightly packed cores at its dimerization interface; each core is defined by the intermolecular interaction between a helical arm from one monomer and a hydrophobic pocket from another monomer. Inhibition and disruption of BMP-2 dimerization have been recognized as an attractive therapeutic strategy against ONFH. Here, we investigate the self-binding behavior of helical arm-derived peptides to the BMP-2 dimerization interface. The native BMP-2 helical arm and its several grafted versions from BMP-4, BMP-6 and BMP-7 are stripped from the intact dimerization interface to generate a number of isolated helical peptides. Computational simulations demonstrate that the stripping does not substantially influence the direct intermolecular interaction between BMP-2 monomer and these helical peptides or desolvation effect upon the interaction. However, the C-terminus of stripped peptides is found to have an intrinsic disorder and large flexibility in the isolated state, which would impair the rebinding of stripped peptides to BMP-2. Next, we rationally design a hydrocarbon bridge across the C-terminal residues 65 and 69 of helical peptides, which can effectively constrain peptide conformational flexibility in the isolated state, thus considerably promoting the binding potency of stripped helical peptides. Circular dichroism (CD) spectroscopy reveals that the peptide helicity increases from 51.8 to 67.9% upon hydrocarbon stapling. Fluorescence polarization assays substantiate that, as designed, the stapling can convert these helical peptides from weak binders to moderate or good binders of BMP-2 protein; their Kd values are improved by up to ~ fourfold.

Keywords

Bone morphogenetic protein-2 Helical peptide Peptide-mediated protein–protein interaction Hydrocarbon stapling Osteonecrosis of femoral head 

Notes

Funding

This work was supported by the National Natural Science Foundation of China (No. 81371962).

Compliance with Ethical Standards

Conflict of interest

The author declares that they have no conflict of interest.

References

  1. 1.
    Chen G, Deng C, Li YP (2012) TGF-β and BMP signaling in osteoblast differentiation and bone formation. Int J Biol Sci 8:272–288CrossRefGoogle Scholar
  2. 2.
    Wu M, Chen G, Li YP (2016) TGF-β and BMP signaling in osteoblast, skeletal development, and bone formation, homeostasis and disease. Bone Res 4:16009CrossRefGoogle Scholar
  3. 3.
    Hogan BL (1996) Bone morphogenetic proteins: multifunctional regulators of vertebrate development. Genes Dev 10:1580–1594CrossRefGoogle Scholar
  4. 4.
    Sykaras N, Opperman LA (2003) Bone morphogenetic proteins (BMPs): how do they function and what can they offer the clinician? J Oral Sci 45:57–73CrossRefGoogle Scholar
  5. 5.
    Chen D, Zhao M, Mundy GR (2004) Bone morphogenetic proteins. Growth Factors 22:233–241CrossRefGoogle Scholar
  6. 6.
    Wang C, Zang H, Zhou D (2018) Bone morphogenetic protein-2 exhibits therapeutic benefits for osteonecrosis of the femoral head through induction of cartilage and bone cells. Exp Ther Med 15:4298–4308PubMedPubMedCentralGoogle Scholar
  7. 7.
    Vandermeer JS, Kamiya N, Aya-ay J, Garces A, Browne R, Kim HK (2011) Local administration of ibandronate and bone morphogenetic protein-2 after ischemic osteonecrosis of the immature femoral head: a combined therapy that stimulates bone formation and decreases femoral head deformity. J Bone Joint Surg Am 93:905–913CrossRefGoogle Scholar
  8. 8.
    Sun W, Li Z, Gao F, Shi Z, Zhang Q, Guo W (2004) Recombinant human bone morphogenetic protein-2 in debridement and impacted bone graft for the treatment of femoral head osteonecrosis. PLoS ONE 9:e100424CrossRefGoogle Scholar
  9. 9.
    Israel DI, Nove J, Kerns KM, Moutsatsos IK, Kaufman RJ (1992) Expression and characterization of bone morphogenetic protein-2 in Chinese hamster ovary cells. Growth Factors 7:139–150CrossRefGoogle Scholar
  10. 10.
    Ruppert R, Hoffmann E, Sebald W (1996) Human bone morphogenetic protein 2 contains a heparin-binding site which modifies its biological activity. Eur J Biochem 237:295–302CrossRefGoogle Scholar
  11. 11.
    Valera E, Isaacs MJ, Kawakami Y, Izpisúa Belmonte JC, Choe S (2010) BMP-2/6 heterodimer is more effective than BMP-2 or BMP-6 homodimers as inductor of differentiation of human embryonic stem cells. PLoS ONE 5:e11167CrossRefGoogle Scholar
  12. 12.
    Morimoto T, Kaito T, Matsuo Y, Sugiura T, Kashii M, Makino T, Iwasaki M, Yoshikawa H (2015) The bone morphogenetic protein-2/7 heterodimer is a stronger inducer of bone regeneration than the individual homodimers in a rat spinal fusion model. Spine J 15:1379–1390CrossRefGoogle Scholar
  13. 13.
    Scheufler C, Sebald W, Hülsmeyer M (1999) Crystal structure of human bone morphogenetic protein-2 at 2.7 Å resolution. J Mol Biol 287:103–115CrossRefGoogle Scholar
  14. 14.
    Petsalaki E, Russell RB (2008) Peptide-mediated interactions in biological systems: new discoveries and applications. Curr Opin Biotechnol 19:344–350CrossRefGoogle Scholar
  15. 15.
    Zhou P, Hou S, Bai Z, Li Z, Wang H, Chen Z, Meng Y (2018) Disrupting the intramolecular interaction between proto-oncogene c-Src SH3 domain and its self-binding peptide PPII with rationally designed peptide ligands. Artif Cells Nanomed Biotechnol 46:1122–1131CrossRefGoogle Scholar
  16. 16.
    Zhu Z, Zhang C, Song W (2017) Rational derivation, extension, and cyclization of self-inhibitory peptides to target TGF-β/BMP signaling in ONFH. Amino Acids 49:283–290CrossRefGoogle Scholar
  17. 17.
    Zhou P, Wang C, Ren Y, Yang C, Tian F (2013) Computational peptidology: a new and promising approach to therapeutic peptide design. Curr Med Chem 20:1985–1996CrossRefGoogle Scholar
  18. 18.
    Zhou P, Yang C, Ren Y, Wang C, Tian F (2013) What are the ideal properties for functional food peptides with antihypertensive effect? A computational peptidology approach. Food Chem 141:2967–2973CrossRefGoogle Scholar
  19. 19.
    Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235–242CrossRefGoogle Scholar
  20. 20.
    Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935CrossRefGoogle Scholar
  21. 21.
    Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24:1999–2012CrossRefGoogle Scholar
  22. 22.
    Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668–1688CrossRefGoogle Scholar
  23. 23.
    Joseph TL, Lane DP, Verma CS (2012) Stapled BH3 peptides against MCL-1: mechanism and design using atomistic simulations. PLoS ONE 7:e43985CrossRefGoogle Scholar
  24. 24.
    Yang C, Wang C, Zhang S, Huang J, Zhou P (2015) Structural and energetic insights into the intermolecular interaction among human leukocyte antigens, clinical hypersensitive drugs and antigenic peptides. Mol Simul 41:741–751CrossRefGoogle Scholar
  25. 25.
    Yang C, Zhang S, He P, Wang C, Huang J, Zhou P (2015) Self-binding peptides: folding or binding. J Chem Inf Model 55:329–342CrossRefGoogle Scholar
  26. 26.
    Yang C, Zhang S, Bai Z, Hou S, Wu D, Huang J, Zhou P (2016) A two-step binding mechanism for the self-binding peptide recognition of target domains. Mol Biosyst 12:1201–1213CrossRefGoogle Scholar
  27. 27.
    Bai Z, Hou S, Zhang S, Li Z, Zhou P (2017) Targeting self-binding peptides as a novel strategy to regulate protein activity and function: a case study on the proto-oncogene tyrosine protein kinase c-Src. J Chem Inf Model 57:835–845CrossRefGoogle Scholar
  28. 28.
    Ryckaert JP, Ciccotti G, Berendsen HJC (1997) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327–341CrossRefGoogle Scholar
  29. 29.
    Darden T, York D, Pedersen L (1993) Particale mesh Ewald and N·log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092CrossRefGoogle Scholar
  30. 30.
    Homeyer N, Gohlke H (2012) Free energy calculations by the molecular mechanics Poisson-Boltzmann surface area method. Mol Inf 31:114–122CrossRefGoogle Scholar
  31. 31.
    Tian F, Lv Y, Zhou P, Yang L (2011) Characterization of PDZ domain-peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses. J Comput Aided Mol Des 25:947–958CrossRefGoogle Scholar
  32. 32.
    Tian F, Tan R, Guo T, Zhou P, Yang L (2013) Fast and reliable prediction of domain-peptide binding affinity using coarse-grained structure models. Biosystems 113:40–49CrossRefGoogle Scholar
  33. 33.
    Tian F, Yang C, Wang C, Guo T, Zhou P (2014) Mutatomics analysis of the systematic thermostability profile of Bacillus subtilis lipase A. J Mol Model 20:2257CrossRefGoogle Scholar
  34. 34.
    Phillips C, Roberts LR, Schade M, Bazin R, Bent A, Davies NL, Moore R, Pannifer AD, Pickford AR, Prior SH, Read CM, Scott A, Brown DG, Xu B, Irving SL (2011) Design and structure of stapled peptides binding to estrogen receptors. J Am Chem Soc 133:9696–9699CrossRefGoogle Scholar
  35. 35.
    Wu T, He P, Wu W, Chen Y, Lv F (2018) Targeting oncogenic transcriptional corepressor Nac1 POZ domain with conformationally constrained peptides by cyclization and stapling. Bioorg Chem 80:1–10CrossRefGoogle Scholar
  36. 36.
    Yano K, Hoshino M, Ohta Y, Manaka T, Naka Y, Imai Y, Sebald W, Takaoka K (2009) Osteoinductive capacity and heat stability of recombinant human bone morphogenetic protein-2 produced by Escherichia coli and dimerized by biochemical processing. J Bone Miner Metab 27:355–363CrossRefGoogle Scholar
  37. 37.
    Lichtenberger FJ, Montague C, Hunter M, Frambach G, Marsh CB (2006) NAC and DTT promote TGF-β1 monomer formation: demonstration of competitive binding. J Inflamm 3:7CrossRefGoogle Scholar
  38. 38.
    Chen YH, Yang JT, Chau KH (1974) Determination of the helix and beta form of proteins in aqueous solution by circular dichroism. Biochemistry 13:3350–3359CrossRefGoogle Scholar
  39. 39.
    Gopal R, Park JS, Seo CH, Park Y (2012) Applications of circular dichroism for structural analysis of gelatin and antimicrobial peptides. Int J Mol Sci 13:3229–3244CrossRefGoogle Scholar
  40. 40.
    Vallejo LF, Rinas U (2013) Folding and dimerization kinetics of bone morphogenetic protein-2, a member of the transforming growth factor-β family. FEBS J 280:83–92CrossRefGoogle Scholar
  41. 41.
    Luo H, Du T, Zhou P, Yang L, Mei H, Ng H, Zhang W, Shu M, Tong W, Shi L, Mendrick DL, Hong H (2015) Molecular docking to identify associations between drugs and class I human leukocyte antigens for predicting idiosyncratic drug reactions. Comb Chem High Throughput Screen 18:296–304CrossRefGoogle Scholar
  42. 42.
    Ren Y, Chen X, Feng M, Wang Q, Zhou P (2011) Gaussian process: a promising approach for the modeling and prediction of Peptide binding affinity to MHC proteins. Protein Pept Lett 18:670–678CrossRefGoogle Scholar
  43. 43.
    Kortemme T, Kim DE, Baker D (2004) Computational alanine scanning of protein–protein interfaces. Sci STKE 2004:pl2PubMedGoogle Scholar
  44. 44.
    Zhou P, Wang C, Tian F, Ren Y, Yang C, Huang J (2013) Biomacromolecular quantitative structure-activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein–protein binding affinity. J Comput Aided Mol Des 27:67–78CrossRefGoogle Scholar
  45. 45.
    Zhou P, Zhang S, Wang Y, Yang C, Huang J (2016) Structural modeling of HLA-B:1502 peptide carbamazepine T-cell receptor complex architecture: implication for the molecular mechanism of carbamazepine-induced Stevens–Johnson syndrome toxic epidermal necrolysis. J Biomol Struct Dyn 34:1806–1817CrossRefGoogle Scholar
  46. 46.
    Lavery K, Swain P, Falb D, Alaoui-Ismaili MH (2008) BMP-2/4 and BMP-6/7 differentially utilize cell surface receptors to induce osteoblastic differentiation of human bone marrow-derived mesenchymal stem cells. J Biol Chem 283:20948–20958CrossRefGoogle Scholar
  47. 47.
    UniProt C (2015) UniProt: a hub for protein information. Nucleic Acids Res 43:D204–D212CrossRefGoogle Scholar
  48. 48.
    Gouet P, Courcelle E, Stuart DI, Métoz F (1999) ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15:305–308CrossRefGoogle Scholar
  49. 49.
    Krivov GG, Shapovalov MV, Dunbrack RL (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins 77:778–795CrossRefGoogle Scholar
  50. 50.
    Yu H, Zhou P, Deng M, Shang Z (2014) Indirect readout in protein–peptide recognition: a different story from classical biomolecular recognition. J Chem Inf Model 54:2022–2032CrossRefGoogle Scholar
  51. 51.
    Walensky LD, Bird GH (2014) Hydrocarbon-stapled peptides: principles, practice, and progress. J Med Chem 57:6275–6288CrossRefGoogle Scholar
  52. 52.
    Greenfield NJ (2006) Using circular dichroism spectra to estimate protein secondary structure. Nat Protoc 1:2876–2890CrossRefGoogle Scholar
  53. 53.
    Dotyp H (1965) The ultraviolet circular dichroism of polypeptides. J Am Chem Soc 87:218–228CrossRefGoogle Scholar
  54. 54.
    Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637CrossRefGoogle Scholar
  55. 55.
    Zhou P, Tian F, Shang Z (2009) 2D depiction of nonbonding interactions for protein complexes. J Comput Chem 30:940–951CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Wenqi Song
    • 1
    • 2
  • Kunzheng Wang
    • 1
    Email author
  • Wei Wang
    • 1
  • Pei Yang
    • 1
  • Xiaoqian Dang
    • 1
  1. 1.Department of OrthopedicsThe Second Affiliated Hospital of Xi’an Jiao Tong UniversityXi’anChina
  2. 2.Department of OrthopedicsShanghai Jiao Tong University Affiliated Sixth People’s HospitalShanghaiChina

Personalised recommendations