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Molecular Stapling of Human Pediatric RSV Phosphoprotein’s C-terminal Tail-Derived Peptides to Target the Coupled Folding-Upon-Binding Event Between Phosphoprotein and Nucleocapsid

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Abstract

Human respiratory syncytial virus (RSV) has been involved in human pediatric lower respiratory tract infections. The intermolecular interaction between RSV phosphoprotein (P) and nucleoprotein (N) plays a vital role in formation of the viral RNA polymerase, which is formed as a peptide-mediated interaction by binding the flexible C-terminal tail of P protein to the rigid globular domain of N protein. In this study, it is revealed that the free P’s C-terminal tail is intrinsically disordered in unbound state, but would fold into a well-structured helical conformation when binding to N protein, thus characterized by a so-called coupled folding-upon-binding process. The Phe241 residue at the end of P’s C-terminus is responsible for the recognition and binding of P protein to N protein, which serves as an anchor residue to root in the binding pocket of N protein and confers both stability and specificity to the N–P interaction. The C-terminal tail’s peptide segment of 9 amino acids long represents a P-peptide; its binding potency to N protein can be regarded as a compromise between favorable direct readout and unfavorable indirect readout. Here, we rationally designed molecular stapling to constrain the free P-peptide into a native-like conformation in unbound state, thus largely minimizing the unfavorable indirect readout effect upon its binding to N protein. Further biophysical characterizations substantiated that the binding affinities of two stapled P-peptide counterparts, namely hs[234,238]P-peptide and hs[235,239]P-peptide, were improved considerably upon the stapling. The stapled peptides may be further exploited as potent self-inhibitory agents to target and disrupt the coupling event of P protein recognition by N protein as anti-RSV therapeutic strategy.

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References

  • 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 57:835–845

    Article  CAS  Google Scholar 

  • Bao D, Bian H, Xu D, Zhao C, Jin Q, Zhu M, Tao T, Cai J (2019) Rational design of the minimal requirement for helix–helix peptide interactions in the trimer-of-hairpins motif of pediatric pneumonia RSV fusion glycoprotein. Int J Pept Res Ther 25:1087–1093

    Article  CAS  Google Scholar 

  • Chen YH, Yang JT, Chau KH (1974) Determination of the helix and beta form of proteins in aqueous solution by circular dichroism. Biochemistry 13:3350–3359

    Article  CAS  Google Scholar 

  • Chou K, Lu J, Yin X, Xu H, Li L, Ma B (2019) Structure-based derivation and intramolecular cyclization of peptide inhibitors from PD-1/PD-L1 complex interface as immune checkpoint blockade for breast cancer immunotherapy. Biophys Chem 253:106213

    Article  Google Scholar 

  • Corbi-Verge C, Kim PM (2016) Motif mediated protein–protein interactions as drug targets. Cell Commun Signal 14:8

    Article  Google Scholar 

  • Darden T, York D, Pedersen L (1993) Particale mesh Ewald and N.log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092

    Article  CAS  Google Scholar 

  • 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 24:1999–2012

    Article  CAS  Google Scholar 

  • Galloux M, Tarus B, Blazevic I, Fix J, Duquerroy S, Eléouët JF (2012) Characterization of a viral phosphoprotein binding site on the surface of the respiratory syncytial nucleoprotein. J Virol 86:8375–8387

    Article  CAS  Google Scholar 

  • Genheden S, Kuhn O, Mikulskis P, Hoffmann D, Ryde U (2012) The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant. J Chem Inf Model 52:2079–2088

    Article  CAS  Google Scholar 

  • Greenfield NJ (2006) Using circular dichroism spectra to estimate protein secondary structure. Nat Protoc 1:2876–2890

    Article  CAS  Google Scholar 

  • Grosfeld H, Hill MG, Collins PL (1995) RNA replication by respiratory syncytial virus (RSV) is directed by the N, P, and L proteins; transcription also occurs under these conditions but requires RSV superinfection for efficient synthesis of full-length mRNA. J Virol 69:5677–5686

    Article  CAS  Google Scholar 

  • Homeyer N, Gohlke H (2012) Free energy calculations by the molecular mechanics Poisson–Boltzmann surface area method. Mol Inf 31:114–122

    Article  CAS  Google Scholar 

  • Hou T, Li Y, Wang W (2011) Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy. Bioinformatics 27:1814–1821

    Article  CAS  Google Scholar 

  • Joseph TL, Lane DP, Verma CS (2012) Stapled BH3 peptides against MCL-1: mechanism and design using atomistic simulations. PLoS ONE 7:e43985

    Article  CAS  Google Scholar 

  • Lamiable A, Thévenet P, Rey J, Vavrusa M, Derreumaux P, Tufféry P (2016) PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex. Nucleic Acids Res 44:W449–W454

    Article  CAS  Google Scholar 

  • Lin J, Wang S, Wen L, Ye H, Shang S, Li J, Shu J, Zhou P (2023a) Targeting peptide‐mediated interactions in omics. Proteomics.  https://doi.org/10.1002/pmic.202200175

  • Lin J, Wen L, Zhou Y, Wang S, Ye H, Su J, Li J, Shu J, Huang J, Zhou P (2023b) PepQSAR: a comprehensive data source and information platform for peptide quantitative structure–activity relationships. Amino Acids. https://doi.org/10.1007/s00726-022-03219-4

  • Li Z, Miao Q, Yan F, Meng Y, Zhou P (2019) Machine learning in quantitative protein–peptide affinity prediction: implications for therapeutic peptide design. Curr Drug Metab 20:170–176

    Article  CAS  Google Scholar 

  • Liu Q, Zhou J, Gao J, Zhang X, Yang J, Hu C, Chu W, Yao M (2021) Targeting the membrane fusion event of human respiratory syncytial virus with rationally designed α-helical hairpin traps. Life Sci 280:119695

    Article  CAS  Google Scholar 

  • Liu Q, Lin J, Wen L, Wang S, Zhou P, Mei L, Shang S (2022a) Systematic modeling, prediction, and comparison of domain-peptide affinities: does it work effectively with the peptide QSAR methodology? Front Genet 12:800857

    Article  Google Scholar 

  • Liu H, Shen L, Pan C, Huang W (2022b) Structural modeling, energetic analysis and molecular design of a π-stacking system at the complex interface of pediatric respiratory syncytial virus nucleocapsid with the C-terminal peptide of phosphoprotein. Biophys Chem 292:106916

    Article  Google Scholar 

  • London N, Raveh B, Movshovitz-Attias D, Schueler-Furman O (2010) Can self-inhibitory peptides be derived from the interfaces of globular protein–protein interactions? Proteins 78:3140–3149

    Article  CAS  Google Scholar 

  • Nair H, Nokes DJ, Gessner BD, Dherani M, Madhi SA, Singleton RJ, O’Brien KL, Roca A, Wright PF, Bruce N, Chandran A, Theodoratou E, Sutanto A, Sedyaningsih ER, Ngama M, Munywoki PK, Kartasasmita C, Simões EA, Rudan I, Weber MW, Campbell H (2010) Global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: a systematic review and meta-analysis. Lancet 375:1545–1555

    Article  Google Scholar 

  • Ouizougun-Oubari M, Pereira N, Tarus B, Galloux M, Lassoued S, Fix J, Tortorici MA, Hoos S, Baron B, England P, Desmaële D, Couvreur P, Bontems F, Rey FA, Eléouët JF, Sizun C, Slama-Schwok A, Duquerroy S (2015) A druggable pocket at the nucleocapsid/phosphoprotein interaction site of human respiratory syncytial virus. J Virol 89:11129–11143

    Article  CAS  Google Scholar 

  • Pereira N, Cardone C, Lassoued S, Galloux M, Fix J, Assrir N, Lescop E, Bontems F, Eléouët JF, Sizun C (2017) New insights into structural disorder in human respiratory syncytial virus phosphoprotein and implications for binding of protein partners. J Biol Chem 292:2120–2131

    Article  CAS  Google Scholar 

  • Peters S, Rowbotham S, Chisholm A, Wearden A, Moschogianis S, Cordingley L, Baker D, Hyde C, Chew-Graham C (2011) Managing self-limiting respiratory tract infections: a qualitative study of the usefulness of the delayed prescribing strategy. Br J Gen Pract 61:e579–e589

    Article  Google Scholar 

  • Petsalaki E, Russell RB (2008) Peptide-mediated interactions in biological systems: new discoveries and applications. Curr Opin Biotechnol 19:344–350

    Article  CAS  Google Scholar 

  • Robustelli P, Piana S, Shaw DE (2020) Mechanism of coupled folding-upon-binding of an intrinsically disordered protein. J Am Chem Soc 142:11092–11101

    Article  CAS  Google Scholar 

  • 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 23:327–341

    Article  Google Scholar 

  • Tawar RG, Duquerroy S, Vonrhein C, Varela PF, Damier-Piolle L, Castagné N, MacLellan K, Bedouelle H, Bricogne G, Bhella D, Eléouët JF, Rey FA (2009) Crystal structure of a nucleocapsid-like nucleoprotein–RNA complex of respiratory syncytial virus. Science 326:1279–1283

    Article  CAS  Google Scholar 

  • Tran TL, Castagné N, Bhella D, Varela PF, Bernard J, Chilmonczyk S, Berkenkamp S, Benhamo V, Grznarova K, Grosclaude J, Nespoulos C, Rey FA, Eléouët JF (2007) The nine C-terminal amino acids of the respiratory syncytial virus protein P are necessary and sufficient for binding to ribonucleoprotein complexes in which six ribonucleotides are contacted per N protein protomer. J Gen Virol 88:196–206

    Article  CAS  Google Scholar 

  • Walensky LD, Bird GH (2014) Hydrocarbon-stapled peptides: principles, practice, and progress. J Med Chem 57:6275–6288

    Article  CAS  Google Scholar 

  • Wang J, Zhang J, Sun X, Liu C, Li X, Chen L (2019) Molecular design of sequence-minimized, structure-optimized, and hydrocarbon-stapled helix–helix interactions in the trimer-of-hairpins motif of pediatric pneumonia RSV-F protein. Chem Biol Drug Des 94:1292–1299

    Article  CAS  Google Scholar 

  • Xue Y, Shi X, Feng D, Wang Y (2022) The binding affinity of human pediatric respiratory syncytial virus phosphoprotein C-terminal tail to nucleocapsid can be improved by a rationally designed halogen-bonded system. J Mol Graph Model 118:108374

    Article  Google Scholar 

  • 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 54:2022–2032

    Article  CAS  Google Scholar 

  • Zhou P, Miao Q, Yan F, Li Z, Jiang Q, Wen L, Meng Y (2019) Is protein context responsible for peptide-mediated interactions? Mol Omics 15:280–295

    Article  CAS  Google Scholar 

  • Zhou P, Yan F, Miao Q, Chen Z, Wang H (2021a) Why the first self-binding peptide of human c-Src kinase does not contain class II motif but can bind to its cognate src homology 3 domain in class II mode? J Biomol Struct Dyn 39:310–318

    Article  CAS  Google Scholar 

  • Zhou P, Liu Q, Wu T, Miao Q, Shang S, Wang H, Chen Z, Wang S, Wang H (2021b) Systematic comparison and comprehensive evaluation of 80 amino acid descriptors in peptide QSAR modeling. J Chem Inf Model 61:1718–1731

    Article  CAS  Google Scholar 

  • Zhou P, Wen L, Lin J, Mei L, Liu Q, Shang S, Li J, Shu J (2022) Integrated unsupervised-supervised modeling and prediction of protein–peptide affinities at structural level. Brief Bioinform 23:bbac097

    Article  Google Scholar 

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Acknowledgements

This work was supported by the Foundation of Suzhou Kowloon Hospital (Grant Nos. SZJL202111 and SZJL202104).

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  1. Department of Pediatrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, 215000, Suzhou, China

    Leling Zhang, Yong Gong & Lili Shen

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  1. Leling Zhang
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  2. Yong Gong
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Contributions

LZ and YG performed the researches; LZ and LS wrote the main manuscript text; LS proposed and supervised the researches; all authors reviewed the manuscript.

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Correspondence to Lili Shen.

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Zhang, L., Gong, Y. & Shen, L. Molecular Stapling of Human Pediatric RSV Phosphoprotein’s C-terminal Tail-Derived Peptides to Target the Coupled Folding-Upon-Binding Event Between Phosphoprotein and Nucleocapsid. Int J Pept Res Ther 29, 12 (2023). https://doi.org/10.1007/s10989-022-10483-1

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