Analytical and Bioanalytical Chemistry

, Volume 402, Issue 4, pp 1731–1736 | Cite as

Computational analysis of non-covalent polymer–protein interactions governing antibody orientation

  • Leslie R. Farris
  • Melisenda J. McDonald
Technical Note


The ALYGNSA is an affinity-based antibody orientation system produced through the interaction of the polymer poly(methyl methacrylate) (PMMA) and recombinant protein G (rProG), a streptococcal protein. This improved orientation suggests a specific non-covalent attachment of the rProG to PMMA that leaves the IgG binding region of the rProG more readily available. In this study, a full tertiary structure model of the rProG molecule of 198 amino acid residues containing a signal region, two IgG binding domains, and an anchor region, was computationally generated using the iterative threading assembly refinement (I-Tasser) server. The rProG model having the highest confidence score was subject to docking experiments with varied-length short chains of PMMA polymer via the graphic processing units-based Hex server. A five-residue section of the rProG anchor region, with the sequence TPATP, was identified as a potential interaction site. A complete ternary model (rProG, PMMA, and IgG) was assembled and provides insight into a plausible mechanism for non-covalent antibody orientation by the ALYGNSA system.


Protein–polymer interactions Antibody orientation ALYGNSA I-TASSER protein modeling server Hex protein docking server Biosensors 



This work was kindly supported by the US ARMY Research Office (Grant # W911NF: Nanomanufacturing of Multifunctional Sensors) and the UMASS Lowell Nanomanufacturing Center (NSF Grant # EEC-0425826). One of us (LRF) has performed this work as part of the requirements for the Ph.D. degree in Chemistry (Biochemistry Option). The full sequence of rProG was generously provided for use in this study (Recombinant Protein G, 21193; Pierce Protein Research Products, Thermo Fisher Scientific, 3747 N. Meridian Rd., Rockford, IL 61105, USA). Finally, many thanks go to Kevin Morton and Adrianna Morris.


  1. 1.
    Conroy PJ, Hearty S, Leonard P, O’Kennedy RJ (2009) Antibody production, design and use for biosensor-based applications. Semin Cell Dev Biol 20:10–26CrossRefGoogle Scholar
  2. 2.
    Kausaite-Minkstimiene A, Ramanaviciene A, Kirlyte J, Ramanavicius A (2010) Comparative study of random and oriented antibody immobilization techniques on the binding capacity of immunosensor. Anal Chem 82:6401–6408CrossRefGoogle Scholar
  3. 3.
    Clarizia L, Sok D, Wei M, Mead J, Barry C, McDonald M (2009) Antibody orientation enhanced by selective polymer–protein noncovalent interactions. Anal Bioanal Chem 393:1531–1538CrossRefGoogle Scholar
  4. 4.
    Sok D, Clarizia L, Farris L, McDonald M (2009) Novel fluoroimmunoassay for ovarian cancer biomarker CA-125. Anal Bioanal Chem 393:1521–1523CrossRefGoogle Scholar
  5. 5.
    Chourb S, Mackness BC, Farris LR, McDonald MJ (2009) Enhanced immuno-detection of shed extracellular domain of HER-2/neu. Health 1:325–329CrossRefGoogle Scholar
  6. 6.
    Mackness B, Chourb S, Farris L, McDonald M (2010) Polymer protein-enhanced fluoroimmunoassay for prostate-specific antigen. Anal Bioanal Chem 396:681–686CrossRefGoogle Scholar
  7. 7.
    Farris L, Wu N, Wang W, Clarizia L, Wang X, McDonald M (2010) Immuno-interferometric sensor for the detection of influenza A nucleoprotein. Anal Bioanal Chem 396:667–674CrossRefGoogle Scholar
  8. 8.
    Simonelli L, Beltramello M, Yudina Z, Macagno A, Calzolai L, Varani L (2010) Rapid structural characterization of human antibody–antigen complexes through experimentally validated computational docking. J Mol Biol 396:1491–1507CrossRefGoogle Scholar
  9. 9.
    Kmiecik S, Kolinski A (2008) Folding pathway of the B1 domain of protein G explored by multiscale modeling. Biophys J 94:726–736CrossRefGoogle Scholar
  10. 10.
    Allen BD, Nisthal A, Mayo SL (2010) Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles. PNAS 107:19838–19843CrossRefGoogle Scholar
  11. 11.
    Lee W, Chang J, Ju S (2010) Hydrogen-bond structure at the interfaces between water/poly(methyl methacrylate), water/poly(methacrylic acid), and water/poly(2-aminoethylmethacrylamide). Langmuir 26:12640–12647CrossRefGoogle Scholar
  12. 12.
    Gronenborn AM, Filpula DR, Essig NZ, Achari A, Whitlow M, Wingfield PT, Clore GM (1991) A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science 253:657–661CrossRefGoogle Scholar
  13. 13.
    Derrick JP, Wigley DB (1994) The third IgG-binding domain from streptococcal protein G: an analysis by X-ray crystallography of the structure alone and in a complex with fab. J Mol Biol 243:906–918CrossRefGoogle Scholar
  14. 14.
    Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protocols 5:725–738CrossRefGoogle Scholar
  15. 15.
    Farris LR, McDonald MJ, Dissertation Supervisor (2011) Promotion of antibody orientation by unique noncovalent polymer-protein pairing: structural elucidation, mechanistic analysis, and applications in immunoassays and biosensors. University Of Massachusetts Lowell, LowellGoogle Scholar
  16. 16.
    Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera: a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612CrossRefGoogle Scholar
  17. 17.
    Ritchie DW, Venkatraman V (2010) Ultra-fast FFT protein docking on graphics processors. Bioinformatics 26:2398–2405CrossRefGoogle Scholar
  18. 18.
    Tomlinson JH, Craven CJ, Williamson MP, Pandya MJ (2010) Dimerization of protein G B1 domain at low pH: a conformational switch caused by loss of a single hydrogen bond. Proteins: Structure, Function, and Bioinformatics 78:1652–1661CrossRefGoogle Scholar
  19. 19.
    Serizawa T, Sawada T, Matsuno H, Matsubara T, Sato T (2005) A peptide motif recognizing a polymer stereoregularity. J Am Chem Soc 127:13780–13781CrossRefGoogle Scholar
  20. 20.
    Harris LJ, Larson SB, Hasel KW, McPherson A (1997) Refined structure of an intact IgG2a monoclonal antibody. Biochemistry 36:1581–1597CrossRefGoogle Scholar
  21. 21.
    Sauer-Eriksson AE, Kleywegt GJ, Uhlén M, Jones TA (1995) Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG. Structure 3:265–278CrossRefGoogle Scholar
  22. 22.
    Achari A, Hale SP, Howard AJ, Clore GM, Gronenborn AM, Hardman KD, Whitlow M (1992) 1.67-.ANG. X-ray structure of the B2 immunoglobulin-binding domain of streptococcal protein G and comparison to the NMR structure of the B1 domain. Biochemistry 31:10449–10457CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  1. 1.Department of Chemistry, College of SciencesUniversity of Massachusetts LowellLowellUSA

Personalised recommendations