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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

Abstract

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.

Keywords

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

Notes

Acknowledgments

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.

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

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

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