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Title Molecular investigation of polypyrrole and surface recognition by affinity peptides
Publication Date
Date Accessioned
Degree PhD
Discipline/Department Biomedical Engineering
Degree Level doctoral
University/Publisher University of Texas – Austin
Abstract Successful tissue engineering strategies in the nervous system must be carefully crafted to interact favorably with the complex biochemical signals of the native environment. To date, all chronic implants incorporating electrical conductivity degrade in performance over time as the foreign body reaction and subsequent fibrous encapsulation isolate them from the host tissue. Our goal is to develop a peptide-based interfacial biomaterial that will non-covalently coat the surface of the conducting polymer polypyrrole, allowing the implant to interact with the nervous system through both electrical and chemical cues. Starting with a candidate peptide sequence discovered through phage display, we used computational simulations of the peptide on polypyrrole to describe the bound peptide structure, explore the mechanism of binding, and suggest new, better binding peptide sequences. After experimentally characterizing the polymer, we created a molecular mechanics model of polypyrrole using quantum mechanics calculations and compared its in silico properties to experimental observables such as density and chain packing. Using replica exchange molecular dynamics, we then modeled the behavior of affinity binding peptides on the surface of polypyrrole in explicit water and saline environments. Relative measurements of the contributions of each amino acid were made using distance measurements and computational alanine scanning.
Subjects/Keywords Polypyrrole; Conducting polymers; Molecular dynamics; Binding affinity; Computational biology
Contributors Ren, Pengyu (advisor); Schmidt, Christine E. (advisor); Elber, Ron (committee member); Roy, Krishnendu (committee member); Georgiou, George (committee member)
Language en
Country of Publication us
Record ID handle:2152/ETD-UT-2011-12-4408
Repository texas
Date Indexed 2020-10-15
Grantor University of Texas at Austin
Note [] text; [department] Biomedical Engineering;

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…93! Polypyrrole Matrix Formation .............................................................93! Construction of Polypyrrole/Peptide Systems .....................................95! Replica Exchange Molecular Dynamics

…the trajectory of molecular dynamics simulations and to observe trends in the data provides excellent feedback and guidance for designing binding affinity peptides. For quantitative free energy of binding 4 calculations, however, this type of problem…

…detail on the background and significance of polypyrrole as a biomaterial and the current state of molecular simulations. Chapter 3 covers the experimental characterization and in vitro studies we conducted with polypyrrole. When first examining…

…served different implant applications, with trade-offs between conductivity, stability, and cell adhesion. 3 In Chapter 4, we discuss the molecular mechanics model that we created for polypyrrole. Starting from ab initio quantum mechanics calculations…

…requires further growth in efficient sampling methods and computational power. Modeling peptide interactions with complex materials surfaces is a mostly unexplored application of molecular modeling. This work is an early investment in what we hope becomes…

…computational models and techniques employed in this thesis, including quantum mechanics and molecular mechanics. 2.2 CHRONIC IMPLANTS AND THE IMMUNE RESPONSE The definition of what constitutes an “implant” or a “biomaterial” has become blurred as engineers…

…trending research foci of biomedical engineering have evolved from bulk implants and instrumentation to microscale devices and sensors to nano-scale imaging and molecular design. 15 Biological processes natively occur at a molecular level, and modern…

…biomedical laboratories must operate at that level. Traditionally, we leverage equipment and protocols to scale up molecular interactions into macroscopic observables. Techniques such as nuclear magnetic resonance (NMR) spectroscopy, fluorescence…