Understanding biological hydrogel function through design of simplified peptides and polymers

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, June 2017"May 2017." Cataloged from PDF version of thesis.Includes bibliographical references (pages 103-111).Biological hydrogels exhibit complex properties that cannot be recapitulated by current synthetic materials. Examples include mucus, which acts as a barrier against toxins and pathogens while simultaneously hosting trillions of microbes within the gut; cartilage which resists repetitive compressive forces while maintaining highly lubricated layers for efficient movement; and nuclear pore matrices which act as selective barriers in the transport of proteins and nucleic acids. An underlying theme that gives biological hydrogels their unique mechanical and biological functions is the presence of long polymeric molecules. These polymers are typically comprised of repeating subunits that are essential for correct polymer function, such as the phenylalanine-glycine (FG) repeats in nucleoporin proteins of nuclear pore complexes (NPCs) and the proline-threonine-serine (PTS) domains in mucin polymers found in mucus.Although these polymeric subunits are well-identified, to date their structural complexity has limited our understanding of how they contribute to the overall hydrogel function. In this thesis, we focus on two main biological hydrogels: the self-assembled matrix of the nuclear pore complex that controls the passage of molecules between the nucleus and the cytoplasm, and mucus, which protects against invading pathogens and toxins. As both hydrogels consist of functionally redundant polymers and associated factors, understanding the relationship between polymer sequence and hydrogel function is a significant technical challenge. To simplify the problem, we design structurally reduced peptides and polymers with targeted individual biological features such as amino acid identity, spatial localization of charge, and glycosylation identity. We then study the effect of one or a combination of these properties on the overall hydrogel function.Using this technique, we first demonstrate that peptide charge type and amino acid placement are important features for regulating selective transport through NPCs. For mucins, we identify single glycans that are sufficient to recapitulate the biofilm inhibition properties of mucin, and present novel evidence that mucins modulate horizontal gene transfer rates for opportunistic and commensal bacteria.by Wesley George Chen.Ph. D.Ph.D. Massachusetts Institute of Technology, Department of Biological Engineerin