Tuning interfacial biomolecule interactions with massively parallel nanopore arrays
Date
2021
Authors
Wang, Dafu, author
Kipper, Matt J., advisor
Snow, Chris D., advisor
Bailey, Travis S., committee member
Stasevich, Tim J., committee member
Journal Title
Journal ISSN
Volume Title
Abstract
This project studied interfacial interactions of macromolecules with nanoporous materials, with an ultimate goal of exploiting these interactions in functional biomaterials. We quantified interaction forces and energies for guest molecules threaded into the pores of protein crystals via nano-mechanical atomic force microscopy (AFM) pulling experiments. We demonstrated that both double-stranded DNA and poly(ethylene glycol) are rapidly absorbed within porous protein crystals, where they presumably bind to the inner "wall" surfaces of the protein crystal nanopores. These "guest" molecules can be retrieved from the "host" crystal by chemically modified AFM tips, enabling precise measurements of the adhesion forces and interaction energies. Based on these experiments, machine learning approaches were developed to classify hundreds of thousands of individual force-distance curves obtained in the AFM experiments. Furthermore, we showed that the interactions between protein crystal "hosts" and "guest" macromolecules can be used to modulate cell behavior, by presenting cell adhesion ligands tethered to different lengths of macromolecules that thereby modulate the maximum traction force cells can apply before rupturing bonds tethering the adhesion ligand to the porous protein crystal interior. This method affords the opportunity to create biomaterials that store an internal reservoir of cell-specific signals that can be presented to independently modulate the behavior of different cell populations in a single material. In the first chapter, some recent advancements, and methodologies of measuring interfacial biomolecule interactions are reviewed and compared. The reviewed technics include atomic force microscopy, fluorescence recovery after photobleaching, the total internal reflection fluorescence, confocal microscopy, and optical tweezers. Furthermore, this chapter interduces the application of machine learning to assist the interfacial biomolecule interaction studies, especially the AFM measurements. This chapter further prospects of the future of interfacial biomolecule interactions studies. In the second chapter, the methodologies of probing and observing the surface of highly porous Camphylobacter Jejuni formed protein crystals (CJ protein crystals) by high-resolution AFM are introduced. Throughout this chapter, the morphologies of CJ protein crystals are comprehensively investigated by AFM and have been discussed in this chapter. In the third chapter, for the first time, the interactions of DNA with porous protein crystals are quantitatively measured by high-resolution AFM and chemical force microscopy. The surface structure of protein crystals with unusually large pores was observed in liquid via high-resolution AFM. Force-distance (F-D) curves were also obtained using AFM tips modified to present or capture DNA. The interactions of DNA molecules with protein crystals to be quantitatively studied while revealing the morphology of the protein crystal surface in detail, in buffer, reveals how a new protein-based biomaterial can be used to bind DNA guest molecules. In the fourth chapter, strategies of machine learning are introduced which pioneered the use of machine learning to classify and cluster the interaction patterns between DNA and protein crystals, enabling us to process thousands of F-D curves collected by AFM. Finally, in the fifth chapter, we quantitatively measure and take advantage of the interaction between poly(ethylene glycol) (PEG)-arginine-glycine-aspartic acid (RGD) complex and nanoporous protein crystals to understand how non-covalent surface presentation of peptide adhesion ligands can influence cell behavior. Through AFM, F-D curves of interactions between PEG-RGD and host protein crystals were obtained for the first time. Furthermore, a strategy is developed that enables us to design surfaces that non-covalently present multiple different ligands to cells with tunable adhesive strength for each ligand, and with an internal reservoir to replenish the precisely defined crystalline surface.
Description
Rights Access
Subject
interfacial interactions
macromolecules
nanoporous materials
biomaterials
AMF
DNA