(388d) Strategies to Stabilize Proteins On Surfaces From Improved Modeling of Protein-Surface Interactions

Bush, D. B. - Presenter, Brigham Young University
Knotts, T. A. IV, Brigham Young University
Loong, B., Brigham Young University
Schinn, S. M., Brigham Young University

Protein arrays are a potentially disruptive technology—with applications in a variety of fields including medicine, defense, and biology—that have yet to find mainstream use due to unreliability.  Protein arrays function on the principle of molecular recognition between the protein on the surface and a ligand molecule, so the technology can only be as reliable as the recognition is robust.   But tethering proteins to surfaces during fabrication can affect the stability of proteins in ways that compromise the recognition, and a complete understanding of the relevant phenomena remains elusive.  This lack of knowledge not only limits the performance of current microarrays, but also prevents rational design of next-generation platforms.

Studying the stability of proteins on surfaces is difficult because typical experimental techniques to ascertain protein structure (such as NMR and X-ray crystallography) are not transferrable to inhomogeneous environments.  As such, molecular simulation has emerged as the primary method to investigate protein-surface interactions.  Simulation has provided many insights into these processes, but the vast majority of the studies have been done with relatively idealized systems.  The idealities include studying the stability of only one protein on the surface at a time rather than many proteins as would be found in experiment, binding the protein to the surface using only a single tethering molecule attached to a single residue in the protein, and modeling the surface in a rudimentary way such that it interacts with each protein residue with the same energy regardless of the specific chemistries involved.

This presentation will summarize several efforts to move away from the “ideal” case and model the system in a manner that more closely approximates the real system.  Results will be presented that demonstrate: 1) how multiple molecules tethered to the surface interact with each other to change the degree of folding found on the surface at a given temperature, 2) how binding the protein to the surface using multiple tethers on different residues can drastically alter the folding mechanism and lead to either stabilization or destabilization of protein structure, and 3) how modeling the protein-surface interactions with appropriate chemical detail changes many of the prior results seen when using more rudimentary surface models.  This last topic is made possible by using an advanced coarse-grain model that captures chemically-specific, protein-surface interactions in a manner that produces remarkable agreement with experiment.  As a whole, the results offer hope that rational design of future protein arrays is possible.