Thomas A. Knotts IV
Chemical Engineering Department
Brigham Young University
“The DNA Slide and the Protein Swing: Learning the Steps of Biomolecular Dances”
Many of the basic biological processes that occur innumerable times each day are not well understood from a fundamental standpoint. For example, despite all that is known about DNA, the hybridization process itself is still largely a mystery as no experimental techniques exist to follow the event with molecular-level resolution. Protein biochemistry too has yet to be solved as indicated by our inability to predict the manner in which a linear amino acid chain folds into functional protein. This general lack of understanding has made it difficult to optimize technologies involving biological processes. Devices such as DNA and protein microarrays have the potential to create a paradigm shift in drug design, defense, fundamental research, surface biofunctionalization, and healthcare, but designing next-generation platforms is hindered by the deficiency in knowledge about the biophysics involved.
Molecular simulation has the potential to contribute to biotechnology in meaningful ways by providing answers in the absence of experimental results. However, bridging the divide between the “simulator” and “experimentalist” requires the results to be presented in a language both parties speak and not in the dialect of simulation. Thermodynamics is a universal language, but obtaining statistically-relevant and experimentally-relevant thermodynamic properties is difficult in all-atom simulations. This talk will show how a focus on well-parameterized, coarse-grain models can provide the needed insights in terms of Gibbs energies, melting temperatures, and potentials of mean force. The results attest to the importance of molecular simulation in designing technologies involving biomolecules attached to surfaces.
DNA: An experimentally-validated, coarse-grain model of DNA, which will be described, has shown that traditional theories on DNA hybridization are incomplete. The results indicate that DNA does not hybridize through a “zipping” process but rather a “sliding” process—a fact that has far-reaching implications for the future of microarrays. A comparison of hybridization on surfaces and in the bulk shows, contrary to common belief, that surfaces make hybridization more stable for strands of equal length, but less stable for unequal strands. Other results will also be presented concerning tethering the probe to the surface at multiple locations and hybridization of a target to a group of probes. The findings give a more complete picture of surface hybridization than previously understood.
Proteins: An experimentally-validated coarse grain model for protein-surface interactions will be presented that has provided remarkable insight into how surfaces of different chemistries affect protein stability. Key results include how 1) surfaces stabilize proteins entropically and destabilize proteins enthalpically, 2) the entropic effect is centered on the denatured state while the enthalpic effect is centered on the folded state, 3) protein stability for helical peptides can be correlated to the type of loop region where the tether is placed, 4) surfaces can drastically change the folding behavior of proteins, 5) selecting correct tether positions, including using multiple tethers, can remove unstable intermediates and improve stability of enzymes, 6) surface chemistry can stabilize or destabilize tethered antibodies, and 6) the attachment geometry of an antibody fragment relative to the surface can affect antigen binding mechanisms and binding strength. As a whole, the results offer hope that rational design of technologies involving protein-surface interactions, including protein arrays, is possible.