(247z) Combining Spectroscopy Experiments and Molecular Simulation to Determine Structural and Mechanistic Details of Adsorbed Biomolecules

Combining spectroscopy experiments and molecular simulation
to determine structural and mechanistic details of adsorbed biomolecules

Kayla Sprenger¹,
Tobias Weidner², Jim Pfaendtner¹

¹Department
of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA

²Max
Planck Institute for Polymer Research, Mainz, 55128, Germany

ABSTRACT

Proteins and the mechanisms they mediate at solid/liquid
interfaces play a critical role in many processes including surface fouling,
biocatalysis, and biomineralization. Despite their importance, we often lack a
molecularly detailed understanding of interfacial mechanisms such as protein
recognition, binding, and surface-induced conformational change. While
atomistic simulations of protein adsorption have strong potential to combine
with experiments to elucidate structural and mechanistic details at the
interface, challenges of timescale limitations and strong protein/surface
binding have prohibited the progress of such simulations. To-date there are
virtually zero structures of a biomolecule adsorbed to a surface that have been
made accessible in the Protein Data Bank. For the first time results of
molecular simulation, using the enhanced sampling method PTMetaD-WTE¹
to overcome aforementioned challenges, have been combined with experimental
data from solid-state nuclear magnetic resonance (ssNMR), near edge X-ray
adsorption fine structure (NEXAFS), and sum frequency generation spectroscopy
(SFG) to determine the structure and orientation of the SN15 binding domain of the
salivary protein statherin on hydroxyapatite (HAp). Additionally, multiple SN15
peptides have been simulated to represent more closely the experimental
conditions of a crowded microenvironment at the interface. Resulting structural
information is compared to the single protein adsorption results to determine
the role of lateral protein-protein interactions. From this comparison, mechanistic
details of statherin film formation and its control of HAp growth are
hypothesized. This poster will also propose some general principles for
efficiently simulating with metadynamics and computing experimental observables
for protein adsorption systems.

References

[1] Deighan, M.; Bonomi, M.; Pfaendtner, J. Efficient
Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble. JCTC 2012, 8, 2189-2192.