Combining Simulation and Spectroscopy to Determine the Structure and Dynamics of Adsorbed Proteins - Application to Biomass Conversion
Final Report Abstract
This DFG project has lead to improvements of our understanding of protein-surface interactions and paved the way for more high-resolution studies of interfacial protein action. This project has been a transatlantic collaboration of the MD group of Jim Pfaendtner at the University of Washington (Seattle) and the surface spectroscopy group of Tobias Weidner at the Max Planck Institute for Polymer Research in Mainz, Germany. The US-based part of the project has been funded through the National Science Foundation (NSF) of the United States. The aim of the project has been to determine the molecular mechanisms involved in cellulose breakdown by the enzyme cellulase. Unfortunately making relevant cellulose surface has been a challenge. We eventually learned how to produce surfaces coated with highly aligned cellulose fibers. SFG spectra and simulations show that the binding domain of cellulase attaches to the cellulose crystal in an ordered way and the proteins align at the interface. SFG spectra collected at different azimuthal angles are very different, indicting that different aspects of the peptide backbone is samples. This also gives us a unique opportunity to study proteins, literally, from different sides. We are still working on analyzing the data. Since the project proposed to develop methods combining sum frequency generation spectroscopy and molecular simulations to determine the role of folding and side chain structure on surface binding, we decided to study other important protein surface systems and develop methods this way. By studying a wide variety of proteins such as anti-freeze proteins, biomineral proteins, sensor proteins and artificial model systems we did fulfill on our promise to develop techniques to determine backbone and side chains structure and also to follow side motions with sub-picosecond time resolution. The project has lead to a significant improvement of the methods used to determine interfacial protein structure by combining the experimental data directly with simulations via calculated spectra. This is in analogy to the analysis of 2D NMR spectra for protein analysis in solution. This new development makes it now possible to extract the complexity inherent to nonlinear vibrational spectra for a unique assignment to the 3D structure of interfacial proteins of virtually unlimited size. In addition, the combination with experimental data allows to test the quality of force fields and sampling methods of simulations directly. The results have led to numerous follow up studies funded by the European Union, the Lundbeck Fonden and the Villum Foundation and the Carlsberg Foundation.
Publications
- Bovine and human insulin adsorption at lipid monolayers: a comparison. Frontiers in Physics, 3, 51 (2015)
S. Mauri, R. Pandey, I. Rzezicka, H. Lu, M. Bonn, T. Weidner
(See online at https://doi.org/10.3389/fphy.2015.00051) - Ultrafast reorientational dynamics of leucine at the air-water interface. Journal of the American Chemical Society, 138, 5226-5229 (2016)
M. Donovan, Y. Yimer, J. Pfaendtner, E. Backus, M. Bonn, T. Weidner
(See online at https://doi.org/10.1021/jacs.6b01878) - Determination of Absolute Orientation of Protein α-Helices at Interfaces using Phase Resolved SFG Spectroscopy. Journal of Physical Chemistry Letters, 8, 3101-3103 (2017)
L. Schmüser, S.J. Roeters, H. Lutz, S. Woutersen, M. Bonn, T. Weidner
(See online at https://doi.org/10.1021/acs.jpclett.7b01059) - LK peptide side chain dynamics at interfaces are independent of secondary structure. Physical Chemistry – Chemical Physics PCCP, 19, 28507-28511 (2017)
M.A. Donovan, H. Lutz, Y.Y. Yimer, J. Pfaendtner, M. Bonn, T. Weidner
(See online at https://doi.org/10.1039/c7cp05897g) - Predicting the orientation of protein G B1 on hydrophobic surfaces using Monte Carlo simulations. Biointerphases 12, 02D401 (2017)
E.T. Harrison, T. Weidner, D.G. Castner, G. Interlandi
(See online at https://doi.org/10.1116/1.4971381) - Thiolated Lysine‐Leucine Peptides Self‐Assemble into Biosilica Nucleation Pits on Gold Surfaces. Advanced Materials Interfaces, 4, 1700399 (2017)
H. Lu, Y. Yimer, R. Berger, M. Bonn, J. Pfaendtner, T. Weidner
(See online at https://doi.org/10.1002/admi.201700399) - Calcium-Induced Molecular Rearrangement of Peptide Folds Enables Biomineralization of Vaterite Calcium Carbonate. Journal of the American Chemical Society, 140, 2793–2796 (2018)
H. Lu, H. Lutz, S. Roeters, M. Hood, A. Schäfer, R. Muñoz-Espí, R. Berger, M. Bonn, T. Weidner
(See online at https://doi.org/10.1021/jacs.8b00281) - Ice-binding site of surface-bound type III antifreeze protein partially decoupled from water. Physical Chemistry – Chemical Physics PCCP, 20, 26926-26933 (2018)
D. Verreault, S. Alamdari, S. Roeters, Ra. Pandey, J. Pfaendtner, T. Weidner
(See online at https://doi.org/10.1039/c8cp03382j)
