Shape-Shifters: Small Proteins Unexpectedly Shift Their Shape When Coming Together
A team of researchers discovered that peptoids can change shape when they form a nanosheet, which has potential to improve chemical sensors and much more.
The Science
Artificial versions of small proteins, called peptoids, can readily self-assemble into tiny sheets, which gives them a great deal of potential for use in medicine, sensing, and other fields. An international team led by Foundry scientists discovered that peptoids could change shape when they form a nanosheet.
The Impact
This is the first evidence that shows peptoids can change shape. With a better understanding of how peptoid chains organize themselves, this work will open the door to creating new types of durable and engineerable biomimetic nanomaterials. These materials could benefit material design, separations, and sensors.
Summary
Peptoids are artificial versions of nature's peptides that are highly customizable and have opened up new avenues of research in a range of fields, from biomedicine to materials science. Peptoids can readily self-assemble into nanosheets, which are of particular interest because they are biocompatible, highly uniform bilayer structures that are free-floating in water. Nanosheets can serve as templates for the growth of composite materials and hold great potential for use as membranes for separations, or as a platform for chemical and biological sensing.
An international team of researchers discovered that peptoids could change shape when they form a nanosheet. To make this discovery, the team studied the atomic details of the molecular structure of a peptoid nanosheet using the Foundry's computational model in conjunction with a technique called solid-state nuclear magnetic resonance (NMR) spectroscopy. The team synthesized specially labelled peptoids that introduced "probe" atoms at specific locations within the molecule. Solid-state NMR showed exactly where the probes were in relation to each other and revealed some surprising findings.
The team found evidence supporting the brick-like pattern formed by peptoids in nanosheets predicted by the existing model, but also found that some of the bond angles inside individual peptoids did not match as expected. With this new data in hand, the team used multi-scale simulations to create a new computational model using the high-performance computing resources of the National Energy Research Scientific Computing Center.
Version 2.0 of the Foundry's model matched experimental data even better than before and yielded a surprise. The reason that the bond angles didn't match the original model is because peptoids can change shape when they assemble into nanosheets. When peptoids assemble into nanosheets, the "branches" of atoms coming off of the backbone interact with those of neighboring peptoids. These interactions become more favorable when the peptoid is in the cis position. While the peptoid backbone is less stable in the cis form, the atoms branching off of it become more stable and the molecules can be packed more tightly together and become more highly organized. With a better understanding of how peptoid chains organize themselves upon assembly, the researchers expect this work will open the door to engineering new types of durable, biomimetic nanomaterials.
Contact
Ron Zuckermann
Molecular Foundry and Berkeley Lab
rnzuckermann@lbl.gov
Funding
This work was done as part of a user project at the Molecular Foundry at Lawrence Berkeley National Laboratory, supported by the Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences. Additional support was provided by Defense Threat Reduction Agency, Defense Advanced Research Projects Agency (DARPA) Folded Non-Natural Polymers with Biological Function (Fold Fx) program, Air Force Office of Scientific Research Award. Quantum mechanical calculations were carried out on the High-Performance Computing resources at New York University Abu Dhabi. This work used resources of the National Energy Research Scientific Computing Center, which is supported by the DOE Office of Science. Work at the Molecular Foundry was supported by the DOE, Office of Science, Office of Basic Energy Sciences. The authors acknowledge the use of nuclear magnetic resonance (NMR) instruments at the NMR center at the Georgia Institute of Technology.
Publications
B.C. Hudson, A. Battigelli, M.D. Connolly, J. Edison, R.K. Spencer, S. Whitelam, R.N. Zuckermann, and A.K. Paravastu, “Evidence for cis amide bonds in peptoid nanosheets.” Journal of Physical Chemistry Letters 9(10), 2574 (2018). [DOI: 10.1021/acs.jpclett.8b01040]
J. Edison, R.K. Spencer, G.L. Butterfoss, B.C. Hudson, A.I. Hochbaum, A.K. Paravastu, R.N. Zuckermann, and S. Whitelam, "Conformations of peptoids in nanosheets result from the interplay of backbone energetics and intermolecular interactions.” Proceedings of the National Academy of Sciences USA 115, 5647 (2018). [DOI: 10.1073/pnas.1800397115]
Related Links
Molecular Foundry summary: Shape-shifters: Peptoids Unexpectedly Change Shape When Forming Nanosheets
