Peptoid Backbone Flexibilility Dictates Its Interaction with Water and Surfaces: A Molecular Dynamics Investigation
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States; Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
Peptoids are peptide-mimetic biopolymers that are easy-to-synthesize and adaptable for use in drugs, chemical scaffolds, and coatings. However, there is insufficient information about their structural preferences and interactions with the environment in various applications. We conducted a study to understand the fundamental differences between peptides and peptoids using molecular dynamics simulations with semi-empirical (PM6) and empirical (AMBER) potentials, in conjunction with metadynamics enhanced sampling. From studies of single molecules in water and on surfaces, we found that sarcosine (model peptoid) is much more flexible than alanine (model peptide) in different environments. However, the sarcosine and alanine interact similarly with a hydrophobic or a hydrophilic. Finally, this study highlights the conformational landscape of peptoids and the dominant interactions that drive peptoids towards these conformations. ACKNOWLEDGMENT: MD simulations and manuscript preparation were supported by the MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory (PNNL), a multi-program national laboratory operated by Battelle for the U.S. Department of Energy. CJM was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by the US Department of Energy, Office of Basic Energy Sciences, Biomolecular Materials Program at PNNL. Computing resources were generously allocated by University of Washington's IT department and PNNL's Institutional Computing program. The authors greatly acknowledge conversations with Dr. Kayla Sprenger, Josh Smith, and Dr. Yeneneh Yimer.
- Research Organization:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (US)
- Sponsoring Organization:
- USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
- DOE Contract Number:
- AC05-76RL01830
- OSTI ID:
- 1439013
- Report Number(s):
- PNNL-SA-132333; KC0203030
- Journal Information:
- Biomacromolecules, Journal Name: Biomacromolecules Journal Issue: 3 Vol. 19; ISSN 1525-7797
- Publisher:
- American Chemical Society
- Country of Publication:
- United States
- Language:
- English
Similar Records
Controlled synthesis of highly-branched plasmonic gold nanoparticles through peptoid engineering
Local Aqueous Solvation Structure Around Ca2+ During Ca2+---Cl– Pair Formation