1. Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles
- Author
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Siewert J. Marrink, Anna S. Bondarenko, Mathieu Surin, Thomas L. C. Jansen, Gaël Schaeffer, Yigit Altay, Julien Idé, Sijbren Otto, David Beljonne, Pim W. J. M. Frederix, Molecular Dynamics, Synthetic Organic Chemistry, and Theory of Condensed Matter
- Subjects
DYNAMICS ,Circular dichroism ,spectroscopy ,Absorption spectroscopy ,PROTEINS ,Supramolecular chemistry ,General Physics and Astronomy ,Infrared spectroscopy ,Molecular Dynamics Simulation ,010402 general chemistry ,01 natural sciences ,self-replication ,Article ,Molecular dynamics ,0103 physical sciences ,nanostructures ,IMPLEMENTATION ,Molecule ,General Materials Science ,AMPHIPHILES ,Protein secondary structure ,chemistry.chemical_classification ,MOLECULAR SIMULATION ,010304 chemical physics ,Circular Dichroism ,General Engineering ,WATER MODELS ,self-assembly ,DRIVEN ,simulation ,molecular dynamics ,0104 chemical sciences ,Supramolecular polymers ,GROMOS FORCE-FIELD ,SUPRAMOLECULAR POLYMERS ,Crystallography ,chemistry ,Chemical physics ,peptides ,AMYLOID FIBRIL - Abstract
Self-replication at the molecular level is often seen as essential to the early origins of life. Recently a mechanism of self-replication has been discovered in which replicator self-assembly drives the process. We have studied one of the examples of such self-assembling self-replicating molecules to a high level of structural detail using a combination of computational and spectroscopic techniques. Molecular Dynamics simulations of self-assembled stacks of peptide-derived replicators provide insights into the structural characteristics of the system and serve as the basis for semiempirical calculations of the UV-vis, circular dichroism (CD) and infrared (IR) absorption spectra that reflect the chiral organization and peptide secondary structure of the stacks. Two proposed structural models are tested by comparing calculated spectra to experimental data from electron microscopy, CD and IR spectroscopy, resulting in a better insight into the specific supramolecular interactions that lead to self-replication. Specifically, we find a cooperative self-assembly process in which β-sheet formation leads to well-organized structures, while also the aromatic core of the macrocycles plays an important role in the stability of the resulting fibers.
- Published
- 2017