Systems Chemistry and Nested Biomolecular Information

The Plant Microbiome as an External Organ

The rhizosphere is the most complex systems on the planet consisting of microbes, fungi, and complex chemical reaction. Thus far, it has been shown that there is a spatial and temporal relationship that exists within the rhizosphere between plant roots and parasites surrounding plant roots, but thus far we do not know how this spatial temporal relationship is established nor how it works. Currently, the Lynn lab is interested in understanding diffusion in space and time within the rhizosphere between plant roots and microbes and how this spatial temporal relationship impacts climate change.

Organizing the Rhizosphere Participants into a Plant Organ

Reaction-Diffusion Dynamics Hypothesis: Reduced quinones and O2 released from the host plant root diffuse into the rhizosphere, react with bacterial phenazines (methylene blue), to create autocatalytic stationary state Turing patterns that define the spatiotemporal ordering of the external organ.

Amphiphiles and 2-step Nucleation of Biomaterials

Prion-like low complexity domains (PLCD) exist as head-to-tail linked amphiphiles, accessing liquid-liquid phase transitions enable spatiotemporal cellular organization critical in division, signaling, and transcriptional regulation.

Intrinsically disordered (IDP) biomolecular condensates are found in ribonucleoprotein bodies, the nucleolus, and as domain of ~40% of all eukaryotic proteins.

Peptide/Nucleic Acid Co-assemblies

Oligonucleotides can template assembly of positively charged peptides like Ac-KLVIIAG-NH2 and Ac-RLVIIAG-NH2 into well-ordered cross-β peptide leaflets that order into multi-lamellar nanotubes. While these short peptides can self-assemble into fibrillar structures on their own, the presence of polyanionic templates could provide a different pathway for assembly via charge passivation, which result in entirely different morphology (fibers vs. multilamellar nanotubes). Furthermore, the spatial arrangements of negative charges along the template could greatly affect template stability, dictating whether or not cooperative assembly could occur. These interactions can are also seen in proteins and DNA in vivo, and recapitulating such complex phenomena with such minimal model systems could further elucidate the mechanisms that control dynamic supramolecular assemblies seen in cells.

Sticker/Spacer Oligomers as Primitive Proteins Capable of Novel Functions