An Analysis of Nucleotide-Amyloid Interactions Reveals Selective Binding to Codon-Sized RNA.

Interactions between RNA and proteins are the cornerstone of many important biological processes from transcription and translation to gene regulation, yet little is known about the ancient origin of said interactions. We hypothesized that peptide amyloids played a role in the origin of life and that their repetitive structure lends itself to building interfaces with other polymers through avidity. Here, we report that short RNA with a minimum length of three nucleotides binds in a sequence-dependent manner to peptide amyloids. The 3'-5' linked RNA backbone appears to be well-suited to support these interactions, with the phosphodiester backbone and nucleobases both contributing to the affinity. Sequence-specific RNA-peptide interactions of the kind identified here may provide a path to understanding one of the great mysteries rooted in the origin of life: the origin of the genetic code.

Super-resolution NMR spectroscopy.

Spectral resolution is one of the limiting factors in nuclear magnetic resonance (NMR) spectroscopy of biological systems where signal overlap often interferes with chemical shift assignment as well as dynamics and structure analysis. This problem can be addressed in part by using higher magnetic field NMR spectrometers operating at up to 1.2 GHz 1H frequency to enhance the resolution proportionally with the field strength, and by deuteration in combination with transverse relaxation-optimized spectroscopy that reduces the transverse relaxation rate and proportionally the resonance linewidth of the peaks yielding higher spectral resolution. As a complement or alternative to these expensive and often insufficient approaches, we present here a generally applicable method to reduce the linewidth of peaks in indirect dimensions of multi-dimensional NMR spectra by increasing the number of scans per time increment exponentially as a function of time in order to compensate, in part, the decay of the signal caused by transverse relaxation. This enables to achieve a user-defined linewidth of the peaks without undue increase of the noise. Optimization by including in the number of scans also a cosine apodization function as well as processing spectra with an exponential-cosine window function in the direct dimension results typically in a resolution enhancement (linewidth reduction) by a factor of 1.5-2 in comparison to a standard measurement with a constant number of scans per time increment. This is comparable to the 2-fold resolution enhancement that can be obtained by going from a 600 MHz 1H frequency NMR spectrometer to a 1.2 GHz instrument, or from 1.2 GHz to a spectrum measured hypothetically at 2.4 GHz 1H frequency. A factor of two resolution enhancement causes thereby a signal to noise loss of a factor of three. The sensitivity gain by dynamic number of scan sampling is thereby ∼20 % over the use of a digital apodization function.

NMR tools to detect protein allostery.

Allostery is a fundamental mechanism of cellular homeostasis by intra-protein communication between distinct functional sites. It is an internal process of proteins to steer interactions not only with each other but also with other biomolecules such as ligands, lipids, and nucleic acids. In addition, allosteric regulation is particularly important in enzymatic activities. A major challenge in structural and molecular biology today is unraveling allosteric sites in proteins, to elucidate the detailed mechanism of allostery and the development of allosteric drugs. Here we summarize the recently developed tools and approaches which enable the elucidation of regulatory hotspots and correlated motion in biomolecules, focusing primarily on solution-state nuclear magnetic resonance spectroscopy (NMR). These tools open an avenue towards a rational understanding of the mechanism of allostery and provide essential information for the design of allosteric drugs.

Membrane-induced tau amyloid fibrils.

The intrinsically disordered protein tau aggregates into ß-sheet amyloid fibrils that spread in human brains afflicted with Alzheimer's disease and other neurodegenerative diseases. Tau interaction with lipid membranes might play a role in the formation and spreading of these pathological aggregates. Here we investigate the conformation and assembly of membrane-induced tau aggregates using solid-state NMR and transmission electron microscopy. A tau construct that encompasses the microtubule-binding repeats and a proline-rich domain is reconstituted into cholesterol-containing phospholipid membranes. 2D 13C-13C correlation spectra indicate that tau converted from a random coil to a ß-sheet conformation over weeks. Small unilamellar vesicles (SUVs) cause different equilibrium conformations from large unilamellar vesicles (LUVs) and multilamellar vesicles (MLVs). Importantly, SUV-bound tau developed long fibrils that exhibit the characteristic ß-sheet chemical shifts of Tyr310 in heparin-fibrillized tau. In comparison, LUVs and MLVs do not induce fibrils but cause different ß-sheet aggregates. Lipid-protein correlation spectra indicate that these tau aggregates reside at the membrane-water interface, without inserting into the middle of the lipid bilayer. Removal of cholesterol from the SUVs abolished the fibrils, indicating that both membrane curvature and cholesterol are required for tau fibril formation. These results have implications for how lipid membranes might nucleate tau aggregates.