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Biology subjects

Moudgal, N.

Publications and source records attributed to Moudgal, N..

2 recordsLinked to original sources

Fourier Helicity Spectra as Quantifiers of Multiscale Chirality

Quantifying the chirality of three-dimensional (3D) objects is crucial for understanding interactions of nanoscale structures, biological molecules, and hierarchical materials. Although chirality is simultaneously present at multiple scales for each case, existing chirality measures rely only on singular scale-specific quantifiers, and some of them yield incorrect chirality assignments for biomolecules. Here we introduce the Fourier Helicity Spectra, a mathematical framework to decompose geometry of chemical and biological structures encompassing the scale dependence of mirror asymmetry. Fourier decomposition of 3D objects into helical harmonics enables one to compute a handedness-resolved characteristics of complex shapes, while reducing computational cost. We show its applicability for a diverse range of chemical systems, from biomacromolecular electron densities to tomographic reconstructions of inorganic nanostructures. Furthermore, inverse transform of isolated spectral components into real space enables visualization of helicity-matched interfaces, identifying how chirality governs biomolecular interactions. We anticipate that this methodology can be generalized with alternative basis sets to encompass a broad range of chiral symmetries governing biological signaling, polarization optics, drug design, and advanced synthesis.

bioinformatics↗

Using Unassigned NMR Chemical Shifts to Model RNA Secondary Structure

NMR-derived chemical shifts are sensitive probes of RNA structure. However, the need to assign NMR spectra hampers their utility as a direct source of structural information. In this report, we describe a simple method that uses unassigned 2D NMR spectra to model the secondary structure of RNAs. Similar to assigned chemical shifts, we could use unassigned chemical shift data to reweight conformational libraries such that the highest weighted structure closely resembles their reference NMR structure. Furthermore, the application of our approach to the 3- and 5-UTR of the SARS-CoV-2 genome yields structures that are, for the most part, consistent with the secondary structure models derived from chemical probing data. Therefore, we expect the framework we describe here will be useful as a general strategy for rapidly generating preliminary structural RNA models directly from unassigned 2D NMR spectra. As we demonstrated for the 337-nt and 472-nt UTRs of SARS-CoV-2, our approach could be especially valuable for modeling the secondary structures of large RNA.

biophysics↗