Plant cytokinesis, a fundamental process of plant life, involves de novo formation of a ‘cell plate’ partitioning the cytoplasm of dividing cells. Cell plate formation is directed by orchestrated delivery, fusion of cytokinetic vesicles, and membrane maturation to form a nascent cell wall by timely deposition of polysaccharides. During cell plate maturation, the fragile membrane network transitions to a fenestrated sheet and finally a young cell wall. Here, we approximated cell plate sub-structures with testable shapes and adopted the Helfrich free energy model for membranes, including a stabilizing and spreading force, to understand the transition from a vesicular network to a fenestrated sheet and mature cell plate. Regular cell plate development in the model was possible, with suitable bending modulus, for a two-dimensional late stage spreading force of 2-6 pN/nm, an osmotic pressure difference of 2-10 kPa, and spontaneous curvature between 0-0.04 nm−1. With these conditions, stable membrane conformation sizes and morphologies emerged in concordance with stages of cell plate development. To reach a mature cell plate, our model required the late-stage onset of a spreading/stabilizing force coupled with a concurrent loss of spontaneous curvature. Absence of a spreading/stabilizing force predicts failure of maturation. The proposed model provides a framework to interrogate different players in late cytokinesis and potentially other membrane networks that undergo such transitions. Callose, is a polysaccharide that accumulates transiently during cell plate maturation. Callose related observations were consistent with the proposed model’s concept, suggesting that it is one of the factors involved in establishing the spreading force.

The recent emergence of the omicron variant of the SARS-CoV-2 virus with large numbers of mutations has raised concern about a potential new surge in infections. Here we use molecular dynamics to study the biophysics of the interface of the omicron spike protein binding to (i) the ACE2 receptor protein, (ii) antibodies from all known binding regions, and (iii) the furin binding domain. Our simulations suggest that while there is significant reduction of antibody binding strength corresponding to escape, the omicron spike pays a cost in terms of weaker receptor binding. The furin cleavage domain is the same or weaker binding than the alpha variant, suggesting less viral load and disease intensity than the extant delta variant.

We demonstrate that AlphaFold and AlphaFold Multimer, implemented within the ColabFold suite, can accurately predict the structures of the furin enzyme with known six residue inhibitory peptides. Noting the similarity of the peptide inhibitors to polybasic furin cleavage domain insertion region of the SARS-CoV-2, which begins at P681, we implement this approach to study the wild type furin cleavage domain for the virus and several mutants. We introduce mutations in silico for alpha, omicron, and delta variants, for several sequences which have been rarely observed, for sequences which have not yet been observed, for other coronaviruses (NL63, OC43, HUK1a, HUK1b, MERS, and 229E), and for the H5N1 flu. We show that interfacial hydrogen bonds between the furin cleavage domain and furin are a good measure of binding strength that correlate well with endpoint binding free energy estimates, and conclude that among all candidate viral sequences studied, delta is near the very top binding strength within statistical accuracy. However, the binding strength of several rare sequences match delta within statistical accuracy. We find that the furin S1 pocket is optimized for binding arginine as opposed to lysine. This residue, typically at sequence position five, contains the most hydrogen bonds to the furin, and hydrogen bond count for just this residue shows a strong positive correlation with the overall hydrogen bond count . We demonstrate that the root mean square backbone C-alpha fluctuation of the first residue in the furin cleavage domain has a strong negative correlation with the interfacial hydrogen bond count. We show by considering the variation with the number of basic residues that the maximum mean number of interfacial hydrogen bonds expected is 15.7 at 4 basic residues.

Transcriptional and epigenetic regulators shape the chromatin microenvironment and corresponding gene expression during cellular differentiation and homeostasis. Programmable modulators of transcription provide a powerful toolkit for controlling gene dosage in therapeutic applications, but a limited catalog of functional domains constrains their robustness and durability profiles, and large cargo sizes impede clinical delivery. To address these limitations, here we perform high-throughput screening to discover novel classes of transcriptional modulators among human, viral, and archaeal proteomes and characterize their functions in a multitude of endogenous human contexts. We identify compact, potent activators from viral proteomes with exceptional robustness across silent and expressed genes in varied cell types using distinct dCas systems. Insights from predicted 3-dimensional structures and machine learning models enabled us to rationally engineer improved activators, both in potency and persistence. Notably, engineered activators achieved mitotically durable gene activation following transient delivery. Our discovery pipeline provides a predictive rubric for the systematic development of hypercompact activators from unannotated proteomes, yielding superior efficiency and kinetics profiles that broadly expand the epigenetic editing toolkit for therapeutic applications.

Plant cell division involves de novo formation of a 'cell plate' that partitions the cytoplasm of the dividing cell. Cell plate formation is directed by orchestrated delivery of cytokinetic vesicles via the phragmoplast, vesicle fusion, and membrane maturation to the nascent cell wall by the timely deposition of polysaccharides such as callose, cellulose, and crosslinking glycans. In contrast to the role of endomembrane protein regulators the role of polysaccharides, particularly callose, in cell plate development is poorly understood. It has been suggested that the transient accumulation of callose provides an anisotropic spreading force which helps the transition of earlier, membrane-network cell plate stages into a more mature fenestrated sheet stage. Here we present a biophysical model based on the Helfrich free energy for membranes that models this spreading force. We show that proper cell plate development in the model is possible, depending upon the selection of the bending modulus, with a twodimensional spreading force parameter of between 2 − 6 / , an osmotic pressure difference of 2 − 10 , and a range of spontaneous curvature between 0 − 0.04 −1 . With these conditions, we can achieve stable membrane conformations in agreement with observed sizes and morphologies corresponding to intermediate stages of cell plate development. Altogether, our mathematical model predicts that a spreading force generated by callose and/or other polysaccharides, coupled with a concurrent decrease in spontaneous curvature, is vital for the transition of a membrane network to a nearly mature cell plate. Significance StatementPlant cell division features the development of a unique membrane network called the cell plate that matures to a cell wall which separates the two daughter cells. During cell plate development, callose, a β-1-3 glucan polymer, is transiently synthesized at the cell plate only to be replaced by cellulose in mature stages. The role for this transient callose accumulation at the cell plate is unknown. It has been suggested that callose provides mechanical stability, as well as a spreading force that widens and expands tubular and fenestrated cell plate structures to aid the maturation of the cell plate. Chemical inhibition of callose deposition results in the failure of cell plate development supporting this hypothesis. This publication establishes the need for a spreading force in cell plate development using a biophysical model that predicts cell plate development in the presence and the absence of this force. Such models can potentially be used to decipher for the transition/maturation of membrane networks upon the deposition of polysaccharide polymers. Main Text