EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies

A method for detecting structural homologs of components in an intermediate resolution cryo-EM map and their spatial configuration is presented

The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems

Intracellular phase separation is emerging as a universal principle for organizing biochemical reactions in time and space. It remains incompletely resolved how biological function is encoded in these assemblies and whether this depends on their material state. The conserved intrinsically disordered protein PopZ forms condensates at the poles of the bacterium Caulobacter crescentus, which in turn orchestrate cell-cycle regulating signaling cascades. Here we show that the material properties of these condensates are determined by a balance between attractive and repulsive forces mediated by a helical oligomerization domain and an expanded disordered region, respectively. A series of PopZ mutants disrupting this balance results in condensates that span the material properties spectrum, from liquid to solid. A narrow range of condensate material properties supports proper cell division, linking emergent properties to organismal fitness. We use these insights to repurpose PopZ as a modular platform for generating tunable synthetic condensates in human cells

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

A set of software tools for building and distributing models of macromolecular assemblies uses an integrative structure modeling approach, which casts the building of models as a computational optimization problem where information is encoded into a scoring function used to evaluate candidate models

Poly(A)-binding protein is an ataxin-2 chaperone that regulates biomolecular condensates

Biomolecular condensation underlies the biogenesis of an expanding array of membraneless assemblies, including stress granules (SGs), which form under a variety of cellular stresses. Advances have been made in understanding the molecular grammar of a few scaffold proteins that make up these phases, but how the partitioning of hundreds of SG proteins is regulated remains largely unresolved. While investigating the rules that govern the condensation of ataxin-2, an SG protein implicated in neurodegenerative disease, we unexpectedly identified a short 14 aa sequence that acts as a condensation switch and is conserved across the eukaryote lineage. We identify poly(A)-binding proteins as unconventional RNA-dependent chaperones that control this regulatory switch. Our results uncover a hierarchy of cis and trans interactions that fine-tune ataxin-2 condensation and reveal an unexpected molecular function for ancient poly(A)-binding proteins as regulators of biomolecular condensate proteins. These findings may inspire approaches to therapeutically target aberrant phases in disease.Funding: work in the A.D.G. lab is supported by NIH (grant R35NS097263). A.D.G. is a Chan Zuckerberg Biohub investigator. Work in the S.B. lab is supported by CPRIT (RR220094) and NSF (WALII, DBI grant # 2213983). S.B. acknowledges an EMBO Long Term Fellowship. Y.D. was supported by the Stanford Graduate Fellowship in Science and Engineering, Carnegie Institution for Science, and Brigitte Berthelemot. G.K. is supported by a fellowship from the Knight-Hennessy Scholars Program at Stanford University. The Stanford Neuroscience Microscopy Service is supported by NIH (grant NS069375). Work in the I.R.-T. lab was supported by a grant (BFU2017-90114-P) from Ministerio de Economía y Competitividad (MINECO), Agencia Estatal de Investigación (AEI), and Fondo Europeo de Desarrollo Regional (FEDER) to I.R.-T. Work in the R.D. lab was supported by NIH (grant AI140421). Work in the Y.L. lab is supported by the National Natural Science Foundation of China (grant # 32170684). A.S.H. is supported by the Human Frontier Science Program (RGP0015/2022) and NSF (WALII, DBI grant # 2213983). D.G. is supported by an NSF Graduate Research Fellowship (DGE-2139839).Peer reviewe

Toward an Integrated Structural Model of the 26S Proteasome*

The 26S proteasome is the end point of the ubiquitin-proteasome pathway and degrades ubiquitylated substrates. It is composed of the 20S core particle (CP), where degradation occurs, and the 19S regulatory particle (RP), which ensures substrate specificity of degradation. Whereas the CP is resolved to atomic resolution, the architecture of the RP is largely unknown. We provide a comprehensive analysis of the current structural knowledge on the RP, including structures of the RP subunits, physical protein-protein interactions, and cryoelectron microscopy data. These data allowed us to compute an atomic model for the CP-AAA-ATPase subcomplex. In addition to this atomic model, further subunits can be mapped approximately, which lets us hypothesize on the substrate path during its degradation