Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking.

Single-particle cryo-EM is widely used to determine enzyme-nucleosome complex structures. However, cryo-EM sample preparation remains challenging and inconsistent due to complex denaturation at the air-water interface (AWI). To address this issue, we developed graphene-oxide-coated EM grids functionalized with either single-stranded DNA (ssDNA) or thiol-poly(acrylic acid-co-styrene) (TAASTY) co-polymer. These grids protect complexes between the chromatin remodeler SNF2h and nucleosomes from the AWI and facilitated collection of high-quality micrographs of intact SNF2h-nucleosome complexes in the absence of crosslinking. The data yields maps ranging from 2.3 to 3 Å in resolution. 3D variability analysis reveals nucleotide-state linked conformational changes in SNF2h bound to a nucleosome. In addition, the analysis provides structural evidence for asymmetric coordination between two SNF2h protomers acting on the same nucleosome. We envision these grids will enable similar detailed structural analyses for other enzyme-nucleosome complexes and possibly other protein-nucleic acid complexes in general.

Membrane mimetic systems in CryoEM: keeping membrane proteins in their native environment.

Advances in electron microscopes, detectors and data processing algorithms have greatly facilitated the structural determination of many challenging integral membrane proteins that have been evasive to crystallization. These breakthroughs facilitate the application and development of various membrane protein solubilization approaches for structural studies, including reconstitution into lipid nanoparticles. In this review, we discuss various approaches for preparing transmembrane proteins for structural determination with single-particle electron cryo microscopy (cryoEM).

Interactions of a Bacterial Cu(I)-ATPase with a Complex Lipid Environment.

Phospholipids and sterols play multiple roles in cells. In addition to establishing barriers between compartments, they also provide the matrix for assembly and function of a large variety of catalytic processes. Lipid composition is a highly regulated feature of biological membranes, yet its implications for membrane proteins are difficult problems to approach. One obstacle is the inherent complexity of observing and describing these interactions and their dynamics at a molecular and atomic level. However, lipid interactions are pivotal for membrane protein function and should be acknowledged. The enzymatic activity of several different P-type ATPases, one of the major families of ion pumping primary active transporters, has previously been shown to exhibit a strong dependence on phospholipids; however, distinguishing the effects of annular and specific lipid interactions is challenging. Here we show that the hydrolytic activity of a bacterial Cu(I)-transporting P-type ATPase (LpCopA) is stimulated by the bacterial, anionic phospholipid cardiolipin and to some extent by phosphatidylglycerol. Furthermore, multiscale molecular dynamics simulations pinpoint lipid hot spots on the membrane-spanning domain of LpCopA. Thus, using two independent methods, our study shows converging evidence that the lipid membrane composition plays an important role for LpCopA.

Structure of the human TRPM4 ion channel in a lipid nanodisc.

Transient receptor potential (TRP) melastatin 4 (TRPM4) is a widely expressed cation channel associated with a variety of cardiovascular disorders. TRPM4 is activated by increased intracellular calcium in a voltage-dependent manner but, unlike many other TRP channels, is permeable to monovalent cations only. Here we present two structures of full-length human TRPM4 embedded in lipid nanodiscs at ~3-angstrom resolution, as determined by single-particle cryo-electron microscopy. These structures, with and without calcium bound, reveal a general architecture for this major subfamily of TRP channels and a well-defined calcium-binding site within the intracellular side of the S1-S4 domain. The structures correspond to two distinct closed states. Calcium binding induces conformational changes that likely prime the channel for voltage-dependent opening.

Controlling Styrene Maleic Acid Lipid Particles through RAFT.

The ability of styrene maleic acid copolymers to dissolve lipid membranes into nanosized lipid particles is a facile method of obtaining membrane proteins in solubilized lipid discs while conserving part of their native lipid environment. While the currently used copolymers can readily extract membrane proteins in native nanodiscs, their highly disperse composition is likely to influence the dispersity of the discs as well as the extraction efficiency. In this study, reversible addition-fragmentation chain transfer was used to control the polymer architecture and dispersity of molecular weights with a high-precision. Based on Monte Carlo simulations of the polymerizations, the monomer composition was predicted and allowed a structure-function analysis of the polymer architecture, in relation to their ability to assemble into lipid nanoparticles. We show that a higher degree of control of the polymer architecture generates more homogeneous samples. We hypothesize that low dispersity copolymers, with control of polymer architecture are an ideal framework for the rational design of polymers for customized isolation and characterization of integral membrane proteins in native lipid bilayer systems.

Water-mediated interactions influence the binding of thapsigargin to sarco/endoplasmic reticulum calcium adenosinetriphosphatase.

A crystal structure suggests four water molecules are present in the binding cavity of thapsigargin in sarco/endoplasmic reticulum calcium ATPase (SERCA). Computational chemistry indicates that three of these water molecules mediate an extensive hydrogen-bonding network between thapsigargin and the backbone of SERCA. The orientation of the thapsigargin molecule in SERCA is crucially dependent on these interactions. The hypothesis has been verified by measuring the affinity of newly synthesized model compounds, which are prevented from participating in such water-mediated interactions as hydrogen-bond donors.

On allosteric modulation of P-type Cu(+)-ATPases.

P-type ATPases perform active transport of various compounds across biological membranes and are crucial for ion homeostasis and the asymmetric composition of lipid bilayers. Although their functional cycle share principles of phosphoenzyme intermediates, P-type ATPases also show subclass-specific sequence motifs and structural elements that are linked to transport specificity and mechanistic modulation. Here we provide an overview of the Cu(+)-transporting ATPases (of subclass PIB) and compare them to the well-studied sarco(endo)plasmic reticulum Ca(2+)-ATPase (of subclass PIIA). Cu(+) ions in the cell are delivered by soluble chaperones to Cu(+)-ATPases, which expose a putative "docking platform" at the intracellular interface. Cu(+)-ATPases also contain heavy-metal binding domains providing a basis for allosteric control of pump activity. Database analysis of Cu(+) ligating residues questions a two-site model of intramembranous Cu(+) binding, and we suggest an alternative role for the proposed second site in copper translocation and proton exchange. The class-specific features demonstrate that topological diversity in P-type ATPases may tune a general energy coupling scheme to the translocation of compounds with remarkably different properties.