Oliver B. Clarke

Minimal requirements for actin filament disassembly revealed by structural analysis of malaria parasite actin-depolymerizing factor 1

Malaria parasite cell motility is a process that is dependent on the dynamic turnover of parasite-derived actin filaments. Despite its central role, actins polymerization state is controlled by a set of identifiable regulators that is markedly reduced compared with those of other eukaryotic cells. In Plasmodium falciparum, the most virulent species that affects humans, this minimal repertoire includes two members of the actin-depolymerizing factor/cofilin (AC) family of proteins, P. falciparum actin-depolymerizing factor 1 (PfADF1) and P. falciparum actin-depolymerizing factor 2. This essential class of actin regulator is involved in the control of filament dynamics at multiple levels, from monomer binding through to filament depolymerization and severing. Previous biochemical analyses have suggested that PfADF1 sequesters monomeric actin but, unlike most eukaryotic counterparts, has limited potential to bind or depolymerize filaments. The molecular basis for these unusual properties and implications for parasite cell motility have not been established. Here we present the crystal structure of an apicomplexan AC protein, PfADF1. We show that PfADF1 lacks critical residues previously implicated as essential for AC-mediated actin filament binding and disassembly, having a substantially reduced filament-binding loop and C-terminal α4 helix. Despite this divergence in structure, we demonstrate that PfADF1 is capable of efficient actin filament severing. Furthermore, this severing occurs despite PfADF1’s low binding affinity for filaments. Comparative structural analysis along with biochemical and microscopy evidence establishes that severing is reliant on the availability of an exposed basic residue in the filament-binding loop, a conserved minimal requirement that defines AC-mediated filament disassembly across eukaryotic cells.

Structures of aminoarabinose transferase ArnT suggest a molecular basis for lipid A glycosylation

A bacterial defense mechanism Polymyxins are antibiotics that disrupt the bacterial cell membrane and are used to treat multidrug-resistant infections. A bacterial enzyme called ArnT can mediate resistance to polymyxins by transferring a sugar group from a lipid carrier to lipid A, a component of the bacterial outer membrane. Petrou et al. described structures of ArnT alone and in complex with a lipid carrier and identified a cavity where lipid A probably binds. Insights into the enzyme mechanism could be exploited to design drugs that combat polymyxin resistance. Science, this issue p. 608 Structural studies elucidate the mechanism of a reaction that contributes to antibiotic resistance in Gram-negative bacteria. Polymyxins are antibiotics used in the last line of defense to combat multidrug-resistant infections by Gram-negative bacteria. Polymyxin resistance arises through charge modification of the bacterial outer membrane with the attachment of the cationic sugar 4-amino-4-deoxy-l-arabinose to lipid A, a reaction catalyzed by the integral membrane lipid-to-lipid glycosyltransferase 4-amino-4-deoxy-l-arabinose transferase (ArnT). Here, we report crystal structures of ArnT from Cupriavidus metallidurans, alone and in complex with the lipid carrier undecaprenyl phosphate, at 2.8 and 3.2 angstrom resolution, respectively. The structures show cavities for both lipidic substrates, which converge at the active site. A structural rearrangement occurs on undecaprenyl phosphate binding, which stabilizes the active site and likely allows lipid A binding. Functional mutagenesis experiments based on these structures suggest a mechanistic model for ArnT family enzymes.

Structure of the STRA6 receptor for retinol uptake.

A window into the cell for vitamin A Vitamin A is an essential nutrient for mammals, and its metabolites affect diverse biological processes. It is carried in the bloodstream as retinol by retinol binding protein (RBP); a protein called STRA6 is implicated in facilitating retinol translocation across the cell membrane. Chen et al. determined the structure of zebrafish STRA6 to a resolution of 3.9 Å by electron microscopy. A lipophilic cleft is a likely binding site for RBP, and an opening in the cleft may allow retinol to diffuse into the membrane. Unexpectedly, the structure also includes bound calcium-modulated protein, but its function remains unclear. Science, this issue p. 887 The structure of a STRA6-calmodulin complex gives insight into how retinol (vitamin A) enters cells. INTRODUCTION Vitamin A is an essential nutrient for all mammals, being vital for vision and for transcription of a wide array of genes. Retinol (vitamin A alcohol) is the predominant circulating retinoid. In the fasting state, retinol from liver stores is mobilized bound to retinol-binding protein (RBP), which transports this highly hydrophobic molecule in the bloodstream. How retinol is released from RBP and internalized by target cells has been the subject of intense debate. The RBP receptor, STRA6, was cloned in 2007. STRA6 was predicted to be a 75-kDa multipass transmembrane (TM) protein without sequence similarity to any known transporter, channel, or receptor. STRA6 is expressed widely, with particular abundance in the eye and placenta. Mutations in the human STRA6 gene have been linked to Matthew-Wood syndrome, which presents with ocular abnormalities and developmental defects. RATIONALE Despite a wealth of biochemical work aimed at investigating how STRA6 mediates internalization of retinol from RBP, progress at the molecular level has been hindered by the absence of structural information. Purified STRA6 from zebrafish was a detergent-stable dimer in an unexpected association with calmodulin (CaM), forming a 180-kDa complex. RESULTS Using cryo-electron microscopy, we determined the structure of zebrafish STRA6 in complex with CaM to 3.9 Å resolution. The protein is assembled as an intricate dimer with a topology that includes 18 TM helices (nine per protomer) and two long horizontal intramembrane (IM) helices interacting at the dimer core. Each STRA6 protomer comprises an N-terminal domain (NTD) of the first five TM helices, connected by a linker containing the first CaM-binding peptide to a central domain at the dimer interface that includes TMs 6 to 9 and the IM helices, and a cytoplasmic C-terminal segment that interacts with CaM through two additional helices. Each protomer is compactly associated with one molecule of CaM, adopting an unconventional arrangement in which it is bound to three helical regions of STRA6. We characterized the STRA6-CaM interaction biophysically by isothermal titration calorimetry, showing that the affinity of CaM for one STRA6 peptide alone is subnanomolar, and structurally by x-ray crystallography. We also demonstrated that the STRA6-CaM association is physiological by performing immunoprecipitation experiments on native zebrafish tissue. Both the extra- and intracellular surfaces of the NTD feature conserved polar pockets. The outer NTD pocket spans half the bilayer. The central domain of STRA6 defines a large ~20,000 Å3 cleft on the extracellular side, which encompasses the space between previously characterized binding sites for RBP, ~25 Å above the membrane surface, and the IM helices located down at the mid-bilayer level. This outer cleft is hydrophobic, contains two ordered putative cholesterols, and is exposed to the membrane through two symmetry-related lateral windows defined by TMs 8 and 9 and the IM helices. CONCLUSIONS The structure of STRA6 suggests a mechanism for retinol release from RBP into the hydrophobic environment of the outer cleft and direct diffusion into the membrane through the lateral window. Our work also sets the basis for future experiments aimed at investigating how the system is regulated, whether STRA6 also has a role in signaling, and the functional relevance of its association with CaM. The structure of STRA6 in complex with CaM. The STRA6 dimer, drawn as a ribbon representation with one protomer in dark red and the other in black, is associated with two molecules of calmodulin, drawn in gray and gold. The internal volume of the outer cleft is represented as a semitransparent blue surface. Calcium ions are represented as green spheres. Vitamin A homeostasis is critical to normal cellular function. Retinol-binding protein (RBP) is the sole specific carrier in the bloodstream for hydrophobic retinol, the main form in which vitamin A is transported. The integral membrane receptor STRA6 mediates cellular uptake of vitamin A by recognizing RBP-retinol to trigger release and internalization of retinol. We present the structure of zebrafish STRA6 determined to 3.9-angstrom resolution by single-particle cryo-electron microscopy. STRA6 has one intramembrane and nine transmembrane helices in an intricate dimeric assembly. Unexpectedly, calmodulin is bound tightly to STRA6 in a noncanonical arrangement. Residues involved with RBP binding map to an archlike structure that covers a deep lipophilic cleft. This cleft is open to the membrane, suggesting a possible mode for internalization of retinol through direct diffusion into the lipid bilayer.

Structural basis for catalysis in a CDP-alcohol phosphotransferase.

The CDP-alcohol phosphotransferase (CDP-AP) family of integral membrane enzymes catalyzes the transfer of a substituted phosphate group from a CDP-linked donor to an alcohol-acceptor. This is an essential reaction for phospholipid biosynthesis across all kingdoms of life, and it is catalyzed solely by CDP-APs. Here we report the 2.0 Å resolution crystal structure of a representative CDP-AP from Archaeoglobus fulgidus. The enzyme (AF2299) is a homodimer, with each protomer consisting of six transmembrane helices and an N-terminal cytosolic domain. A polar cavity within the membrane accommodates the active site, lined with the residues from an absolutely conserved CDP-AP signature motif (D1xxD2G1xxAR…G2xxxD3xxxD4). Structures in the apo, CMP-bound, CDP-bound and CDP-glycerol-bound states define functional roles for each of these eight conserved residues and allow us to propose a sequential, base-catalyzed mechanism universal for CDP-APs, in which the fourth aspartate (D4) acts as the catalytic base.

Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis.

The attachment of a sugar to a hydrophobic polyisoprenyl carrier is the first step for all extracellular glycosylation processes. The enzymes that perform these reactions, polyisoprenyl-glycosyltransferases (PI-GTs) include dolichol phosphate mannose synthase (DPMS), which generates the mannose donor for glycosylation in the endoplasmic reticulum. Here we report the 3.0Å resolution crystal structure of GtrB, a glucose-specific PI-GT from Synechocystis, showing a tetramer in which each protomer contributes two helices to a membrane-spanning bundle. The active site is 15 Å from the membrane, raising the question of how water-soluble and membrane-embedded substrates are brought into apposition for catalysis. A conserved juxtamembrane domain harbours disease mutations, which compromised activity in GtrB in vitro and in human DPM1 tested in zebrafish. We hypothesize a role of this domain in shielding the polyisoprenyl-phosphate for transport to the active site. Our results reveal the basis of PI-GT function, and provide a potential molecular explanation for DPM1-related disease.

Structures of the colossal RyR1 calcium release channel

Ryanodine receptors (RyRs) are intracellular cation channels that mediate the rapid and voluminous release of Ca2+ from the sarcoplasmic reticulum (SR) as required for excitation-contraction coupling in cardiac and skeletal muscle. Understanding of the architecture and gating of RyRs has advanced dramatically over the past two years, due to the publication of high resolution cryo-electron microscopy (cryoEM) reconstructions and associated atomic models of multiple functional states of the skeletal muscle receptor, RyR1. Here we review recent advances in our understanding of RyR architecture and gating, and highlight remaining gaps in understanding which we anticipate will soon be filled.

Structural basis for phosphatidylinositol-phosphate biosynthesis.

Phosphatidylinositol is critical for intracellular signalling and anchoring of carbohydrates and proteins to outer cellular membranes. The defining step in phosphatidylinositol biosynthesis is catalysed by CDP-alcohol phosphotransferases, transmembrane enzymes that use CDP-diacylglycerol as donor substrate for this reaction, and either inositol in eukaryotes or inositol phosphate in prokaryotes as the acceptor alcohol. Here we report the structures of a related enzyme, the phosphatidylinositol-phosphate synthase from Renibacterium salmoninarum, with and without bound CDP-diacylglycerol to 3.6 and 2.5 Å resolution, respectively. These structures reveal the location of the acceptor site, and the molecular determinants of substrate specificity and catalysis. Functional characterization of the 40%-identical ortholog from Mycobacterium tuberculosis, a potential target for the development of novel anti-tuberculosis drugs, supports the proposed mechanism of substrate binding and catalysis. This work therefore provides a structural and functional framework to understand the mechanism of phosphatidylinositol-phosphate biosynthesis.

Structural basis for catalysis at the membrane-water interface.

The membrane-water interface forms a uniquely heterogeneous and geometrically constrained environment for enzymatic catalysis. Integral membrane enzymes sample three environments - the uniformly hydrophobic interior of the membrane, the aqueous extramembrane region, and the fuzzy, amphipathic interfacial region formed by the tightly packed headgroups of the components of the lipid bilayer. Depending on the nature of the substrates and the location of the site of chemical modification, catalysis may occur in each of these environments. The availability of structural information for alpha-helical enzyme families from each of these classes, as well as several beta-barrel enzymes from the bacterial outer membrane, has allowed us to review here the different ways in which each enzyme fold has adapted to the nature of the substrates, products, and the unique environment of the membrane. Our focus here is on enzymes that process lipidic substrates. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.

Single-channel recordings of RyR1 at microsecond resolution in CMOS-suspended membranes

Significance We present a method for measuring the conductance of ion channels at bandwidths up to 500 kHz by fabricating lipid membranes directly on the surface of a custom amplifier chip. We apply this approach to the RyR1 receptor, enabling us to identify additional closed states for calcium-dependent inactivation at microsecond temporal resolutions. Additional data analysis using extended beta distributions allows us to detect gating events as short as 35 ns, a timescale that approaches that of single-file ion translocation. These measurement techniques hold the promise of reaching timescales for studying the kinetics of ion channels, achievable now only with computer-based molecular dynamics simulations. Single-channel recordings are widely used to explore functional properties of ion channels. Typically, such recordings are performed at bandwidths of less than 10 kHz because of signal-to-noise considerations, limiting the temporal resolution available for studying fast gating dynamics to greater than 100 µs. Here we present experimental methods that directly integrate suspended lipid bilayers with high-bandwidth, low-noise transimpedance amplifiers based on complementary metal-oxide-semiconductor (CMOS) integrated circuits (IC) technology to achieve bandwidths in excess of 500 kHz and microsecond temporal resolution. We use this CMOS-integrated bilayer system to study the type 1 ryanodine receptor (RyR1), a Ca2+-activated intracellular Ca2+-release channel located on the sarcoplasmic reticulum. We are able to distinguish multiple closed states not evident with lower bandwidth recordings, suggesting the presence of an additional Ca2+ binding site, distinct from the site responsible for activation. An extended beta distribution analysis of our high-bandwidth data can be used to infer closed state flicker events as fast as 35 ns. These events are in the range of single-file ion translocations.