Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily.

The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH) domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the largest protein superfamilies, and have diverged to regulate many different signaling proteins and modules such as Dbl homology (DH) and Tec homology (TH) domains. The ligands of approximately 70 PH domains have been validated by binding assays and complexed structures, allowing meaningful extrapolation across the entire superfamily. Here the Membrane Optimal Docking Area (MODA) program is used at a genome-wide level to identify all membrane docking PH structures and map their lipid-binding determinants. In addition to the linear sequence motifs which are employed for phosphoinositide recognition, the three dimensional structural features that allow peripheral membrane domains to approach and insert into the bilayer are pinpointed and can be predicted ab initio. The analysis shows that conserved structural surfaces distinguish which PH domains associate with membrane from those that do not. Moreover, the results indicate that lipid-binding PH domains can be classified into different functional subgroups based on the type of membrane insertion elements they project towards the bilayer

Ice-rich permafrost thaw under sub-aquatic conditions

Degradation of sub-aquatic permafrost can release large quantities of methane into the atmosphere, impact offshore drilling activities, and affect coastal erosion. The degradation rate depends on the duration of inundation, warming rate, sediment characteristics, the coupling of the bottom to the atmosphere through bottom-fast ice, and brine injections into the sediment. The relative importance of these controls on the rate of sub-aquatic permafrost degradation, however, remains poorly understood. This poster presents a conceptual evaluation of sub-aquatic permafrost thaw mechanisms and an approach to their representation using one-dimensional modelling of heat and dissolved salt diffusion. We apply this model to permafrost degradation observed below Peatball Lake on the Alaska North Slope and compare modelling results to talik geometry information inferred from transient electromagnetic (TEM) soundings

Size and conformation limits to secretion of disulfide-bonded loops in autotransporter proteins

Autotransporters are a superfamily of virulence factors typified by a channel-forming C terminus that facilitates translocation of the functional N-terminal passenger domain across the outer membrane of Gram-negative bacteria. This final step in the secretion of autotransporters requires a translocation-competent conformation for the passenger domain that differs markedly from the structure of the fully folded secreted protein. The nature of the translocation-competent conformation remains controversial, in particular whether the passenger domain can adopt secondary structural motifs, such as disulfide- bonded segments, while maintaining a secretion-competent state. Here, we used the endogenous and closely spaced cysteine residues of the plasmid-encoded toxin (Pet) from enteroaggregative Escherichia coli to investigate the effect of disulfide bond-induced folding on translocation of an auto-transporter passenger domain. We reveal that rigid structural elements within disulfide-bonded segments are resistant to autotransporter-mediated secretion. We define the size limit of disulfide-bonded segments tolerated by the autotransporter system demonstrating that, when present, cysteine pairs are intrinsically closely spaced to prevent congestion of the translocator pore by large disulfide-bonded regions. These latter data strongly support the hairpin mode of autotransporter biogenesis

Advancing membrane biology with poly(styrene-co-maleic acid)-based native nanodiscs

CITATION: Overduin, M. & Klumperman, B. 2019. Advancing membrane biology with poly(styrene-co-maleic acid)-based native nanodiscs. European Polymer Journal, 110:63-68, doi:10.1016/j.eurpolymj.2018.11.015.The original publication is available at https://www.sciencedirect.com/science/article/pii/S0014305718311364ENGLISH ABSTRACT: The elucidation of the structures and interactions of proteins and lipids in intact biological membranes remains largely uncharted territory. However, this information is crucial for understanding how organelles are assembled and how transmembrane machines transduce signals. The challenge of seeing how lipids and proteins engage each other in vivo remains difficult but is being aided by a group of amphipathic copolymers that spontaneously fragment native membranes into native nanodiscs. Poly(styrene-co-maleic acid) (SMA) copolymers have proven adept at converting membranes, cells and tissues directly into SMA lipid particles (SMALPs), allowing endogenous lipid: protein complexes to be prepared and analyzed. Unlike other amphipathic polymers such as amphipols, SMALP formation requires no conventional detergents, which typically strip lipid molecules from proteins and can destabilize multimers. A collaborative community of hundreds of investigators known as the SMALP network has emerged to develop and apply new technologies and identify new challenges and design potential solutions. In this contribution, we review recent practices and progress, focusing on novel SMA copolymers, modifications, alternatives and mechanisms. In addition, a brief overview will be provided, with reference to the further contributions to this special issue on the SMALP technology.https://www.sciencedirect.com/science/article/pii/S0014305718311364https://www.sciencedirect.com/science/article/pii/S0014305718311364Publisher's versio

Simulating Saline Permafrost and Cryopeg Evolution Using a Coupled Heat and Salt Diffusion Model

Saline permafrost is primarily found in marine deposits beneath shallow shelf seas and can often extend several kilometres inland from present Arctic coastlines. On land, saline permafrost forms when previously submerged marine sediments are exposed to the atmosphere, either through a sea level regression or post-glacial rebound. Cryopegs are perennially cryotic layers or pockets within permafrost that remain unfrozen due to their high salt content. While heat and salt flow models have been applied to study subsea permafrost degradation, adapting these models to terrestrial saline permafrost remains a significant gap in model development. We utilize a version of the CryoGrid modelling suite that couples heat and salt diffusion. This enables us to simulate the formation of saline permafrost and the development of cryopegs during transitions from sub-aquatic to sub-aerial conditions. As the freezing front descends, ice forms in the sediment matrix, expulsing salts into the remaining unfrozen liquid water at sub-zero temperatures. The increased unfrozen porewater salt concentration gradient increases the rate at which salt diffuses downwards into the sediment column. Over time the thermal gradient weakens, potentially allowing a more effective salt build-up ahead of the freezing front.</jats:p

Mapping subsea permafrost around Tuktoyaktuk Island (Northwest Territories, Canada) using electrical resistivity tomography

Along much of the Arctic coast, shoreline retreat and sea level rise combine to inundate permafrost. Once inundated by seawater, permafrost usually begins to degrade. Tuktoyaktuk Island (Beaufort Sea, Northwest Territories, Canada) is an important natural barrier protecting the harbor of Tuktoyaktuk but will likely be breached within the next 2 decades. The state of subsea permafrost and its depth distribution around the island are, however, still largely unknown. We collected marine electrical resistivity tomography (ERT) surveys (vertical electrical soundings) north and south of Tuktoyaktuk Island using a floating cable with 13 electrodes in a quasi-symmetric Wenner–Schlumberger array configuration. We filtered the data with a new approach to eliminate potentially incorrect measurements due to a curved cable and inverted the profiles with a variety of parameterizations to estimate the position of the ice-bearing permafrost table (IBPT) below the seafloor. Our results indicate that north of Tuktoyaktuk Island, where coastal erosion is considerably faster, IBPT depths range from 5 m below sea level (120 m from the shoreline) to around 20 m b.s.l. (up to 800 m from the shoreline). South of the island, the IBPT dips more steeply and lies at 10 m b.s.l. a few meters from the shore, and 200 m from the shore, it is more than 30 m b.s.l. We discuss how marine ERT can be improved by accurately recording electrode positions, although choices made during data inversion are likely a greater source of uncertainty in the determination of the IBPT position. At Tuktoyaktuk Island, IBPT depths below the seafloor increase with distance from the shoreline; comparing the northern and southern sides of the island, the inclination is inversely proportional to coastline retreat rates. On the island’s north side, the historical coastal retreat rate suggests a mean permafrost degradation rate of 5.3 ± 4.0 cm yr−

Secondary structure and 1H, 13C, 15N resonance assignments of the endosomal sorting protein sorting nexin 3

Sorting nexin 3 (SNX3) belongs to a sub-family of sorting nexins that primarily contain a single Phox homology domain capable of binding phosphoinositides and membranes. We report the complete 1H, 13C and 15N resonance assignments of the full-length human SNX3 protein and identification of its secondary structure elements, revealing a canonical fold and unstructured termini