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Release of crude oil from reservoir rock by low-salinity waterflooding is thought to occur by decreasing the advancing crude oil/brine/rock water contact angle to depin three-phase contact lines (i.e., by increasing reservoir water wettability). Crude oil likely adheres locally to reservoir rock asperities by deposition of asphaltene agglomerates formed at the crude oil/brine interface, following collapse of protective water films. One mechanism proposed for asphaltene adhesion and subsequent release is ion bridging of asphaltenic carboxylate groups protruding through molecularly thin water layers to calcium-occupied rock surface exchange sites, the so-called multicomponent ion exchange mechanism. To our knowledge, however, no experimental evidence directly establishes divalent cation bridging of aqueous carboxylates to anionic mineral surfaces. Using a quartz crystal microbalance with dissipation, we measure adsorption of aqueous carboxylates (benzoate, pentanoate, and hexanoate) onto silica, with and without calcium ion present at near-neutral pH. We find little to no adsorption on a silica surface to within the detection limit of our measurement (±1 Hz, 0.18 mg/m 2 ). Modeling of the silica surface chemistry, using classical ion-complexing triple-layer formalism, reveals that less than 10% of surface-hydroxylated sites actually ionize at pH 7. Of these, not all bind calcium ions. Accordingly, the calcium ion surface density is insufficient to reverse the negative surface charge of silica or to promote significant ion bridging of aqueous carboxylates. In so far as aqueous-soluble carboxylic acids mimic those incorporated in crude oil asphaltenes, we conclude that calcium ion bridging alone does not adhere asphaltenes to silica surfaces.

Asphaltenes in crude oil play a pivotal role in reservoir oil production because they control rock-surface wettability. Upon crude oil invasion into a brine-filled reservoir trap, rock adherence of sticky asphaltene agglomerates formed at the crude oil/brine interface can change the initially water-wet porous medium into mixed-oil wetting. If thick, stable water films coat the rock surfaces, however, asphaltenic-oil adhesion is thought to be prevented. We investigate whether water films influence the uptake of asphaltenes in crude oil onto silica surfaces. Water films of known thickness are formed at a silica surface in a quartz crystal microbalance with dissipation and contacted by toluene-solubilized asphaltene. We confirm that thick water films prevent asphaltene molecular contact with the silica surface blocking asphaltene adhesion. The thicker the water film, the smaller is the amount of asphaltene deposited. Film thickness necessary for complete blockage onto silica is greater than about 500 nm, well beyond the range of molecular-chain contact. Water films of thickness less than 500 nm, sandwiched between toluene and solid silica, apparently rupture into thick water pockets and interposed molecularly thin water layers that permit asphaltene adherence.

De novo design provides an attractive approach to test the mechanism by which metalloproteins define the geometry and reactivity of their metal ion cofactors. While there has been considerable progress in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments has not been accomplished. Here, we describe the design of tetranuclear clusters, consisting of four Zn2+ and four carboxylate oxygens situated at the vertices of a distorted cube-like structure. The tetra-Zn2+ clusters are bound at a buried site within a four-helix bundle, with each helix donating a single carboxylate (Glu or Asp) and imidazole (His) ligand, as well as second- and third-shell ligands. Overall, the designed site consists of four Zn2+ and 16 polar side chains in a fully connected hydrogen-bonded network. The designed proteins have apolar cores at the top and bottom of the bundle, which drive the assembly of the liganding residues near the center of the bundle. The steric bulk of the apolar residues surrounding the binding site was varied to determine how subtle changes in helix-helix packing affect the binding site. The crystal structures of two of four proteins synthesized were in good agreement with the overall design; both formed a distorted cuboidal site stabilized by flanking second- and third-shell interactions that stabilize the primary ligands. A third structure bound a single Zn2+ in an unanticipated geometry, and the fourth bound multiple Zn2+ at multiple sites at partial occupancy. The metal-binding and conformational properties of the helical bundles in solution, probed by circular dichroism spectroscopy, analytical ultracentrifugation, and NMR, were consistent with the crystal structures.

A protective HIV vaccine will likely need to induce broadly neutralizing antibodies (bnAbs). Vaccination with the germline-targeting immunogen eOD-GT8 60mer adjuvanted with AS01B was found to induce VRC01-class bnAb precursors in 97% of vaccine recipients in the IAVI G001 phase 1 clinical trial; however, heterologous boost immunizations with antigens more similar to the native glycoprotein will be required to induce bnAbs. Therefore, we designed core-g28v2 60mer, a nanoparticle immunogen to be used as a first boost after eOD-GT8 60mer priming. We found, using a humanized mouse model approximating human conditions of VRC01-class precursor B cell diversity, affinity, and frequency, that both protein- and mRNA-based heterologous prime-boost regimens induced VRC01-class antibodies that gained key mutations and bound to near-native HIV envelope trimers lacking the N276 glycan. We further showed that VRC01-class antibodies induced by mRNA-based regimens could neutralize pseudoviruses lacking the N276 glycan. These results demonstrated that heterologous boosting can drive maturation toward VRC01-class bnAb development and supported the initiation of the IAVI G002 phase 1 trial testing mRNA-encoded nanoparticle prime-boost regimens. Editor's summary: For a vaccine regimen to be effective against HIV infection, it will need to elicit broadly neutralizing antibodies (bnAbs). However, strategies to elicit bnAbs in humans with a vaccine have not been successful to date. A different strategy, germline-targeting vaccine design, relies on a priming immunogen to first induce bnAb precursors and then a series of heterologous boosters to drive the maturation of bnAb precursors to produce bnAbs. The first step in this process, elicitation of bnAb precursors, has proven successful in clinical trials. Here, Cottrell et al. take the next step by designing and testing the first booster immunogen in the shepherding process. Vaccination of eOD-GT8 60mer-primed humanized mice with their immunogen, core-g28v2 60mer, in either protein or mRNA form resulted in antibodies that were closer to bnAbs than those that received a placebo booster. These data support the ongoing clinical trial testing core-g28v2 60mer mRNA as a booster vaccine. —Courtney Malo [ABSTRACT FROM AUTHOR]

Germline-targeting (GT) protein immunogens to induce VRC01-class broadly neutralizing antibodies (bnAbs) to the CD4-binding site of the HIV envelope (Env) have shown promise in clinical trials. Here, we preclinically validated a lipid nanoparticle–encapsulated nucleoside mRNA (mRNA-LNP) encoding eOD-GT8 60mer as a soluble self-assembling nanoparticle in mouse models. In a model with three humanized B cell lineages bearing distinct VRC01-precursor B cell receptors (BCRs) with similar affinities for eOD-GT8, all lineages could be simultaneously primed and undergo diversification and affinity maturation without exclusionary competition. Boosts drove precursor B cell participation in germinal centers; the accumulation of somatic hypermutations, including in key VRC01-class positions; and affinity maturation to boost and native-like antigens in two of the three precursor lineages. We have preclinically validated a prime-boost regimen of soluble self-assembling nanoparticles encoded by mRNA-LNP, demonstrating that multiple lineages can be primed, boosted, and diversified along the bnAb pathway. Editor's summary: Germline-targeting (GT) vaccination is a promising approach to elicit broadly neutralizing antibodies against conserved sites within the variable HIV envelope (Env) protein. GT vaccination uses an initial "prime" to activate B cells expressing anti-Env bnAb precursors and recruit them into germinal centers. Env-like immunogens are then administered as a "boost," driving increased antibody potency and breadth. Wang et al. characterize mRNA-LNP vaccination with an Env immunogen (eOD-GT8 60mer) as well as three different boost-phase immunogens in mice that had received an adoptive transfer of three distinct knock-in B cell lines, mimicking the competition that occurs in humans between anti-Env precursors. All three precursor lineages showed noncompetitive priming by the same immunogen but disparate responses at the boost stage, providing an important proof of concept for current approaches to GT vaccination. —Seth Thomas Scanlon [ABSTRACT FROM AUTHOR]

Enzymes fold into unique three-dimensional structures, which underlie their remarkable catalytic properties. The requirement to adopt a stable, folded conformation is likely to contribute to their relatively large size (>10,000 Da). However, much shorter peptides can achieve well-defined conformations through the formation of amyloid fibrils. To test whether short amyloid-forming peptides might in fact be capable of enzyme-like catalysis, we designed a series of seven-residue peptides that act as Zn(2+)-dependent esterases. Zn(2+) helps stabilize the fibril formation, while also acting as a cofactor to catalyse acyl ester hydrolysis. These results indicate that prion-like fibrils are able to not only catalyse their own formation, but they can also catalyse chemical reactions. Thus, they might have served as intermediates in the evolution of modern-day enzymes. These results also have implications for the design of self-assembling nanostructured catalysts including ones containing a variety of biological and non-biological metal ions.

Agrobacterium tumefaciens is a broad host range plant pathogen that combinatorially recognizes diverse host molecules including phenolics, low pH, and aldose monosaccharides to activate its pathogenic pathways. Chromosomal virulence gene E (chvE) encodes a periplasmic-binding protein that binds several neutral sugars and sugar acids, and subsequently interacts with the VirA/VirG regulatory system to stimulate virulence (vir) gene expression. Here, a combination of genetics, X-ray crystallography, and isothermal calorimetry reveals how ChvE binds the different monosaccharides and also shows that binding of sugar acids is pH dependent. Moreover, the potency of a sugar for vir gene expression is modulated by a transport system that also relies on ChvE. These two circuits tune the overall system to respond to sugar concentrations encountered in vivo. Finally, using chvE mutants with restricted sugar specificities, we show that there is host variation in regard to the types of sugars that are limiting for vir induction.

We have designed a highly specific inhibitor of calpain by mimicking a natural protein-protein interaction between calpain and its endogenous inhibitor calpastatin. To enable this goal we established a new method of stabilizing an α-helix in a small peptide by screening 24 commercially available cross-linkers for successful cysteine alkylation in a model peptide sequence. The effects of cross-linking on the α-helicity of selected peptides were examined by CD and NMR spectroscopy, and revealed structurally rigid cross-linkers to be the best at stabilizing α-helices. We applied this strategy to the design of inhibitors of calpain that are based on calpastatin, an intrinsically unstable polypeptide that becomes structured upon binding to the enzyme. A two-turn α-helix that binds proximal to the active site cleft was stabilized, resulting in a potent and selective inhibitor for calpain. We further expanded the utility of this inhibitor by developing irreversible calpain family activity-based probes (ABPs), which retained the specificity of the stabilized helical inhibitor. We believe the inhibitor and ABPs will be useful for future investigation of calpains, while the cross-linking technique will enable exploration of other protein-protein interactions.

In order to evaluate the ability of building sealing materials to resist mould infection, the testing method of mould resistance of building sealing materials was studied. The suitable sample thickness was obtained by comparing the three kinds of sample thickness. The matching sample size and inoculation method were obtained by comparing the sample size and inoculation method. Through the screening test of many kinds of mold, select the representative test strains. The results can provide reference for improving the mold resistance testing method of building sealing materials. [ABSTRACT FROM AUTHOR]