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Open Access Publications from the University of California

Scholarly Works (6 results)

  • Article
  • Peer Reviewed
UC San Francisco Previously Published Works (2013)
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.
    Cover page: Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals
    • Article
    • Peer Reviewed
    UC San Francisco Previously Published Works (2014)
    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.
      Cover page: Short peptides self-assemble to produce catalytic amyloids.
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2019)
      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.
        Cover page: Asphaltene Adsorption from Toluene onto Silica through Thin Water Layers
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2018)

        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.

          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2019)
          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.
            Cover page: Calcium Ion Bridging of Aqueous Carboxylates onto Silica: Implications for Low-Salinity Waterflooding
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2012)
            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.
              Cover page: Development of α‑Helical Calpain Probes by Mimicking a Natural Protein–Protein Interaction
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