Search for: All records

The α/β-hydrolase fold superfamily includes esterases and hydroxynitrile lyases which, despite catalyzing different reactions, share a Ser–His–Asp catalytic triad. We report a 1.99 Å resolution crystal structure of HNL6V, an engineered variant of hydroxynitrile lyase fromHevea brasiliensis(HbHNL) containing seven amino-acid substitutions (T11G, E79H, C81L, H103V, N104A, G176S and K236M). The structure reveals that HNL6V maintains the characteristic α/β-hydrolase fold while exhibiting systematic shifts in backbone and catalytic atom positions. Compared with wild-typeHbHNL, the C^αpositions in HNL6V differ by a mean of 0.2 ± 0.1 Å, representing a statistically significant displacement. Importantly, the catalytic triad and oxyanion-hole atoms have moved 0.2–0.8 Å closer to their corresponding positions in SABP2, although they remain 0.3–1.1 Å from fully achieving the configuration of SABP2. The substitutions also increase local flexibility, particularly in the lid domain covering the active site. This structural characterization demonstrates that targeted amino-acid substitutions can systematically shift catalytic geometries towards those of evolutionarily related enzymes. 

Hydroxynitrile lyase fromHevea brasiliensis(HbHNL) and the esterase SABP2 fromNicotiana tabacumshare the α/β-hydrolase fold, a Ser–His–Asp catalytic triad and 44% sequence identity, yet catalyze different reactions. Prior studies showed that three active-site substitutions inHbHNL conferred weak esterase activity. To investigate how regions beyond the active site influence catalytic efficiency and active-site geometry, we engineeredHbHNL variants with increasing numbers of substitutions to match SABP2. Variant HNL16 has all amino acids within 6.5 Å of the active site identical to SABP2, HNL40 those within 10 Å and HNL71 those within 14 Å. HNL16 exhibited poor esterase activity, whereas both HNL40 and HNL71 showed efficient esterase catalysis, demonstrating that residues beyond the immediate active site are critical for functional conversion. X-ray structures of HNL40 and HNL71 reveal a progressive shift in backbone positions toward those of SABP2, with r.m.s.d. values of 0.51 Å (HNL40) and 0.41 Å (HNL71) over the C^αatoms, and even smaller r.m.s.d.s within the active-site region. Both HNL40 and HNL71 show a restored oxyanion hole and an additional tunnel connecting the active site to the protein surface. This work demonstrates the essential role of distant, indirectly acting residues to catalysis in α/β-hydrolase enzymes. 

Porphyry Cu ± Mo ± Au and iron oxide-apatite (IOA) deposits rarely occur in spatial and temporal proximity in Phanerozoic arc-related settings, and the formation of these mineral deposit types in an evolving arc setting remains poorly understood. Specifically, the roles of magma composition and the tectonic regime remain the subject of some debate. Here, we systematically estimated the P-T-fO2 conditions and H2O-S-Cl contents for dioritic to granodioritic source magmas for porphyry and skarn Cu ± Au (150–135 Ma) and IOA deposits (~130 Ma) that formed in transpressional and transtensional settings in the Middle-Lower Yangtze River metallogenic belt, China. Our estimates show that, compared to IOA deposits, the porphyry- and skarn-related magmas were relatively felsic, cooler, and more hydrous. These geochemical features are consistent with the tectonic transition from subduction to slab rollback of the paleo-Pacific plate in the East Asia continental margin at <135 Ma and concomitant crustal extension and steepening of the regional geothermal gradient. Apatite data reveal that the silicate melts associated with the porphyry and skarn Cu ± Au and IOA deposits had comparable predegassed S concentrations (~0.13 ± 0.06 wt % vs. ~0.16 ± 0.09 wt % on average), but that IOA-related melts contained higher predegassed Cl/H2O ratios (~0.11 ± 0.03 vs. ~0.04 ± 0.03 for porphyry- and skarn-related magmas) that decreased by one order of magnitude after magmatic degassing. Magmatic fO2 estimated using zircon and amphibole, reported in log units relative to the fayalite-magnetite-quartz (FMQ) redox buffer, gradually increased during cooling of the porphyry- and skarn-related magmas (ΔFMQ +0.7 to +2.5) at 950° to 800°C and decreased to ΔFMQ +1 at 700°C owing to fractionation of Fe2+-rich minerals and subsequent S degassing, respectively. In contrast, the magmatic fO2 values for the IOA-related source magmas varied significantly from ΔFMQ –1.5 to ΔFMQ +2.5 but generally show an increasing trend with cooling from 970° to 700°C that probably resulted from variable degrees of evaporite assimilation, fractionation of Fe2+-rich minerals, and Cl degassing. These results are consistent with the hypothesis that Cl enrichment of the IOA-related source magmas played a determinant role in their formation. We propose that the porphyry and skarn Cu ± Au deposits in the Middle-Lower Yangtze River metallogenic belt formed in a transpressional setting in response to paleo-Pacific flat-slab subduction that favored storage and evolution of S-rich hydrous ore-forming magmas at variable crustal levels. A subsequent extensional setting formed due to slab rollback, leading to rapid degassing of Cl-rich IOA-related magmas. For the latter scenario, assimilation of evaporite by mafic to intermediate magmas would lead to an enrichment of Cl in the predegassed magmas and subsequent exsolution of hypersaline magmatic-hydrothermal fluid enriched in Fe as FeCl2. This Fe-rich ore fluid efficiently transported Fe to the apical parts of the magma bodies and overlying extensional normal faults where IOA mineralization was localized. The concomitant loss of S, H2O, and Cu with Cl by volcanic outgassing may have inhibited sulfide mineralization at lower temperatures. 

Abstract We begin with a treatment of the Caputo time‐fractional diffusion equation, by using the Laplace transform, to obtain a Volterra integro‐differential equation. We derive and utilize a numerical scheme that is derived in parallel to the L1‐method for the time variable and a standard fourth‐order approximation in the spatial variable. The main method derived in this article has a rate of convergence ofO(k^α + h⁴)foru(x,t) ∈ C^α([0,T];C⁶(Ω)),0 < α < 1, which improves previous regularity assumptions that requireC²[0,T]regularity in the time variable. We also present a novel alternative method for a first‐order approximation in time, under a regularity assumption ofu(x,t) ∈ C¹([0,T];C⁶(Ω)), while exhibiting order of convergence slightly more thanO(k)in time. This allows for a much wider class of functions to be analyzed which was previously not possible under the L1‐method. We present numerical examples demonstrating these results and discuss future improvements and implications by using these techniques.