Critical mineral deposits commonly form in magmatic-hydrothermal systems including carbonatites and/or alkaline syenites, and more evolved peralkaline granites where the rare earth element (REE) undergo a complex array of partitioning, transport and mineralization. Significant alteration and veining zones develop in these deposits and can be used to vector ore zones in the field [1]. The REE ore minerals typically reflect the characteristics of these systems, which are enriched in carbonate, fluoride, and phosphate or a combination thereof. The REE can also be incorporated into vein minerals such as calcite, fluorite and apatite where the REE3+ exchange for Ca2+ on the crystal lattice [2]. These minerals give us clues about the hydrothermal reaction paths of REE in critical mineral deposits. This study aims to: 1) present our recent findings from hydrothermal fluid-mineral REE partitioning experiments, 2) discuss thermodynamic models to simulate REE in critical mineral deposits, and 3) link the thermodynamic simulations to field observations.
Hydrothermal fluid-calcite partitioning experiments were conducted between 100 and 200 °C by hydrothermal fluid mixing and precipitation [2] at near neutral to mildly alkaline pH (6 – 9). The REE concentrations in synthetic calcite crystals and aqueous fluids sampled in situ were used to fit the data to the lattice strain model [3] and using the Dual Thermodynamic approach [4]. A second type of experiment consisted of reacting natural fluorite and apatite crystals with acidic to mildly acidic (pH of 2 – 4) aqueous fluids in batch-type reactors to study the behavior of REE and mineral dissolution-precipitation reactions near crystal surfaces. The GEMS code package [5] was used to implement these new data into a thermodynamic model and simulate possible REE reaction paths in hydrothermal fluids. Two REE mineral deposits in New Mexico (Lemitar and Gallinas Mountains) present ideal case studies to illustrate how these models can be linked to field observations from natural systems.
[1] Gysi et al. (2016), Econ. Geol. 111, 1241-1276; [2] Perry and Gysi (2020), Geochim. Cosmochim. Acta 286, 177-197; [3] Blundy and Wood (1994) Nature 372, 452-454; [4] Kulik (2006), Chem. Geol. 225, 189-212; [5] Kulik et al. (2013), Computat. Geosci. 17, 1-24.
more »
« less
Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl−/H+ Antiporter
Intracellular transport of chloride by members of the CLC transporter family involves a coupled exchange between a Cl− anion and a proton (H+), which makes the transport function dependent on ambient pH. Transport activity peaks at pH 4.5 and stalls at neutral pH. However, a structure of the WT protein at acidic pH is not available, making it difficult to assess the global conformational rearrangements that support a pH-dependent gating mechanism. To enable modeling of the CLC-ec1 dimer at acidic pH, we have applied molecular dynamics simulations (MD) featuring a new force field modification scheme—termed an Equilibrium constant pH approach (ECpH). The ECpH method utilizes linear interpolation between the force field parameters of protonated and deprotonated states of titratable residues to achieve a representation of pH-dependence in a narrow range of physiological pH values. Simulations of the CLC-ec1 dimer at neutral and acidic pH comparing ECpH-MD to canonical MD, in which the pH-dependent protonation is represented by a binary scheme, substantiates the better agreement of the conformational changes and the final model with experimental data from NMR, cross-link and AFM studies, and reveals structural elements that support the gate-opening at pH 4.5, including the key glutamates Gluin and Gluex.
more »
« less
- Award ID(s):
- 1841758
- NSF-PAR ID:
- 10355280
- Date Published:
- Journal Name:
- Molecules
- Volume:
- 26
- Issue:
- 22
- ISSN:
- 1420-3049
- Page Range / eLocation ID:
- 6956
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
more » « less
EmrE is an
Escherichia coli multidrug efflux pump and member of the small multidrug resistance (SMR) family that transports drugs as a homodimer by harnessing energy from the proton motive force. SMR family transporters contain a conserved glutamate residue in transmembrane 1 (Glu14 in EmrE) that is required for binding protons and drugs. Yet the mechanism underlying proton-coupled transport by the two glutamate residues in the dimer remains unresolved. Here, we used NMR spectroscopy to determine acid dissociation constants (pK a ) for wild-type EmrE and heterodimers containing one or two Glu14 residues in the dimer. For wild-type EmrE, we measured chemical shifts of the carboxyl side chain of Glu14 using solid-state NMR in lipid bilayers and obtained unambiguous evidence on the existence of asymmetric protonation states. Subsequent measurements of pK a values for heterodimers with a single Glu14 residue showed no significant differences from heterodimers with two Glu14 residues, supporting a model where the two Glu14 residues have independent pK a values and are not electrostatically coupled. These insights support a transport pathway with well-defined protonation states in each monomer of the dimer, including a preferred cytoplasmic-facing state where Glu14 is deprotonated in monomer A and protonated in monomer B under pH conditions in the cytoplasm ofE. coli . Our findings also lead to a model, hop-free exchange, which proposes how exchangers with conformation-dependent pK a values reduce proton leakage. This model is relevant to the SMR family and transporters comprised of inverted repeat domains. -
more » « less
Abstract Oxalate decarboxylase from
Bacillus subtilis is a binuclear Mn‐dependent acid stress response enzyme that converts the mono‐anion of oxalic acid into formate and carbon dioxide in a redox neutral unimolecular disproportionation reaction. A π‐stacked tryptophan dimer, W96 and W274, at the interface between two monomer subunits facilitates long‐range electron transfer between the two Mn ions and plays an important role in the catalytic mechanism. Substitution of W96 with the unnatural amino acid 5‐hydroxytryptophan leads to a persistent EPR signal which can be traced back to the neutral radical of 5‐hydroxytryptophan with its hydroxyl proton removed. 5‐Hydroxytryptophan acts as a hole sink preventing the formation of Mn(III) at the N‐terminal active site and strongly suppresses enzymatic activity. The lower boundary of the standard reduction potential for the active site Mn(II)/Mn(III) couple can therefore be estimated as 740 mV against the normal hydrogen electrode at pH 4, the pH of maximum catalytic efficiency. Our results support the catalytic importance of long‐range electron transfer in oxalate decarboxylase while at the same time highlighting the utility of unnatural amino acid incorporation and specifically the use of 5‐hydroxytryptophan as an energetic sink for hole hopping to probe electron transfer in redox proteins. -
more » « less
Abstract Bor1p is a secondary transporter in yeast that is responsible for boron transport. Bor1p belongs to the SLC4 family which controls bicarbonate exchange and pH regulation in animals as well as borate uptake in plants. The SLC4 family is more distantly related to members of the Amino acid‐Polyamine‐organoCation (APC) superfamily, which includes well studied transporters such as LeuT, Mhp1, AdiC, vSGLT, UraA, SLC26Dg. Their mechanism generally involves relative movements of two domains: a core domain that binds substrate and a gate domain that in many cases mediates dimerization. To shed light on conformational changes governing transport by the SLC4 family, we grew helical membrane crystals of Bor1p from
Saccharomyces mikatae and determined a structure at ∼6 Å resolution using cryo‐electron microscopy. To evaluate the conformation of Bor1p in these crystals, a homology model was built based on the related anion exchanger from red blood cells (AE1). This homology model was fitted to the cryo‐EM density map using the Molecular Dynamics (MD) Flexible Fitting method and then relaxed by all‐atom MD simulation in explicit solvent and membrane. Mapping of water accessibility indicates that the resulting structure represents an inward‐facing conformation. Comparisons of the resulting Bor1p model with the X‐ray structure of AE1 in an outward‐facing conformation, together with MD simulations of inward‐facing and outward‐facing Bor1p models, suggest rigid body movements of the core domain relative to the gate domain. These movements are consistent with the rocking‐bundle transport mechanism described for other members of the APC superfamily. -
The production of atmospheric organic nitrates (RONO2) has a large impact on air quality and climate due to their contribution to secondary organic aerosol and influence on tropospheric ozone concentrations. Since organic nitrates control the fate of gas phase NOx (NO + NO2), a byproduct of anthropogenic combustion processes, their atmospheric production and reactivity is of great interest. While the atmospheric reactivity of many relevant organic nitrates is still uncertain, one significant reactive pathway, condensed phase hydrolysis, has recently been identified as a potential sink for organic nitrate species. The partitioning of gas phase organic nitrates to aerosol particles and subsequent hydrolysis likely removes the oxidized nitrogen from further atmospheric processing, due to large organic nitrate uptake to aerosols and proposed hydrolysis lifetimes, which may impact long-range transport of NOx, a tropospheric ozone precursor. Despite the atmospheric importance, the hydrolysis rates and reaction mechanisms for atmospherically derived organic nitrates are almost completely unknown, including those derived from α-pinene, a biogenic volatile organic compound (BVOC) that is one of the most significant precursors to biogenic secondary organic aerosol (BSOA). To better understand the chemistry that governs the fate of particle phase organic nitrates, the hydrolysis mechanism and rate constants were elucidated for several organic nitrates, including an α-pinene-derived organic nitrate (APN). A positive trend in hydrolysis rate constants was observed with increasing solution acidity for all organic nitrates studied, with the tertiary APN lifetime ranging from 8.3 min at acidic pH (0.25) to 8.8 h at neutral pH (6.9). Since ambient fine aerosol pH values are observed to be acidic, the reported lifetimes, which are much shorter than that of atmospheric fine aerosol, provide important insight into the fate of particle phase organic nitrates. Along with rate constant data, product identification confirms that a unimolecular specific acid-catalyzed mechanism is responsible for organic nitrate hydrolysis under acidic conditions. The free energies and enthalpies of the isobutyl nitrate hydrolysis intermediates and products were calculated using a hybrid density functional (ωB97X-V) to support the proposed mechanisms. These findings provide valuable information regarding the organic nitrate hydrolysis mechanism and its contribution to the fate of atmospheric NOx, aerosol phase processing, and BSOA composition.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3390/molecules26226956
