DP/MM: A Hybrid Model for Zinc–Protein Interactions in Molecular Dynamics

Zinc-containing proteins are vital for many biological processes, yet accurately modeling them using classical force fields is hindered by complicated polarization and charge transfer effects. This study introduces DP/MM, a hybrid force field scheme that utilizes a deep potential model to correct the atomic forces of zinc ions and their coordinated atoms, elevating them from MM to QM levels of accuracy. Trained on the difference between MM and QM atomic forces across diverse zinc coordination groups, the DP/MM model faithfully reproduces structural characteristics of zinc coordination during simulations, such as the tetrahedral coordination of Cys4 and Cys3His1 groups. Furthermore, DP/MM allows water exchange in the zinc coordination environment. With its unique blend of accuracy, efficiency, flexibility, and transferability, DP/MM serves as a valuable tool for studying structures and dynamics of zinc-containing proteins and also represents a pioneering approach in the evolving landscape of machine learning potentials for molecular modeling

DP/MM: A Hybrid Model for Zinc–Protein Interactions in Molecular Dynamics

Zinc-containing proteins are vital for many biological processes, yet accurately modeling them using classical force fields is hindered by complicated polarization and charge transfer effects. This study introduces DP/MM, a hybrid force field scheme that utilizes a deep potential model to correct the atomic forces of zinc ions and their coordinated atoms, elevating them from MM to QM levels of accuracy. Trained on the difference between MM and QM atomic forces across diverse zinc coordination groups, the DP/MM model faithfully reproduces structural characteristics of zinc coordination during simulations, such as the tetrahedral coordination of Cys4 and Cys3His1 groups. Furthermore, DP/MM allows water exchange in the zinc coordination environment. With its unique blend of accuracy, efficiency, flexibility, and transferability, DP/MM serves as a valuable tool for studying structures and dynamics of zinc-containing proteins and also represents a pioneering approach in the evolving landscape of machine learning potentials for molecular modeling

Arbuscular Mycorrhizal Colonization Alters Subcellular Distribution and Chemical Forms of Cadmium in <em>Medicago sativa</em> L. and Resists Cadmium Toxicity

<div><p>Some plants can tolerate and even detoxify soils contaminated with heavy metals. This detoxification ability may depend on what chemical forms of metals are taken up by plants and how the plants distribute the toxins in their tissues. This, in turn, may have an important impact on phytoremediation. We investigated the impact of arbuscular mycorrhizal (AM) fungus, <em>Glomus intraradices</em>, on the subcellular distribution and chemical forms of cadmium (Cd) in alfalfa (<em>Medicago sativa</em> L.) that were grown in Cd-added soils. The fungus significantly colonized alfalfa roots by day 25 after planting. Colonization of alfalfa by <em>G. intraradices</em> in soils contaminated with Cd ranged from 17% to 69% after 25–60 days and then decreased to 43%. The biomass of plant shoots with AM fungi showed significant 1.7-fold increases compared to no AM fungi addition under the treatment of 20 mg·kg⁻¹ Cd. Concentrations of Cd in the shoots of alfalfa under 0.5, 5, and 20 mg·kg⁻¹ Cd without AM fungal inoculation are 1.87, 2.92, and 2.38 times higher, respectively, than those of fungi-inoculated plants. Fungal inoculation increased Cd (37.2–80.5%) in the cell walls of roots and shoots and decreased in membranes after 80 days of incubation compared to untreated plants. The proportion of the inactive forms of Cd in roots was higher in fungi-treated plants than in controls. Furthermore, although fungi-treated plants had less overall Cd in subcellular fragments in shoots, they had more inactive Cd in shoots than did control plants. These results provide a basis for further research on plant-microbe symbioses in soils contaminated with heavy metals, which may potentially help us develop management regimes for phytoremediation.</p> </div

Supplementary document for Optical Center of a Luminescent Solar Concentrator - 6030370.pdf

Supporting content

Light micrographs of mouthpart components.

<p>(A) Labrum in frontal view, male. (B) Left mandible, female. Arrow shows the condyles. (C) Inner lateral view of right maxillae, male. (D) Posterior lateral view of right maxillae, male; (E) Labium in posterior view, male. cd, cardo; cly, clypeus; gl, galea; lbr, labrum; lc, lacinia; lp1,2, labial palpomere I and II; m, mentum; mp, maxillary palp; pm, prementum; ppf, palpifer; ppg, palpiger; sm, submentum; st, stipes. Scale bars  = 200 μm.</p

Accumulated Cd in alfalfa inoculated with <i>G. intraradices</i> after 80 days of seedling growth.

<p>Sharing a common lowercase are not significantly different in the Cd concentration in plant shoots and the same capital are not significantly different in the Cd concentration in plant roots (<i>P</i><0.05).</p

Presentation_1_Lanthanide-Dependent Methanol Dehydrogenases of XoxF4 and XoxF5 Clades Are Differentially Distributed Among Methylotrophic Bacteria and They Reveal Different Biochemical Properties.PDF

<p>Lanthanide-dependent alcohol dehydrogenases have recently emerged as environmentally important enzymes, most prominently represented in methylotrophic bacteria. The diversity of these enzymes, their environmental distribution, and their biochemistry, as well as their evolutionary relationships with their calcium-dependent counterparts remain virtually untapped. Here, we make important advances toward understanding lanthanide-dependent methylotrophy by assessing the distribution of XoxF4 and XoxF5 clades of lanthanide methanol dehydrogenases among, respectively, Methylophilaceae and non-Methylophilaceae methylotrophs, and we carry out comparative biochemical characterization of XoxF4 and XoxF5 enzymes, demonstrating differences in their properties, including catalytic efficiencies. We conclude that one subtype of the XoxF4 enzyme, XoxF4-1 is the dominant type in nature while other XoxF4 subtypes appear to be auxiliary, representatives of this clade only found in the Methylophilaceae (Betaproteobacteria). In contrast, we demonstrate that XoxF5 enzymes are widespread among Alpha-, Beta-, and Gammaproteobacteria. We purified and biochemically characterized two XoxF4 enzymes (XoxF4-1 and XoxF4-2), both from Methylotenera mobilis, and one XoxF5 enzyme, from Methylomonas sp., after expressing their His-tagged versions in respective natural hosts. All three enzymes showed broad specificities toward alcohols and aldehydes and strict dependence on lighter lanthanides. However, they revealed differences in their properties in terms of optimal pH for in vitro activity, ammonia dependence, the range of lanthanides that could serve as cofactors, and in kinetic properties. Overall, our data advance the understanding of the biochemistry and environmental distribution of these recently discovered enzymes that appear to be key enzymes in lanthanide-dependent methylotrophy.</p

Presentation_3_Lanthanide-Dependent Methanol Dehydrogenases of XoxF4 and XoxF5 Clades Are Differentially Distributed Among Methylotrophic Bacteria and They Reveal Different Biochemical Properties.PDF

<p>Lanthanide-dependent alcohol dehydrogenases have recently emerged as environmentally important enzymes, most prominently represented in methylotrophic bacteria. The diversity of these enzymes, their environmental distribution, and their biochemistry, as well as their evolutionary relationships with their calcium-dependent counterparts remain virtually untapped. Here, we make important advances toward understanding lanthanide-dependent methylotrophy by assessing the distribution of XoxF4 and XoxF5 clades of lanthanide methanol dehydrogenases among, respectively, Methylophilaceae and non-Methylophilaceae methylotrophs, and we carry out comparative biochemical characterization of XoxF4 and XoxF5 enzymes, demonstrating differences in their properties, including catalytic efficiencies. We conclude that one subtype of the XoxF4 enzyme, XoxF4-1 is the dominant type in nature while other XoxF4 subtypes appear to be auxiliary, representatives of this clade only found in the Methylophilaceae (Betaproteobacteria). In contrast, we demonstrate that XoxF5 enzymes are widespread among Alpha-, Beta-, and Gammaproteobacteria. We purified and biochemically characterized two XoxF4 enzymes (XoxF4-1 and XoxF4-2), both from Methylotenera mobilis, and one XoxF5 enzyme, from Methylomonas sp., after expressing their His-tagged versions in respective natural hosts. All three enzymes showed broad specificities toward alcohols and aldehydes and strict dependence on lighter lanthanides. However, they revealed differences in their properties in terms of optimal pH for in vitro activity, ammonia dependence, the range of lanthanides that could serve as cofactors, and in kinetic properties. Overall, our data advance the understanding of the biochemistry and environmental distribution of these recently discovered enzymes that appear to be key enzymes in lanthanide-dependent methylotrophy.</p

Components of maxilla.

<p>(A) Anterior view of the mouthparts with the labrum and mandibles removed, female. (B) Magnification of the thick spines on the maxilla apex. Inset shows the cuticular shafts with several pores (arrowheads), male. (C) The first two segments of the maxillary palp. Arrowheads show campaniform sensilla, male. (D) The distal segment of the maxillary palp, showing the two groups of short basiconic sensilla and campaniform sensilla (arrowheads), male. bb, Böhm's bristles; bs, basiconic sensilla; gl, galea; lc, lacinia; lp, labial palp; mp, maxillary palp; r1–2, ridge I–II. Scale bars: (A)  = 250 μm; (B) and (C)  = 50 μm; (D)  = 25 μm.</p

Solid-State NMR Analyses Reveal the Structure Dependence of the Molecular Dynamics for ω-Amino Acids

The molecular dynamics of metabolites is structure dependent and vitally important for the interactive functions in their potential applications as natural materials. To understand the relationship between molecular structure and dynamics, the molecular motions of four structurally related ω-amino acids (β-alanine, γ-aminobutyric acid, 5-aminovaleric acid, and 6-aminocaproic acid) were investigated by measuring their proton spin–lattice relaxation times (<i>T</i>₁, <i>T</i>_1ρ) as a function of temperature (180–440 K). ¹³C CPMAS NMR and DSC analyses were performed to obtain complementary information. All of these ω-amino acids showed no phase transition in the temperature range studied but had outstandingly long proton <i>T</i>₁ at 300 MHz and even at 20 MHz for the deuterated forms. The molecular dynamics of all these ω-amino acids were dominated by the reorientation motions of amino groups and backbone motions except in β-alanine. The activation energies for amino group reorientations were positively correlated with the strength of hydrogen bonds involving these groups in the crystals and the carbon-chain lengths, whereas such energies for the backbone motions were inversely correlated with the carbon-chain lengths. These findings provided essential information for the molecular dynamics of ω-amino acids and demonstrated the combined solid-state NMR methods as a useful approach for understanding the structural dependence of molecular dynamics