Zn Binding Sites Research Articles

The SBP-box transcription factor PlSPL2 negatively regulates stem development in herbaceous peony.

The SBP-box transcription factor PlSPL2 silencing in herbaceous peony enhanced stem strength by regulating xylem development, whereas its overexpression in tobacco resulted in weaker stem strength and undeveloped xylem. The strength of plant stems is a critical determinant of lodging resistance of plants, which significantly affects crop yield and cut-flower quality. Squamosa promoter binding (SBP) protein-like (SPL) transcription factors (TFs), participate in multiple regulatory processes, particularly in stem development. In this study, PlSPL2, an orthologous gene of Arabidopsis AtSPL2 in herbaceous peony, was isolated and found to contain a conserved SBP domain featuring two typical Zn-binding sites, as well as a nuclear localization sequence (NLS). Subsequently, transient infection of tobacco leaf epidermal cells using Agrobacterium confirmed the nuclear localization of PISPL2 protein. Additionally, gene expression analyses revealed that PlSPL2 was preferentially expressed in stems, and demonstrated a download trend in expression levels within vascular bundles during stem cell wall development. Furthermore, silencing of PlSPL2 in herbaceous peony enhanced stem strength. The silenced plants exhibited more developed xylems with wider radii and higher numbers of cell layers. Overexpression of PlSPL2 in tobacco, however, resulted in weaker stem strength, accompanied by a narrower radius of the xylem. These findings suggested that PlSPL2 was a negative regulator of herbaceous peony stem development, and its discovery and research could significantly contribute to a deeper understanding of stem growth and development mechanisms.

Pathogenic R163W Variant of the Copper Chaperone for Sod1 (Ccs) Functions as an Anti-chaperone.

The copper chaperone for Sod1 (Ccs) is a metallochaperone that plays a multifaceted role in the maturation of Cu,Zn superoxide dismutase (Sod1). The Ccs mutation R163W was identified in an infant with fatal neurological abnormalities. Based on a comprehensive structural and functional analysis, we developed the first data-driven model for R163W-related pathogenic phenotypes. The work here confirms previous findings that the substitution of arginine with tryptophan at this site, which is located adjacent to a conserved Zn binding site, creates an unstable Zn-deficient protein that loses its ability to efficiently activate Sod1. Intriguingly, R163W Ccs can reduce copper (i.e., Cu(II) → Cu(I)) bound in its Sod1-like domain (D2), and this novel redox event is accompanied by disulfide bond formation. The loss of Zn binding, along with the unusual ability to bind copper in D2, diverts R163W Ccs toward aggregation. The remarkably high affinity of D2 Cu(I) binding converts R163W from a Cu chaperone to a Cu scavenger that accelerates Sod1 deactivation (i.e., an Anti-chaperone). Overall, these findings present a first-of-its-kind molecular mechanism for Ccs dysfunction that leads to pathogenesis in humans.

Unraveling Protein-Metabolite Interactions in Precision Nutrition: A Case Study of Blueberry-Derived Metabolites Using Advanced Computational Methods.

Metabolomics, the study of small-molecule metabolites within biological systems, has become a potent instrument for understanding cellular processes. Despite its profound insights into health, disease, and drug development, identifying the protein partners for metabolites, especially dietary phytochemicals, remains challenging. In the present study, we introduced an innovative in silico, structure-based target prediction approach to efficiently predict protein targets for metabolites. We analyzed 27 blood serum metabolites from nutrition intervention studies' blueberry-rich diets, known for their health benefits, yet with elusive mechanisms of action. Our findings reveal that blueberry-derived metabolites predominantly interact with Carbonic Anhydrase (CA) family proteins, which are crucial in acid-base regulation, respiration, fluid balance, bone metabolism, neurotransmission, and specific aspects of cellular metabolism. Molecular docking showed that these metabolites bind to a common pocket on CA proteins, with binding energies ranging from -5.0 kcal/mol to -9.0 kcal/mol. Further molecular dynamics (MD) simulations confirmed the stable binding of metabolites near the Zn binding site, consistent with known compound interactions. These results highlight the potential health benefits of blueberry metabolites through interaction with CA proteins.

Combining Native Mass Spectrometry and Proteomics to Differentiate and Map the Metalloform Landscape in Metallothioneins.

Within the intricate landscape of the proteome, approximately 30% of all proteins bind metal ions. This repertoire is even larger when considering all the different forms of a protein, known as proteoforms. Here, we propose the term "metalloforms" to refer to different structural or functional variations of a protein resulting from the binding of various hetero- or homogeneous metal ions. Using human Cu(I)/Zn(II)-metallothionein-3 as a representative model, we developed a chemical proteomics strategy to simultaneously differentiate and map Zn(II) and Cu(I) metal binding sites. In the first labeling step, N-ethylmaleimide reacts with Cysteine (Cys), resulting in the dissociation of all Zn(II) ions while Cu(I) remains bound to the protein. In the second labeling step, iodoacetamide is utilized to label Cu(I)-bound Cys residues. Native mass spectrometry (MS) was used to determine the metal/labeling protein stoichiometries, while bottom-up/top-down MS was used to map the Cys-labeled residues. Next, we used a developed methodology to interrogate an isolated rabbit liver metallothionein fraction containing three metallothionein-2 isoforms and multiple Cd(II)/Zn(II) metalloforms. The approach detailed in this study thus holds the potential to decode the metalloproteoform diversity within other proteins.

The zinc absorption of the novel peptide-Zn complex in Caco-2 cells: effects of soybean peptides charge and hydrophobicity.

The supplemental effect of zinc depends not only on adequate intake, but also on how efficiently it is absorbed in the small intestine. In the present study, weak hydrophobic peptides (WHP), strong hydrophobic peptides (SHP), positively charged peptides (PCP) and negatively charged peptides (NCP) were isolated from soybean peptides (SP). The peptide-Zn complexes (PCP-Zn, NCP-Zn, WHP-Zn, SHP-Zn and SP-Zn) were prepared to compare their promotion zinc absorption capacity in the Caco-2 cells monolayers model. We found that the carboxyl, carbonyl and amino groups in peptide were the primary binding sites of Zn. Compared with zinc sulfate, the peptide-Zn complexes with different charge and hydrophobic peptides could improve zinc solubility at different pH. NCP-Zn had a lower Zn-binding capacity but a higher zinc absorption capacity compared to that of PCP-Zn in Caco-2 cells. In addition, the capacity of PCP-Zn to promote zinc absorption was lower than the control group (SP-Zn). There were no significant differences in transport rates, retention rates and uptake rates of WHP-Zn, SHP-Zn and SP-Zn. NCP-Zn could improve the activity of Zn-related enzymes, and the expression levels of PepT1 and ZnT1 were higher than other peptide-Zn complexes. The promotion zinc absorption capacity of peptide-Zn complexes was not completely dependent on the Zn-binding capacity, but also depended on the charge and hydrophobicity of peptides. © 2024 Society of Chemical Industry.

Role of Histidine 310 in Amydetes vivianii firefly luciferase pH and metal sensitivities and improvement of its color tuning properties.

Firefly luciferases emit yellow-green light and are pH-sensitive, changing the bioluminescence color to red in the presence of heavy metals, acidic pH and high temperatures. These pH and metal-sensitivities have been recently harnessed for intracellular pH indication and toxic metal biosensing. However, whereas the structure of the pH sensor and the metal binding site, which consists mainly of two salt bridges that close the active site (E311/R337 and H310/E354), has been identified, the specific role of residue H310 in pH and metal sensing is still under debate. The Amydetes vivianii firefly luciferase has one of the lowest pH sensitivities among the group of pH-sensitive firefly luciferases, displaying high bioluminescent activity and special spectral selectivity for cadmium and mercury, which makes it a promising analytical reagent. Using site-directed mutagenesis, we have investigated in detail the role of residue H310 on pH and metal sensitivity in this luciferase. Negatively charged residues at position 310 increase the pH sensitivity and metal sensitivity; H310G considerably increases the size of the cavity, severely impacting the activity, H310R closes the cavity, and H310F considerably decreases both pH and metal sensitivities. However, no substitution completely abolished pH and metal sensitivities. The results indicate that the presence of negatively charged and basic side chains at position 310 is important for pH sensitivity and metals coordination, but not essential, indicating that the remaining side chains of E311 and E354 may still coordinate some metals in this site. Furthermore, a metal binding site search predicted that H310 mutations decrease the affinity mainly for Zn, Ni and Hg but less for Cd, and revealed the possible existence of additional binding sites for Zn, Ni and Hg.

Characterization of Copper(II) and Zinc(II) Complexes of Peptides Mimicking the CuZnSOD Enzyme.

Antimicrobial peptides are short cationic peptides that are present on biological surfaces susceptible to infection, and they play an important role in innate immunity. These peptides, like other compounds with antimicrobial activity, often have significant superoxide dismutase (SOD) activity. One direction of our research is the characterization of peptides modeling the CuZnSOD enzyme and the determination of their biological activity, and these results may contribute to the development of novel antimicrobial peptides. In the framework of this research, we have synthesized 10, 15, and 16-membered model peptides containing the amino acid sequence corresponding to the Cu(II) and Zn(II) binding sites of the CuZnSOD enzyme, namely the Zn(II)-binding HVGD sequence (80-83. fragments), the Cu(II)-binding sequence HVH (fragments 46-48), and the histidine (His63), which links the two metal ions as an imidazolate bridge: Ac-FHVHEGPHFN-NH2 (L1(10)), Ac-FHVHAGPHFNGGHVG-NH2 (L2(15)), and Ac-FHVHEGPHFNGGHVGD-NH2 (L3(16)). pH-potentiometric, UV-Vis-, and CD-spectroscopy studies of the Cu(II), Zn(II), and Cu(II)-Zn(II) mixed complexes of these peptides were performed, and the SOD activity of the complexes was determined. The binding sites preferred by Cu(II) and Zn(II) were identified by means of CD-spectroscopy. From the results obtained for these systems, it can be concluded that in equimolar solution, the -(NGG)HVGD- sequence of the peptides is the preferred binding site for copper(II) ion. However, in the presence of both metal ions, according to the native enzyme, the -HVGD- sequence offers the main binding site for Zn(II), while the majority of Cu(II) binds to the -FHVH- sequence. Based on the SOD activity assays, complexes of the 15- and 16-membered peptide have a significant SOD activity. Although this activity is smaller than that of the native CuZnSOD enzyme, the complexes showed better performance in the degradation of superoxide anion than other SOD mimics. Thus, the incorporation of specific amino acid sequences mimicking the CuZnSOD enzyme increases the efficiency of model systems in the catalytic decomposition of superoxide anion.

Role of amino acid functional group in alga-amino acid-Zn ternary complexes

The bioaccumulation of heavy metals (HMs) at the water-algal interface determines their threat degree to aquatic ecosystem. Amino acids (AAs), as predominant components of dissolved organic matter (DOM), play pivotal roles in shaping the speciation of HMs in water and their subsequent accumulation by algae. However, the diverse nature of amino acid poses a challenge in generalizing the underlying mechanisms. This study explores four amino acids (asparagine, aspartic acid, glycine, lysine), each possessing distinct amino and carboxyl groups, and investigates their impact on zinc (Zn) bioaccumulation through batch experiments. Upon the introduction of AAs, the adsorption process obeyed the pseudo-second-order kinetic adsorption model demonstrating chemisorption (R2 >0.99), and it affected Zn externalization (up to 3.994 mmol g-1). This phenomenon followed a two-step model, indicating multilayer adsorption. The study proposed that the protonated amino group of AA could serve as a link between Zn-AA complex and microalgae. Amino acids adsorbed onto the surface of microalgae via protonated amino groups did not occupy the Zn-binding sites, instead, they furnished additional functional groups. This differs from the previous results of organic acids containing only carboxyl functional groups as DOM. Multiple linear regression equations and correlation analyses were used to explain the effects of amino and carboxyl morphology on microalgae accumulation of Zn. The equation showed that the leading model terms explain 75.8% of the accumulation amount variance. This study enhances our understanding of the effects of functional group-different DOM on the accumulation of heavy metals in microalgae, offering insights for future research and prediction.

Reversible Zn electrodeposition enabled by interfacial chemistry manipulation for high-energy anode-free Zn batteries

Aqueous Zn batteries have attracted intensive interest in terms of the high safety and sustainable raw materials with low cost. However, the excess use of Zn anode greatly limits the practical energy density of batteries and arouses a threat to their real-life application. Here, a robust heterointerface composed of 0D metal nanodots and 2D metal carbide nanosheets with triple synergistic effects is designed to manipulate interfacial chemistry for anode-free Zn batteries. An interface of in situ anchoring ultrafine Sn nanodots on Na+ decorated MXene nanosheets is used as a model. The 2D Na-MXene promotes the Zn plating/stripping kinetics and homogenizes the distributions of electric field and ion flux. The high-affinity Zn binding sites of 0D Sn nanodots reduce the plating energy barrier and consequently manipulate the uniform Zn nucleation/growth. The in situ formed ZnF2 layer during Zn plating allows Zn ions to diffuse and shields side reactions. Consequently, the stable Zn plating/stripping with a high accumulated areal capacity of 5,000 mAh cm−2 is realized at high current density and plating capacity (10 mA cm−2∼20 mAh cm−2). Benefitting from triply synergistic effects derived from built cooperative interfaces, an anode-free Zn cell is constructed, proving ameliorative cyclic stability.

A Specific Guide for Metalloenzyme Designers: Introduction and Evolution of Metal-Coordination Spheres Embedded in Protein Environments.

ConspectusMetalloproteins establish a comprehensive molecular space by combining inorganic cofactors with protein environments. The chemical interplay between a metal element and a protein matrix is remarkable yet elusive, as the chemical properties of metal ions do not directly translate into those of metalloenzymes when placed within a protein matrix. Instead, the biochemical context determines the metal-coordination geometries, reaction kinetics, and thermodynamic parameters, such as redox potential and Lewis acidity/basicity. The molecular design of novel metalloproteins, which involves varying the combination of the two major components, metal ion and protein, allows us to validate our current understanding of their chemical interactions, modulate protein structure and function toward specific directions, and create protein-based functional biomaterials and biocatalysts. Considering theoretically possible protein sequence combinations and several metal elements at several oxidation states, artificial metalloenzyme design is analogous to the drawing of new paintings with multiple colors and brush strokes.Our laboratory has developed minimalistic strategies to transform diverse proteins into artificial metalloproteins with novel architectures or catalytic functions. First, we analyzed the geometric parameters of native Zn-binding sites to introduce a tetrahedral zinc-binding motif to a non-α-helical protein scaffold that shows neither pre-existing affinity to any metal ion nor catalytic activity, such as the β-barrel outer membrane protein OmpF. We created a series of artificial Zn-binding OmpF variants that possess coordinatively unsaturated mononuclear Zn-ligation sites and exhibit hydrolytic activities with esters, β-lactams, and β-glycosides. The OmpF variants were further evolved to zinc-dependent glycosidases, addressing a central question in bioinorganic chemistry: can zinc ions directly associate with the hydrolytic cleavage of glycosidic bonds in sugars?To expand the scope of metalloprotein design, we also utilized a metal-chelating noncanonical amino acid, bipyridine-alanine, and constructed tunable dicopper-dependent oxidases and nickel/iridium-dependent photocatalytic cross-coupling enzymes. These advancements increased the complexity and precision of metalloenzyme design, revealing how protein matrices, in conjunction with metallocofactors in aqueous media, facilitate electron transfer and mediate multiple chemical events, such as proton transfer, substrate access, and product release, while suppressing adventitious reactions.Furthermore, we redesigned the secondary and tertiary metal-coordination spheres of manganese-dependent quercetin dioxygenase and zinc-dependent β-lactamase, respectively. Biochemical characterizations of the evolved enzymes revealed that metal ions harmoniously and selectively cooperate with protein environments such that seemingly unimportant residues play critical roles in tuning the electronic structures of the enzymes or determining the metal-dependent reactivity. Thus, our work establishes the fundamental basis of how metalloenzymes function via long-range intermolecular interactions and how we can control their structure and function in specific directions. Consequently, these novel metalloenzymes have provided possible snapshots of how they could have evolved under controlled chemical environments and potential prospects for how to design more sophisticated and efficient biocatalysts with accuracy at the molecular level.

A conserved zinc-binding site in Acinetobacter baumannii PBP2 required for elongasome-directed bacterial cell shape

Acinetobacter baumannii is a gram-negative bacterial pathogen that causes challenging nosocomial infections. β-lactam targeting of penicillin-binding protein (PBP)-mediated cell wall peptidoglycan (PG) formation is a well-established antimicrobial strategy. Exposure to carbapenems or zinc (Zn)-deprived growth conditions leads to a rod-to-sphere morphological transition in A. baumannii, an effect resembling that caused by deficiency in the RodA-PBP2 PG synthesis complex required for cell wall elongation. While it is recognized that carbapenems preferentially acylate PBP2 in A. baumannii and therefore block the transpeptidase function of the RodA-PBP2 system, the molecular details underpinning cell wall elongation inhibition upon Zn starvation remain undefined. Here, we report the X-ray crystal structure of A. baumannii PBP2, revealing an unexpected Zn coordination site in the transpeptidase domain required for protein stability. Mutations in the Zn-binding site of PBP2 cause a loss of bacterial rod shape and increase susceptibility to β-lactams, therefore providing a direct rationale for cell wall shape maintenance and Zn homeostasis in A. baumannii. Furthermore, the Zn-coordinating residues are conserved in various β- and γ-proteobacterial PBP2 orthologs, consistent with a widespread Zn-binding requirement for function that has been previously unknown. Due to the emergence of resistance to virtually all marketed antibiotic classes, alternative or complementary antimicrobial strategies need to be explored. These findings offer a perspective for dual inhibition of Zn-dependent PG synthases and metallo-β-lactamases by metal chelating agents, considered the most sought-after adjuvants to restore β-lactam potency against gram-negative bacteria.

Design and directed evolution of noncanonical β-stereoselective metalloglycosidases

Metallohydrolases are ubiquitous in nearly all subclasses of hydrolases, utilizing metal elements to activate a water molecule and facilitate its subsequent dissociation of diverse chemical bonds. However, such a catalytic role of metal ions is rarely found with glycosidases that hydrolyze the glycosidic bonds in sugars. Herein, we design metalloglycosidases by constructing a hydrolytically active Zn-binding site within a barrel-shaped outer membrane protein OmpF. Structure- and mechanism-based redesign and directed evolution have led to the emergence of Zn-dependent glycosidases with catalytic proficiency of 2.8 × 109 and high β-stereoselectivity. Biochemical characterizations suggest that the Zn-binding site constitutes a key catalytic motif along with at least one adjacent acidic residue. This work demonstrates that unprecedented metalloenzymes can be tailor-made, expanding the scope of inorganic reactivities in proteinaceous environments, resetting the structural and functional diversity of metalloenzymes, and providing the potential molecular basis of unidentified metallohydrolases and novel whole-cell biocatalysts.

Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase.

The evolution of zinc (Zn) as a protein cofactor altered the functional landscape of biology, but dependency on Zn also created an Achilles' heel, necessitating adaptive mechanisms to ensure Zn availability to proteins. A debated strategy is whether metallochaperones exist to prioritize essential Zn-dependent proteins. Here, we present evidence for a conserved family of putative metal transferases in human and fungi, which interact with Zn-dependent methionine aminopeptidase type I (MetAP1/Map1p/Fma1). Deletion of the putative metal transferase in Saccharomyces cerevisiae (ZNG1; formerly YNR029c) leads to defective Map1p function and a Zn-deficiency growth defect. Invitro, Zng1p can transfer Zn2+ or Co2+ to apo-Map1p, but unlike characterized copper chaperones, transfer is dependent on GTP hydrolysis. Proteomics reveal mis-regulation of the Zap1p transcription factor regulon because of loss of ZNG1 and Map1p activity, suggesting that Zng1p is required to avoid a compounding effect of Map1p dysfunction on survival during Zn limitation.

A role for bioinorganic chemistry in the reactivation of mutant p53 in cancer.

Metal ion dysregulation has been implicated in a number of diseases from neurodegeneration to cancer. While defective metal ion transport mechanisms are known to cause specific diseases of genetic origin, the role of metal dysregulation in many diseases has yet to be elucidated due to the complicated function (both good and bad!) of metal ions in the body. A breakdown in metal ion speciation can manifest in several ways from increased reactive oxygen species (ROS) generation to an increase in protein misfolding and aggregation. In this review, we will discuss the role of Zn in the proper function of the p53 protein in cancer. The p53 protein plays a critical role in the prevention of genome mutations via initiation of apoptosis, DNA repair, cell cycle arrest, anti-angiogenesis, and senescence pathways to avoid propagation of damaged cells. p53 is the most frequently mutated protein in cancer and almost all cancers exhibit malfunction along the p53 pathway. Thus, there has been considerable effort dedicated to restoring normal p53 expression and activity to mutant p53. This includes understanding the relative populations of the Zn-bound and Zn-free p53 in wild-type and mutant forms, and the development of metallochaperones to re-populate the Zn binding site to restore mutant p53 activity. Parallels will be made to the development of multifunctional metal binding agents for modulating the aggregation of the amyloid-beta peptide in Alzheimer's Disease (AD).

Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind’s AlphaFold2 Program Dramatically Expands the Metalloproteome

DeepMind’s AlphaFold2 software has ushered in a revolution in high quality, 3D protein structure prediction. In very recent work by the DeepMind team, structure predictions have been made for entire proteomes of twenty-one organisms, with >360,000 structures made available for download. Here we show that thousands of novel binding sites for iron-sulfur (Fe-S) clusters and zinc (Zn) ions can be identified within these predicted structures by exhaustive enumeration of all potential ligand-binding orientations. We demonstrate that AlphaFold2 routinely makes highly specific predictions of ligand binding sites: for example, binding sites that are comprised exclusively of four cysteine sidechains fall into three clusters, representing binding sites for 4Fe-4S clusters, 2Fe-2S clusters, or individual Zn ions. We show further: (a) that the majority of known Fe-S cluster and Zn binding sites documented in UniProt are recovered by the AlphaFold2 structures, (b) that there are occasional disputes between AlphaFold2 and UniProt with AlphaFold2 predicting highly plausible alternative binding sites, (c) that the Fe-S cluster binding sites that we identify in E. coli agree well with previous bioinformatics predictions, (d) that cysteines predicted here to be part of ligand binding sites show little overlap with those shown via chemoproteomics techniques to be highly reactive, and (e) that AlphaFold2 occasionally appears to build erroneous disulfide bonds between cysteines that should instead coordinate a ligand. These results suggest that AlphaFold2 could be an important tool for the functional annotation of proteomes, and the methodology presented here is likely to be useful for predicting other ligand-binding sites.

Four alternative splicing transcripts of intracellular copper/zinc superoxide dismutase 1 in Oxya chinensis

In this study, we obtained four alternative splicing transcripts of intracellular copper/zinc superoxide dismutase 1 (icCuZnSOD1) in Oxya chinensis. OcicCuZnSOD1a has all common characteristics of CuZnSOD family and is a canonical CuZnSOD. OcicCuZnSOD1b is missing a Zn binding site. OcicCuZnSOD1c lacks Zn ion and is a Cu-only SOD. OcicCuZnSOD1d is missing a CuZnSOD conserved sequence and lacks the E-loop, a conserved disulfide bond, and an active site arginine. OcicCuZnSOD1a was the most heat-resistant and OcicCuZnSOD1c was the most unstable at high temperatures above 55 °C. They were stable at a wide pH range, especially in alkaline conditions. The four variants expressed at the throughout developmental stages and had various tissue expression patterns. OcicCuZnSOD1a and OcicCuZnSOD1d were significantly induced by 8.79 mM CuCl2 and OcicCuZnSOD1b was significantly up-regulated by 14.67 mM CuCl2. OcicCuZnSOD1a was significantly inhibited by 19.13 mM ZnSO4 while OcicCuZnSOD1d were significantly induced by 22.61 mM ZnSO4. Disc diffusion assay showed that the four isoforms of OcicCuZnSOD1 made the killing zones smaller surrounding the CdCl2-soaked filter discs. However, the reduction ratios of OcicCuZnSOD1a were the highest. These results implied that the four transcripts played roles in defense against CdCl2-induced oxidative stress while OcicCuZnSOD1a had stronger antioxidant capacity.

The structure of neurofibromin isoform 2 reveals different functional states

The autosomal dominant monogenetic disease neurofibromatosis type 1 (NF1) affects approximately one in 3,000 individuals and is caused by mutations in the NF1 tumour suppressor gene, leading to dysfunction in the protein neurofibromin (Nf1)1,2. As a GTPase-activating protein, a key function of Nf1 is repression of the Ras oncogene signalling cascade. We determined the human Nf1 dimer structure at an overall resolution of 3.3 Å. The cryo-electron microscopy structure reveals domain organization and structural details of the Nf1 exon 23a splicing3 isoform 2 in a closed, self-inhibited, Zn-stabilized state and an open state. In the closed conformation, HEAT/ARM core domains shield the GTPase-activating protein-related domain (GRD) so that Ras binding is sterically inhibited. In a distinctly different, open conformation of one protomer, a large-scale movement of the GRD occurs, which is necessary to access Ras, whereas Sec14-PH reorients to allow interaction with the cellular membrane4. Zn incubation of Nf1 leads to reduced Ras-GAP activity with both protomers in the self-inhibited, closed conformation stabilized by a Zn binding site between the N-HEAT/ARM domain and the GRD–Sec14-PH linker. The transition between closed, self-inhibited states of Nf1 and open states provides guidance for targeted studies deciphering the complex molecular mechanism behind the widespread neurofibromatosis syndrome and Nf1 dysfunction in carcinogenesis.

Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function.

Understanding the structural and functional implications of metal ions is of pivotal significance to chemical biology. Herein, we report first time the evidence of spodium bonds (SpB’s, an attractive noncovalent force involving elements from group 12 and electron-rich species) in tetrahedral Zn-binding sites. Through a combined crystallographic (PDB analysis) and computational (ab initio calculations) study, we demonstrate that Zn SpB’s are abundant and might be involved in protein structure and enzyme inhibition.

Multiscale Quantum Refinement Approaches for Metalloproteins.

Biomolecules with metal ion(s) (e.g., metalloproteins) play many important biological roles. However, accurate structural determination of metalloproteins, particularly those containing transition metal ion(s), is challenging due to their complicated electronic structure, complex bonding of metal ions, and high number of conformations in biomolecules. Quantum refinement, which was proposed to combine crystallographic data with computational chemistry methods by several groups, can improve the local structures of some proteins. In this study, a quantum refinement method combining several multiscale computational schemes with experimental (X-ray diffraction) information was developed for metalloproteins. Various quantum refinement approaches using different ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) combinations of quantum mechanics (QM), semiempirical (SE), and molecular mechanics (MM) methods were conducted to assess the performance and reliability on the refined local structure in two metalloproteins. The structures for two (Cu- or Zn-containing) metalloproteins were refined by combining two-layer ONIOM2(QM1/QM2) and ONIOM2(QM/MM) and three-layer ONIOM3(QM1/QM2/MM) schemes with experimental data. The accuracy of the quantum-refined metal binding sites was also examined and compared in these multiscale quantum refinement calculations. ONIOM3(QM/SE/MM) schemes were found to give good results with lower computational costs and were proposed to be a good choice for the multiscale computational scheme for quantum refinement calculations of metal binding site(s) in metalloproteins with high efficiency. Additionally, a two-center ONIOM approach was employed to speed up the quantum refinement calculations for the Zn metalloprotein with two remote active sites/ligands. Moreover, a recent quantum-embedding wavefunction-in-density functional theory (WF-in-DFT) method was also adopted as the high-level method in unprecedented ONIOM2(CCSD-in-B3LYP/MM) and ONIOM3(CCSD-in-B3LYP/SE/MM) calculations, which can be regarded as novel pseudo-three- and pseudo-four-layer ONIOM methods, respectively, to refine the key Zn binding site at the coupled-cluster singles and doubles (CCSD) level. These refined results indicate that multiscale quantum refinement schemes can be used to improve the structural accuracy obtained for local metal binding site(s) in metalloproteins with high efficiency.

Toward Planar and Dendrite-Free Zn Electrodepositions by Regulating Sn-Crystal Textured Surface.

The propensity of Zn-metal anodes to form non-uniform or dendritic electrodeposits is bound up with the nature of the electrode surface. However, the effect of surface structure on the inherent nucleation and deposition of Zn is not yet well understood. Here, the surface structure of a Zn-metal anode is reconstructed with Sn-crystal textures via a facile chemical displacement reaction. Compared to the bare Zn, the high-affinity Zn binding sites of Sn afford lower deposition energy barrier, which promotes deposition kinetics. What is more, a Sn-textured surface with moderate Zn affinity but high average surface energy ensures a better wettability from the deposits, leading to the lateral growth of Zn crystals. The resultant Sn-textured Zn-metal anode exhibits an extremely low voltage hysteresis of 20mV and achieves a prolonged cycling stability over 500 h cycles without dendrite formation. This work provides new insights into the crystal-texture-dependent Zn electrodeposition process and offers direction for direct surface texturing to better stabilize Zn-metal anodes with improved reversibility.