Structural insights into the elevator-type transport mechanism of a bacterial ZIP metal transporter

Data- and knowledge-derived functional landscape of human solute carriers

The human solute carrier (SLC) superfamily of ~460 membrane transporters remains the largest understudied protein family despite its therapeutic potential. To advance SLC research, we developed a comprehensive knowledgebase that integrates systematic multi-omics data sets with selected curated information from public sources. We annotated SLC substrates through literature curation, compiled SLC disease associations using data mining techniques, and determined the subcellular localization of SLCs by combining annotations from public databases with an immunofluorescence imaging approach. This SLC-centric knowledge is made accessible to the scientific community via a web portal featuring interactive dashboards and visualization tools. Utilizing this systematically collected and curated resource, we computationally derived an integrated functional landscape for the entire human SLC superfamily. We identified clusters with distinct properties and established functional distances between transporters. Based on all available data sets and their integration, we assigned biochemical/biological functions to each SLC, making this study one of the largest systematic annotations of human gene function and a potential blueprint for future research endeavors.

Ion-Induced Dipole Interactions Matter in Metadynamics Simulation of Transition Metal Ion Transporters

Metal transporters play crucial roles in the homeostasis and detoxification of beneficial and toxic metals in the human body. Due to experimental limitations in studying some metal transporters, numerous simulation studies have been conducted to understand the mechanisms of metal transport. However, studying the transport of divalent metal ions across the plasma membrane by metal transporters has been challenging with traditional molecular dynamics (MD) simulations. The metal ions often become trapped inside the transporter due to encountering high energy barriers during the transport process. In this study, we combined a recently developed metadynamics setup, known as well-tempered (WT) volume-based MTD, with the 12-6-4 Lennard-Jones (LJ) model representing transition metal-His/Asp/Glu side chain interactions. We used this approach to investigate the mechanism of action of a Zrt-/Irt-like protein (ZIP) transporter and compared the results with simulations using standard 12-6 LJ parameters for the transition metal-His/Asp/Glu side chain interactions. Our results show that the 12-6-4 LJ model for transition metal-His/Asp/Glu side chain interactions samples conformational space more broadly than the standard 12-6 LJ model for the same interactions in MTD simulations, facilitating the sampling of states that are hard to reach with the standard 12-6 model within the same time scale. This is even more remarkable given the fact that the model is dominated by 12-6 LJ interactions for the majority of the system, while the transition metal-His/Asp/Glu side chain interactions are the only interactions using the 12-6-4 LJ model. Hence, a small subset of interactions significantly modifies the states sampled by the entire protein leading to a more frequent observation of the transport of the transition metal ion. Overall, using 12-6-4 LJ to model the transition metal-His/Asp/Glu side chain interactions increases the potential for discovering additional metastable states by enabling metal ions to traverse more freely along the defined transport pathways.

Probing the substrate binding-induced conformational change of a ZIP metal transporter using a sandwich ELISA

Zrt-/Irt-like proteins (ZIPs), a family of divalent metal transporters, are crucial for maintaining the homeostasis of zinc, an essential trace element involved in numerous biological processes. While extensive research on the prototypical ZIP from Bordetella bronchiseptica (BbZIP) have suggested an elevator transport mechanism, the dynamic conformational changes during the transport cycle have not been thoroughly studied. In this work, we developed a sandwich ELISA using a custom anti-BbZIP monoclonal antibody to investigate the conformational change induced by the metal binding to the transport site. This was achieved by determining the accessibility of a cysteine residue introduced at a position exposed to the solvent only when the transporter adopts an outward-facing conformation. This assay allowed us to report the dissociation constants of BbZIP for Zn2+ and Cd2+ at low and sub-micromolar levels, respectively. Notably, the installation of a positive charge at the M2 site drastically reduced metal binding at the M1 site, consistent with an auxiliary role for the M2 site in metal transport. We also demonstrated that this assay can be used to rapidly screen variants for subsequent structural study. We anticipate that other transporters where substrate binding induces large conformational changes can also be studied using this method.

Molecular insights into substrate translocation in an elevator-type metal transporter

The Zrt/Irt-like protein (ZIP) metal transporters are key players in maintaining the homeostasis of a panel of essential microelements. The prototypical ZIP from Bordetella bronchiseptica (BbZIP) is an elevator transporter, but how the metal substrate moves along the transport pathway and how the transporter changes conformation to allow alternating access remain to be elucidated. Here, we combine structural, biochemical, and computational approaches to investigate the process of metal substrate translocation along with the global structural rearrangement. Our study reveals an upward hinge motion of the transport domain in a high-resolution crystal structure of a cross-linked variant, elucidates the mechanisms of metal release from the transport site into the cytoplasm and activity regulation by a cytoplasmic metal-binding loop, and unravels an unusual elevator mode in enhanced sampling simulations that distinguishes BbZIP from other elevator transporters. This work provides important insights into the metal transport mechanism of the ZIP family.

Advances in mechanism for the microbial transformation of heavy metals: implications for bioremediation strategies

Heavy metals are extensively discharged through various anthropogenic activities, resulting in an environmental risk on a global scale. In this case, microorganisms can survive in an extreme heavy metal-contaminated environment via detoxification or resistance, playing a pivotal role in the speciation, bioavailability, and mobility of heavy metals. Therefore, studies on the mechanism for the microbial transformation of heavy metals are of great importance and can provide guidance for heavy metal bioremediation. Current research studies on the microbial transformation of heavy metals mainly focus on the single oxidation, reduction and methylation pathways. However, complex microbial transformation processes and corresponding bioremediation strategies have never been clarified, which may involve the inherent physicochemical properties of heavy metals. To uncover the underlying mechanism, we reclassified heavy metals into three categories based on their biological transformation pathways, namely, metals that can be chelated, reduced or oxidized, and methylated. Firstly, we comprehensively characterized the difference in transmembrane pathways between heavy metal cations and anions. Further, biotransformation based on chelation by low-molecular-weight organic complexes is thoroughly discussed. Moreover, the progress and knowledge gaps in the microbial redox and (de)methylation mechanisms are discussed to establish a connection linking theoretical advancements with solutions to the heavy metal contamination problem. Finally, several efficient bioremediation strategies for heavy metals and the limitations of bioremediation are proposed. This review presents a solid contribution to the design of efficient microbial remediation strategies applied in the real environment.

Evolution, classification, and mechanisms of transport, activity regulation, and substrate specificity of ZIP metal transporters

The Zrt/Irt-like protein (ZIP) family consists of ubiquitously expressed divalent d-block metal transporters that play central roles in the uptake, secretion, excretion, and distribution of several essential and toxic metals in living organisms. The past few years has witnessed rapid progress in the molecular basis of these membrane transport proteins. In this critical review, we summarize the research progress at the molecular level of the ZIP family and discuss the future prospects. Furthermore, an evolutionary path for the unique ZIP fold and a new classification of the ZIP family are proposed based on the presented structural and sequence analyses.

Molecular insights into substrate translocation in an elevator-type metal transporter

The Zrt/Irt-like protein (ZIP) metal transporters are key players in maintaining the homeostasis of a panel of essential microelements. The prototypical ZIP from Bordetella bronchiseptica (BbZIP) is an elevator transporter, but how the metal substrate moves along the transport pathway and how the transporter changes conformation to allow alternating access remain to be elucidated. Here, we combined structural, biochemical, and computational approaches to investigate the process of metal substrate translocation along with the global structural rearrangement. Our study revealed an upward hinge motion of the transport domain in a high-resolution crystal structure of a cross-linked variant, elucidated the mechanisms of metal release from the transport site into the cytoplasm and activity regulation by a cytoplasmic metal-binding loop, and unraveled an unusual elevator mode in enhanced sampling simulations that distinguishes BbZIP from other elevator transporters. This work provides important insights into the metal transport mechanism of the ZIP family.

Determination of metal ion transport rate of human ZIP4 using stable zinc isotopes

The essential microelement zinc is absorbed in the small intestine mainly by the zinc transporter ZIP4, a representative member of the Zrt/Irt-like protein (ZIP) family. ZIP4 is reportedly upregulated in many cancers, making it a promising oncology drug target. To date, there have been no reports on the turnover number of ZIP4, which is a crucial missing piece of information needed to better understand the transport mechanism. In this work, we used a nonradioactive zinc isotope, 70Zn, and inductively coupled plasma mass spectrometry to study human ZIP4 (hZIP4) expressed in Human embryonic kidney 293 cells. Our data showed that 70Zn can replace the radioactive 65Zn as a tracer in kinetic evaluation of hZIP4 activity. This approach, combined with the quantification of the cell surface expression of hZIP4 using biotinylation or surface-bound antibody, allowed us to estimate the apparent turnover number of hZIP4 to be in the range of 0.08 to 0.2 s-1. The turnover numbers of the truncated hZIP4 variants are significantly smaller than that of the full-length hZIP4, confirming a crucial role for the extracellular domain in zinc transport. Using 64Zn and 70Zn, we measured zinc efflux during the cell-based transport assay and found that it has little effect on the zinc import analysis under these conditions. Finally, we demonstrated that use of laser ablation inductively coupled plasma-TOF-mass spectrometry on samples applied to a solid substrate significantly increased the throughput of the transport assay. We envision that the approach reported here can be applied to the studies of metal transporters beyond the ZIP family.

The Manganese-Bone Connection: Investigating the Role of Manganese in Bone Health

The complex relationship between trace elements and skeletal health has received increasing attention in the scientific community. Among these minerals, manganese (Mn) has emerged as a key element affecting bone metabolism and integrity. This review examines the multifaceted role of Mn in bone health, including its effects on bone regeneration, mineralization, and overall skeletal strength. This review article is based on a synthesis of experimental models, epidemiologic studies, and clinical trials of the mechanisms of the effect of Mn on bone metabolism. Current research data show that Mn is actively involved in the processes of bone remodeling by modulating the activity of osteoblasts and osteoclasts, as well as the main cells that regulate bone formation and resorption. Mn ions have a profound effect on bone mineralization and density by intricately regulating signaling pathways and enzymatic reactions in these cells. Additionally, Mn superoxide dismutase (MnSOD), located in bone mitochondria, plays a crucial role in osteoclast differentiation and function, protecting osteoclasts from oxidative damage. Understanding the nuances of Mn's interaction with bone is essential for optimizing bone strategies, potentially preventing and managing skeletal diseases. Key findings include the stimulation of osteoblast proliferation and differentiation, the inhibition of osteoclastogenesis, and the preservation of bone mass through the RANK/RANKL/OPG pathway. These results underscore the importance of Mn in maintaining bone health and highlight the need for further research into its therapeutic potential.

Structures, Mechanisms, and Physiological Functions of Zinc Transporters in Different Biological Kingdoms

Zinc transporters take up/release zinc ions (Zn2+) across biological membranes and maintain intracellular and intra-organellar Zn2+ homeostasis. Since this process requires a series of conformational changes in the transporters, detailed information about the structures of different reaction intermediates is required for a comprehensive understanding of their Zn2+ transport mechanisms. Recently, various Zn2+ transport systems have been identified in bacteria, yeasts, plants, and humans. Based on structural analyses of human ZnT7, human ZnT8, and bacterial YiiP, we propose updated models explaining their mechanisms of action to ensure efficient Zn2+ transport. We place particular focus on the mechanistic roles of the histidine-rich loop shared by several zinc transporters, which facilitates Zn2+ recruitment to the transmembrane Zn2+-binding site. This review provides an extensive overview of the structures, mechanisms, and physiological functions of zinc transporters in different biological kingdoms.

Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation

Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.

Metalation and activation of Zn2+ enzymes via early secretory pathway-resident ZNT proteins

Zinc (Zn2+), an essential trace element, binds to various proteins, including enzymes, transcription factors, channels, and signaling molecules and their receptors, to regulate their activities in a wide range of physiological functions. Zn2+ proteome analyses have indicated that approximately 10% of the proteins encoded by the human genome have potential Zn2+ binding sites. Zn2+ binding to the functional site of a protein (for enzymes, the active site) is termed Zn2+ metalation. In eukaryotic cells, approximately one-third of proteins are targeted to the endoplasmic reticulum; therefore, a considerable number of proteins mature by Zn2+ metalation in the early secretory pathway compartments. Failure to capture Zn2+ in these compartments results in not only the inactivation of enzymes (apo-Zn2+ enzymes), but also their elimination via degradation. This process deserves attention because many Zn2+ enzymes that mature during the secretory process are associated with disease pathogenesis. However, how Zn2+ is mobilized via Zn2+ transporters, particularly ZNTs, and incorporated in enzymes has not been fully elucidated from the cellular perspective and much less from the biophysical perspective. This review focuses on Zn2+ enzymes that are activated by Zn2+ metalation via Zn2+ transporters during the secretory process. Further, we describe the importance of Zn2+ metalation from the physiopathological perspective, helping to reveal the importance of understanding Zn2+ enzymes from a biophysical perspective.

Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models

Protein engineering is an emerging field in biotechnology that has the potential to revolutionize various areas, such as antibody design, drug discovery, food security, ecology, and more. However, the mutational space involved is too vast to be handled through experimental means alone. Leveraging accumulative protein databases, machine learning (ML) models, particularly those based on natural language processing (NLP), have considerably expedited protein engineering. Moreover, advances in topological data analysis (TDA) and artificial intelligence-based protein structure prediction, such as AlphaFold2, have made more powerful structure-based ML-assisted protein engineering strategies possible. This review aims to offer a comprehensive, systematic, and indispensable set of methodological components, including TDA and NLP, for protein engineering and to facilitate their future development.

Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models

Protein engineering is an emerging field in biotechnology that has the potential to revolutionize various areas, such as antibody design, drug discovery, food security, ecology, and more. However, the mutational space involved is too vast to be handled through experimental means alone. Leveraging accumulative protein databases, machine learning (ML) models, particularly those based on natural language processing (NLP), have considerably expedited protein engineering. Moreover, advances in topological data analysis (TDA) and artificial intelligence-based protein structure prediction, such as AlphaFold2, have made more powerful structure-based ML-assisted protein engineering strategies possible. This review aims to offer a comprehensive, systematic, and indispensable set of methodological components, including TDA and NLP, for protein engineering and to facilitate their future development.

Rational engineering of an elevator-type metal transporter ZIP8 reveals a conditional selectivity filter critically involved in determining substrate specificity

Engineering of transporters to alter substrate specificity as desired holds great potential for applications, including metabolic engineering. However, the lack of knowledge on molecular mechanisms of substrate specificity hinders designing effective strategies for transporter engineering. Here, we applied an integrated approach to rationally alter the substrate preference of ZIP8, a Zrt-/Irt-like protein (ZIP) metal transporter with multiple natural substrates, and uncovered the determinants of substrate specificity. By systematically replacing the differentially conserved residues with the counterparts in the zinc transporter ZIP4, we created a zinc-preferring quadruple variant (Q180H/E343H/C310A/N357H), which exhibited largely reduced transport activities towards Cd2+, Fe2+, and Mn2+ whereas increased activity toward Zn2+. Combined mutagenesis, modeling, covariance analysis, and computational studies revealed a conditional selectivity filter which functions only when the transporter adopts the outward-facing conformation. The demonstrated approach for transporter engineering and the gained knowledge about substrate specificity will facilitate engineering and mechanistic studies of other transporters.

Expression, purification, and crystallization of the extracellular domain of a mammalian ZIP4

Zinc transporters are of vital importance in maintaining zinc homeostasis in all living organisms. In humans, ZIP4 is exclusive for dietary zinc uptake. Obtaining enough purified protein by heterologous expression is necessary for structural characterization to understand working mechanisms at the atomic level. However, due to the major obstacle in membrane protein expression, there is no structural information of the full-length human ZIP4 till now. A "divide and conquer" strategy has been applied to ZIP4 to study the extracellular domain (ECD) and the transmembrane domain separately, which has led to the first ECD structure in the entire ZIP family. In this chapter, we provide detailed protocols for the expression, purification, and crystallization of ZIP4-ECD from a mammalian species.

Considerations in production of the prokaryotic ZIP family transporters for structural and functional studies

Zinc ions play essential roles as components of enzymes and many other important biomolecules, and are associated with numerous diseases. The uptake of Zn2+ and other metal ions require a widely distributed transporter protein family called Zrt/Irt-like Proteins (ZIP family), the majority members of which tend to have eight transmembrane helices with both N- and C- termini located on the extracellular or periplasmic side. Their small sizes and dynamic conformations bring many difficulties in their production for structural studies either by crystallography or Cryo-EM. Here, we summarize the problems that may encounter at the various steps of processing the ZIP proteins from gene to structural and functional studies, and provide some solutions and examples from our and other labs for the cloning, expression, purification, stability screening, metal ion transport assays and structural studies of prokaryotic ZIP family transporters using Escherichia coli as a heterologous host.

High-resolution structure of a mercury cross-linked ZIP metal transporter reveals delicate motions and metal relay for regulated zinc transport

Zrt-/Irt-like protein (ZIP) divalent metal transporters play a central role in maintaining trace element homeostasis. The prototypical ZIP from Bordetella bronchiseptica (BbZIP) is an elevator-type transporter, but the dynamic motions and detailed transport mechanism remain to be elucidated. Here, we report a high-resolution crystal structure of a mercury-crosslinked BbZIP variant at 1.95 Å, revealing an upward rotation of the transport domain in the new inward-facing conformation and a water-filled metal release channel that is divided into two parallel pathways by the previously disordered cytoplasmic loop. Mutagenesis and transport assays indicated that the newly identified high-affinity metal binding site in the primary pathway acts as a "metal sink" to reduce the transport rate. The discovery of a hinge motion around an extracellular axis allowed us to propose a sequential hinge-elevator-hinge movement of the transport domain to achieve alternating access. These findings provide key insights into the transport mechanisms and activity regulation.