GO:0032767 copper-dependent protein binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0032767 (copper-dependent protein binding) is a molecular function defined as binding to a protein or protein complex in the presence of copper.
• Copper binding can be intrinsic or extrinsic to known copper-binding motifs, as shown for the prion protein and the bacterial YcnI protein.
• Copper-dependent protein interactions are central to cuproptosis, a copper-induced cell death pathway targeting lipoylated TCA cycle proteins.
• Copper homeostasis and copper-dependent protein binding are implicated in neurodegeneration, cancer, and metabolic diseases [2,5].
• Key proteins include DLAT, DLST, GPX4, SELENBP1, HKDC1, and prion protein (PRNP), each with distinct copper-dependent functions [1,3,4,7,8].
• CRISPR knockout, point mutation, knock-in, and overexpression models enable causal dissection of copper-dependent protein binding in disease.
Description
Copper is an essential trace element that serves as a cofactor for numerous enzymes, but it can also drive toxic protein interactions when dysregulated. The Gene Ontology term GO:0032767, copper-dependent protein binding, captures the molecular function of binding to a protein or protein complex specifically in the presence of copper. This term is distinct from generic copper ion binding because it requires a protein partner and copper as a contextual cofactor. Understanding this function is critical for researchers studying cuproptosis, neurodegeneration, and cancer, where copper-dependent protein interactions determine cell fate [1,5]. Recent work has shown that copper directly binds lipoylated TCA cycle proteins, triggering their aggregation and cell death. Other studies demonstrate copper-dependent degradation of GPX4 during ferroptosis and copper-dependent thiol oxidase activity of SELENBP1. These examples highlight the broad biological impact of copper-dependent protein binding. This article synthesizes authoritative QuickGO data and verified PubMed literature to provide a research-grade overview of GO:0032767, its mechanisms, key genes, disease links, and experimental methods.
copper-dependent protein binding At A Glance
| GO ID | GO:0032767 |
|---|---|
| GO term | copper-dependent protein binding |
| Ontology | molecular_function |
| Synonym | None |
| Definition | Binding to a protein or protein complex, in the presence of copper. |
| Major function | Mediates protein-protein interactions that require copper ions as a cofactor or allosteric regulator. |
| Related processes | Cuproptosis, ferroptosis, copper homeostasis, neurodegeneration, cancer. |
| Example proteins | DLAT, DLST, GPX4, SELENBP1, HKDC1, PRNP. |
| Research methods | CRISPR KO/point mutation/knock-in/overexpression, proteomics, binding assays. |
What Is GO:0032767?
GO:0032767 (copper-dependent protein binding) is defined by QuickGO as the binding to a protein or protein complex, in the presence of copper. This means the interaction between a copper-binding molecule (often a protein or small molecule) and its protein target requires copper ions to occur or is stabilized by copper. The term does not describe copper binding to a protein per se, but rather the copper-dependent association with another protein or protein complex. It is a molecular function that can be studied using biochemical binding assays, structural biology, and genetic perturbations.
Why Is copper-dependent protein binding Important in Cell Biology?
Copper-dependent protein binding is important because it links copper homeostasis to fundamental cellular processes such as mitochondrial metabolism, oxidative stress response, and cell death. Dysregulation of this function contributes to diseases including cancer, neurodegenerative disorders, and metabolic syndromes [2,5]. For researchers, GO:0032767 provides a framework to study how copper modulates protein interactions and to identify therapeutic targets.
• Copper-dependent binding of lipoylated TCA cycle proteins triggers cuproptosis, a novel form of cell death.
• Copper-dependent autophagic degradation of GPX4 promotes ferroptosis, linking copper to lipid peroxidation.
• SELENBP1 functions as a copper-dependent thiol oxidase, affecting redox signaling.
• Copper homeostasis and copper-dependent protein interactions are implicated in Alzheimer's and Parkinson's diseases.
• The prion protein binds copper extrinsic to its octarepeat region, influencing prion biology.
• Bacterial YcnI contains a copper-binding domain, highlighting evolutionary conservation.
• HKDC1 mediates LPS-induced cuproptosis and inflammation in macrophages.
• Copper-dependent protein binding is a potential target for cancer therapy via cuproptosis induction [1,2].
• Understanding this term aids in designing CRISPR screens for copper-related genes.
• It provides a molecular basis for developing copper-chelating or copper-ionophore drugs.
Molecular Mechanism of copper-dependent protein binding
Copper as a Cofactor for Protein-Protein Interactions
In simple terms: Copper acts like a molecular glue that helps two proteins stick together.
In many cases, copper ions bind to one protein and induce a conformational change that enables binding to a partner protein. For example, copper binds to lipoylated DLAT and promotes its aggregation, a key step in cuproptosis. This interaction is dependent on the presence of copper and specific lipoylation marks.
Copper-Dependent Degradation of GPX4
In simple terms: Copper helps tag the antioxidant enzyme GPX4 for destruction, leading to ferroptosis.
Copper promotes autophagic degradation of GPX4, a glutathione peroxidase that protects against lipid peroxidation. This copper-dependent process drives ferroptosis and involves binding of copper to GPX4 or associated proteins.
Extrinsic Copper Binding to Prion Protein
In simple terms: The prion protein can bind copper outside its known copper-binding repeats.
The prion protein (PRNP) binds copper not only via its octarepeat region but also through extrinsic sites. This copper-dependent binding may modulate prion protein function and aggregation.
Copper-Binding Domains in Bacterial Proteins
In simple terms: Bacteria also use copper-dependent protein binding for their own physiology.
The YcnI protein from Bacillus subtilis contains a copper-binding domain, demonstrating that copper-dependent protein binding is conserved across kingdoms. This domain may mediate protein-protein interactions required for bacterial copper homeostasis.
Regulation by Copper Homeostasis
In simple terms: Cells control copper levels to regulate these binding events.
Copper homeostasis proteins, such as copper chaperones and transporters, maintain appropriate copper concentrations. Disruption of homeostasis alters copper-dependent protein binding and can trigger cuproptosis or ferroptosis [2,5].
Key Genes Involved in GO:0032767 copper-dependent protein binding
The following genes and proteins are experimentally linked to copper-dependent protein binding or its downstream effects.
| Gene | Major Role | Research Relevance |
|---|---|---|
| DLAT | Lipoylated TCA cycle protein; binds copper to form aggregates | Central to cuproptosis; target for cancer therapy |
| DLST | Lipoylated TCA cycle protein; copper-dependent aggregation | Cuproptosis marker; studied in metabolic diseases |
| GPX4 | Glutathione peroxidase; copper-dependent degradation | Ferroptosis regulator; cancer and neurodegeneration |
| SELENBP1 | Copper-dependent thiol oxidase | Redox signaling; cancer biomarker |
| HKDC1 | Hexokinase domain containing 1; mediates LPS-induced cuproptosis | Inflammation and macrophage biology |
| PRNP | Prion protein; binds copper extrinsically | Neurodegeneration; prion diseases |
| YcnI | Bacterial copper-binding protein | Model for copper-dependent protein binding |
| ATP7A | Copper-transporting ATPase | Copper homeostasis; Menkes disease |
| ATP7B | Copper-transporting ATPase | Copper homeostasis; Wilson disease |
| SLC31A1 | Copper transporter 1 (CTR1) | Copper uptake; cuproptosis sensitivity |
| ATOX1 | Copper chaperone | Delivers copper to ATP7A/B; homeostasis |
| CCS | Copper chaperone for SOD1 | Copper-dependent SOD1 activation |
| SOD1 | Cu/Zn superoxide dismutase | Copper-dependent antioxidant defense |
| MT1A | Metallothionein 1A | Copper sequestration; stress response |
| FDX1 | Ferredoxin 1; reduces Cu(II) to Cu(I) | Regulates cuproptosis |
| LIAS | Lipoyl synthase | Required for lipoylation of DLAT/DLST |
| LIPT1 | Lipoyltransferase 1 | Lipoylation of TCA enzymes |
| GLS | Glutaminase | Glutamine metabolism linked to cuproptosis |
How Is copper-dependent protein binding Regulated?
Copper-dependent protein binding is regulated by cellular copper homeostasis, which involves copper transporters (SLC31A1, ATP7A, ATP7B), chaperones (ATOX1, CCS), and metallothioneins. Additionally, the lipoylation status of target proteins such as DLAT and DLST, controlled by enzymes like LIAS and LIPT1, determines their ability to bind copper and trigger cuproptosis. Ferredoxin 1 (FDX1) reduces Cu(II) to Cu(I), a step required for copper-dependent protein binding and subsequent cell death. Inflammatory signals such as LPS can upregulate HKDC1, which mediates cuproptosis in macrophages. These regulatory layers ensure that copper-dependent protein interactions are tightly controlled and context-dependent.
copper-dependent protein binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| DLAT | Cuproptosis; cancer | Knockout and point mutation in cancer cell lines |
| GPX4 | Ferroptosis; neurodegeneration | Overexpression and knockout in neuronal cells |
| PRNP | Prion diseases; Alzheimer's | Knock-in of copper-binding mutants in mice |
| HKDC1 | Inflammation; sepsis | Knockout in THP-1 macrophages |
| SELENBP1 | Cancer; redox imbalance | Overexpression in cancer cell lines |
Copper-Dependent Protein Binding in Cancer
Cuproptosis, driven by copper-dependent binding to lipoylated TCA cycle proteins, is a novel cell death pathway that can be exploited for cancer therapy. Many cancers exhibit altered copper metabolism, making them sensitive to copper ionophores. Targeting copper-dependent protein binding may overcome apoptosis resistance.
Neurodegenerative Diseases
Copper dyshomeostasis and aberrant copper-dependent protein binding are implicated in Alzheimer's disease, Parkinson's disease, and prion disorders [5,8]. The prion protein binds copper extrinsically, and this interaction may influence protein aggregation and neurotoxicity. Copper chelation or modulation is being explored as a therapeutic strategy.
Ferroptosis and Inflammatory Diseases
Copper-dependent degradation of GPX4 promotes ferroptosis, a form of lipid peroxidation-driven cell death involved in ischemia-reperfusion injury and neurodegeneration. In macrophages, LPS induces HKDC1-mediated cuproptosis and inflammation, linking copper-dependent protein binding to innate immunity.
From copper-dependent protein binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of DLAT prevent cuproptosis? | DLAT knockout cell lines |
| Does a copper-binding point mutation in GPX4 alter ferroptosis? | GPX4 point-mutant knock-in |
| Can overexpression of SELENBP1 protect against oxidative stress? | SELENBP1 overexpression |
| Does HKDC1 mediate LPS-induced cuproptosis? | HKDC1 knockout in THP-1 |
| Does prion protein copper binding affect aggregation? | PRNP knock-in with mutated copper sites |
| Can CRISPR screen identify new copper-dependent protein binders? | Genome-wide CRISPR knockout library [1,2] |
How to Study the copper-dependent protein binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| ITC | Binding affinity and thermodynamics | Copper-protein interactions |
| SPR | Real-time binding kinetics | Copper-dependent protein-protein binding |
| AP-MS | Protein complex composition | Interactome in presence of copper |
| CRISPR screen | Gene essentiality for phenotype | Identify regulators of cuproptosis [1,2] |
| Live-cell imaging | Subcellular localization and aggregation | Monitor copper-induced protein aggregation |
| Western blot | Protein expression and degradation | GPX4 degradation |
| qPCR | mRNA expression | Copper homeostasis genes |
Biochemical Binding Assays
Copper-dependent protein binding can be measured using isothermal titration calorimetry (ITC), surface plasmon resonance (SPR), or pull-down assays in the presence and absence of copper. These methods quantify binding affinity and stoichiometry [6,8].
Proteomics and Interactomics
Copper-dependent interactomes can be mapped using affinity purification mass spectrometry (AP-MS) with copper supplementation. This approach identifies protein complexes that form only when copper is present [1,4].
CRISPR Screening
Genome-wide CRISPR knockout or activation screens can identify genes that regulate copper-dependent protein binding and downstream phenotypes such as cuproptosis [1,2].
Live-Cell Imaging
Fluorescently tagged proteins and copper sensors enable real-time visualization of copper-dependent protein interactions and aggregation in living cells [1,5].
How CRISPR Can Be Used to Study GO:0032767 copper-dependent protein binding
Knockout
CRISPR knockout of genes such as DLAT, GPX4, or HKDC1 can abolish copper-dependent protein binding and downstream cell death, providing causal evidence [1,3,7].
Point Mutation
Introducing point mutations in copper-binding residues (e.g., in PRNP or SELENBP1) allows precise dissection of copper coordination and its role in protein binding [4,8].
Knock-in
Knock-in of tagged or mutant alleles (e.g., HA-tagged DLAT) enables affinity purification and imaging of copper-dependent protein complexes.
Overexpression
Overexpression of copper-binding proteins such as SELENBP1 or GPX4 can test gain-of-function effects on copper-dependent binding and cell survival [3,4].
How EDITGENE Supports copper-dependent protein binding Research
Researchers studying copper-dependent protein binding-related genes often need to determine whether a candidate gene is causally involved in copper-induced phenotypes, such as cuproptosis or ferroptosis. This requires precise genetic models that can knockout, mutate, tag, or overexpress the gene of interest in relevant cell types.
Contact EDITGENE today to design your custom CRISPR model for copper-dependent protein binding research.
Frequently Asked Questions About copper-dependent protein binding
What is GO:0032767 copper-dependent protein binding?
GO:0032767 is a Gene Ontology molecular function term defined as binding to a protein or protein complex, in the presence of copper.
What genes are involved in copper-dependent protein binding?
Key genes include DLAT, DLST, GPX4, SELENBP1, HKDC1, PRNP, and bacterial YcnI, among others [1,3,4,6,7,8].
How does copper induce cuproptosis?
Copper binds to lipoylated TCA cycle proteins like DLAT, causing their aggregation and cell death, a process called cuproptosis.
What is the role of GPX4 in copper-dependent protein binding?
Copper promotes autophagic degradation of GPX4, leading to ferroptosis.
Which diseases are linked to copper-dependent protein binding?
Cancer, neurodegenerative diseases (Alzheimer's, Parkinson's, prion diseases), and inflammatory conditions [2,5,7,8].
How can I study copper-dependent protein binding in the lab?
Use biochemical binding assays, proteomics, CRISPR screens, and live-cell imaging [1,4,6,8].
What CRISPR models are available for copper-dependent protein binding research?
Knockout, point mutation, knock-in, and overexpression models can be custom-generated by EDITGENE [1,3,4,7].
Is copper-dependent protein binding conserved in bacteria?
Yes, the YcnI protein from Bacillus subtilis contains a copper-binding domain, indicating conservation.
What is the prion protein's role in copper binding?
The prion protein binds copper extrinsically to its octarepeat region, which may affect its function and aggregation.
How does SELENBP1 function as a copper-dependent protein?
SELENBP1 is a copper-dependent thiol oxidase, involved in redox regulation.
Conclusion
GO:0032767 copper-dependent protein binding is a molecular function with broad implications for cell death, metabolism, and disease. The integration of QuickGO definitions with verified literature reveals key proteins such as DLAT, GPX4, and SELENBP1 that mediate copper-dependent interactions. Understanding these mechanisms offers opportunities for therapeutic intervention in cancer and neurodegeneration. EDITGENE provides comprehensive CRISPR services to accelerate research in this field.
References
- 1. Tsvetkov P et al.. 2022. Copper induces cell death by targeting lipoylated TCA cycle proteins.. Science 375(6586):1254-1261 PMID: 35298263
- 2. Chen L et al.. 2022. Copper homeostasis and cuproptosis in health and disease.. Signal Transduct Target Ther 7(1):378 PMID: 36414625
- 3. Xue Q et al.. 2023. Copper-dependent autophagic degradation of GPX4 drives ferroptosis.. Autophagy 19(7):1982-1996 PMID: 36622894
- 4. Philipp TM et al.. 2023. Selenium-binding protein 1 (SELENBP1) is a copper-dependent thiol oxidase.. Redox Biol 65:102807 PMID: 37437449
- 5. Wang Y et al.. 2025. Copper homeostasis and neurodegenerative diseases.. Neural Regen Res 20(11):3124-3143 PMID: 39589160
- 6. Damle MS et al.. 2021. The YcnI protein from Bacillus subtilis contains a copper-binding domain.. J Biol Chem 297(3):101078 PMID: 34400169
- 7. Ou L et al.. 2025. LPS mediates cuproptosis and inflammation in THP-1 macrophages through HKDC1.. Acta Biochim Biophys Sin (Shanghai) 57(12):1953-68 PMID: 40692442
- 8. Walter ED et al.. 2009. Copper binding extrinsic to the octarepeat region in the prion protein.. Curr Protein Pept Sci 10(5):529-35 PMID: 19538144
