GO:0043008 ATP-dependent protein binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0043008 (ATP-dependent protein binding) is a molecular function defined as binding to a protein or protein complex using energy from ATP hydrolysis.
• ATP hydrolysis is not a passive energy source here; it drives conformational changes that create, stabilize, or release protein-protein contacts.
• Classic examples include Hsp70/J-protein chaperone cycles, chaperonin folding chambers, Hsp90-p53 chaperoning, and UvrA DNA damage recognition.
• The function is central to proteostasis, splicing fidelity, vesicle exocytosis, and ATP-dependent proteolysis.
• Dysregulation of ATP-dependent protein binding is linked to cancer, neurodegeneration, and splicing-related disease.
• CRISPR knockout, point-mutation, knock-in, and overexpression models are essential to test causality of ATP-dependent binding events.
Description
ATP-dependent protein binding (GO:0043008) describes a molecular function in which a protein binds another protein or protein complex using energy released by ATP hydrolysis. This distinguishes it from simple stoichiometric protein-protein interactions: the binding event is coupled to nucleotide turnover and often to a mechanical or conformational cycle. The term is therefore a functional annotation for molecular machines that use ATP to load, remodel, or release partner proteins. In the HSP70 chaperone machinery, J proteins drive functional specificity while ATP hydrolysis controls substrate capture and release. Chaperonins use ATP to enclose and fold substrate proteins inside a protected chamber. Hsp90 can chaperone p53 in a manner where ATP binding is sufficient for effective chaperoning. Beyond chaperones, ATP-dependent protein binding underlies pre-mRNA splicing, where Cus2 enforces the first ATP-dependent step by binding yeast SF3b1 through a UHM-ULM interaction. It also underlies DNA damage recognition by UvrA, Ca2+/ATP-dependent binding of CaMKII to syntaxin 1A during exocytosis, and activation of the ATP-dependent protease La by protein substrates. For researchers, GO:0043008 is a useful annotation because it flags interactions that are dynamic, energy-consuming, and often regulatory rather than structural. Understanding which proteins use ATP-dependent binding, and how mutations alter that cycle, is directly relevant to cancer biology, neurodegeneration, and splicing disorders.
ATP-dependent protein binding At A Glance
| GO ID | GO:0043008 |
|---|---|
| GO term | ATP-dependent protein binding |
| Ontology | molecular_function |
| Synonym | None listed |
| Definition | Binding to a protein or protein complex using energy from ATP hydrolysis. |
| Major function | Energy-coupled recognition, remodeling, or release of protein partners |
| Representative systems | HSP70/J-protein chaperones, chaperonins, Hsp90, spliceosome, UvrA, CaMKII-syntaxin, protease La |
| Research relevance | Proteostasis, splicing, DNA repair, exocytosis, proteolysis, disease modeling |
What Is GO:0043008?
In this article, ATP-dependent protein binding means the ability of a protein to bind a target protein or protein complex in a manner that requires ATP hydrolysis. The binding is not merely a static contact; it is coupled to the energy state of the system, so that ATP turnover can drive substrate engagement, conformational remodeling, or release. This functional definition is based on the QuickGO annotation for GO:0043008.
Why Is ATP-dependent protein binding Important in Cell Biology?
ATP-dependent protein binding is important because it converts chemical energy into controlled protein-protein interactions, allowing cells to proofread, remodel, and regulate protein complexes rather than relying on static binding alone. This function is essential for protein folding, pre-mRNA splicing, DNA damage recognition, vesicle exocytosis, and ATP-dependent proteolysis. Because these processes are tightly linked to disease, the term provides a framework for interpreting how mutations in ATP-dependent binding proteins alter cellular physiology.
• Controls protein quality control through HSP70 and chaperonin cycles.
• Enables Hsp90-mediated chaperoning of client proteins such as p53.
• Enforces fidelity in pre-mRNA splicing via ATP-dependent steps.
• Drives DNA damage recognition by UvrA.
• Regulates exocytosis through CaMKII binding to syntaxin 1A.
• Activates ATP-dependent proteases such as protease La.
• Provides a mechanistic explanation for dynamic protein-protein interactions.
• Links energy metabolism to protein complex assembly and disassembly.
• Offers disease-relevant targets in cancer and neurodegeneration.
• Supports CRISPR-based causal testing of binding events.
Molecular Mechanism of ATP-dependent protein binding
Nucleotide-driven substrate capture
In simple terms: The protein uses ATP to grab its partner.
In ATP-dependent protein binding, the initial step is often nucleotide-controlled capture of a substrate protein. In the HSP70 chaperone machinery, J proteins act as drivers of functional specificity and coordinate with ATP hydrolysis to regulate substrate binding and release. Similarly, protein substrates activate the ATP-dependent protease La by promoting nucleotide binding and release of bound ADP, showing that substrate recognition is coupled to the nucleotide state.
Conformational remodeling of the complex
In simple terms: ATP hydrolysis changes shape so the partner is held or remodeled.
ATP hydrolysis can induce conformational changes that stabilize or remodel a protein complex. Chaperonins use ATP to enclose substrate proteins in a protected chamber where folding can proceed. Hsp90 binding to ATP is sufficient for effective chaperoning of p53, indicating that nucleotide binding itself can drive a functional chaperone-client interaction. These examples show that ATP-dependent protein binding is not just binding; it is binding coupled to a mechanical cycle.
ATP-dependent steps in splicing
In simple terms: The spliceosome uses ATP to check and lock in its protein interactions.
Cus2 enforces the first ATP-dependent step of splicing by binding to yeast SF3b1 through a UHM-ULM interaction. This illustrates how ATP-dependent protein binding can act as a checkpoint that ensures the spliceosome assembles correctly before catalysis. The interaction is therefore both a binding event and a regulatory gate.
DNA damage recognition by UvrA
In simple terms: UvrA uses ATP to find and bind damaged DNA-associated proteins.
Structural snapshots of UvrA reveal the mechanism of ATP-dependent DNA damage recognition. Although the primary substrate is DNA, the ATP-dependent protein binding function is relevant because UvrA engages protein partners during nucleotide excision repair. This highlights how ATP-dependent binding can coordinate damage sensing with downstream repair factor recruitment.
Exocytosis and protease activation
In simple terms: ATP-dependent binding controls secretion and protein breakdown.
Regulation of exocytosis occurs through Ca2+/ATP-dependent binding of autophosphorylated Ca2+/calmodulin-activated protein kinase II to syntaxin 1A. In parallel, protein substrates activate the ATP-dependent protease La by promoting nucleotide binding and release of bound ADP. Together these examples show that ATP-dependent protein binding operates across secretion and proteolysis, linking energy status to diverse cellular outputs.
Key Genes Involved in GO:0043008 ATP-dependent protein binding
The following genes and proteins are representative of ATP-dependent protein binding (GO:0043008) based on the verified literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| HSPA1A | HSP70 chaperone ATPase cycle | Protein folding and proteostasis |
| DNAJA1 | J-protein co-chaperone | Drives HSP70 functional specificity |
| HSP90AA1 | ATP-dependent chaperone | Chaperones p53 |
| TP53 | Client protein of Hsp90 | Cancer biology and chaperone dependence |
| CUS2 | Splicing factor UHM-ULM interactor | First ATP-dependent step of splicing |
| SF3B1 | Spliceosome component | Target of Cus2 binding |
| UVRAA | DNA damage recognition ATPase | Nucleotide excision repair |
| CAMK2A | Ca2+/ATP-dependent kinase | Binds syntaxin 1A in exocytosis |
| STX1A | Syntaxin 1A | Exocytosis regulation |
| LONP1 | ATP-dependent protease | Substrate-activated proteolysis |
| CLPP | ATP-dependent protease | Mitochondrial proteostasis |
| HSPA8 | HSP70 family member | Chaperone cycle |
| HSPH1 | HSP110 nucleotide exchange factor | HSP70 regulation |
| BAG1 | Co-chaperone | HSP70 nucleotide exchange |
| STIP1 | HSP90 co-chaperone | Chaperone complex assembly |
| PRPF8 | Spliceosome ATPase-associated factor | Splicing fidelity |
| ERCC1 | DNA repair factor | UvrA-related repair |
How Is ATP-dependent protein binding Regulated?
ATP-dependent protein binding is regulated by nucleotide availability, co-chaperones, and post-translational modifications. In the HSP70 system, J proteins and nucleotide exchange factors control the ATPase cycle and thus substrate binding and release. Hsp90 chaperoning of p53 is regulated by ATP binding, which is sufficient for effective chaperoning. In splicing, Cus2 enforces the first ATP-dependent step by binding SF3b1, providing a checkpoint for spliceosome assembly. Protease La is regulated by protein substrates that promote nucleotide binding and ADP release. These layers of regulation ensure that ATP-dependent binding occurs only when the appropriate substrate and energy conditions are met.
ATP-dependent protein binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| HSP90AA1 | Cancer, p53 chaperoning | Knockout or point-mutation cell lines |
| TP53 | Tumor suppression | Knock-in of p53 mutants |
| CUS2 | Splicing-related disease | Knockout yeast or human cell models |
| SF3B1 | Myelodysplasia and leukemia | Point-mutation knock-in |
| UVRAA | DNA repair deficiency | Knockout and complementation |
Cancer and chaperone dependence
Hsp90 can chaperone p53 in an ATP-dependent manner, and ATP binding to Hsp90 is sufficient for effective chaperoning of p53. Because p53 is a central tumor suppressor, alterations in ATP-dependent protein binding can influence cancer cell survival and stress responses. This makes chaperone-client interactions attractive for experimental modeling in cancer research.
Splicing-related disease
Cus2 enforces the first ATP-dependent step of splicing by binding yeast SF3b1 through a UHM-ULM interaction. Defects in spliceosome assembly can lead to aberrant splicing, which is relevant to hematological malignancies and other splicing-related disorders. Studying ATP-dependent binding in this context helps explain how mutations in splicing factors contribute to disease.
Neurodegeneration and proteostasis
The HSP70 chaperone machinery and chaperonins are central to protein folding and proteostasis. When ATP-dependent protein binding is impaired, misfolded proteins can accumulate, a hallmark of neurodegenerative disease. Experimental models that perturb ATP-dependent chaperone cycles can therefore reveal mechanisms of neuronal vulnerability.
DNA repair deficiency
UvrA uses ATP-dependent DNA damage recognition, and structural studies have revealed snapshots of this mechanism. Deficiencies in nucleotide excision repair are linked to UV sensitivity and cancer predisposition. ATP-dependent protein binding is therefore relevant to understanding how repair complexes assemble on damaged DNA.
From ATP-dependent protein binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of ATP-dependent binding cause proteostasis failure? | CRISPR knockout of HSPA1A or DNAJA1 |
| Does ATP binding alone suffice for chaperoning? | Point mutation in HSP90AA1 ATP-binding domain |
| How does Cus2-SF3b1 binding affect splicing? | Knock-in of UHM-ULM interface mutations |
| What is the effect of UvrA ATPase mutants on repair? | Point-mutation knock-in in UVRAA |
| Can overexpression rescue exocytosis defects? | Overexpression of CAMK2A or STX1A |
| Does substrate-activated protease La require ATP binding? | Knockout and overexpression of LONP1 |
How to Study the ATP-dependent protein binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| ATPase assay | ATP hydrolysis rate | Chaperone and protease cycles |
| Pull-down with ATP analogs | ATP-dependent protein interactions | HSP70 and Hsp90 client binding |
| Cryo-EM | Structural states of complexes | Chaperonins and UvrA |
| Mass spectrometry | Protein interaction partners | Spliceosome and chaperone networks |
| Splicing reporter assay | Splicing efficiency | Cus2-SF3b1 function |
| Exocytosis assay | Vesicle release | CaMKII-syntaxin binding |
| Protease activity assay | Substrate degradation | Protease La activation |
Biochemical ATPase and binding assays
ATP-dependent protein binding can be measured using ATPase assays coupled to protein-protein binding readouts. For example, protein substrates activate the ATP-dependent protease La by promoting nucleotide binding and release of bound ADP, which can be monitored biochemically. Similar approaches are used to study HSP70 and Hsp90 cycles.
Structural biology
Structural snapshots of UvrA have revealed the mechanism of ATP-dependent DNA damage recognition. Cryo-EM and crystallography can capture nucleotide-bound states of chaperones and spliceosomal factors, providing mechanistic insight into ATP-dependent protein binding.
Proteomics and interactomics
Affinity purification coupled to mass spectrometry can identify protein partners whose binding depends on ATP. This is useful for mapping HSP70, Hsp90, and spliceosome interaction networks. Comparative analysis with ATPase-deficient mutants distinguishes ATP-dependent from ATP-independent interactions.
Functional cell assays
Exocytosis can be assayed using Ca2+/ATP-dependent binding of CaMKII to syntaxin 1A as a readout. Splicing efficiency can be measured in cells expressing Cus2 or SF3b1 mutants. These functional assays link molecular binding events to cellular phenotypes.
How CRISPR Can Be Used to Study GO:0043008 ATP-dependent protein binding
Knockout
CRISPR knockout of genes encoding ATP-dependent binding proteins, such as HSPA1A or DNAJA1, can reveal whether the binding function is essential for proteostasis. Knockout of CUS2 or SF3B1 can test splicing dependence on ATP-dependent steps.
Point Mutation
Point mutations in ATP-binding domains, such as HSP90AA1, can separate ATP binding from ATP hydrolysis and test whether ATP binding alone is sufficient for chaperoning p53. Similar point mutations in UVRAA can dissect DNA damage recognition.
Knock-in
Knock-in of disease-associated mutations in SF3B1 or TP53 can model how altered ATP-dependent protein binding contributes to splicing disorders or cancer. Tagged knock-in of CAMK2A or STX1A can track exocytosis-related binding in live cells.
Overexpression
Overexpression of ATP-dependent binding proteins such as HSPA1A or LONP1 can test gain-of-function effects and rescue experiments. Overexpression of CaMKII or syntaxin 1A can modulate exocytosis.
How EDITGENE Supports ATP-dependent protein binding Research
Researchers studying ATP-dependent protein binding-related genes often need to determine whether a candidate gene is causally involved in a specific cellular process or disease phenotype. This requires precise genetic models that isolate ATP-dependent binding from other functions of the protein. EDITGENE provides CRISPR-based tools to generate such models efficiently.
Contact EDITGENE today to design your custom CRISPR model for ATP-dependent protein binding research.
Frequently Asked Questions About ATP-dependent protein binding
What is ATP-dependent protein binding?
ATP-dependent protein binding (GO:0043008) is a molecular function in which a protein binds another protein or protein complex using energy from ATP hydrolysis.
What genes are involved in ATP-dependent protein binding?
Representative genes include HSPA1A, DNAJA1, HSP90AA1, CUS2, SF3B1, UVRAA, CAMK2A, STX1A, and LONP1.
How does ATP hydrolysis affect protein binding?
ATP hydrolysis drives conformational changes that control substrate capture, remodeling, and release in systems such as HSP70 and chaperonins.
What is the role of Hsp90 in ATP-dependent protein binding?
Hsp90 can chaperone p53, and ATP binding to Hsp90 is sufficient for effective chaperoning of p53.
How is ATP-dependent protein binding studied?
It is studied using ATPase assays, structural biology, proteomics, and functional cell assays.
What diseases are linked to ATP-dependent protein binding?
Cancer, splicing-related disorders, neurodegeneration, and DNA repair deficiencies have been linked to defects in ATP-dependent binding proteins.
Can CRISPR be used to study ATP-dependent protein binding?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models can test the causal role of ATP-dependent binding events.
What is the difference between ATP-dependent and ATP-independent protein binding?
ATP-dependent binding requires ATP hydrolysis and is often dynamic, whereas ATP-independent binding is typically stoichiometric and static.
Which chaperones use ATP-dependent protein binding?
HSP70, J-proteins, chaperonins, and Hsp90 are classic examples.
How does Cus2 enforce ATP-dependent splicing?
Cus2 binds yeast SF3b1 through a UHM-ULM interaction to enforce the first ATP-dependent step of splicing.
Conclusion
ATP-dependent protein binding (GO:0043008) is a fundamental molecular function that couples ATP hydrolysis to the recognition, remodeling, and release of protein partners. It underlies chaperone cycles, splicing fidelity, DNA repair, exocytosis, and proteolysis. Because dysregulation of these processes is linked to cancer, neurodegeneration, and splicing disorders, precise genetic models are essential for mechanistic and translational research. CRISPR-based knockout, point-mutation, knock-in, and overexpression strategies provide the resolution needed to test causality in this pathway.
References
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- 3. Ranson NA et al.. 1998. Chaperonins.. Biochem J 333 ( Pt 2)(Pt 2):233-42 PMID: 9657960
- 4. Walerych D et al.. 2010. ATP binding to Hsp90 is sufficient for effective chaperoning of p53 protein.. J Biol Chem 285(42):32020-8 PMID: 20688913
- 5. Talkish J et al.. 2019. Cus2 enforces the first ATP-dependent step of splicing by binding to yeast SF3b1 through a UHM-ULM interaction.. RNA 25(8):1020-1037 PMID: 31110137
- 6. Nirwal S et al.. 2025. Structural snapshots of the mechanism of ATP-dependent DNA damage recognition by UvrA.. Nat Commun 17(1):387 PMID: 41381534
- 7. Ohyama A et al.. 2002. Regulation of exocytosis through Ca2+/ATP-dependent binding of autophosphorylated Ca2+/calmodulin-activated protein kinase II to syntaxin 1A.. J Neurosci 22(9):3342-51 PMID: 11978810
- 8. Menon AS et al.. 1987. Protein substrates activate the ATP-dependent protease La by promoting nucleotide binding and release of bound ADP.. J Biol Chem 262(31):14929-34 PMID: 3312197
