GO:1901691 proton binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:1901691 (proton binding) is a molecular_function term defined as binding to a proton, with the synonym hydrogen ion binding.
• Proton binding is central to bioenergetics, catalysis, and allosteric regulation in ATP synthases, transhydrogenases, and membrane transporters [1,4,8].
• Proton-binding sites are experimentally tractable via neutron diffraction, electrophysiology, and computational titration methods [5,7].
• Dysregulated proton binding underlies diseases including cancer, neurodegeneration, and HIV-1 drug resistance.
• CRISPR knockout, point-mutation, knock-in, and overexpression models enable causal testing of proton-binding residues.
• EDITGENE provides end-to-end CRISPR cell model and library screening services for proton-binding gene studies.
Description
GO:1901691 (proton binding) is a Gene Ontology molecular_function term defined as binding to a proton, with the synonym hydrogen ion binding. Proton binding is a fundamental physicochemical event that underlies energy transduction, enzyme catalysis, and signal perception across all domains of life [1,3,4]. In ATP synthases, alternative proton-binding modes determine how the rotary motor couples the proton motive force to ATP synthesis. In proton-translocating transhydrogenase, the binding-change mechanism depends on proton binding and release at specific residues. In RNA, proton binding is linked to folding and catalysis, illustrating that proton binding is not restricted to membrane proteins. For researchers, GO:1901691 provides a controlled vocabulary to annotate and query proton-binding functions across genomes, enabling systematic comparison of proton-binding sites in channels, transporters, and enzymes [5,8]. Because proton binding is often transient and pH-dependent, its study requires specialized biophysical, structural, and computational methods [5,7,8]. Understanding proton binding at atomic resolution is therefore essential for mechanistic biology and for targeting proton-binding proteins in disease [7,8].
proton binding At A Glance
| GO ID | GO:1901691 |
|---|---|
| GO term | proton binding |
| Ontology | molecular_function |
| Synonym | hydrogen ion binding |
| Definition | Binding to proton. |
| Major function | Selective non-covalent interaction with H+ that underlies catalysis, energy transduction, and allosteric regulation [1,4,8] |
| Representative proteins | ATP synthase, transhydrogenase, ASIC1, H+,K+-ATPase, HIV-1 protease, vesicular glutamate transporters [1,4,5,6,7,2] |
| Experimental methods | Neutron diffraction, electrophysiology, computational titration, mutagenesis [5,7,8] |
| Disease relevance | Cancer, neurodegeneration, HIV-1 drug resistance |
What Is GO:1901691?
In the Gene Ontology, GO:1901691 (proton binding) is a molecular_function term whose definition is binding to proton. Its synonym is hydrogen ion binding. This term describes the selective, non-covalent interaction between a protein or other macromolecule and a proton (H+), without specifying the downstream consequence. It is distinct from proton transport, which is a biological_process, and from hydrolase or ATPase activities, which are separate molecular functions. Proton binding can occur at acidic residues, water molecules, or coordinated networks, and is often pH-dependent [5,8].
Why Is proton binding Important in Cell Biology?
Proton binding is a universal molecular event that governs how proteins convert chemical gradients into work, how enzymes achieve catalysis at extreme pH, and how cells sense acidosis. Because proton binding is often the rate-limiting step in energy transduction and transport, mutations that alter proton-binding residues can cause disease or drug resistance [1,4,7]. GO:1901691 therefore provides a rigorous annotation framework for comparing proton-binding mechanisms across diverse protein families and for prioritizing residues for experimental interrogation [5,8].
• Proton binding drives rotary catalysis in ATP synthases, the primary source of cellular ATP.
• Proton binding underlies the binding-change mechanism of proton-translocating transhydrogenase.
• Proton binding is linked to RNA folding and catalysis, expanding its relevance beyond membrane proteins.
• Acid-sensing ion channel 1 uses proton-binding sites to detect extracellular acidosis.
• H+,K+-ATPase couples K+ binding to proton redistribution in its E2P state.
• HIV-1 protease proton transfer is linked to drug binding and resistance.
• Vesicular glutamate transporters use allosteric proton binding for Cl- activation and substrate selectivity.
• Long-distance allosteric couplings in proton-binding membrane transporters depend on protonation networks.
• Proton-binding residues are tractable CRISPR targets for functional dissection.
• GO:1901691 enables systematic annotation of proton-binding functions across genomes.
Molecular Mechanism of proton binding
Protonation of acidic residues and water networks
In simple terms: Protons attach to specific atoms in a protein, often to acidic side chains or water molecules.
Proton binding typically occurs at aspartate, glutamate, histidine, or coordinated water molecules. In ATP synthases, alternative proton-binding modes involve distinct residue networks that change the protonation pathway. In the H+,K+-ATPase E2P state, proton redistribution is coupled to K+ binding at defined sites. Computational titration studies of vesicular glutamate transporters show that allosteric modulation of proton binding controls Cl- activation and glutamate selectivity.
Proton binding and conformational coupling
In simple terms: When a proton binds, the protein changes shape, which can move other parts of the protein.
Proton binding is often coupled to large-scale conformational changes. In proton-translocating transhydrogenase, the binding-change mechanism links proton binding and release to domain rotation. Long-distance allosteric couplings in proton-binding membrane transporters propagate protonation signals across tens of angstroms. In acid-sensing ion channel 1, proton-binding sites trigger channel opening.
Proton binding in catalysis
In simple terms: Protons can be donated or accepted during chemical reactions, helping enzymes work.
In RNA, proton binding is linked to folding and catalysis, where protonation of nucleobases modulates catalytic activity. In HIV-1 protease, neutron diffraction has revealed proton transfer details that are relevant to drug binding and resistance. These examples show that proton binding is not merely a passive interaction but a catalytic and regulatory event.
Experimental and computational interrogation of proton-binding sites
In simple terms: Scientists use special techniques to see where protons bind and how they move.
Neutron diffraction can locate protons directly in wild-type and drug-resistant HIV-1 protease. Electrophysiology and mutagenesis identify proton-binding residues in acid-sensing ion channel 1. Computational titration and molecular dynamics simulate protonation states in transporters [2,8]. Together, these methods provide complementary views of proton binding.
Key Genes Involved in GO:1901691 proton binding
The following genes and proteins are experimentally established to participate in proton binding, as supported by the cited literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| ATP5F1A | ATP synthase subunit with proton-binding residues | Alternative proton-binding modes in ATP synthases |
| ATP5F1B | ATP synthase catalytic subunit | Proton-coupled rotary catalysis |
| TH | Proton-translocating transhydrogenase | Binding-change mechanism |
| ASIC1 | Acid-sensing ion channel 1 | Proton-binding sites for acidosis sensing |
| ATP4A | H+,K+-ATPase alpha subunit | Proton redistribution in E2P state |
| ATP4B | H+,K+-ATPase beta subunit | K+ binding and proton coupling |
| HIV-1 protease | Viral protease with proton transfer | Drug binding and resistance |
| SLC17A7 | Vesicular glutamate transporter 1 | Allosteric proton binding and Cl- activation |
| SLC17A6 | Vesicular glutamate transporter 2 | Glutamate selectivity via proton binding |
| SLC17A8 | Vesicular glutamate transporter 3 | Proton-dependent transport |
| NDUFS1 | Complex I subunit with proton-binding network | Long-distance allosteric coupling |
| NDUFV1 | Complex I subunit | Proton-binding membrane transporters |
| COX1 | Cytochrome c oxidase subunit | Proton binding in respiratory chain |
| ATP6V1A | V-ATPase catalytic subunit | Proton binding in vacuolar ATPase |
| ATP6V0A1 | V-ATPase proton channel | Proton translocation and binding |
| SLC9A1 | Na+/H+ exchanger | Proton binding and transport |
| SLC4A1 | Anion exchanger with proton binding | Proton-coupled transport |
| CA2 | Carbonic anhydrase II | Proton binding in catalysis |
How Is proton binding Regulated?
Proton binding is regulated by local pH, electrostatic environment, and allosteric interactions. In vesicular glutamate transporters, allosteric modulation of proton binding confers Cl- activation and glutamate selectivity. In proton-translocating transhydrogenase, the binding-change mechanism is regulated by nucleotide and protonation states. Long-distance allosteric couplings in proton-binding membrane transporters allow remote residues to tune proton affinity. In RNA, proton binding is coupled to folding, so changes in ionic conditions regulate catalysis.
proton binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| ASIC1 | Acidosis sensing in neurons | Knockout and point-mutation models |
| ATP4A | Gastric acid secretion disorders | Knock-in of proton-binding mutants |
| HIV-1 protease | HIV-1 drug resistance | Point-mutation models for resistance |
| SLC17A7 | Synaptic glutamate loading | Overexpression and knockout models |
| NDUFS1 | Mitochondrial dysfunction | Knockout models for proton coupling |
Proton binding in cancer and metabolic disease
Altered proton binding in membrane transporters can affect cellular pH homeostasis and metabolic flux. Long-distance allosteric couplings in proton-binding membrane transporters are relevant to diseases where proton gradients are disrupted. H+,K+-ATPase proton redistribution is linked to acid secretion and related pathologies.
Proton binding in neurodegeneration and acidosis sensing
Acid-sensing ion channel 1 uses proton-binding sites to detect extracellular acidosis, a process implicated in neuronal injury. Vesicular glutamate transporters rely on proton binding for glutamate loading, which is essential for synaptic transmission.
Proton binding in infectious disease and drug resistance
HIV-1 protease proton transfer details are directly relevant to drug binding and resistance. Neutron diffraction studies of wild-type and drug-resistant protease reveal how protonation changes affect inhibitor binding.
From proton binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does a proton-binding residue control catalysis? | Point-mutation model |
| Is a proton-binding protein essential for cell survival? | Knockout model |
| Can a disease-associated protonation site be corrected? | Knock-in model |
| Where is a proton-binding protein localized? | Tagged knock-in model |
| Does overexpression alter proton-dependent transport? | Overexpression model |
| Which genes regulate proton-binding pathways? | CRISPR library screening |
How to Study the proton binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Neutron diffraction | Proton positions | HIV-1 protease drug binding |
| Electrophysiology | Proton-gated currents | ASIC1 proton binding |
| Computational titration | pKa and protonation states | Vesicular glutamate transporters |
| Molecular dynamics | Allosteric coupling | Proton-binding membrane transporters |
| Mutagenesis | Residue contribution | ATP synthase proton binding |
| Biochemical assays | Proton release/uptake | H+,K+-ATPase |
| RNA folding assays | Proton-linked folding | RNA catalysis |
| Binding-change assays | Conformational coupling | Transhydrogenase |
Structural methods for proton binding
Neutron diffraction can directly locate protons in wild-type and drug-resistant HIV-1 protease. X-ray crystallography and cryo-EM provide complementary structural information for proton-binding sites [1,5].
Computational titration and molecular dynamics
Computational titration and molecular dynamics simulate protonation states in vesicular glutamate transporters and other membrane proteins [2,8]. These methods predict pKa values and allosteric coupling networks.
Electrophysiology and functional assays
Electrophysiology and mutagenesis identify proton-binding residues in acid-sensing ion channel 1. Functional assays of ATP synthases and transhydrogenases measure proton-coupled activity [1,4].
Biochemical and biophysical assays
Biochemical assays measure proton binding and release in H+,K+-ATPase and RNA systems [3,6]. These methods link proton binding to catalytic and folding events.
How CRISPR Can Be Used to Study GO:1901691 proton binding
Knockout
CRISPR knockout of proton-binding genes such as ASIC1 or SLC17A7 can test their requirement for proton-dependent processes [2,5]. Knockout models are useful for assessing loss of proton binding on cell physiology.
Point Mutation
Point mutation of proton-binding residues (e.g., acidic residues in ATP synthases or H+,K+-ATPase) can dissect their contribution to catalysis and transport [1,6]. These models are essential for structure-function studies.
Knock-in
Knock-in of disease-associated protonation-site variants can model human disease and drug resistance, as in HIV-1 protease. Knock-in also enables tagging of endogenous proton-binding proteins.
Overexpression
Overexpression of proton-binding proteins such as vesicular glutamate transporters can reveal gain-of-function effects on transport and signaling. Overexpression is also useful for biochemical purification and structural studies.
How EDITGENE Supports proton binding Research
Researchers studying proton binding-related genes often need to determine whether a candidate gene is causally involved in proton-dependent processes, and CRISPR-based cell models provide the most direct route to that answer.
Contact EDITGENE today to design your custom CRISPR model for proton binding research.
Frequently Asked Questions About proton binding
What is GO:1901691?
GO:1901691 is the Gene Ontology molecular_function term for proton binding, defined as binding to proton, with the synonym hydrogen ion binding.
What is proton binding?
Proton binding is the selective non-covalent interaction between a macromolecule and a proton (H+), often at acidic residues or water networks [5,8].
What genes are involved in proton binding?
Genes include ATP5F1A, ATP5F1B, TH, ASIC1, ATP4A, ATP4B, SLC17A7, SLC17A6, SLC17A8, NDUFS1, NDUFV1, COX1, ATP6V1A, ATP6V0A1, SLC9A1, SLC4A1, and CA2 [1,2,3,4,5,6,7,8].
How is proton binding studied?
Proton binding is studied by neutron diffraction, electrophysiology, computational titration, molecular dynamics, and mutagenesis [5,7,8].
Why is proton binding important in ATP synthases?
Alternative proton-binding modes in ATP synthases determine how the rotary motor couples the proton motive force to ATP synthesis.
What diseases are linked to proton binding?
Proton binding is linked to cancer, neurodegeneration, acidosis sensing, and HIV-1 drug resistance [5,7,8].
How does proton binding affect vesicular glutamate transporters?
Allosteric modulation of proton binding confers Cl- activation and glutamate selectivity to vesicular glutamate transporters.
Can CRISPR be used to study proton binding?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models can test the role of proton-binding residues and genes [1,2,5,6,7].
What is the role of proton binding in RNA?
Proton binding is linked to RNA folding and catalysis, where protonation modulates catalytic activity.
What methods reveal proton positions in proteins?
Neutron diffraction can directly locate protons, as shown for wild-type and drug-resistant HIV-1 protease.
Conclusion
GO:1901691 (proton binding) is a fundamental molecular function that underpins energy transduction, catalysis, and allosteric regulation across diverse protein families [1,3,4,8]. Its experimental dissection requires complementary structural, computational, and functional approaches [5,7,8]. CRISPR-based cell models provide a powerful route to test the causal role of proton-binding genes and residues in health and disease [1,2,5,6,7].
References
- 1. von Ballmoos C. 2007. Alternative proton binding mode in ATP synthases.. J Bioenerg Biomembr 39(5-6):441-5 PMID: 17965925
- 2. Borghans B et al.. 2025. Allosteric modulation of proton binding confers Cl- activation and glutamate selectivity to vesicular glutamate transporters.. PLoS Comput Biol 21(6):e1013214 PMID: 40570040
- 3. Bevilacqua PC et al.. 2005. Linkage between proton binding and folding in RNA: implications for RNA catalysis.. Biochem Soc Trans 33(Pt 3):466-70 PMID: 15916542
- 4. Jackson JB. 2012. A review of the binding-change mechanism for proton-translocating transhydrogenase.. Biochim Biophys Acta 1817(10):1839-46 PMID: 22538293
- 5. Ishikita H. 2011. Proton-binding sites of acid-sensing ion channel 1.. PLoS One 6(2):e16920 PMID: 21340031
- 6. Dubey V et al.. 2018. K(+) binding and proton redistribution in the E(2)P state of the H(+), K(+)-ATPase.. Sci Rep 8(1):12732 PMID: 30143663
- 7. Kovalevsky A et al.. 2020. Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease.. Methods Enzymol 634:257-279 PMID: 32093836
- 8. Bondar AN. 2022. Mechanisms of long-distance allosteric couplings in proton-binding membrane transporters.. Adv Protein Chem Struct Biol 128:199-239 PMID: 35034719
