GO:0001786 phosphatidylserine binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0001786 phosphatidylserine binding is a molecular function defined as binding to phosphatidylserine, a glycophospholipid in which a phosphatidyl group is esterified to the hydroxyl group of L-serine.
• Phosphatidylserine is normally confined to the inner leaflet of the plasma membrane, and its exposure on the outer leaflet serves as a key signal in apoptosis, efferocytosis, and coagulation.
• Proteins that bind phosphatidylserine include annexin A5, coagulation factor X, CKLF1, and various synthetic or natural ligands used to detect extracellular vesicles.
• Phosphatidylserine binding is critical for microglial efferocytosis after ischemic stroke, where CKLF1 competes with phosphatidylserine to disrupt clearance of dying cells.
• Annexin A5 is a widely used phosphatidylserine-binding reagent for detecting apoptotic cells and extracellular vesicles, and its binding is Ca2+-dependent.
• CRISPR-based knockout, point-mutation, knock-in, and overexpression models enable causal interrogation of phosphatidylserine-binding proteins in disease and cell clearance.
Description
Phosphatidylserine binding (GO:0001786) is a molecular function that mediates the specific recognition of phosphatidylserine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of L-serine. This binding event is fundamental to many biological processes, including apoptotic cell clearance, blood coagulation, and extracellular vesicle turnover. Phosphatidylserine is normally restricted to the inner leaflet of the plasma membrane, but its exposure on the outer leaflet acts as a signal for phagocytes and other cells. Proteins that bind phosphatidylserine therefore serve as sensors and effectors in these processes. Researchers study phosphatidylserine binding to understand how cells recognize and respond to phosphatidylserine signals in health and disease. For example, CKLF1 disrupts microglial efferocytosis after acute ischemic stroke by binding to phosphatidylserine, thereby impairing clearance of dead cells. Coagulation factor X contains a unique phosphatidylserine binding site that is essential for its function in the coagulation cascade. Annexin A5 is a well-characterized phosphatidylserine-binding protein used as a tool to detect apoptotic cells and extracellular vesicles. Synthetic ligands that bind phosphatidylserine have been developed to target cells for phagocytic clearance. This article provides a comprehensive overview of phosphatidylserine binding, covering its definition, key genes and proteins, molecular mechanisms, disease relevance, and research methods. All facts are based on published literature and the QuickGO definition for GO:0001786.
phosphatidylserine binding At A Glance
| GO ID | GO:0001786 |
|---|---|
| GO term | phosphatidylserine binding |
| Ontology | molecular_function |
| Synonym | none |
| Major function | Binding to phosphatidylserine, a glycophospholipid, enabling cellular recognition and signaling |
| Definition source | QuickGO |
| Related processes | Apoptotic cell clearance, coagulation, extracellular vesicle turnover |
| Representative proteins | Annexin A5, coagulation factor X, CKLF1, synthetic phosphatidylserine-binding ligands |
What Is GO:0001786?
Phosphatidylserine binding (GO:0001786) is the molecular function of selectively interacting with phosphatidylserine, a phospholipid in which the phosphatidyl group is esterified to the hydroxyl group of L-serine. This binding is typically non-covalent and can be mediated by specific protein domains or motifs that recognize the phosphatidylserine headgroup. The function is defined in the Gene Ontology under the molecular_function aspect.
Why Is phosphatidylserine binding Important in Cell Biology?
Phosphatidylserine binding is important because it underpins essential biological processes such as the recognition and removal of apoptotic cells, blood coagulation, and the clearance of extracellular vesicles. Dysregulation of phosphatidylserine binding can lead to impaired efferocytosis, contributing to inflammation and tissue damage after ischemic stroke. In coagulation, phosphatidylserine binding by factor X is critical for the assembly of the prothrombinase complex. Furthermore, phosphatidylserine-binding reagents are widely used in research and diagnostics to detect apoptotic cells and extracellular vesicles. Understanding phosphatidylserine binding also informs the development of synthetic ligands for targeted cell clearance.
• Mediates recognition of apoptotic cells by phagocytes during efferocytosis.
• Essential for blood coagulation through phosphatidylserine-dependent assembly of coagulation factors.
• Enables detection of extracellular vesicles and apoptotic cells using annexin A5 and other reagents.
• Plays a role in microglial clearance after ischemic stroke, where CKLF1 disrupts efferocytosis.
• Provides a target for synthetic ligands that promote phagocytic clearance of targeted cells.
• Involved in the distribution and function of phosphatidylserine in cellular membranes.
• Phosphatidylserine-binding proteins are studied for their roles in signal transduction and membrane trafficking.
• Annexin A5 binding to phosphatidylserine is Ca2+-dependent and used in anticoagulant assays.
• Phosphatidylserine exposure is a hallmark of apoptosis and is recognized by multiple phosphatidylserine-binding proteins.
• Understanding phosphatidylserine binding aids in the development of therapeutics for stroke, thrombosis, and inflammatory diseases.
What Happens During phosphatidylserine binding?
Exposure of phosphatidylserine on the cell surface
In simple terms: Phosphatidylserine moves from the inside to the outside of the cell membrane.
Under normal conditions, phosphatidylserine is confined to the inner leaflet of the plasma membrane, but during apoptosis or activation, it becomes exposed on the outer leaflet. This exposure serves as a signal for recognition by phosphatidylserine-binding proteins.
Recognition by phosphatidylserine-binding proteins
In simple terms: Proteins that can bind phosphatidylserine attach to it on the cell surface.
Proteins such as annexin A5, coagulation factor X, and CKLF1 specifically bind to exposed phosphatidylserine. This binding is often mediated by structural motifs that recognize the phosphatidylserine headgroup.
Downstream signaling and effector functions
In simple terms: Once bound, these proteins trigger responses like cell clearance or blood clotting.
Binding of phosphatidylserine by phagocyte receptors leads to engulfment of apoptotic cells, a process called efferocytosis. In coagulation, phosphatidylserine binding by factor X facilitates the assembly of coagulation complexes on activated platelets.
Regulation and competition
In simple terms: Other molecules can interfere with phosphatidylserine binding.
CKLF1 competes with phosphatidylserine for binding to microglial receptors, thereby disrupting efferocytosis after ischemic stroke. Synthetic ligands can also be designed to bind phosphatidylserine and promote targeted cell clearance.
Key Genes Involved in GO:0001786 phosphatidylserine binding
The following genes and proteins are key players in phosphatidylserine binding and its associated functions.
| Gene | Major Role | Research Relevance |
|---|---|---|
| ANXA5 | Ca2+-dependent phosphatidylserine-binding protein | Used as a probe for apoptotic cells and extracellular vesicles |
| F10 | Coagulation factor X; contains a unique phosphatidylserine binding site | Essential for coagulation cascade; studied for anticoagulant therapies |
| CKLF1 | Chemokine-like factor 1; binds phosphatidylserine and disrupts microglial efferocytosis | Implicated in ischemic stroke pathology |
| MFGE8 | Milk fat globule-EGF factor 8; bridges phosphatidylserine on apoptotic cells to phagocytes | Mediates efferocytosis; studied in inflammation and tissue repair |
| GAS6 | Growth arrest-specific 6; binds phosphatidylserine and activates TAM receptors | Regulates cell survival, proliferation, and immune responses |
| PROS1 | Protein S; binds phosphatidylserine and functions as a cofactor for protein C | Anticoagulant pathway; studied in thrombosis |
| TIMD4 | T-cell immunoglobulin and mucin domain containing 4; phosphatidylserine receptor | Mediates apoptotic cell clearance; studied in immune tolerance |
| STAB1 | Stabilin-1; scavenger receptor that binds phosphatidylserine | Involved in clearance of apoptotic cells and extracellular vesicles |
| STAB2 | Stabilin-2; phosphatidylserine-binding scavenger receptor | Roles in clearance and immune regulation |
| AXL | Receptor tyrosine kinase; binds GAS6-phosphatidylserine complexes | Promotes efferocytosis and cancer progression |
| MERTK | Receptor tyrosine kinase; recognizes phosphatidylserine via GAS6 | Critical for retinal pigment epithelium function and efferocytosis |
| CD300A | Inhibitory receptor that binds phosphatidylserine | Regulates immune cell activation |
| CD300LF | Activating receptor that binds phosphatidylserine | Modulates immune responses |
| RAGE | Receptor for advanced glycation end products; binds phosphatidylserine | Involved in inflammation and clearance |
| SCARB1 | Scavenger receptor class B member 1; binds phosphatidylserine | Roles in lipid metabolism and clearance |
| LAMP1 | Lysosomal-associated membrane protein 1; may bind phosphatidylserine | Marker for lysosomes; potential role in vesicle trafficking |
| SYNTHETIC LIGAND | Engineered phosphatidylserine-binding molecule | Used to target cells for phagocytic clearance |
How Is phosphatidylserine binding Regulated?
Phosphatidylserine binding is regulated at multiple levels. The exposure of phosphatidylserine on the cell surface is controlled by phospholipid scramblases and flippases. Calcium ions are required for the binding of annexin A5 and other annexin family proteins to phosphatidylserine. Competition by soluble factors such as CKLF1 can modulate phosphatidylserine binding to receptors, as shown in microglial efferocytosis after stroke. Additionally, the expression levels of phosphatidylserine-binding proteins and their receptors influence the efficiency of downstream processes like efferocytosis and coagulation.
phosphatidylserine binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| CKLF1 | Ischemic stroke; disrupted efferocytosis | Knockout mouse or microglial cell line with CKLF1 KO |
| F10 | Thrombosis; coagulation disorders | Point-mutation knock-in of factor X phosphatidylserine binding site |
| ANXA5 | Apoptosis detection; extracellular vesicle turnover | Overexpression or tagged knock-in of ANXA5 for imaging |
| MFGE8 | Inflammation; impaired efferocytosis | Knockout mouse model to study clearance |
| AXL | Cancer; immune evasion | Kinase-dead point mutation or knockout in cancer cell lines |
Ischemic stroke and neuroinflammation
After acute ischemic stroke, CKLF1 binds to phosphatidylserine and disrupts microglial efferocytosis, leading to impaired clearance of dead cells and exacerbated neuroinflammation. This highlights phosphatidylserine binding as a potential therapeutic target for stroke.
Coagulation disorders and thrombosis
Coagulation factor X contains a unique phosphatidylserine binding site that is essential for its function in the coagulation cascade. Dysregulation of phosphatidylserine binding can contribute to thrombotic disorders, and factor X is a target for anticoagulant drugs.
Cancer and immune evasion
Phosphatidylserine exposure on tumor cells and extracellular vesicles can promote immune evasion by engaging phosphatidylserine receptors on immune cells. Synthetic ligands that bind phosphatidylserine are being explored to target cancer cells for phagocytic clearance.
Extracellular vesicle turnover and diagnostics
Phosphatidylserine-binding reagents are used to assess extracellular vesicle turnover in vivo, providing insights into vesicle biology and potential biomarkers for disease.
From phosphatidylserine binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of CKLF1 restore microglial efferocytosis after stroke? | CKLF1 knockout mouse or microglial cell line |
| What is the role of factor X phosphatidylserine binding in coagulation? | Point mutation of the phosphatidylserine binding site in F10 |
| Can annexin A5 be used to track extracellular vesicles in vivo? | Tagged knock-in of ANXA5 with fluorescent protein |
| Does overexpression of MFGE8 enhance clearance of apoptotic cells? | MFGE8 overexpression in phagocytes |
| Can synthetic phosphatidylserine ligands target specific cells for clearance? | Knock-in of synthetic ligand receptor or overexpression |
| How does phosphatidylserine exposure regulate immune responses? | Knockout of scramblase or flippase genes |
How to Study the phosphatidylserine binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Annexin A5 flow cytometry | Phosphatidylserine exposure on cell surface | Apoptosis detection |
| Extracellular vesicle imaging | Turnover of phosphatidylserine-positive vesicles | In vivo vesicle tracking |
| Coagulation assay | Factor X activity and phosphatidylserine-dependent coagulation | Thrombosis research |
| CRISPR knockout screen | Genes required for phosphatidylserine binding | Identify novel regulators |
| Surface plasmon resonance | Binding affinity to phosphatidylserine | Characterize phosphatidylserine-protein interactions |
| Lipid overlay assay | Phosphatidylserine binding specificity | Screen for phosphatidylserine-binding proteins |
| Phagocytosis assay | Efferocytosis of phosphatidylserine-coated targets | Study microglial clearance |
| Synthetic ligand binding assay | Targeted cell clearance | Develop therapeutic ligands |
Flow cytometry with annexin A5
Annexin A5 conjugated to fluorophores is widely used to detect phosphatidylserine exposure on apoptotic cells by flow cytometry. This method allows quantification of apoptosis and phosphatidylserine externalization.
Extracellular vesicle detection
Highly sensitive phosphatidylserine-binding reagents enable assessment of extracellular vesicle turnover in vivo, as demonstrated by Flaskamp et al.. These reagents can be used in imaging and biochemical assays.
Coagulation assays
Phosphatidylserine binding by factor X can be studied using coagulation assays that measure thrombin generation or factor X activity in the presence of phospholipid vesicles.
CRISPR-based genetic screens
CRISPR knockout or activation screens can identify genes that regulate phosphatidylserine binding and efferocytosis. For example, synthetic ligands that bind phosphatidylserine can be used to select for resistant or sensitive cells.
How CRISPR Can Be Used to Study GO:0001786 phosphatidylserine binding
Knockout
CRISPR knockout of genes encoding phosphatidylserine-binding proteins (e.g., CKLF1, ANXA5) can reveal their roles in efferocytosis, coagulation, and vesicle turnover. Knockout cell models are essential for loss-of-function studies.
Point Mutation
Point mutations can be introduced into phosphatidylserine-binding domains to abrogate binding without affecting protein expression. For example, mutating the phosphatidylserine binding site in factor X can clarify its role in coagulation.
Knock-in
Knock-in of tagged versions of phosphatidylserine-binding proteins (e.g., fluorescently tagged annexin A5) allows real-time imaging of phosphatidylserine exposure and vesicle tracking.
Overexpression
Overexpression of phosphatidylserine-binding proteins such as MFGE8 or synthetic ligands can enhance clearance of apoptotic cells and be used to study gain-of-function effects.
How EDITGENE Supports phosphatidylserine binding Research
Researchers studying phosphatidylserine binding-related genes often need to determine whether a candidate gene is causally involved in phosphatidylserine recognition, efferocytosis, or coagulation. EDITGENE provides comprehensive CRISPR gene editing services to create precisely engineered cell models for such investigations.
Contact EDITGENE today to design your custom CRISPR model for phosphatidylserine binding research.
Frequently Asked Questions About phosphatidylserine binding
What is phosphatidylserine binding?
Phosphatidylserine binding is a molecular function (GO:0001786) that mediates specific recognition of phosphatidylserine, a phospholipid exposed on the outer leaflet of cells during apoptosis and activation.
What genes are involved in phosphatidylserine binding?
Key genes include ANXA5, F10, CKLF1, MFGE8, GAS6, and various receptors such as TIMD4 and MERTK.
How is phosphatidylserine binding measured?
Common methods include annexin A5 flow cytometry, extracellular vesicle imaging, and coagulation assays.
What is the role of phosphatidylserine binding in stroke?
CKLF1 binds phosphatidylserine and disrupts microglial efferocytosis after ischemic stroke, impairing clearance of dead cells.
Which proteins bind phosphatidylserine in coagulation?
Coagulation factor X contains a unique phosphatidylserine binding site essential for coagulation cascade assembly.
Can CRISPR be used to study phosphatidylserine binding?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models enable functional studies of phosphatidylserine-binding proteins.
What is annexin A5 and how does it relate to phosphatidylserine?
Annexin A5 is a Ca2+-dependent phosphatidylserine-binding protein widely used to detect apoptotic cells and extracellular vesicles.
How does phosphatidylserine exposure signal cell clearance?
Phosphatidylserine on the outer leaflet is recognized by phagocyte receptors, triggering engulfment of apoptotic cells.
What diseases are linked to phosphatidylserine binding?
Diseases include ischemic stroke, thrombosis, cancer, and inflammatory conditions.
What are synthetic phosphatidylserine-binding ligands?
Synthetic ligands are engineered molecules that bind phosphatidylserine and can target cells for phagocytic clearance.
Conclusion
Phosphatidylserine binding (GO:0001786) is a fundamental molecular function that mediates critical biological processes, including apoptotic cell clearance, coagulation, and extracellular vesicle turnover. Dysregulation of phosphatidylserine binding contributes to diseases such as ischemic stroke, thrombosis, and cancer. Advances in CRISPR gene editing and phosphatidylserine-binding reagents continue to illuminate the mechanisms and therapeutic potential of this function. Researchers can leverage EDITGENE's comprehensive CRISPR services to create knockout, point-mutation, knock-in, and overexpression models for studying phosphatidylserine-binding proteins in health and disease.
References
- 1. Fan PL et al.. 2025. CKLF1 disrupts microglial efferocytosis following acute ischemic stroke by binding to phosphatidylserine.. Cell Death Differ 32(8):1499-1517 PMID: 40057593
- 2. Leventis PA et al.. 2010. The distribution and function of phosphatidylserine in cellular membranes.. Annu Rev Biophys 39:407-27 PMID: 20192774
- 3. Stace CL et al.. 2006. Phosphatidic acid- and phosphatidylserine-binding proteins.. Biochim Biophys Acta 1761(8):913-26 PMID: 16624617
- 4. Flaskamp L et al.. 2025. Assessing Extracellular Vesicle Turnover In Vivo Using Highly Sensitive Phosphatidylserine-Binding Reagents.. Adv Sci (Weinh) 12(40):e07624 PMID: 40817753
- 5. van Genderen HO et al.. 2008. Extracellular annexin A5: functions of phosphatidylserine-binding and two-dimensional crystallization.. Biochim Biophys Acta 1783(6):953-63 PMID: 18334229
- 6. Paul D et al.. 2022. Stoichiometric analysis reveals a unique phosphatidylserine binding site in coagulation factor X.. J Thromb Haemost 20(3):600-604 PMID: 34894064
- 7. Nakayama M et al.. 2020. Annexin Lectins: Ca(2+)-Dependent Heparin-Binding Activity, Phosphatidylserine-Binding Activity, and Anticoagulant Activity.. Methods Mol Biol 2132:661-668 PMID: 32306365
- 8. Yamato Y et al.. 2026. Phagocytic clearance of targeted cells with a synthetic ligand.. Nat Biomed Eng 10(3):584-601 PMID: 40903592
