User talk:Mousumi Kandangkel
From Proteopedia
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| - | <Structure load='9OVR' size='350' frame='true' align='right' caption=' | + | <Structure load='9OVR' size='350' frame='true' align='right' caption='CryoEM structure of human NBCn1 (PDB 9OVR) showing the homodimeric assembly with each protomer containing 14 transmembrane helices organized into gate and core domains.' scene='Insert optional scene name here' /> |
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== CryoEM and Computational Modeling Structural Insights into the pH Regulator NBCn1 == | == CryoEM and Computational Modeling Structural Insights into the pH Regulator NBCn1 == | ||
| - | === Function === | + | === Function: Physiological Role and Cancer Dependence === |
| - | NBCn1 (SLC4A7) | + | The electroneutral sodium–bicarbonate cotransporter NBCn1 (SLC4A7) functions as a critical "base loader" for cellular physiology. By importing base equivalents to neutralize metabolic acid, NBCn1 maintains intracellular pH homeostasis. In the context of pathology, NBCn1 is frequently overexpressed in breast cancer cells. Its elevated activity drives sustained cytosolic alkalinization, a condition that favors tumor proliferation and survival despite the highly acidic microenvironment typical of solid tumors. |
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| + | === Structural Architecture (PDB: 9OVR) === | ||
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| + | The cryoEM study resolves the full-length human NBCn1 at near-atomic resolution, providing the first definitive look at its architecture. The protein assembles as a homodimer, with each protomer containing 14 transmembrane helices organized into two distinct functional domains: a rigid gate domain that serves as a membrane scaffold and a mobile core domain that houses the ion-binding sites. The resolved structure captures the transporter in an outward-facing state, characterized by a large, solvent-accessible vestibule that opens to the extracellular space while sealing off the intracellular pathway. | ||
| - | === | + | === Mechanism: The Carbonate Hypothesis === |
| - | + | A pivotal finding of this study is the revision of the transport substrate identity. While long assumed to be a simple bicarbonate transporter, the structural and computational data argue for a Carbonate (CO₃²⁻) Symport mechanism. The density maps reveal coordination sites for two Sodium ions (2Na⁺) and one Carbonate ion (CO₃²⁻). This 2:1 stoichiometry perfectly balances the charges, resulting in net zero charge transfer consistent with NBCn1's electroneutral behavior. Transporting CO₃²⁻ is thermodynamically superior to transporting HCO₃⁻ in acidic conditions, as carbonate carries two base equivalents, achieving double the neutralizing power per transport cycle. | |
| - | === | + | === Structural Dynamics: The "Fast Elevator" Model === |
| - | + | Molecular Dynamics simulations elucidate an Elevator-Type Alternating Access Mechanism. Unlike rocker-switch transporters, NBCn1 functions like an elevator where the core domain slides vertically through the membrane plane against the static gate domain. The vertical shift required to transition between outward-facing and inward-facing states is remarkably small—approximately 5 Å. This minimal structural rearrangement implies a flat free-energy landscape with very low activation barriers, which explains the exceptionally high turnover rate of approximately 15,000 s⁻¹. NBCn1 is built for speed, functioning almost as fast as an ion channel while maintaining strict transporter coupling. | |
| - | === | + | === Biological and Medical Implications === |
| - | + | Structure-guided cysteine-scanning mutagenesis confirmed that residues lining the predicted translocation pathway are essential, with modifications abolishing transport and validating the elevator interface. Current inhibitors of acid-base transporters are often non-specific, but the unique structure of the NBCn1 extracellular vestibule provides a specific pocket for drug design. Because breast cancer cells are "addicted" to NBCn1 for pH survival while normal cells have redundant mechanisms, high-affinity inhibitors or monoclonal antibodies that lock the elevator in a single conformation could suffocate tumors by allowing lethal cytosolic acidification. | |
| - | === | + | === Key Findings Summary === |
| - | + | This research transforms NBCn1 from a kinetic concept into a defined structural machine. It demonstrates that NBCn1 is a high-velocity, carbonate-preferring elevator transporter. By utilizing a compact 5 Å vertical slide, it achieves rapid base influx necessary to sustain aggressive breast cancer metabolism. The structure (PDB 9OVR) now serves as a template for structure-based drug discovery aimed at disrupting tumor pH regulation. | |
| - | === | + | ===Course code : BI3323 === |
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Current revision
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Contents |
CryoEM and Computational Modeling Structural Insights into the pH Regulator NBCn1
Function: Physiological Role and Cancer Dependence
The electroneutral sodium–bicarbonate cotransporter NBCn1 (SLC4A7) functions as a critical "base loader" for cellular physiology. By importing base equivalents to neutralize metabolic acid, NBCn1 maintains intracellular pH homeostasis. In the context of pathology, NBCn1 is frequently overexpressed in breast cancer cells. Its elevated activity drives sustained cytosolic alkalinization, a condition that favors tumor proliferation and survival despite the highly acidic microenvironment typical of solid tumors.
Structural Architecture (PDB: 9OVR)
The cryoEM study resolves the full-length human NBCn1 at near-atomic resolution, providing the first definitive look at its architecture. The protein assembles as a homodimer, with each protomer containing 14 transmembrane helices organized into two distinct functional domains: a rigid gate domain that serves as a membrane scaffold and a mobile core domain that houses the ion-binding sites. The resolved structure captures the transporter in an outward-facing state, characterized by a large, solvent-accessible vestibule that opens to the extracellular space while sealing off the intracellular pathway.
Mechanism: The Carbonate Hypothesis
A pivotal finding of this study is the revision of the transport substrate identity. While long assumed to be a simple bicarbonate transporter, the structural and computational data argue for a Carbonate (CO₃²⁻) Symport mechanism. The density maps reveal coordination sites for two Sodium ions (2Na⁺) and one Carbonate ion (CO₃²⁻). This 2:1 stoichiometry perfectly balances the charges, resulting in net zero charge transfer consistent with NBCn1's electroneutral behavior. Transporting CO₃²⁻ is thermodynamically superior to transporting HCO₃⁻ in acidic conditions, as carbonate carries two base equivalents, achieving double the neutralizing power per transport cycle.
Structural Dynamics: The "Fast Elevator" Model
Molecular Dynamics simulations elucidate an Elevator-Type Alternating Access Mechanism. Unlike rocker-switch transporters, NBCn1 functions like an elevator where the core domain slides vertically through the membrane plane against the static gate domain. The vertical shift required to transition between outward-facing and inward-facing states is remarkably small—approximately 5 Å. This minimal structural rearrangement implies a flat free-energy landscape with very low activation barriers, which explains the exceptionally high turnover rate of approximately 15,000 s⁻¹. NBCn1 is built for speed, functioning almost as fast as an ion channel while maintaining strict transporter coupling.
Biological and Medical Implications
Structure-guided cysteine-scanning mutagenesis confirmed that residues lining the predicted translocation pathway are essential, with modifications abolishing transport and validating the elevator interface. Current inhibitors of acid-base transporters are often non-specific, but the unique structure of the NBCn1 extracellular vestibule provides a specific pocket for drug design. Because breast cancer cells are "addicted" to NBCn1 for pH survival while normal cells have redundant mechanisms, high-affinity inhibitors or monoclonal antibodies that lock the elevator in a single conformation could suffocate tumors by allowing lethal cytosolic acidification.
Key Findings Summary
This research transforms NBCn1 from a kinetic concept into a defined structural machine. It demonstrates that NBCn1 is a high-velocity, carbonate-preferring elevator transporter. By utilizing a compact 5 Å vertical slide, it achieves rapid base influx necessary to sustain aggressive breast cancer metabolism. The structure (PDB 9OVR) now serves as a template for structure-based drug discovery aimed at disrupting tumor pH regulation.
