Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter
Intracellular transport of chloride by members of the CLC transporter family involves a coupled exchange between a Cl<sup>−</sup> anion and a proton (H<sup>+</sup>), which makes the transport function dependent on ambient pH. Transport activity peaks at pH 4.5 and stalls at n...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-11-01
|
| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/26/22/6956 |
| _version_ | 1797509143808966656 |
|---|---|
| author | Ekaterina Kots Derek M. Shore Harel Weinstein |
| author_facet | Ekaterina Kots Derek M. Shore Harel Weinstein |
| author_sort | Ekaterina Kots |
| collection | DOAJ |
| description | Intracellular transport of chloride by members of the CLC transporter family involves a coupled exchange between a Cl<sup>−</sup> anion and a proton (H<sup>+</sup>), which makes the transport function dependent on ambient pH. Transport activity peaks at pH 4.5 and stalls at neutral pH. However, a structure of the WT protein at acidic pH is not available, making it difficult to assess the global conformational rearrangements that support a pH-dependent gating mechanism. To enable modeling of the CLC-ec1 dimer at acidic pH, we have applied molecular dynamics simulations (MD) featuring a new force field modification scheme—termed an Equilibrium constant pH approach (ECpH). The ECpH method utilizes linear interpolation between the force field parameters of protonated and deprotonated states of titratable residues to achieve a representation of pH-dependence in a narrow range of physiological pH values. Simulations of the CLC-ec1 dimer at neutral and acidic pH comparing ECpH-MD to canonical MD, in which the pH-dependent protonation is represented by a binary scheme, substantiates the better agreement of the conformational changes and the final model with experimental data from NMR, cross-link and AFM studies, and reveals structural elements that support the gate-opening at pH 4.5, including the key glutamates Glu<sub>in</sub> and Glu<sub>ex</sub>. |
| first_indexed | 2024-03-10T05:14:01Z |
| format | Article |
| id | doaj.art-3fcb8aab014141448b78da10c6219dc3 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T05:14:01Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-3fcb8aab014141448b78da10c6219dc32023-11-23T00:36:20ZengMDPI AGMolecules1420-30492021-11-012622695610.3390/molecules26226956Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> AntiporterEkaterina Kots0Derek M. Shore1Harel Weinstein2Department of Physiology and Biophysics, Weill Cornell Medical School, New York, NY 10065, USADepartment of Physiology and Biophysics, Weill Cornell Medical School, New York, NY 10065, USADepartment of Physiology and Biophysics, Weill Cornell Medical School, New York, NY 10065, USAIntracellular transport of chloride by members of the CLC transporter family involves a coupled exchange between a Cl<sup>−</sup> anion and a proton (H<sup>+</sup>), which makes the transport function dependent on ambient pH. Transport activity peaks at pH 4.5 and stalls at neutral pH. However, a structure of the WT protein at acidic pH is not available, making it difficult to assess the global conformational rearrangements that support a pH-dependent gating mechanism. To enable modeling of the CLC-ec1 dimer at acidic pH, we have applied molecular dynamics simulations (MD) featuring a new force field modification scheme—termed an Equilibrium constant pH approach (ECpH). The ECpH method utilizes linear interpolation between the force field parameters of protonated and deprotonated states of titratable residues to achieve a representation of pH-dependence in a narrow range of physiological pH values. Simulations of the CLC-ec1 dimer at neutral and acidic pH comparing ECpH-MD to canonical MD, in which the pH-dependent protonation is represented by a binary scheme, substantiates the better agreement of the conformational changes and the final model with experimental data from NMR, cross-link and AFM studies, and reveals structural elements that support the gate-opening at pH 4.5, including the key glutamates Glu<sub>in</sub> and Glu<sub>ex</sub>.https://www.mdpi.com/1420-3049/26/22/6956CLC transporterspH-dependent activitymolecular dynamics (MD) simulationshigh-resolution atomic force microscopy (HR-AFM)protonation state representationsnet charge conservation protocol |
| spellingShingle | Ekaterina Kots Derek M. Shore Harel Weinstein Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter Molecules CLC transporters pH-dependent activity molecular dynamics (MD) simulations high-resolution atomic force microscopy (HR-AFM) protonation state representations net charge conservation protocol |
| title | Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter |
| title_full | Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter |
| title_fullStr | Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter |
| title_full_unstemmed | Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter |
| title_short | Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl<sup>−</sup>/H<sup>+</sup> Antiporter |
| title_sort | simulation of ph dependent conformational transitions in membrane proteins the clc ec1 cl sup sup h sup sup antiporter |
| topic | CLC transporters pH-dependent activity molecular dynamics (MD) simulations high-resolution atomic force microscopy (HR-AFM) protonation state representations net charge conservation protocol |
| url | https://www.mdpi.com/1420-3049/26/22/6956 |
| work_keys_str_mv | AT ekaterinakots simulationofphdependentconformationaltransitionsinmembraneproteinstheclcec1clsupsuphsupsupantiporter AT derekmshore simulationofphdependentconformationaltransitionsinmembraneproteinstheclcec1clsupsuphsupsupantiporter AT harelweinstein simulationofphdependentconformationaltransitionsinmembraneproteinstheclcec1clsupsuphsupsupantiporter |