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Equilibrated atomic models of outward-facing P-glycoprotein and effect of ATP binding on structural dynamics.

Pan L, Aller SG - Sci Rep (2015)

Bottom Line: Three long lasting (>100 ns) meta-stable states were apparent in the presence of MgATP revealing new insights into alternating access.The two ATP-binding pockets are highly asymmetric resulting in differential control of overall structural dynamics and allosteric regulation of the drug-binding pocket.Equilibrated Pgp has a considerably different electrostatic profile compared to Sav1866 that implicates significant kinetic and thermodynamic differences in transport mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL, 35205 USA.

ABSTRACT
P-glycoprotein (Pgp) is an ATP-binding cassette (ABC) transporter that alternates between inward- and outward-facing conformations to capture and force substrates out of cells like a peristaltic pump. The high degree of similarity in outward-facing structures across evolution of ABC transporters allowed construction of a high-confidence outward-facing Pgp atomic model based on crystal structures of outward-facing Sav1866 and inward-facing Pgp. The model adhered to previous experimentally determined secondary- and tertiary- configurations during all-atom molecular dynamics simulations in the presence or absence of MgATP. Three long lasting (>100 ns) meta-stable states were apparent in the presence of MgATP revealing new insights into alternating access. The two ATP-binding pockets are highly asymmetric resulting in differential control of overall structural dynamics and allosteric regulation of the drug-binding pocket. Equilibrated Pgp has a considerably different electrostatic profile compared to Sav1866 that implicates significant kinetic and thermodynamic differences in transport mechanisms.

No MeSH data available.


Related in: MedlinePlus

Solvent Accessible Surface Area (SASA).The SASA are measured using the last 50 ns trajectories and averaged over the triplicate simulations for both apo-Pgp and Pgp-MgATP models. The changes of SASA are calculated against the initial structure. The apo-Pgp showed larger total SASA increase (3.0%) than Pgp-MgATP (0.6%). The apo-Pgp demonstrated larger decreases (−7.8% vs. −3.6%) in TMDs and larger increases in NBDs (11.3% vs. 4.3%) compared Pgp-MgATP.
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f7: Solvent Accessible Surface Area (SASA).The SASA are measured using the last 50 ns trajectories and averaged over the triplicate simulations for both apo-Pgp and Pgp-MgATP models. The changes of SASA are calculated against the initial structure. The apo-Pgp showed larger total SASA increase (3.0%) than Pgp-MgATP (0.6%). The apo-Pgp demonstrated larger decreases (−7.8% vs. −3.6%) in TMDs and larger increases in NBDs (11.3% vs. 4.3%) compared Pgp-MgATP.

Mentions: In addition to ligand effects (drug-binding and ATP-binding/hydrolysis), water is a major driving force of protein conformational change by hydrophobic effect and hydrostatic pressure on both sides of the membrane. Solvent accessible surface area (SASA) is an indirect measurement for conformational change. For both models, SASA of TMDs decreases while the SASA of NBDs increases, which indicates that the closure of TMDs is coupled with the opening of NBDs. The results suggest water efflux from the TMDs and water influx into the NBDs due to the change of conformation in these areas (Figure 7). Such water flux is directly quantifiable using the change of SASA in percentage compared to that of initial structure. The results indicated that the efflux of water from the TMDs and the influx of water into the NBDs are strongly correlated processes. It also showed that the MgATP binding provided the counterforce in this process to maintain a different hydration distribution favoring the outward facing conformation as opposed to that of apo-Pgp, which favors the inward-facing conformation.


Equilibrated atomic models of outward-facing P-glycoprotein and effect of ATP binding on structural dynamics.

Pan L, Aller SG - Sci Rep (2015)

Solvent Accessible Surface Area (SASA).The SASA are measured using the last 50 ns trajectories and averaged over the triplicate simulations for both apo-Pgp and Pgp-MgATP models. The changes of SASA are calculated against the initial structure. The apo-Pgp showed larger total SASA increase (3.0%) than Pgp-MgATP (0.6%). The apo-Pgp demonstrated larger decreases (−7.8% vs. −3.6%) in TMDs and larger increases in NBDs (11.3% vs. 4.3%) compared Pgp-MgATP.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4389535&req=5

f7: Solvent Accessible Surface Area (SASA).The SASA are measured using the last 50 ns trajectories and averaged over the triplicate simulations for both apo-Pgp and Pgp-MgATP models. The changes of SASA are calculated against the initial structure. The apo-Pgp showed larger total SASA increase (3.0%) than Pgp-MgATP (0.6%). The apo-Pgp demonstrated larger decreases (−7.8% vs. −3.6%) in TMDs and larger increases in NBDs (11.3% vs. 4.3%) compared Pgp-MgATP.
Mentions: In addition to ligand effects (drug-binding and ATP-binding/hydrolysis), water is a major driving force of protein conformational change by hydrophobic effect and hydrostatic pressure on both sides of the membrane. Solvent accessible surface area (SASA) is an indirect measurement for conformational change. For both models, SASA of TMDs decreases while the SASA of NBDs increases, which indicates that the closure of TMDs is coupled with the opening of NBDs. The results suggest water efflux from the TMDs and water influx into the NBDs due to the change of conformation in these areas (Figure 7). Such water flux is directly quantifiable using the change of SASA in percentage compared to that of initial structure. The results indicated that the efflux of water from the TMDs and the influx of water into the NBDs are strongly correlated processes. It also showed that the MgATP binding provided the counterforce in this process to maintain a different hydration distribution favoring the outward facing conformation as opposed to that of apo-Pgp, which favors the inward-facing conformation.

Bottom Line: Three long lasting (>100 ns) meta-stable states were apparent in the presence of MgATP revealing new insights into alternating access.The two ATP-binding pockets are highly asymmetric resulting in differential control of overall structural dynamics and allosteric regulation of the drug-binding pocket.Equilibrated Pgp has a considerably different electrostatic profile compared to Sav1866 that implicates significant kinetic and thermodynamic differences in transport mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL, 35205 USA.

ABSTRACT
P-glycoprotein (Pgp) is an ATP-binding cassette (ABC) transporter that alternates between inward- and outward-facing conformations to capture and force substrates out of cells like a peristaltic pump. The high degree of similarity in outward-facing structures across evolution of ABC transporters allowed construction of a high-confidence outward-facing Pgp atomic model based on crystal structures of outward-facing Sav1866 and inward-facing Pgp. The model adhered to previous experimentally determined secondary- and tertiary- configurations during all-atom molecular dynamics simulations in the presence or absence of MgATP. Three long lasting (>100 ns) meta-stable states were apparent in the presence of MgATP revealing new insights into alternating access. The two ATP-binding pockets are highly asymmetric resulting in differential control of overall structural dynamics and allosteric regulation of the drug-binding pocket. Equilibrated Pgp has a considerably different electrostatic profile compared to Sav1866 that implicates significant kinetic and thermodynamic differences in transport mechanisms.

No MeSH data available.


Related in: MedlinePlus