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Reversible pH-controlled DNA-binding peptide nanotweezers: an in-silico study.

Sharma G, Rege K, Budil DE, Yarmush ML, Mavroidis C - Int J Nanomedicine (2008)

Bottom Line: Modulating the solution pH between neutral and acidic values results in the reversible movement of helices toward and away from each other and creates a complete closed-open-closed transition cycle between the helices.The efficacy of the mutant that demonstrated the most significant reversible actuation for environmentally responsive modulation of DNA-binding activity was also demonstrated.Our results have significant implications in bioseparations and in the engineering of novel transcription factors.

View Article: PubMed Central - PubMed

Affiliation: Department of Mechanical and Industrial Engineering, Northeastern University, Boston, MA 02115, USA.

ABSTRACT
We describe the molecular dynamics (MD)-aided engineering design of mutant peptides based on the alpha-helical coiled-coil GCN4 leucine zipper peptide (GCN4-p1) in order to obtain environmentally-responsive nanotweezers. The actuation mechanism of the nanotweezers depends on the modification of electrostatic charges on the residues along the length of the coiled coil. Modulating the solution pH between neutral and acidic values results in the reversible movement of helices toward and away from each other and creates a complete closed-open-closed transition cycle between the helices. Our results indicate that the mutants show a reversible opening of up to 15 A (1.5 nm; approximately 150% of the initial separation) upon pH actuation. Investigation on the physicochemical phenomena that influence conformational properties, structural stability, and reversibility of the coiled-coil peptide-based nanotweezers revealed that a rationale- and design-based approach is needed to engineer stable peptide or macromolecules into stimuli-responsive devices. The efficacy of the mutant that demonstrated the most significant reversible actuation for environmentally responsive modulation of DNA-binding activity was also demonstrated. Our results have significant implications in bioseparations and in the engineering of novel transcription factors.

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Related in: MedlinePlus

a) Snapshots of a 5 ns simulation of open-to-close transition to                        show the reversible motion of mutant M3. For reversible motion the His, Glu                        and Asp residues were unprotonated to simulate neutral pH. Due to lack of                        ionic repulsions at neutral pH and also due to the attractive hydrophobic                        interactions the actuator chains rapidly reclosed. The final state closely                        resembles the initial NMR structure; b) Reversible motion                        dynamics for mutant M3 at neutral pH. The distance between the two chains                        after 5 ns simulation time was 10 Å which is in good agreement                        with the separation between the helices in the initial NMR structure.
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f7-ijn-3-505: a) Snapshots of a 5 ns simulation of open-to-close transition to show the reversible motion of mutant M3. For reversible motion the His, Glu and Asp residues were unprotonated to simulate neutral pH. Due to lack of ionic repulsions at neutral pH and also due to the attractive hydrophobic interactions the actuator chains rapidly reclosed. The final state closely resembles the initial NMR structure; b) Reversible motion dynamics for mutant M3 at neutral pH. The distance between the two chains after 5 ns simulation time was 10 Å which is in good agreement with the separation between the helices in the initial NMR structure.

Mentions: Figure 7a shows snapshots of a 5 ns-long reversible-motion simulation of M3. Increasing the pH back to neutral triggered the reversible transition of the mutant and the final conformation generated by this simulation resembles the initial starting structure from the closed-to-open simulation (Figure 5b). Figure 7b shows the dynamics of the reversible motion of M3 over the simulation time. As mentioned in the previous section, the ‘open’ state generated at the end of the close-to-open simulation of M3 at low pH was in a state of dynamic equilibrium. This means that the peptide was in a ‘tensed’ state wherein the restituting forces due to helices elasticity and the hydrophobic attractions near the C-terminal of the peptide chains balanced the repulsive electrostatic forces of the ionized histidine residues. At neutral pH, the force-generating capability vanished due to histidine neutralization, leading to the restitution of the ‘relaxed’ state. The reversible transition of the mutant at neutral pH was exactly as hypothesized and verifies the concept of designing a nanotweezer element whose actuation can be modulated by pH.


Reversible pH-controlled DNA-binding peptide nanotweezers: an in-silico study.

Sharma G, Rege K, Budil DE, Yarmush ML, Mavroidis C - Int J Nanomedicine (2008)

a) Snapshots of a 5 ns simulation of open-to-close transition to                        show the reversible motion of mutant M3. For reversible motion the His, Glu                        and Asp residues were unprotonated to simulate neutral pH. Due to lack of                        ionic repulsions at neutral pH and also due to the attractive hydrophobic                        interactions the actuator chains rapidly reclosed. The final state closely                        resembles the initial NMR structure; b) Reversible motion                        dynamics for mutant M3 at neutral pH. The distance between the two chains                        after 5 ns simulation time was 10 Å which is in good agreement                        with the separation between the helices in the initial NMR structure.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2636583&req=5

f7-ijn-3-505: a) Snapshots of a 5 ns simulation of open-to-close transition to show the reversible motion of mutant M3. For reversible motion the His, Glu and Asp residues were unprotonated to simulate neutral pH. Due to lack of ionic repulsions at neutral pH and also due to the attractive hydrophobic interactions the actuator chains rapidly reclosed. The final state closely resembles the initial NMR structure; b) Reversible motion dynamics for mutant M3 at neutral pH. The distance between the two chains after 5 ns simulation time was 10 Å which is in good agreement with the separation between the helices in the initial NMR structure.
Mentions: Figure 7a shows snapshots of a 5 ns-long reversible-motion simulation of M3. Increasing the pH back to neutral triggered the reversible transition of the mutant and the final conformation generated by this simulation resembles the initial starting structure from the closed-to-open simulation (Figure 5b). Figure 7b shows the dynamics of the reversible motion of M3 over the simulation time. As mentioned in the previous section, the ‘open’ state generated at the end of the close-to-open simulation of M3 at low pH was in a state of dynamic equilibrium. This means that the peptide was in a ‘tensed’ state wherein the restituting forces due to helices elasticity and the hydrophobic attractions near the C-terminal of the peptide chains balanced the repulsive electrostatic forces of the ionized histidine residues. At neutral pH, the force-generating capability vanished due to histidine neutralization, leading to the restitution of the ‘relaxed’ state. The reversible transition of the mutant at neutral pH was exactly as hypothesized and verifies the concept of designing a nanotweezer element whose actuation can be modulated by pH.

Bottom Line: Modulating the solution pH between neutral and acidic values results in the reversible movement of helices toward and away from each other and creates a complete closed-open-closed transition cycle between the helices.The efficacy of the mutant that demonstrated the most significant reversible actuation for environmentally responsive modulation of DNA-binding activity was also demonstrated.Our results have significant implications in bioseparations and in the engineering of novel transcription factors.

View Article: PubMed Central - PubMed

Affiliation: Department of Mechanical and Industrial Engineering, Northeastern University, Boston, MA 02115, USA.

ABSTRACT
We describe the molecular dynamics (MD)-aided engineering design of mutant peptides based on the alpha-helical coiled-coil GCN4 leucine zipper peptide (GCN4-p1) in order to obtain environmentally-responsive nanotweezers. The actuation mechanism of the nanotweezers depends on the modification of electrostatic charges on the residues along the length of the coiled coil. Modulating the solution pH between neutral and acidic values results in the reversible movement of helices toward and away from each other and creates a complete closed-open-closed transition cycle between the helices. Our results indicate that the mutants show a reversible opening of up to 15 A (1.5 nm; approximately 150% of the initial separation) upon pH actuation. Investigation on the physicochemical phenomena that influence conformational properties, structural stability, and reversibility of the coiled-coil peptide-based nanotweezers revealed that a rationale- and design-based approach is needed to engineer stable peptide or macromolecules into stimuli-responsive devices. The efficacy of the mutant that demonstrated the most significant reversible actuation for environmentally responsive modulation of DNA-binding activity was also demonstrated. Our results have significant implications in bioseparations and in the engineering of novel transcription factors.

Show MeSH
Related in: MedlinePlus