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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) Residue sequence of the GCN4mT peptide. The basic DNA-binding                        region is grafted at the N-terminus of the mutant M3 design; Snapshots of                        the SMD simulation to study DNA-binding modulation; b) at                        neutral pH the DNA molecule is tightly bound to the peptide chains and                        cannot break free when pulled using an external force; c) At                        low pH the conformational changes in the GCN4mT peptide reduces the strength                        of DNA-binding and when pulled the DNA molecule is rapidly released from the                        peptide-binding cavity; d) Force required pulling the DNA out                        of the GCN4mT-binding cavity. The Left and Bottom axis are for data at low                        pH while the Top and Right axis are for neutral pH data. As hypothesized the                        force required to pull the DNA is considerably smaller at low pH.
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f9-ijn-3-505: a) Residue sequence of the GCN4mT peptide. The basic DNA-binding region is grafted at the N-terminus of the mutant M3 design; Snapshots of the SMD simulation to study DNA-binding modulation; b) at neutral pH the DNA molecule is tightly bound to the peptide chains and cannot break free when pulled using an external force; c) At low pH the conformational changes in the GCN4mT peptide reduces the strength of DNA-binding and when pulled the DNA molecule is rapidly released from the peptide-binding cavity; d) Force required pulling the DNA out of the GCN4mT-binding cavity. The Left and Bottom axis are for data at low pH while the Top and Right axis are for neutral pH data. As hypothesized the force required to pull the DNA is considerably smaller at low pH.

Mentions: The pH dependent conformational change of the nanotweezer can be employed for modulating the DNA-binding affinity of the parent GCN4 transcription activator protein. The design principle can also be employed to generate proteins with distinct DNA-binding specificities and different physiological targets thereby having implications in engineering of novel transcription factors and ligand design for DNA purification. To demonstrate the DNA-binding modulation capability of the nanotweezer a new peptide was designed in which the DNA-binding basic region of the parent GCN4 peptide was grafted at the end of the N-terminus of the nanotweezer based on the M3 mutant design (henceforth called GCN4mT). The residue sequence of the resulting GCN4mT peptide is shown in Figure 9a.


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) Residue sequence of the GCN4mT peptide. The basic DNA-binding                        region is grafted at the N-terminus of the mutant M3 design; Snapshots of                        the SMD simulation to study DNA-binding modulation; b) at                        neutral pH the DNA molecule is tightly bound to the peptide chains and                        cannot break free when pulled using an external force; c) At                        low pH the conformational changes in the GCN4mT peptide reduces the strength                        of DNA-binding and when pulled the DNA molecule is rapidly released from the                        peptide-binding cavity; d) Force required pulling the DNA out                        of the GCN4mT-binding cavity. The Left and Bottom axis are for data at low                        pH while the Top and Right axis are for neutral pH data. As hypothesized the                        force required to pull the DNA is considerably smaller at low pH.
© Copyright Policy
Related In: Results  -  Collection

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

f9-ijn-3-505: a) Residue sequence of the GCN4mT peptide. The basic DNA-binding region is grafted at the N-terminus of the mutant M3 design; Snapshots of the SMD simulation to study DNA-binding modulation; b) at neutral pH the DNA molecule is tightly bound to the peptide chains and cannot break free when pulled using an external force; c) At low pH the conformational changes in the GCN4mT peptide reduces the strength of DNA-binding and when pulled the DNA molecule is rapidly released from the peptide-binding cavity; d) Force required pulling the DNA out of the GCN4mT-binding cavity. The Left and Bottom axis are for data at low pH while the Top and Right axis are for neutral pH data. As hypothesized the force required to pull the DNA is considerably smaller at low pH.
Mentions: The pH dependent conformational change of the nanotweezer can be employed for modulating the DNA-binding affinity of the parent GCN4 transcription activator protein. The design principle can also be employed to generate proteins with distinct DNA-binding specificities and different physiological targets thereby having implications in engineering of novel transcription factors and ligand design for DNA purification. To demonstrate the DNA-binding modulation capability of the nanotweezer a new peptide was designed in which the DNA-binding basic region of the parent GCN4 peptide was grafted at the end of the N-terminus of the nanotweezer based on the M3 mutant design (henceforth called GCN4mT). The residue sequence of the resulting GCN4mT peptide is shown in Figure 9a.

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