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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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Comparison of opening dynamics for various mutants at low pH. M3 showed the                        maximum opening of 1.6 nm during the simulation time. The control mutant                        M3CT initially followed a similar dynamics but lags the net opening of M3 by                        0.4 nm. The dynamics of wild-type (WT) and mutants M1, M2 are explained                        previously.
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f6-ijn-3-505: Comparison of opening dynamics for various mutants at low pH. M3 showed the maximum opening of 1.6 nm during the simulation time. The control mutant M3CT initially followed a similar dynamics but lags the net opening of M3 by 0.4 nm. The dynamics of wild-type (WT) and mutants M1, M2 are explained previously.

Mentions: In order to gain insights into the mechanisms of action of M3, we designed a control mutant, M3CT, by replacing the N-terminal histidines in M3 by an equivalent number of glycine residues. This design enables an investigation into the contribution of the five histidine residues within the coiled-coil core towards the conformational dynamics of the resulting GCN4-LZ mutant, without additional contributions from the distal His-tags. Glycine was chosen since it is a neutral, α-helix breaking amino acid (Aurora et al 1994) and therefore, has no secondary structural or charge contributions to the resulting M3CT mutant. Figure 6 compares the actuation dynamics of all five mutants plotted against time. Mutant M3 shows the most significant actuation followed by the M3CT mutant, further reinforcing the observation that while the N-terminal His-tag contributes towards the actuation, the His mutations in the parent GCN4-LZ structure play the critical role. These results are consistent with the lack of closed-to-open transition for M1. The WT and M2 mutants did not show any transition during the simulation as discussed earlier.


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)

Comparison of opening dynamics for various mutants at low pH. M3 showed the                        maximum opening of 1.6 nm during the simulation time. The control mutant                        M3CT initially followed a similar dynamics but lags the net opening of M3 by                        0.4 nm. The dynamics of wild-type (WT) and mutants M1, M2 are explained                        previously.
© Copyright Policy
Related In: Results  -  Collection

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

f6-ijn-3-505: Comparison of opening dynamics for various mutants at low pH. M3 showed the maximum opening of 1.6 nm during the simulation time. The control mutant M3CT initially followed a similar dynamics but lags the net opening of M3 by 0.4 nm. The dynamics of wild-type (WT) and mutants M1, M2 are explained previously.
Mentions: In order to gain insights into the mechanisms of action of M3, we designed a control mutant, M3CT, by replacing the N-terminal histidines in M3 by an equivalent number of glycine residues. This design enables an investigation into the contribution of the five histidine residues within the coiled-coil core towards the conformational dynamics of the resulting GCN4-LZ mutant, without additional contributions from the distal His-tags. Glycine was chosen since it is a neutral, α-helix breaking amino acid (Aurora et al 1994) and therefore, has no secondary structural or charge contributions to the resulting M3CT mutant. Figure 6 compares the actuation dynamics of all five mutants plotted against time. Mutant M3 shows the most significant actuation followed by the M3CT mutant, further reinforcing the observation that while the N-terminal His-tag contributes towards the actuation, the His mutations in the parent GCN4-LZ structure play the critical role. These results are consistent with the lack of closed-to-open transition for M1. The WT and M2 mutants did not show any transition during the simulation as discussed earlier.

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