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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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a) Opening dynamics of M3 at varying pH. The trajectories                        plotted at each pH are the average values for two separate MD runs with                        different initial random seed. The opening at intermediate pH lags that at                        low pH by 5 Å thereby suggesting the potential use of the                        nanotweezer as a pH sensor; b) Root mean squared deviations                        (RMSD) of individual residues of the M3 mutant during the opening and                        closing mechanism. The plot helps to identify the more flexible region of                        the protein.
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f8-ijn-3-505: a) Opening dynamics of M3 at varying pH. The trajectories plotted at each pH are the average values for two separate MD runs with different initial random seed. The opening at intermediate pH lags that at low pH by 5 Å thereby suggesting the potential use of the nanotweezer as a pH sensor; b) Root mean squared deviations (RMSD) of individual residues of the M3 mutant during the opening and closing mechanism. The plot helps to identify the more flexible region of the protein.

Mentions: In order to probe the physicochemical contributions to the actuation mechanism, we first examined the closed-to-open actuation behavior of M3 at three different pH values: neutral, intermediate, and low. The objective of these simulations was to ascertain if the nanotweezer design based on M3 mutant is sensitive to smaller changes in pH. Figure 8a shows the plots of opening dynamics of M3 at three pH values. As expected, no opening was observed in the mutant at neutral pH due the absence of ionic repulsions in the chains as the His residues are not ionized at neutral pH. The distance between the two helices at the end of closed-to-open simulation at neutral pH is 7 Å which is in good agreement with the distance observed between the helices at the end of the open-to-closed simulation of M3 (Figure 7). At intermediate pH, where the Glu and Asp residues are assumed to be unprotonated and the His residues protonated, the transition closely followed the low pH trajectory until approximately 2.2 ns, at which point the distance between the two chains was 24 Å. From 2.2–3 ns the separation reduced by 4 Å and the two chains finally stabilized at a distance of 20 Å during the last nanosecond. Thus, at intermediate pH the final inter-helical opening was 9 Å, in contrast to the separation of 16 Å seen at low pH. Each chain of mutant M3 has five glutamic acids (Glu254, Glu258, Glu268, Glu270, Glu280) and one aspartic acid (Asp255) residue. These residues are negatively charged at intermediate pH and can be expected to contribute to the overall ionic repulsion, resulting in increased separation between the two chains. However, the opening of M3 at intermediate pH was less than that at low pH by 7 Å. One explanation for this reduced opening lies in the location of the Glu and Asp residues along the protein chain. The Asp255 and Glu280 residues are at the f and c position respectively on the helical wheel diagram (Figure 1c) of the protein. The f and c positions are at the outer periphery of the protein and thus these residues are not expected to participate in any interhelical ionic interactions. On the other hand, three salt-pairs (Glu268A–Lys263B, Lys275A–Glu270B, Lys275B–Glu270A) contribute to interhelical ionic attractions at the intermediate pH thereby significantly reducing the total ionic repulsions between the two chains resulting in a reduced separation between the chains. These salt-pairs are absent at low pH due to the protonation of Glu residues which permits greater opening between the helices. This qualitative explanation neglects the fact that the Glu, Asp, and His residues are most likely only partially protonated at intermediate pH values, and also neglects possible cooperative effects in the acid-base equilibria of adjacent residues. Nevertheless, these approximations do not alter the overall conclusion that the results at intermediate and low pH support our hypothesis that the opening of the nanotweezer can be modulated simply by varying the pH of its environment.


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) Opening dynamics of M3 at varying pH. The trajectories                        plotted at each pH are the average values for two separate MD runs with                        different initial random seed. The opening at intermediate pH lags that at                        low pH by 5 Å thereby suggesting the potential use of the                        nanotweezer as a pH sensor; b) Root mean squared deviations                        (RMSD) of individual residues of the M3 mutant during the opening and                        closing mechanism. The plot helps to identify the more flexible region of                        the protein.
© Copyright Policy
Related In: Results  -  Collection

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

f8-ijn-3-505: a) Opening dynamics of M3 at varying pH. The trajectories plotted at each pH are the average values for two separate MD runs with different initial random seed. The opening at intermediate pH lags that at low pH by 5 Å thereby suggesting the potential use of the nanotweezer as a pH sensor; b) Root mean squared deviations (RMSD) of individual residues of the M3 mutant during the opening and closing mechanism. The plot helps to identify the more flexible region of the protein.
Mentions: In order to probe the physicochemical contributions to the actuation mechanism, we first examined the closed-to-open actuation behavior of M3 at three different pH values: neutral, intermediate, and low. The objective of these simulations was to ascertain if the nanotweezer design based on M3 mutant is sensitive to smaller changes in pH. Figure 8a shows the plots of opening dynamics of M3 at three pH values. As expected, no opening was observed in the mutant at neutral pH due the absence of ionic repulsions in the chains as the His residues are not ionized at neutral pH. The distance between the two helices at the end of closed-to-open simulation at neutral pH is 7 Å which is in good agreement with the distance observed between the helices at the end of the open-to-closed simulation of M3 (Figure 7). At intermediate pH, where the Glu and Asp residues are assumed to be unprotonated and the His residues protonated, the transition closely followed the low pH trajectory until approximately 2.2 ns, at which point the distance between the two chains was 24 Å. From 2.2–3 ns the separation reduced by 4 Å and the two chains finally stabilized at a distance of 20 Å during the last nanosecond. Thus, at intermediate pH the final inter-helical opening was 9 Å, in contrast to the separation of 16 Å seen at low pH. Each chain of mutant M3 has five glutamic acids (Glu254, Glu258, Glu268, Glu270, Glu280) and one aspartic acid (Asp255) residue. These residues are negatively charged at intermediate pH and can be expected to contribute to the overall ionic repulsion, resulting in increased separation between the two chains. However, the opening of M3 at intermediate pH was less than that at low pH by 7 Å. One explanation for this reduced opening lies in the location of the Glu and Asp residues along the protein chain. The Asp255 and Glu280 residues are at the f and c position respectively on the helical wheel diagram (Figure 1c) of the protein. The f and c positions are at the outer periphery of the protein and thus these residues are not expected to participate in any interhelical ionic interactions. On the other hand, three salt-pairs (Glu268A–Lys263B, Lys275A–Glu270B, Lys275B–Glu270A) contribute to interhelical ionic attractions at the intermediate pH thereby significantly reducing the total ionic repulsions between the two chains resulting in a reduced separation between the chains. These salt-pairs are absent at low pH due to the protonation of Glu residues which permits greater opening between the helices. This qualitative explanation neglects the fact that the Glu, Asp, and His residues are most likely only partially protonated at intermediate pH values, and also neglects possible cooperative effects in the acid-base equilibria of adjacent residues. Nevertheless, these approximations do not alter the overall conclusion that the results at intermediate and low pH support our hypothesis that the opening of the nanotweezer can be modulated simply by varying the pH of its environment.

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