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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) Snapshots of a 4 ns simulation of mutant M2 at various time                        instances. The position of histidine residues are shown in dark shades. The                        α-helical structure in chain B was disrupted during the                        simulation implying that some of the mutations are inherently destabilizing                        for its secondary structure; b) Evolution of the secondary                        structure elements of M2 as a function of time. The coloring scheme is                        indicated at the top right. The upper and lower halves corresponds to chain                        A and B respectively while the Y-axis denotes the residue number. The early                        disruption of the α-helical structure in chain B is evident from                        the figure.
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f4-ijn-3-505: a) Snapshots of a 4 ns simulation of mutant M2 at various time instances. The position of histidine residues are shown in dark shades. The α-helical structure in chain B was disrupted during the simulation implying that some of the mutations are inherently destabilizing for its secondary structure; b) Evolution of the secondary structure elements of M2 as a function of time. The coloring scheme is indicated at the top right. The upper and lower halves corresponds to chain A and B respectively while the Y-axis denotes the residue number. The early disruption of the α-helical structure in chain B is evident from the figure.

Mentions: Figure 4a shows the snapshots of a 4 ns simulation of M2 at low pH. Mutant M2 was not stable during the course of the simulation as indicated by the disruption of the α-helix in chain B. Moreover, no significant opening was observed in the mutant, implying that either the electrostatic forces were not sufficient or the mutation sites were not well-selected. To gain further insight into the stability of the structure we plotted the evolution of the secondary structure elements of M2 over the simulation time (Figure 4b). Unfolding of the α-helix begins during the first nanosecond of the simulation itself, implying that these mutations were inherently destabilizing to the secondary structure. One explanation for the unfolding of the α-helix lies in the nature of the N264H mutation. The location of the two asparagines (Asn264A and Asn264B) is unique in that they are the only polar residues in the core positions (a and d) of the GCN4-LZ. The Asn264A–Asn264B interhelical interaction is the strongest favorable interaction between individual groups in the GCN4-LZ and stabilizes the coiled-coil structure by contributing −2.1 kcal/mole towards the free energy of the structure (Hendsch and Tidor 1999). This strong interaction arises from the fact that the two Asn residues are buried and packed in the ‘knobs-into-holes’ pattern described by Crick (1953). The N264H mutation replaces this stabilizing interaction of Asn residues with the destabilizing ionic repulsions of the charged His residues thereby disrupting the coiled-coil structure. The resulting structural instability obviates the use of M2 as a potential design since maintaining structural rigidity during the course of operation is an important design requirement for the nanotweezer.


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 4 ns simulation of mutant M2 at various time                        instances. The position of histidine residues are shown in dark shades. The                        α-helical structure in chain B was disrupted during the                        simulation implying that some of the mutations are inherently destabilizing                        for its secondary structure; b) Evolution of the secondary                        structure elements of M2 as a function of time. The coloring scheme is                        indicated at the top right. The upper and lower halves corresponds to chain                        A and B respectively while the Y-axis denotes the residue number. The early                        disruption of the α-helical structure in chain B is evident from                        the figure.
© Copyright Policy
Related In: Results  -  Collection

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

f4-ijn-3-505: a) Snapshots of a 4 ns simulation of mutant M2 at various time instances. The position of histidine residues are shown in dark shades. The α-helical structure in chain B was disrupted during the simulation implying that some of the mutations are inherently destabilizing for its secondary structure; b) Evolution of the secondary structure elements of M2 as a function of time. The coloring scheme is indicated at the top right. The upper and lower halves corresponds to chain A and B respectively while the Y-axis denotes the residue number. The early disruption of the α-helical structure in chain B is evident from the figure.
Mentions: Figure 4a shows the snapshots of a 4 ns simulation of M2 at low pH. Mutant M2 was not stable during the course of the simulation as indicated by the disruption of the α-helix in chain B. Moreover, no significant opening was observed in the mutant, implying that either the electrostatic forces were not sufficient or the mutation sites were not well-selected. To gain further insight into the stability of the structure we plotted the evolution of the secondary structure elements of M2 over the simulation time (Figure 4b). Unfolding of the α-helix begins during the first nanosecond of the simulation itself, implying that these mutations were inherently destabilizing to the secondary structure. One explanation for the unfolding of the α-helix lies in the nature of the N264H mutation. The location of the two asparagines (Asn264A and Asn264B) is unique in that they are the only polar residues in the core positions (a and d) of the GCN4-LZ. The Asn264A–Asn264B interhelical interaction is the strongest favorable interaction between individual groups in the GCN4-LZ and stabilizes the coiled-coil structure by contributing −2.1 kcal/mole towards the free energy of the structure (Hendsch and Tidor 1999). This strong interaction arises from the fact that the two Asn residues are buried and packed in the ‘knobs-into-holes’ pattern described by Crick (1953). The N264H mutation replaces this stabilizing interaction of Asn residues with the destabilizing ionic repulsions of the charged His residues thereby disrupting the coiled-coil structure. The resulting structural instability obviates the use of M2 as a potential design since maintaining structural rigidity during the course of operation is an important design requirement for the nanotweezer.

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