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Computational Studies of the Effect of Shock Waves on the Binding of Model Complexes.

Kaminski GA - J Chem Theory Comput (2014)

Bottom Line: The behavior of the protein systems was more complex, yet significant disruption of the binding and geometry was also observed.The rationale of the studies was in attempting to understand the strong effects that irradiation with a low-intensity ultrasound can have on biomolecular systems, because such ultrasound irradiation can cause cavitation bubbles to be produced and collapse, thus leading to local shock wave generation.The long-term objective is to contribute to future design of synergetic ultrasound and chemical drug strategy of protein inhibition.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, Worcester Polytechnic Institute , Worcester, Massachusetts 01609, United States.

ABSTRACT
We have simulated effects of a shock wave in water that would result from the collapse of a cavitation bubble on binding in model complexes. We have considered a benzene dimer, a pair of uracil molecules, a complex of fragments of the X-linked inhibitor of apoptosis and caspase-9, and a fragment of c-Myc oncoprotein in binding with its dimerization partner Max. The effect of the shock waves was simulated by adding a momentum to a slab of solvent water molecules and observing the system as the slab moved and caused changes. In the cases of the small molecular pairs, the passage of the shock waves lead to dissociation of the complexes. The behavior of the protein systems was more complex, yet significant disruption of the binding and geometry was also observed. In all the cases, the effects did not occur during the immediate impact of the high-momentum solvent molecules, but rather during the expansion of the compressed system that followed the passage of the waves. The rationale of the studies was in attempting to understand the strong effects that irradiation with a low-intensity ultrasound can have on biomolecular systems, because such ultrasound irradiation can cause cavitation bubbles to be produced and collapse, thus leading to local shock wave generation. The long-term objective is to contribute to future design of synergetic ultrasound and chemical drug strategy of protein inhibition.

No MeSH data available.


Related in: MedlinePlus

Evolution of density distribution of the systemin the solvatedbenzene dimer simulations. The time positions in the legend are givenrelative to the moment of the increase in the linear momentum.
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fig7: Evolution of density distribution of the systemin the solvatedbenzene dimer simulations. The time positions in the legend are givenrelative to the moment of the increase in the linear momentum.

Mentions: Results of simulationsof the benzene dimer are given on Figures 7–10. The size of the equilibrated cellwas 343.6 Å × 25.8 Å × 25.8 Å, not very differentfrom the size observed for the pure water system. Figures 7 and 8 demonstrate the evolutionof the density and velocity distribution with the passage of timeafter the shock wave is generated. The behavior of the system in theserespects is essentially the same as in the case of the pure watersimulations described above.


Computational Studies of the Effect of Shock Waves on the Binding of Model Complexes.

Kaminski GA - J Chem Theory Comput (2014)

Evolution of density distribution of the systemin the solvatedbenzene dimer simulations. The time positions in the legend are givenrelative to the moment of the increase in the linear momentum.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230379&req=5

fig7: Evolution of density distribution of the systemin the solvatedbenzene dimer simulations. The time positions in the legend are givenrelative to the moment of the increase in the linear momentum.
Mentions: Results of simulationsof the benzene dimer are given on Figures 7–10. The size of the equilibrated cellwas 343.6 Å × 25.8 Å × 25.8 Å, not very differentfrom the size observed for the pure water system. Figures 7 and 8 demonstrate the evolutionof the density and velocity distribution with the passage of timeafter the shock wave is generated. The behavior of the system in theserespects is essentially the same as in the case of the pure watersimulations described above.

Bottom Line: The behavior of the protein systems was more complex, yet significant disruption of the binding and geometry was also observed.The rationale of the studies was in attempting to understand the strong effects that irradiation with a low-intensity ultrasound can have on biomolecular systems, because such ultrasound irradiation can cause cavitation bubbles to be produced and collapse, thus leading to local shock wave generation.The long-term objective is to contribute to future design of synergetic ultrasound and chemical drug strategy of protein inhibition.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, Worcester Polytechnic Institute , Worcester, Massachusetts 01609, United States.

ABSTRACT
We have simulated effects of a shock wave in water that would result from the collapse of a cavitation bubble on binding in model complexes. We have considered a benzene dimer, a pair of uracil molecules, a complex of fragments of the X-linked inhibitor of apoptosis and caspase-9, and a fragment of c-Myc oncoprotein in binding with its dimerization partner Max. The effect of the shock waves was simulated by adding a momentum to a slab of solvent water molecules and observing the system as the slab moved and caused changes. In the cases of the small molecular pairs, the passage of the shock waves lead to dissociation of the complexes. The behavior of the protein systems was more complex, yet significant disruption of the binding and geometry was also observed. In all the cases, the effects did not occur during the immediate impact of the high-momentum solvent molecules, but rather during the expansion of the compressed system that followed the passage of the waves. The rationale of the studies was in attempting to understand the strong effects that irradiation with a low-intensity ultrasound can have on biomolecular systems, because such ultrasound irradiation can cause cavitation bubbles to be produced and collapse, thus leading to local shock wave generation. The long-term objective is to contribute to future design of synergetic ultrasound and chemical drug strategy of protein inhibition.

No MeSH data available.


Related in: MedlinePlus