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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 ofdensity distribution of the system in the pure watersimulation. The time positions in the legend are given relative tothe moment of the increase in the linear momentum.
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fig5: Evolution ofdensity distribution of the system in the pure watersimulation. The time positions in the legend are given relative tothe moment of the increase in the linear momentum.

Mentions: Figure 5 shows the evolution of the density distributionin the pure water system after the increase of the linear momentumof the solvent slab at the leftmost part of the total simulation cell.At the beginning, the density is roughly uniform (the black line).The moving water molecules then create a spike in the density in theleft part of the system (as illustrated for the 1 ps time by the redline). The spike moves to the right and reaches the middle of thesystem between 2 and 3 ps of the simulation time. Once the front ofthe shock wave reaches the rightmost edge of the system, density binsbeyond those filled in the beginning become populated, as can be seenfor the density curves at 5, 6, and 7 ps. Finally, the density insidethe simulation cell falls to its initial equilibration value at ca.7 ps. Thus, we can say that results for the first 7 ps after the generationof the shock wave are physically more relevant than those producedfor the times after 7 ps, and the latter should only be consideredin qualitative and approximate descriptions of the process.


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

Kaminski GA - J Chem Theory Comput (2014)

Evolution ofdensity distribution of the system in the pure watersimulation. The time positions in the legend are given relative tothe moment of the increase in the linear momentum.
© Copyright Policy
Related In: Results  -  Collection

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

fig5: Evolution ofdensity distribution of the system in the pure watersimulation. The time positions in the legend are given relative tothe moment of the increase in the linear momentum.
Mentions: Figure 5 shows the evolution of the density distributionin the pure water system after the increase of the linear momentumof the solvent slab at the leftmost part of the total simulation cell.At the beginning, the density is roughly uniform (the black line).The moving water molecules then create a spike in the density in theleft part of the system (as illustrated for the 1 ps time by the redline). The spike moves to the right and reaches the middle of thesystem between 2 and 3 ps of the simulation time. Once the front ofthe shock wave reaches the rightmost edge of the system, density binsbeyond those filled in the beginning become populated, as can be seenfor the density curves at 5, 6, and 7 ps. Finally, the density insidethe simulation cell falls to its initial equilibration value at ca.7 ps. Thus, we can say that results for the first 7 ps after the generationof the shock wave are physically more relevant than those producedfor the times after 7 ps, and the latter should only be consideredin qualitative and approximate descriptions of the process.

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