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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 densitydistribution in the solvated XIAP–caspase-9dimer simulations. The time positions in the legend are given relativeto the moment of the increase in the linear momentum.
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fig15: Evolution of densitydistribution in the solvated XIAP–caspase-9dimer simulations. The time positions in the legend are given relativeto the moment of the increase in the linear momentum.

Mentions: Thesize of the simulation cell for the protein dimers was differentfrom that for pure water and small molecular dimers. The dimensionsof the equilibrated cell for the XIAP–caspase-9 complex were225.3 Å × 45.6 Å × 45.6 Å. Qualitatively,the behavior of the density and velocity distributions was similarto that in the previous cases, except that the smaller size alongthe X-axis lead to a somewhat shorter time frameof the passing of the shock wave through the system. (See Figures 15 and 16.)


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

Kaminski GA - J Chem Theory Comput (2014)

Evolution of densitydistribution in the solvated XIAP–caspase-9dimer simulations. The time positions in the legend are given relativeto 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

fig15: Evolution of densitydistribution in the solvated XIAP–caspase-9dimer simulations. The time positions in the legend are given relativeto the moment of the increase in the linear momentum.
Mentions: Thesize of the simulation cell for the protein dimers was differentfrom that for pure water and small molecular dimers. The dimensionsof the equilibrated cell for the XIAP–caspase-9 complex were225.3 Å × 45.6 Å × 45.6 Å. Qualitatively,the behavior of the density and velocity distributions was similarto that in the previous cases, except that the smaller size alongthe X-axis lead to a somewhat shorter time frameof the passing of the shock wave through the system. (See Figures 15 and 16.)

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