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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

Three stages of the simulations: (a) a slab of water molecules(one-fifth of the system on the left) is given an additional linermomentum; (b) a region of increased density has been created and isapproaching the solutes; (c) the front of the shock wave has passedthe location of the solutes.
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fig1: Three stages of the simulations: (a) a slab of water molecules(one-fifth of the system on the left) is given an additional linermomentum; (b) a region of increased density has been created and isapproaching the solutes; (c) the front of the shock wave has passedthe location of the solutes.

Mentions: This initial configuration of the shock wave propagation intheequilibrated cell is shown in Figure 1a. Thevelocities have already been set, but the density is not yet distorted.The solute molecules (in this case, a fragment of the c-Myc in complexwith Max) is visible near the center of the cell. The MD simulationsproceed further in the NVE ensemble. The periodicity is preservedonly in the Y- and X-directions,and the value of the period in along the X-axis isset to infinity. The time step is reduced to 0.2 fs at this stageof the simulations.


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

Kaminski GA - J Chem Theory Comput (2014)

Three stages of the simulations: (a) a slab of water molecules(one-fifth of the system on the left) is given an additional linermomentum; (b) a region of increased density has been created and isapproaching the solutes; (c) the front of the shock wave has passedthe location of the solutes.
© Copyright Policy
Related In: Results  -  Collection

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

fig1: Three stages of the simulations: (a) a slab of water molecules(one-fifth of the system on the left) is given an additional linermomentum; (b) a region of increased density has been created and isapproaching the solutes; (c) the front of the shock wave has passedthe location of the solutes.
Mentions: This initial configuration of the shock wave propagation intheequilibrated cell is shown in Figure 1a. Thevelocities have already been set, but the density is not yet distorted.The solute molecules (in this case, a fragment of the c-Myc in complexwith Max) is visible near the center of the cell. The MD simulationsproceed further in the NVE ensemble. The periodicity is preservedonly in the Y- and X-directions,and the value of the period in along the X-axis isset to infinity. The time step is reduced to 0.2 fs at this stageof the simulations.

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