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Computational Studies of the Effect of Shock Waves on the Binding of Model Complexes
[Image: see text] 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,...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American
Chemical Society
2014
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230379/ https://www.ncbi.nlm.nih.gov/pubmed/25400519 http://dx.doi.org/10.1021/ct500461s |
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author | Kaminski, George A. |
author_facet | Kaminski, George A. |
author_sort | Kaminski, George A. |
collection | PubMed |
description | [Image: see text] 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. |
format | Online Article Text |
id | pubmed-4230379 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | American
Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-42303792015-09-25 Computational Studies of the Effect of Shock Waves on the Binding of Model Complexes Kaminski, George A. J Chem Theory Comput [Image: see text] 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. American Chemical Society 2014-09-25 2014-11-11 /pmc/articles/PMC4230379/ /pubmed/25400519 http://dx.doi.org/10.1021/ct500461s Text en Copyright © 2014 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes. |
spellingShingle | Kaminski, George A. Computational Studies of the Effect of Shock Waves on the Binding of Model Complexes |
title | Computational
Studies of the Effect of Shock Waves
on the Binding of Model Complexes |
title_full | Computational
Studies of the Effect of Shock Waves
on the Binding of Model Complexes |
title_fullStr | Computational
Studies of the Effect of Shock Waves
on the Binding of Model Complexes |
title_full_unstemmed | Computational
Studies of the Effect of Shock Waves
on the Binding of Model Complexes |
title_short | Computational
Studies of the Effect of Shock Waves
on the Binding of Model Complexes |
title_sort | computational
studies of the effect of shock waves
on the binding of model complexes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230379/ https://www.ncbi.nlm.nih.gov/pubmed/25400519 http://dx.doi.org/10.1021/ct500461s |
work_keys_str_mv | AT kaminskigeorgea computationalstudiesoftheeffectofshockwavesonthebindingofmodelcomplexes |