Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein
Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be...
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| Format: | Article |
| Language: | English |
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Wiley
2015-01-01
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| Series: | Journal of Chemistry |
| Online Access: | http://dx.doi.org/10.1155/2015/908204 |
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| author | Raiker Witter Margit Möllhoff Frank-Thomas Koch Ulrich Sternberg |
| author_facet | Raiker Witter Margit Möllhoff Frank-Thomas Koch Ulrich Sternberg |
| author_sort | Raiker Witter |
| collection | DOAJ |
| description | Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT). Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges of ab initio calculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation of R=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus. Our calculations show that moderate changes of side chain torsion angle χ1 and small variations of χ2 of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism. |
| format | Article |
| id | doaj-art-51fb1da9672441f3958ff85275e672de |
| institution | Kabale University |
| issn | 2090-9063 2090-9071 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Chemistry |
| spelling | doaj-art-51fb1da9672441f3958ff85275e672de2025-02-03T01:28:06ZengWileyJournal of Chemistry2090-90632090-90712015-01-01201510.1155/2015/908204908204Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel ProteinRaiker Witter0Margit Möllhoff1Frank-Thomas Koch2Ulrich Sternberg3Technomedicum, Tallinn University of Technology, Ehitajate Tee 5, 19086 Tallinn, EstoniaLos Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM 87545, USAMax Planck Institute of Biogeochemistry, Hans-Knöll-Strasse 10, 07745 Jena, GermanyTechnomedicum, Tallinn University of Technology, Ehitajate Tee 5, 19086 Tallinn, EstoniaPolarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT). Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges of ab initio calculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation of R=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus. Our calculations show that moderate changes of side chain torsion angle χ1 and small variations of χ2 of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism.http://dx.doi.org/10.1155/2015/908204 |
| spellingShingle | Raiker Witter Margit Möllhoff Frank-Thomas Koch Ulrich Sternberg Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein Journal of Chemistry |
| title | Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein |
| title_full | Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein |
| title_fullStr | Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein |
| title_full_unstemmed | Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein |
| title_short | Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein |
| title_sort | fast atomic charge calculation for implementation into a polarizable force field and application to an ion channel protein |
| url | http://dx.doi.org/10.1155/2015/908204 |
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