Simulated Annealing Method for the Automated Simulation of DNA Dynamics in the HhaI Protein Binding Site
Solid-state deuterium NMR is well suited to the study of the conformational dynamics of DNA. Deuterium quadrupole echo spectra for a particular motional model can be calculated and matched to the experimental spectrum to extract information on the DNA dynamics; however, doing so can be very time-int...
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| Language: | English |
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Wiley
2023-01-01
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| Series: | Concepts in Magnetic Resonance: Part A, Bridging Education and Research |
| Online Access: | http://dx.doi.org/10.1155/2023/6235105 |
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| author | Kari Pederson Michael Groves Gary P. Drobny |
| author_facet | Kari Pederson Michael Groves Gary P. Drobny |
| author_sort | Kari Pederson |
| collection | DOAJ |
| description | Solid-state deuterium NMR is well suited to the study of the conformational dynamics of DNA. Deuterium quadrupole echo spectra for a particular motional model can be calculated and matched to the experimental spectrum to extract information on the DNA dynamics; however, doing so can be very time-intensive. The two-axis motion used to model the dynamics of either 2″ or 5′/5″ furanose ring deuteron is particularly complex with up to ten independent variables that can be optimized. Here, we present a program which automates both the input script generation and searches the parameter space for the best fit using a simulated annealing algorithm. The parameter, χred2, provides a relative measure of goodness of fit. This method reduces the overall time to determine the best fit of a line shape to a few days, in most cases, when running on a low-power desktop PC. The automated fitting program presented here can be easily modified to generate input scripts for new models, incorporate a weighting factor to the χred2 calculation to emphasize key line shape features, or fit nonsymmetrized data. This adaptable program will make simulation of solid-state deuterium spectra accessible to a broader audience. |
| format | Article |
| id | doaj-art-45b34c2625b648abb8a0fdc7930b1d94 |
| institution | DOAJ |
| issn | 1552-5023 |
| language | English |
| publishDate | 2023-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Concepts in Magnetic Resonance: Part A, Bridging Education and Research |
| spelling | doaj-art-45b34c2625b648abb8a0fdc7930b1d942025-08-20T02:39:18ZengWileyConcepts in Magnetic Resonance: Part A, Bridging Education and Research1552-50232023-01-01202310.1155/2023/6235105Simulated Annealing Method for the Automated Simulation of DNA Dynamics in the HhaI Protein Binding SiteKari Pederson0Michael Groves1Gary P. Drobny2Department of Chemistry & BiochemistryGrant NMR CenterDepartment of ChemistrySolid-state deuterium NMR is well suited to the study of the conformational dynamics of DNA. Deuterium quadrupole echo spectra for a particular motional model can be calculated and matched to the experimental spectrum to extract information on the DNA dynamics; however, doing so can be very time-intensive. The two-axis motion used to model the dynamics of either 2″ or 5′/5″ furanose ring deuteron is particularly complex with up to ten independent variables that can be optimized. Here, we present a program which automates both the input script generation and searches the parameter space for the best fit using a simulated annealing algorithm. The parameter, χred2, provides a relative measure of goodness of fit. This method reduces the overall time to determine the best fit of a line shape to a few days, in most cases, when running on a low-power desktop PC. The automated fitting program presented here can be easily modified to generate input scripts for new models, incorporate a weighting factor to the χred2 calculation to emphasize key line shape features, or fit nonsymmetrized data. This adaptable program will make simulation of solid-state deuterium spectra accessible to a broader audience.http://dx.doi.org/10.1155/2023/6235105 |
| spellingShingle | Kari Pederson Michael Groves Gary P. Drobny Simulated Annealing Method for the Automated Simulation of DNA Dynamics in the HhaI Protein Binding Site Concepts in Magnetic Resonance: Part A, Bridging Education and Research |
| title | Simulated Annealing Method for the Automated Simulation of DNA Dynamics in the HhaI Protein Binding Site |
| title_full | Simulated Annealing Method for the Automated Simulation of DNA Dynamics in the HhaI Protein Binding Site |
| title_fullStr | Simulated Annealing Method for the Automated Simulation of DNA Dynamics in the HhaI Protein Binding Site |
| title_full_unstemmed | Simulated Annealing Method for the Automated Simulation of DNA Dynamics in the HhaI Protein Binding Site |
| title_short | Simulated Annealing Method for the Automated Simulation of DNA Dynamics in the HhaI Protein Binding Site |
| title_sort | simulated annealing method for the automated simulation of dna dynamics in the hhai protein binding site |
| url | http://dx.doi.org/10.1155/2023/6235105 |
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