{"title":"Simulated Annealing Method for the Automated Simulation of DNA Dynamics in the HhaI Protein Binding Site","authors":"Kari Pederson, Michael Groves, Gary P. Drobny","doi":"10.1155/2023/6235105","DOIUrl":null,"url":null,"abstract":"<div>\n <p>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, <span></span><math></math>, 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 <span></span><math></math> 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.</p>\n </div>","PeriodicalId":55216,"journal":{"name":"Concepts in Magnetic Resonance Part A","volume":"2023 1","pages":""},"PeriodicalIF":0.4000,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2023/6235105","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Concepts in Magnetic Resonance Part A","FirstCategoryId":"92","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1155/2023/6235105","RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
引用次数: 0
Abstract
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, , 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 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.
期刊介绍:
Concepts in Magnetic Resonance Part A brings together clinicians, chemists, and physicists involved in the application of magnetic resonance techniques. The journal welcomes contributions predominantly from the fields of magnetic resonance imaging (MRI), nuclear magnetic resonance (NMR), and electron paramagnetic resonance (EPR), but also encourages submissions relating to less common magnetic resonance imaging and analytical methods.
Contributors come from academic, governmental, and clinical communities, to disseminate the latest important experimental results from medical, non-medical, and analytical magnetic resonance methods, as well as related computational and theoretical advances.
Subject areas include (but are by no means limited to):
-Fundamental advances in the understanding of magnetic resonance
-Experimental results from magnetic resonance imaging (including MRI and its specialized applications)
-Experimental results from magnetic resonance spectroscopy (including NMR, EPR, and their specialized applications)
-Computational and theoretical support and prediction for experimental results
-Focused reviews providing commentary and discussion on recent results and developments in topical areas of investigation
-Reviews of magnetic resonance approaches with a tutorial or educational approach