Document Detail


Predicting ion-nucleic acid interactions by energy landscape-guided sampling.
MedLine Citation:
PMID:  23002389     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
The recently developed Tightly Bound Ion (TBI) model offers improved predictions for ion effect in nucleic acid systems by accounting for ion correlation and fluctuation effects. However, further application of the model to larger systems is limited by the low computational efficiency of the model. Here, we develop a new computational efficient TBI model using free energy landscape-guided sampling method. The method leads to drastic reduction in the computer time by a factor of 50 for RNAs of 50-100 nucleotides long. The improvement in the computational efficiency would be more significant for larger structures. To test the new method, we apply the model to predict the free energies and the number of bound ions for a series of RNA folding systems. The validity of this new model is supported by the nearly exact agreement with the results from the original TBI model and the agreement with the experimental data. The method may pave the way for further applications of the TBI model to treat a broad range of biologically significant systems such as tetraloop-receptor and riboswitches.
Authors:
Zhaojian He; Shi-Jie Chen
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-4-30
Journal Detail:
Title:  Journal of chemical theory and computation     Volume:  8     ISSN:  1549-9626     ISO Abbreviation:  J Chem Theory Comput     Publication Date:  2012 Jun 
Date Detail:
Created Date:  2012-9-24     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101232704     Medline TA:  J Chem Theory Comput     Country:  -    
Other Details:
Languages:  ENG     Pagination:  2095-2101     Citation Subset:  -    
Affiliation:
Department of Physics, Department of Biochemistry, and Informatics Institute University of Missouri, Columbia, MO 65211.
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