NDLI: RNA structure refinement and force field evaluation using molecular dynamics simulations

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RNA structure refinement and force field evaluation using molecular dynamics simulations

Content Provider	ACM Digital Library
Author	Cheatham, Thomas E. Henriksen, Niel
Abstract	In this study we investigated the structure of two similar RNA hairpins using molecular dynamics. Both structures were originally determined using solution NMR. Despite having a nearly identical base sequence, the published 3D structures have striking differences. To further understand these differences we used the AMBER suite of simulation software to perform a series of explicitly solvated simulations with the experimental structure restraints enforced. These simulations revealed incorrect restraints in one hairpin and a problematic nucleotide conformation in the other. Removal of the bad restraints and addition of a heating step to the structure refinement procedure yielded two high quality structural ensembles with very low pairwise RMSD to one another. Thus our restrained simulations suggest that these two RNA hairpins have quite similar 3D structures and the differences in the published structures are likely due to refinement problems. In addition to the structure refinement study, we were also interested in how the AMBER RNA force fields performed in unrestrained simulations. We found that non-canonical features, such as bulge and loop regions, were modeled very poorly. In some cases, pathological conformations dominated the entire simulation trajectory. The results of both the restrained and unrestrained simulations show that while the molecular dynamics environment is a powerful tool for structure refinement of RNA, unrestrained simulations must be treated with great caution until force field performance is improved.
Starting Page	1
Ending Page	1
Page Count	1
File Format	PDF
ISBN	9781450308885
DOI	10.1145/2016741.2016745
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2011-07-18
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Amber Rna Structure refinement Force field Molecular dynamics simulations
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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