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All-atom Monte Carlo simulation of GCAA RNA folding.
| Content Provider | Semantic Scholar |
|---|---|
| Author | Nivon, Lucas G. Shakhnovich, Eugene I. |
| Copyright Year | 2004 |
| Abstract | We report a detailed all-atom simulation of the folding of the GCAA RNA tetraloop. The GCAA tetraloop motif is a very common and thermodynamically stable secondary structure in natural RNAs. We use our simulation methods to study the folding behavior of a 12-base GCAA tetraloop structure with a four-base helix adjacent to the tetraloop proper. We implement an all-atom Monte Carlo (MC) simulation of RNA structural dynamics using a Go potential. Molecular dynamics (MD) simulation of RNA and protein has realistic energetics and sterics, but is extremely expensive in terms of computational time. By coarsely treating non-covalent energetics, but retaining all-atom sterics and entropic effects, all-atom MC techniques are a useful method for the study of protein and now RNA. We observe a sharp folding transition for this structure, and in simulations at room temperature the state histogram shows three distinct minima: an unfolded state (U), a more narrow intermediated state (I), and a narrow folded state (F). The intermediate consists primarily of structures with the GCAA loop and some helix hydrogen bonds formed. Repeated kinetic folding simulations reveal that the number of helix base-pairs forms a simple 1D reaction coordinate for the I-->N transition. |
| Starting Page | 29 |
| Ending Page | 45 |
| Page Count | 17 |
| File Format | PDF HTM / HTML |
| Alternate Webpage(s) | http://faculty.washington.edu/nivon/pdfs/nivon_shakhnovich.pdf |
| PubMed reference number | 15504400v1 |
| Volume Number | 344 |
| Issue Number | 1 |
| Journal | Journal of molecular biology |
| Language | English |
| Access Restriction | Open |
| Subject Keyword | Covalent Interaction Hydrogen Immunoreceptor Tyrosine-Based Activation Motif Kinetics Leucaena pulverulenta Molecular Dynamics Monte Carlo Method Protein Domain RNA Folding |
| Content Type | Text |
| Resource Type | Article |
