| Full text | |
| Author(s): |
Viegas, Rafael G.
;
Sanches, Murilo N.
;
Chen, Alan A. A.
;
Paulovich, Fernando V.
;
Garcia, Angel E.
;
Leite, Vitor B. P.
Total Authors: 6
|
| Document type: | Journal article |
| Source: | JOURNAL OF CHEMICAL INFORMATION AND MODELING; v. 63, n. 17, p. 9-pg., 2023-08-22. |
| Abstract | |
Moleculardynamics (MD) simulations have become increasingly powerfuland can now describe the folding/unfolding of small biomolecules inatomic detail. However, a major challenge in MD simulations is torepresent the complex energy landscape of biomolecules using a smallnumber of reaction coordinates. In this study, we investigate thefolding pathways of an RNA tetraloop, gcGCAAgc, using five classicalMD simulations with a combined simulation time of approximately 120 & mu;s. Our approach involves analyzing the tetraloop dynamics,including the folding transition state ensembles, using the energylandscape visualization method (ELViM). The ELViM is an approach thatuses internal distances to compare any two conformations, allowingfor a detailed description of the folding process without requiringroot mean square alignment of structures. This method has previouslybeen applied to describe the energy landscape of disordered & beta;-amyloidpeptides and other proteins. The ELViM results in a non-linear projectionof the multidimensional space, providing a comprehensive representationof the tetraloop's energy landscape. Our results reveal fourdistinct transition-state regions and establish the paths that leadto the folded tetraloop structure. This detailed analysis of the tetraloop'sfolding process has important implications for understanding RNA folding,and the ELViM approach can be used to study other biomolecules. (AU) | |
| FAPESP's process: | 21/15028-4 - Elucidating the functional plasticity of intrinsically disordered proteins by the study of energy landscape |
| Grantee: | Murilo Nogueira Sanches |
| Support Opportunities: | Scholarships in Brazil - Doctorate |
| FAPESP's process: | 19/22540-3 - Studies of energy landscapes of biological macromolecules |
| Grantee: | Vitor Barbanti Pereira Leite |
| Support Opportunities: | Regular Research Grants |
| FAPESP's process: | 23/02219-1 - Understanding functional mechanisms of proteins and RNAs through energy landscapes |
| Grantee: | Vitor Barbanti Pereira Leite |
| Support Opportunities: | Regular Research Grants |