Dataset Information

Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures.

ABSTRACT: It is an outstanding problem to clarify how the RNA sequence is related to its structure and biological functions. We developed a simplified definition of a metric for tree representation of RNA secondary structures and analyzed the conformational energy landscapes of human spliceosomal snRNAs. We discuss the structural properties of the biological sequence by calculating the conformational energy landscapes based on the structural distance between each of the pairs in the set of suboptimal structures. The new index value is introduced for estimating the shapes of distribution patterns in conformational energy landscapes. We apply our method to the five human snRNAs and show that U1 snRNA has a multi-valley profile of the landscape, whereas the landscapes of the other four snRNAs have one steep valley. This result reflects different biological functions of these snRNAs in the pre-mRNA splicing process. The results of analyzing tRNAs and rRNAs show that the conformational energy landscapes of these sequences have multi-valley profiles.

SUBMITTER: Kitagawa J

PROVIDER: S-EPMC152804 | biostudies-literature | 2003 Apr

REPOSITORIES: biostudies-literature

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Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures.

Kitagawa Junji J Futamura Yasuhiro Y Yamamoto Kenji K

Nucleic acids research 20030401 7

It is an outstanding problem to clarify how the RNA sequence is related to its structure and biological functions. We developed a simplified definition of a metric for tree representation of RNA secondary structures and analyzed the conformational energy landscapes of human spliceosomal snRNAs. We discuss the structural properties of the biological sequence by calculating the conformational energy landscapes based on the structural distance between each of the pairs in the set of suboptimal stru ...[more]

PMID: 12655018

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Project description:Extra unmatched nucleotides (single base bulges) are common structural motifs in folded RNA molecules and can participate in RNA-ligand binding and RNA tertiary structure formation. Often these processes are associated with conformational transitions in the bulge region such as flipping out of the bulge base from an intrahelical stacked toward a looped out state. Knowledge of the flexibility of bulge structures and energetics of conformational transitions is an important prerequisite to better understand the function of this RNA motif. Molecular dynamics simulations were performed on single uridine and adenosine bulge nucleotides at the center of eight basepair RNA molecules and indicated larger flexibility of the bulge bases compared to basepaired regions. The umbrella sampling method was applied to study the bulge base looping out process and accompanying conformational and free energy changes. Looping out toward the major groove resulted in partial disruption of adjacent basepairs and was found to be less favorable compared to looping out toward the minor groove. For both uridine and adenosine bulges, a positive free energy change for full looping out was obtained which was approximately 1.5 kcal mol-1 higher in the case of the adenosine compared to the uridine bulge system. The simulations also indicated stable partially looped out states with the bulge bases located in the RNA minor groove and forming base triples with 5'-neighboring basepairs. In the case of the uridine bulge this state was more stable than the intrahelical stacked bulge structure. Induced looping out toward the minor groove involved crossing of an energy barrier of approximately 3.5 kcal mol-1 before reaching the base triple state. A continuum solvent analysis of intermediate bulge states indicated that electrostatic interactions stabilize looped out and base triple states, whereas van der Waals interactions and nonpolar contributions favor the stacked bulge conformation.

Dataset Information

Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures.

Publications

Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures.

Similar Datasets

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