Coarse-grained Modeling For Double-stranded RNA 3D Structure And Thermal Stability

RNAs are known as very important functioning biomolecules,among which,noncoding RNAs are involved in many key processes of cell metabolism including gene expression regulation and catalytic biochemical reaction.The function of RNA molecule is closely related to its compact folded three-dimensional(3D)structure and its corresponding thermodynamical stability.Therefore,the knowledge of 3D structure and thermodynamical stability of RNAs in salt solutions is important for understanding their biological functions,and is also the guidance for the design of artificial biological functional molecules and drugs.However,it is still time-consuming and expensive to experimentally derive high-resolution 3D structures of RNAs.As a result,there are still limited available structures of RNAs deposited in RNA 3D structure data base.The experimental measurements for thermodynamic information of RNA molecules also cannot meet the rapid growth of research needs.Therefore,computational methods for predicting the 3D structure and thermodynamics of RNA molecules have been developed in recent years.At the two-dimensional level,effective RNA secondary structure and thermodynamic predicting models have been well developed.However,due to the more complex tertiary structures,the predictions of 3D structures of RNAs are still in the initial stage.As RNA molecules are highly sensitive to the environment including ions,which makes enormous challenges for the existing predicting models.Recent development of the coarse-grained model of Efold makes it possible to predict the 3D structure and thermal stability of RNA molecule at monovalent/divalent ion conditions from its sequence.But the model can only predict single-stranded RNAs,and cannot make any predictions for double-stranded(ds)RNA or RNA complexes.Based on the previous Efold model,this thesis further developed its predictive ability of dsRNA and RNA complex,and successfully predicted the 3D structures and thermal stability of dsRNAs as well as RNA kissing complexes at different monovalent/divalent ion concentrations.The main contents of the thesis are as follow:(1)Developing a coarse-grained model for double-stranded RNAsBased on the existing structure model and energy functions of Efold,we introduced inter-strand translation/rotation sampling for dsRNA conformations in finite-size boxes to predict 3D structures of dsRNAs,and a structure-based implicit electrostatic potential which can consider the influence of non-uniform negative charge density on the conterions condensed on negatively charged RNAs.Through the theoretical correction of the finite-size simulations,the newly developed Efold model can make reliable predictions of 3D structure and thermal stabilty for dsRNAs in monovalent/divalent ion sonutions for their sequences.(2)Predicting 3D structure,stability,flexibility and unfolding pathway of dsRNAsWe predictes 3D structures from sequences for extensive dsRNAs with/without bulge/internal loops in monovalent/divalent ion solutions with overall mean RMSD <3.5 ?,and the involvement of the structure-based electrostatic potential and corresponding experimental ion conditions generally improves the structure predictions with smaller RMSDs for dsRNAs in ion solutions.Our predictions on the stability for dsRNAs with extensive sequences over wide ranges of monovalent/divalent ion concentrations have the mean deviation < 2 ?,and our analyses show that the thermally unfolding pathway of a dsRNA is depending on its length as well as its sequence.The salt-dependent flexibility of dsRNAs can be captured and the predicted salt-dependent persistence lengths are in good accordance with experiments.(3)Predicting 3D structure,stability and folding pathway of RNA kissing complexesBy employing the Efold model,we predicted 3D structures,thermal stability and folding pathways for RNA kissing complexes in monovalent/divalent ion solutions.From the sequences,we successfully predicted the native-like 3D structures with overall mean RMSD of 5.4 ? as well as the thermal stability with an overall mean deviation of ~2.4 ? in melting temperature from the experimental data.Our analyses showed that the coaxial stacking interaction and salt condition can play important roles in maintaining and stabilizing their 3D structures.Our comprehensive analyses on thermally folding pathways of typical RNA kissing complexes revealed that the folding pathways as well as final folded structures are mainly determined by the relative stability between different states,which could be significantly modulated by their sequences.(4)Predicting sequence/salt-modulated folding pathway of RNA kissing complexesConsidering the folding pathways as well as final folded structures are mainly determined by the relative stability between different states,and the stability of the kissing complex and the extended duplex of a same RNA sequence can be differently influenced by monovalent/divalent ion solutions,we further predicted the folding pathways of RNA kissing complexes with different sequences at different monovalent/divalent ion concentrations.Our predictions revealed that the sequence of a complex determines the folding path by assigning the relative stability of each possible state,and ions modulat the folding path of a complex by adjusting the relative stability of each possible state.