Simulation Study On Folding Mechanism Of RNA Molecule

RNA is an important macromolecule in living organisms.To perform their functions,RNAs need to fold into correct three-dimensional（tertiary）structures.Hence,studying the folding mechanism of RNA is of great significance for understanding how they perform their functions.This thesis will study some of the basic problems of RNA folding by using all-atom molecular dynamics simulation to further understand the physical mechanism of RNA folding.The main research contents and results include:1)The mechanism of base-pair formation:Base paring is a fundamental step in the RNA folding process.The mechanism of its formation is still not completely understood.We studied the free folding of a short RNA with 12 nucleotides（PDB ID:1zih）and obtained162 independent events of base-pair formation.By analyzing the simulation results,we have found that there are four ways of base pairing formation:stable,bridging,rotation and shifting ways.The first two involve direct coupling of cations,and the latter two do not.We have also found that cations tend to stablely or dynamically interact with negative atoms unprotonated within bases.These results show that the cations may have different roles in base pairing.2)Folding path of RNA hairpin structure:The hairpin structure is the basic unit of RNA structure.From the perspective of thermodynamics,the folding path of RNA hairpin should adopt the simple zipper mode.Due to the limitation of nucleic acid molecular force field,the convetional all-atom molecular dynamics method has not successfully simulated the folding process of RNAs,even small RNA hairpin.In order to overcome this difficulty,we simulate the folding behavior of a hairpin structure（PDB ID:1zih）back to the native state after opening different number of base pairs from the end.The hairpin formed a total of 4 base pairs.The results suggest that the folding of this RNA hairpin indeed can adopt zipper mode,and the formation of the first base pair closest to the loop region may be a key step.3)Sequence dependence of RNA folded structures:The change of a small number of key residues in RNA sequence will affect the folded structure.A typical example is the aptamer of TTE and BSU pre Q₁ riboswitches.They have different frre-state tertiary structures.The significantly different region between them is their L2 loop region in which the BSU pre Q₁ riboswitches have two more uracil than TTE pre Q₁ riboswitches.Therefore,it is intersting to understand whether this sequence difference is the reason of affecting their free-state folded structure.We simulated their unfolding processes starting from the bound-state structure without the ligand and with different mutations of L2 sequence.The results show that BSU pre Q₁ riboswitches can have relatively stable free-state folded structure after the residues mutaions.This indicates that the small residue difference in sequences can indeed affect the stability of folded structures of these two RNAs.