本文利用分子動力學模擬賴氨酸轉移核醣核酸(tRNALys3)與訊息核醣核酸(mRNA)密碼子之交互作用結構穩定性，其密碼子分別為AAA與AAG，並且使用GROMACS分子動力學模擬軟體，以及選擇GROMOS96作用力場當作模擬的勢能，模擬的環境為水溶液中，共加入了79個鈉離子(Na+)來中和整體系統的電性。由RMSD值的結果顯示，tRNALys3的反密碼子與mRNA的密碼子AAG間的擾動相較於其與密碼子AAA間的擾動還來的大，這意味著tRNALys3與mRNA的密碼子AAA結合後，整體結構呈現較穩定的趨勢。此外，由RMSF值的結果顯示，經過修飾後的第34與第37個位置的核苷酸，與mRNA的密碼子產生交互作用後，此兩個特定位置的核苷酸其擾動會比無交互作用時大。最後，在整個模擬過程中，我們發現單獨tRNALys3的反密碼子臂和環(anticodon stem and loop；ASL)結構會呈現穩定的螺旋二級結構，反觀tRNALys3與密碼子AAA以及AAG結合後，其ASL結構將會旋開，而呈現另一種穩定的U形結構，此構形的轉換可能影響tRNALys3在轉譯過程中從核醣體的A位點到P位點的易位。

In this paper, the structual stability of the interactions between wild-type tRNALys3 and mRNA codon, i.e. AAA and AAG, have been performed using molecular dynamics (MD) simulations. The simulated models contain the individual tRNALys3, interaction between tRNALys3 and AAA codon, and interaction between tRNALys3 and AAG codon. MD simulations were performed using the GROMACS simulation program using the GROMOS96 (ffG43a1) force field. From the RMSD measurement, the results indicated the interaction between tRNALys3 and AAG codon has larger fluctuation than AAA codon. This phenomenon implies that the structure is more stable while tRNALys3 interacts to AAA codon. Furthermore, from the RMSF calculations, it is show that the modified tRNALys3 at specific 34 and 37 bases bear larger fluctuations while tRNALys3 interacts to AAA or AAG codons. Finally, the secondary structure of individual tRNALys3, i.e. anticodon stem and loop (ASL), displaying the structurally stable preference during the entire simulation time, whereas the ASL structure produce rotation and further form the U-shape while tRNALys3 bound to the AAA and AAG codons. The structural switch from the helix to U-shape may affect the translocation of ribosome from the A-site to P-site.

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