| Summary: | 碩士 === 國立臺灣師範大學 === 化學研究所 === 89 === Cardiotoxins (CTX) from venom of Taiwan cobra (Naja naja atra) are small 5-β strand and 3-loop basic proteins of 60 amino acids. The two-strand β34-sheet conformations of peptides of 20 residues, which are located at the initial folding site, obtained from NMR structure of CTX, were examined using molecular dynamics (MD) simulation with the locally enhanced sampling (LES) method. The trajectories showed that the peptide of CTX3 (CTX2), starting from CTX2 (CTX3) β conformation, is able to transit and move close to CTX3 (CTX2) β conformation with LES at <300 ps while the conformation transition was not seen up to 1 ns without LES. The effects of number of copies and copy region of LES method in the simulation results were examined. Molecular interactions at the site of conformation transition were analyzed and discussed. These results give us indications of how to examine structural stability, and to predict correct structures for mutants of proteins/peptides.
In additions, an unfolding/refolding MD simulation for CTX3 was carried out to examine the folding/unfolding pathway of this protein. Unlike a previous simulations for ubiquitin, which refolded within several nanoseconds in simulation due to rather strong hydrophobic interaction of this protein, the present CTX3 simulation did not refold in sub-nano second simulation trajectories. This should be because that the non-polar residues of CTX3 are mostly located at turn position of loop seqments. Besides, MD simulations for CTX2 and CTX4 at root temperature were carried out as well to examine the backbone mobility of these proteins. The accuracy of calculated order parameters for Cα-H bonds of CTX2 and CTX4, and their differences are discussed. Relation of these calculated results to the structural stability and dominant interactions of these proteins is discussed.
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