在此章節，需要RasMol software以執行.spt檔案。 RasMol script指令從*.spt文字檔中依序解讀一組RasMol指令，並且執行這些檔案。這可使得一般用於RasMol的序列可被儲存且用一個指令執行。RasMol software is required to run the .spt files found in this section. The RasMol script command reads a set of RasMol commands sequentially from a text file with the *.spt file extension and executes them. This allows sequences of commonly used RasMol commands to be stored and performed by a single command.
單元1-3之分子視覺化練習。Molecular Visualization Exercises For Modules 1-3.
單元1: 細胞的大小與組成，以及此與調節的關連性。Module 1: Size and Components of Cells and Implications with respect to Regulation
自PDB網站查看下列的結構：M. Tuberculosis Enoyl-Acp Reductase (Inha) In Complex With Nad+ and C16-Fatty-Acyl-Substrate (1bvr)
View the following structure from the PDB Web site:
M. Tuberculosis Enoyl-Acp Reductase (Inha) In Complex With Nad+ and C16-Fatty-Acyl-Substrate (1bvr)
單元2: 脂肪酸合成酶 (FAS)，聚酮合成酶(PKS)，以及非核糖體多胜肽生成酶(NRPS)。Module 2: Fatty Acid Synthases (FAS), Polyketide Synthases (PKS), and Non-ribosomal Polypeptide Synthases (NRPS)
自PDB網站查看下列的結構：
B-Ketoacyl-[Acyl Carrier Protein] Synthase I In Complex With Thiolactomycin (1FJ4)
B-Ketoacyl-[Acyl Carrier Protein] Synthase I In Complex With Cerulenin (1FJ8)
View the following structures from the PDB Web site:
B-Ketoacyl-[Acyl Carrier Protein] Synthase I In Complex With Thiolactomycin (1FJ4)
B-Ketoacyl-[Acyl Carrier Protein] Synthase I In Complex With Cerulenin (1FJ8)
為了與所查看的結構相連結，請參考下列文獻：In conjunction with viewing the structures, refer to the following paper:
Price, A. C. et al. 〈Thiolactomycin與Cerulenin抑制B-Ketoacyl-Acyl 攜帶蛋白合成酶〉 《生物化學期刊》 276 (2001): 6551-9.Price, A. C. et al. "Inhibition of B-Ketoacyl-Acyl Carrier Protein Synthases by Thiolactomycin and Cerulenin." J. Biol. Chem. 276 (2001): 6551-9.
單元3: 轉譯：載入、起始、延長、以及終止 – 動作之機制；G蛋白質之導論：開關或啟動者。Module 3: Translation: Loading, Initiation, Elongation, and Termination - A Machine in Action; Introduction to G-proteins: Switches or Motors
請自網站下載適合的Rasmol版本。Download the appropriate version of Rasmol from this Web site.
接下來請下載於下表中的每個script檔案以及pdb檔案，並將全部檔案儲存於Rasmol同一個資料夾內。 然後，在Rasmol命令列打上：
script <spt file name>
檔案將被開啟，且命列列視窗應該會顯示出有關結構與顏色的資訊，此資訊亦列於下表。
Next download each script file and pdb file in the following table and save them all in the same folder as you have saved Rasmol. Then in the Rasmol command line type:
script <spt file name>
"The file should open and the command line window should display information about the structure and coloring which is also given in the table below.
| EF-Tu ，GDPNP，以及 tRNAEF-Tu and GDPNP and tRNA |
1ttt (SPT) |
1ttt (PDB) |
| EF-Tu與GDP (P loop是洋紅色, switch 1是綠色, switch 2是藍色, domain 2是紅色, domain 3是洋紅色)EF-Tu and GDP (P loop is magenta, switch 1 is green, switch 2 is blue, domain 2 is red, domain 3 is magenta) |
1tui (SPT) |
1tui (PDB) |
| Editing domain是紅色, active site 是綠色, conserved residues HIGH 64-67是洋紅色, KMSKS 545-548是黃色Editing domain in red, active site in green, conserved residues HIGH 64-67 in magenta, KMSKS 545-548 in yellow |
1ile (SPT) |
1ile (PDB) |
| IleRS之3'端摺疊入活化位IleRS with 3' end folded into active site |
1gtr (SPT) |
1gtr (PDB) |
| IleRS with pseudomonic acidIleRS with pseudomonic acid |
1qu2 (SPT) |
1qu2 (PDB) |
|
結構參考文獻Structure References
Ban, N., P. Nissen, J. Hansen, P. B. Moore, and T. A. Steitz. 〈於2.4 A 的解析度中，大核醣體次單元的完整分子結構〉 《科學》289 (2000): 905-20. (H. marismortui)Ban, N., P. Nissen, J. Hansen, P. B. Moore, and T. A. Steitz. "The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution." Science 289 (2000): 905-20. (H. marismortui)
Yusupov, M. M., G. Z. Yusupova, A. Baucom, K. Lieberman, T. N. Earnest, J. H. Cate, and H. F. Noller. 〈於5.5 A的解析度中，核醣體的結晶結構〉 《科學》 292 (2001): 883-96. (T. thermophilus)Yusupov, M. M., G. Z. Yusupova, A. Baucom, K. Lieberman, T. N. Earnest, J. H. Cate, and H. F. Noller. "Crystal Structure of the Ribosome at 5.5 Å Resolution." Science 292 (2001): 883-96. (T. thermophilus)
Wimberly, B. T., D. E. Brodersen, W. M. Clemons, Jr., R. J. Morgan-Warren, A. P. Carter, C. Vonrhein, T. Hartsch, and V. Ramakrishnan. 〈30S核醣體次單元的結構〉 《自然》 407 (2000): 327-39.Wimberly, B. T., D. E. Brodersen, W. M. Clemons, Jr., R. J. Morgan-Warren, A. P. Carter, C. Vonrhein, T. Hartsch, and V. Ramakrishnan. "Structure of the 30S Ribosomal Subunit." Nature 407 (2000): 327-39.
Carter, A. P., W. M. Clemons, D. E. Brodersen, R. J. Morgan-Warren, B. T. Wimberly, and V. Ramakrishnan. 〈自30S核醣體次單元的結構，及其與抗生素的交互作用中，洞察其功能性。〉 《自然》 407 (2000): 340-8.Carter, A. P., W. M. Clemons, D. E. Brodersen, R. J. Morgan-Warren, B. T. Wimberly, and V. Ramakrishnan. "Functional Insights from the Structure of the 30S Ribosomal Subunit and Its Interactions with Antibiotics." Nature 407 (2000): 340-8.
Schlunzen F., R. Zarivach, J. Harms, A. Bashan, A. Tocilj, R. Albrecht, A. Yonath, and F. Franceschi. 〈真性細菌的胜肽轉移酶中心，其與抗生素交互作用的結構性基礎〉 《自然》 413 (2001): 814-21. (D. radiodurans)Schlunzen F., R. Zarivach, J. Harms, A. Bashan, A. Tocilj, R. Albrecht, A. Yonath, and F. Franceschi. "Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Centre in Eubacteria." Nature 413 (2001): 814-21. (D. radiodurans)
Steitz, T. A., and P. B. Moore. 〈RNA，第一個巨分子催化劑:核醣體是核醣體？〉 《生物化學科學趨勢》 28, no. 8 (2003): 411-418. (50S structure)Steitz, T. A., and P. B. Moore. "RNA, the First Macromolecular Catalyst: The Ribosome is a Ribozyme." TIBS 28, no. 8 (2003): 411-418. (50S structure)
