ubiquitin是一個具有72個胺基酸的小蛋白質，整個分子的二級結構具有五股β摺版和一股α螺旋鏈，在N端位置上17個胺基酸的胜月太 片段則為兩股反平行的β摺版，且其在水溶液中能夠形成單一的β髮夾狀結構。我們使用GB/SA方法做分子動力學的模擬，研究β突起( β bulge )存在與否和置換折彎（turn）上胺基酸次序對ubiquitin N端之蛋白質胜月太片段的二級結構穩定性影響。模擬結果支持實驗的論點，顯示由Gly10形成的β bulge對ubiquitin蛋白質二級結構的維持有明顯的效應。而ubiquitin原先turn的次序（type I turn，TLTGK）對β髮夾結構的穩定性較優於其它常見折彎處次序為NG、AG、GD、NPDGT的胜月太片段。
在第二部分我們根據文獻所提出的NG turn能夠幫助兩股形成穩定的二級結構，設計了一小段胜月太 鏈，兩股上多為非極性胺基酸，從直線的結構做常溫300 K折疊模擬，於50 ps時產生β摺版的二級結構，且維持了1.6 ns以上，其穩定性與一實驗上所提出的結果相符。而在置換成GD次序後，胜月太 鏈的結構明顯變得不穩定，顯示此置換會影響骨架的二面角，支鏈的位向以及氫鍵的生成，甚至整個結構的穩定性。
最後，在研究整個蛇毒蛋白分子CTX2和CTX3的構形轉換上，我們使用Locally Enhanced Sampling方法(簡稱LES)模擬。利用LES方法可以多次複製以及自行選定複製區域的優點，克服骨架上能障較高的部位，成功地從CTX3轉換為CTX2構形。而CTX2並未完全轉換為CTX3結構，其因素包括：不佳的起始構形，Pro 30和Pro 33對β34骨架二面角之影響等，以及β34構形轉換受到兩旁β12和β5牽制的立體障礙等，文中將討論這些因素。

Ubiquitin is a protein of abundant experimental data for stability and folding/unfolding studies. It consists of five beta + one helix strands. The N-terminal segment of Res1-17 is one of the few cases where a short peptide can populate the monomeric beta hairpin conformation in aqueous solution. In the present study, we carried out molecular dynamics (MD) simulation to examine conformational stability for this peptide and its mutants using GB/SA solvation model. Delection of glycine at turn segment of this ubiquitin peptide destabilizes the β-hairpin as observed in experiment. In addition, we replaced the turn segment of TLTGK with several turn-location-favored segments, including NPDGT, NG, AG, and, GD, in this peptide. The simulation results shows that the TLTGK is more stable than NPDGT segment for this beta hairpin peptide, consistent with experimental observation. Other turn mutations also showed less stability compared with the original TLTGK segment in this ubiquitin peptide.
In addition, we carried out a folding MD simulation of a peptide of NG turn and non-polar residues on the strands at 300 K. Starting from unfolded structure, the trajectory showed that the beta hairpin formed at 50 ps and maintains up to 1.6 ns. The fast folding is consistent with experimental observation. With a mutation of GD segment with NG segment, the beta hairpin structure significantly destablized. The backbone dihedral angles, orientation of side chains and formation of hydrogen bonds will be reported and analyzed.
Finally, we examined the conformational transition between two cardiotoxins, CTX2 and CTX3, which differ six residues in their sequence. The simulation results show that the mutation from CTX3 to CTX2 can get close to CTX2 structure but not reverse. With implement of a locally enhanced sampling (LES) method, the conformational transition is enhanced to some extend. The factors influencing the simulated results, including presence of prolines, steric effect etc., will be
analyzed and discussed.

Alexeev, D., and Sawyer, L., Biochem. J. 1994, 299, 159-163.
Allen, M. and Tildesley, D. Computer simulation of liquids. 1989, Oxford Science Publications, Oxford.
Alonso, D. and Daggett, V. Protein Science 1998, 7, 860-874.
Anderson AG, Hermans J., Proteins, 1998, 3, 262-265
Arunkumar, A., Kumar, T., and Yu. C. Biochim. Biophys. Acta. 1997, 1338, 69-76.
Axe, D. D., Foster, N. W., and Fersht, A. R. J. Mol. Biol., 1999, 286, 1471-1485
Babu, K. R., Moradian, A., and Douglas, D. J. J. Am. Soc. Mass. Spectrom 2001, 12, 317-328
Bhaskaran, P., Huang, C. C., Tsai, Y. C., Jayaraman, G., Chang, D. K., and Yu, C. J. Biol. Chem. 1994, 269, 23500-23508.
Bhaskaran, R., Yu, C., and Yang, C. J. Protein Chem. 1994c, 13, 503-504.
Blanco, F. J., Jimenez, M. A., Rico. M., Santoro. J., Herranz. J., and Nieto. J. L., Eur. J. Biochem. 1991, 200, 345-351
Blanco, F. J., Jimenez, M. A., Rico. M., Santoro. J., Herranz. J., and Nieto. J. L., J. Am. Chem. Soc. 1993, 115, 5887-5888
Blanco, F. J.; Rivas, G.; Serrano, L. Nat. Struct. Biol. 1994, 1, 584-590.
Blasie, C. A.; Berg, J. M. Biochemistry, 1997, 36, 6218-6222.
Bonvin, A. M. and Gunsteren, W. F., J. Mol. Biol. 2000, 296, 255-268
Borer, P. N., LaPlante, S. R., Kumer, A., Zanatta, N., Martin, A., Hakkinen, A., and Levy, G. C. Biochemistry, 1994, 33, 2441-2450.
Buyong M. and Ruth N. J. Mol. Biol. 2000, 296, 1091-1104.
Chan. A.W. E., Hutchinson, E. G., Harris, D., and Thornton, J. M., Protein Sci. 1993, 2,1574-1590
Chandrasekhar, K., Profy. A. T., and Dyson, H. J., Biochemistry 1991, 30,9187-9194
Cheatham, T., and Kollman, P. J. Am. Chem. Soc. 1997b, 119, 4805-4825.
Cheatham, T., and Kollman, P. Structure. 1997a, 5, 1297-1311.
Cheatham, T., Crowley, M., Fox, T., and Kollman, P. Proc. Natl. Acad. Sci. USA 1997a, 94, 9626-9630.
Cheatham, T., Miller, J., Fox, T., and Kollman, P. J. Am. Chem. Soc. 1995, 117, 4193-4194.
Chen, P.Y., Gopalacushina, B.G., Yang, C.C., Chan, S.I., and Evans, P.A., Protein Science. 2001, 10, 2063-2074
Chien, K. Y., Chiang, C. M., Hseu, Y. C. Vyas, A. A., Rule, G. S., Wu, W. G. J. Biol. Chem. 1994, 269, 14473-14483.
Chien, K. Y., Huang, W. N., Jean, J. H., and Wu, W. G. J. Biol. Chem. 1991, 266, 3252-3259.
Ciechanover, A. EMBO J. 1998, 17, 7150-7160
Cieplak, P., Cheatham, T., Kollman, P. J. Am. Chem. Soc. 1997, 119, 6722-6730.
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merx, Jr. K. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A., J. Am. Chem. Soc. 1995,117, 5179.
Daggett, V., and Levitt, M. J. Mol. Biol. 1992, 223, 1121-1138.
Daggett, V., and Levitt, M. J. Mol. Biol. 1993, 232, 600-619.
Daggett, V., Li, A., Itzhaki, L. S., Otzen, D. E., and Fersht, A. R., J. Mol. Biol. 1996, 257, 430-440
Darden, T., York, D., and Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092.
de Alba, E., Jimenez, M. A.; Rico, M., and Nieto, J. L., Folding & Design 1996, 1, 133-144
de Alba, E.; Jimenez, M. A.; Rico, M. J. Am. Chem. Soc. 1997, 119, 175-183
de Alba, E., Rico, M., and Jimenez, M. A., Protein Sci. 1999, 8, 2234-2244
Demand, J., Alberti, S., Patterson, C., and Höhfeld, J., Current Biology, 2001, 11, 1569-1577
Dill, K. Biochemistry 1990, 29, 7133-7155.
Dill, K., Bromberg, S., Yue, K., Fiebig, K., Yee, D., Thomas, P., and Chan, H. Protein Sci. 1995, 4, 561-602.
Duan, Y. and Kollman, P. Science 1998, 282, 740-744.
Dyson, H. J., Cross, K. J., Houghten, R. A., Wilson, I. A., Wright, P. E., and Lemer, R. A., Nature 1985, 318, 480-483
Elber, R., Karplus, M. J. Am. Chem. Soc. 1990, 112, 9161.
Ervin, J., Sabelko, J., Gruebele, M., J. Photochem. Photobiol. B: Biol, 2000, 54, 1-15
Ewald, P. Ann. Phys. 1921, 64, 253-287.
Fernandez A., Colubri, A., Appignanesi, G., and Burastero, T., Physica A, 2001, 293, 358-384
Galluzzi, L., Paiardini, M., Lecomte, M. C., and Magnani, M. FEBS letters 2001, 489, 254-258.
Garicia, A., Hummer, G., and Soumpasis, D. Proteins 1997, 27, 471-480.
Griffiths-Jones, S. R., Maynard, A. J., and Searle, M. S., J. Mol. Biol. 1997, 273, 898-912
Griffiths-Jones, S. R., Maynard, A. J., and Searle, M. S., J. Mol. Biol. 1999, 292, 1051-1069
Hamilton, K. S., Ellison, M. J., Barber, K. R., Williams, R. S., Huzil, J. T., McKenna, S., Ptak, C., Glover, M., and Shaw, G. S., Structure, 2001, 9, 897-904
Haque, T. S.; Gellman, S. H. J. Am. Chem. Soc. 1997, 119, 2303-2304
Jang, J., Kumar, T., Jayaraman, G., Yang, P., and Yu, C. Biochemistry 1997, 36, 14635-14641.
Jayaram, B., Liu, Y., Beveridge, D. J. Chem. Phys. 1998, 109, 1465.
Jayaram, B., Sprous, D., and Beveridge, D. L., J Phys. Chem. B , 1998,102,9571-9576
Jayaraman, F., Kumar, T., and Yu, C. Annual meeting of Chinese Chemical Society 1997.
Johnson, E. C., Lazar, G. A., Desjarlais, J., and Handel, T. M., Structure, 1999, 7, 967-976
Kemp, D. S.; Oslick, S. L.; Allen, T. J. J. Am. Chem. Soc. 1996, 118, 4249-4250.
Khorasanizadeh, S., Peters, I. D., Butt,T. R., and Roder, H., Biochemistry, 1993, 32, 7054-7063
Kim, K., Ramanathan, R., and Frieden, C., Protein Sci. 1997, 6, 364-372
Kumar, T. K. S., Lee, C. S., and Yu, C. Natural Toxins 1996, pages 115-129.
Kumar, T., Jayaraman, G., Lee, C., Arunkumar, A., Sivaraman, T., Samuel, D., and Yu, C. J. Biolmol. Struc. Dyna. 1997, 15, 431-463.
Kumar, T., Jayaraman, G., Lee, C., Sivaraman, T., Lin, W., and Yu, C. Biophys. Res. Commun. 1995, 207, 536-543.
Kumar, T., Pandian, S., Jayaraman, G., Peng, H., Yu, C. Proc. Natl. Sci. Counc. ROC(A) 1999, 23, 1-19.
Lee, C., Kumar, T., Lian, L., Cheng, J., and Yu. C. Biochemistry, 1998, 37, 155-164.
Lenkinski, R. E., Chen, D. M., Gilckson, J. D., and Goldstein, G., Biochim. Biophys. Acta. 1997,494,126-130
Levy, R. M., Karplus, M., and Wolynes, P. G. J. Am. Chem. Soc. 1981, 103, 5998-6011.
Maynard, A. J., Sharman, G. J., Searle, M. S., J. Am. Chem. Soc. 1998, 120, 1996-2007
Miller, J. and Kollman, P. J. Mol. Biol. 1997, 270, 436-450.
Miller-White, E. J., and Poet, R., Trends Biochem. Sci. 1987,12,189-192
Muñoz, V.; Serrano, L. Proteins 1994, 20, 301-311.
Muñoz, V.; Thompson, P.A.; Hofrichter, J.; Eaton, W.A. Nature 1997, 390, 196-199.
O’Connell, J., Bougis, P., and Wuthrich, K. Eur. J. Biochem. 1993, 213, 891-900.
Olejniczak, E. T., Dobson, C. M., Karplus, M., and Levy, R. M. J. Am. Chem. Soc. 1984, 106, 1923-1930.
Palmer, A. G. and Case, D. A. J. Am. Chem. Soc. 1992, 114, 9059-9067.
Palmer, A., Rance, M., and Wright, P. J. Am. Chem. Soc. 1991, 113, 4371-4380.
Patel, H. V., Vyas, A. A., Vyas, K. A., Liu, Y. S., Chiang, C. M., Chi, L. M. and Wu, W. G. J. Biol. Chem. 1997, 272, 1484-1492.
Pearlman, D., Case, D., Caldwell, J., Ross, W., Cheatham, T., DeBolt, S., Ferguson, D., Seibel, G., and Kollman, P., AMBER6.0 Univ. of Cal., San Francisco, San Francisco, 1999.
Peng, S. S., Kumar, T. K. S., Jayaramna, G., Chang, C. C., and Yu, C. J. Biol. Chem. 1997, 272, 7817-7823.
Predki, P. F., Agrawal, V., Brunger, A. T., and Regan, L., Nat. Struct. Biol. 1996, 3,54-58
Prevost, M., Wodak, S., Tidor, B., Karplus, M. Proc. Natl. Acad, Sci. USA 1991, 88, 10880-10884.
Ramirez-Alvarado, M.; Blanco, F. J.; Niemann, H.; Serrano, L. J. Mol. Biol., 1997, 273, 898-912.
Ramirez-Alvarado, M.; Blanco, F. J.; Serrano, L. Nature Struct. Biol., 1996, 3, 604-612.
Ramirez-Alvarado, M.; Serrano, L., and Blanco, F. J., Protein Sci. 1997, 6,162-174
Roitberg, A., Elber, R. J. Chem. Phys. 1991, 95, 9277-9287.
Searle, M. S.; Zerella, R.; Williams, D. H.; Packman, L. C. Protein Eng. 1996, 9, 559-565.
Searle, M. S.; Williams, D. H., and Packman, L. C., Nature Struct. Biol., 1995, 2, 999-1006.
Sharman, G. J., Searle, M. S., J. Am. Chem. Soc. 1998, 120, 5291-5300
Shin, H. C., Merutka, G., Waltho, J. P., Wright, P. E., and Dyson, H. J., Biochemistry 1993, 32, 6348-6355
Sibanda, B. L.; Blundell, T. L.; Thornton, J. M. J. Mol. Biol. 1989, 206, 759-777.
Sibanda, B. L., and Thornton, J. M., Methods Enzylmol 1991, 202, 59-82
Simmerling, C., Elber, R. J. Am. Chem. Soc. 1994, 116, 2534.
Simmerling, C., Fox, T., Kollman, P. A. J. Am. Chem. Soc. 1998a, 120, 5771.
Simmerling, C., Lee, M., Ortiz, A., Kolinski, A. Skolnick, J. Kollman, P. J. Am. Chem. Soc. 2000, 122, 8392-8402.
Simmerling, C., Miller, J. L., Kollman, P. A. J. Am. Chem. Soc. 1998b, 120, 7149-7155.
Singhal, A. K., Chien, K. Y., Wu, W., and Rule, G. S., Biochemistry 1993, 32, 8036.
Sivaraman, T., Kumar, T. and Yu, C. Biological Macromolecules 1996, 19, 235-239.
Sivaraman, T., Kumar, T. K. S., Chang, D., Lin, W., and Yu, C. J. Biol. Chem. 1998, 273, 10181-10189.
Smith, P. E., van Schaik, R. C., Szyperski, T., Wuthrich, K., and van Gunsteren, W. F. J. Mol. Biol. 1995, 246, 356-365.
Spector, T., Cheatham, T., and Kollman, P. J. Am. Chem. Soc. 1997, 119, 7095-7104.
Still, W. C., Tempczak, A., Hawley, R. C., Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127.
Sue, S. C., Rajan, P. K., Chen, T. S., Hsieh, C. H., and Wu, W., Biochemistry 1997, 32, 9826.
Sunada, S. and Go, N. J. Chem. Phys. 1996, 44, 4768-4775.
Sung, S. S. Biophys. J. 1994, 66, 1796-1803.
Sung, S. S. Biophys. J. 1999, 76, 164-175.
Sung, S. S.; Wu, X. W. Proteins 1996, 25, 202-214.
Surewicz, W., Stepanik, T., Szabo, A., and Mantsch, H. J. Biol. Chem. 1988, 263, 786-790.
Vijay-kumar, S., Bugg, C. E., and Cook, W. J., J. Mol. Biol. 1987, 194. 531-544
Wang, H. and Sung, S. S. J. Am. Chem. Soc. 2000, 122, 1999-2009.
Wang, H. and Sung, S. S. Biopolymers. 1999a, 50, 7, 763-776
Wang, H.; Varady, J.; Ng, L.; Sung, S. S. Proteins 1999b, 37, 325-333.
Wang L., Duan, Y., Shortle, R., IMPERIALI, B., and Kollman, P. A., Protein Science, 1999c, 8, 1292-1304
Weerasinghe, S., Smith, P., Mohan, V., Chemg, Y., and Pettitt, B. J. Am. Chem. Soc. 1995, 117, 2147-2158.
Zerella, R., Evans, P. A., lonides, J. M. C., Williams, D. H., Trotter, B. W., and Mackay, J. P., Protein Science, 1999, 8, 1320-1331
吳姿嫻，國立台灣師範大學碩士論文， 2001