研究生: |
嚴正奇 Jeng-chiy Yian |
---|---|
論文名稱: |
心臟毒蛋白之分子動力學模擬:蛋白質反折疊 Molecular Dynamics Simulations of Cardiotoxins: Protein Unfolding |
指導教授: |
孫英傑
Sun, Ying-Chieh |
學位類別: |
碩士 Master |
系所名稱: |
化學系 Department of Chemistry |
畢業學年度: | 87 |
語文別: | 中文 |
論文頁數: | 110 |
中文關鍵詞: | 分子動力學模擬 、台灣眼鏡蛇心臟毒蛋白 、蛋白質反折疊 、展開路徑 、疏水聚集現象 、中間態結構 、變異 |
英文關鍵詞: | Molecular Dynamics Simulation, Cardiotoxins, Protein unfolding, unfolding pathway, hydrophobic clustering effect, intermediate, mutation |
論文種類: | 學術論文 |
相關次數: | 點閱:345 下載:0 |
分享至: |
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報 |
台灣眼鏡蛇毒液心臟毒蛋白是一個具有60個胺基酸殘基,結構上僅具由五個β股所形成的雙股與三股β摺板二級結構,分子中有四個雙硫鍵連接分子的骨架結構。本論文利用升溫分子動力學模擬方法以檢視鹼性的台灣眼鏡蛇毒CTXⅢ於水溶液中展開的情形。模擬的結果顯示,於天然結構中所形成β1與β2間的氫鍵,於計算平衡結構時就不再形成,因此說明於CTXⅢ中β1-β2形成的雙股β摺板較β3-β4-β5所形成的三股β摺板結構不穩定,此模擬得到現象與實驗得到的結果相符合;可能因為三股β摺板間的氫鍵間的合作效應較雙股β摺板結構間的氫鍵明顯,而幫助穩定三股β摺板的結構。另外根據RMSD、二維構形簇、氫鍵的分析並觀察模擬軌跡中之結構變化得到的資訊,建議CTXⅢ的展開在β1與β2的結構展開後,可能經由兩個主要的路徑展開;此二可能路徑為經過β3與β4間的氫鍵先斷或是β3與β5間的氫鍵先斷的的中間態,由於可能的氫鍵之合作效應作用於兩兩β股間的氫鍵,因此得到此二中間態。另外計算所有軌跡之非極性胺基酸支鏈的旋度半徑之後並建議於摺疊的先期發現有疏水聚集的效應。並透過計算α螺旋的二級結構,建議於展開路徑中可能形成α螺旋結構之CTXⅢ的胺基酸片段。本論文中另外亦對計算與實驗的結果相關性進行討論。最後,我們亦進行了CTXⅡ與R36A CTXⅢ變異的模擬,這些結果並與得到的CTXⅢ結果進行比較,希望這些資料可以幫助對CTXⅢ展開的了解。
Thermal denaturation molecular dynamics simulation of cardiotoxin III from Taiwan cobra venom in solution were carried out to examine the unfolding of this small basic protein of 60 amino acids. The simulations showed that the hydrogen bonds between b1-b2 sheet loosed in the computed equilibrium structure, showing that the stability of b1-b2 sheet is weaker than b3-b5 sheet, consistent with experimental results. This should be due to the larger cooperation effect of hydrogen bonds in the latter larger b-sheet. Based on the results of RMSD, 2D-conformational analysis, breaking/formation of H-bonds, and observation of structure along the computed MD trajectories, the present simulations suggest that the unfolding of CTX III might go through two main pathways: after the b1-b2 sheet turns into a loop, either the hydrogen bonds between b3 and b4 strands or the b3 and b5 strands break first due to the cooperative effect of hydrogen bonds between two strands. Calculation of radius of gyration for non-polar residues along the trajectories suggests a hydrophobic clustering in the early stage of folding. A calculation of a-helix structure in the unfolding trajectories gave the segments of residues which may form a-helix in the folding/unfolding pathway(s). Other calculated results were correlated with experimental results and discussed. Finally, we carried out the simulations for CTX II and R36A CTX III mutant as well. The results were discussed and compared with the results of CTX III, and hope these results give a better understanding of the unfolding of CTXs.
Agashe, V., Shastry, M., and Udgaonkar, J. (1995). Initial hydrophobic collapse in
the folding of barstar. Nature, 377:754--757.
Allen, M. and Tildesley, D. (1989). Computer simulation of liquids. Oxford Science
Publications, Oxford.
Bai, V., Milne, J., Mayne, L., and Englander, S. (1993). Primary structure effects on
peptide group hydrogen exchange. Proteins: Struc. Func. Genet., 17:75--85.
Berendsen, H., Postma, J., van Gunsteren, W., DiNola, A., and Haak, J. (1984).
Molecular dynamics with coupling to an external both. J. Chem. Phys., 81:3684--
3690.
Bertsch, R., Vaideh, N., Chan, S., and III, W. G. (1998). Kinetic steps for alpha-helix
formation. Proteins, 33:3:343--357.
Bhaskaran, R., Huang, C., Chang, D., and Yu, C. (1994a). Cardiotoxin iii from
the taiwan cobra (naja naja atra) determination of structure in solution and
comparison with short neurotoxins. J. Mol. Biol., 235:1291--1301.
Bhaskaran, R., Huang, C. C., Tsai, Y. C., Jayaraman, G., Chang, D. K., and Yu,
C. (1994b). Cardiotoxin ii from taiwan cobra venom, naja naja atra. structure
in solution and comparison among homologous cardiotoxins. J. Biol. Chem.,
269:23500--23508.
Bhaskaran, R., Yu, C., and Yang, C. (1994c). Solution structures and functional
implications of the toxins from taiwan cobra venom, naja naja atra. J. Protein
Chem., 13:503--504.
Bilwes, A., Rees, B., Moras, D., Menea, R., and Menez, A. (1994). X-ray structure
at 1.55 a of toxin r, a cardiotoxin from naja nigricollis venom, crystal packing
reveals a model for insertion into membranes. J. Mol. Biol., 239:122--136.
Bishop, M. and Saltiel, C. (1993). Radius of gyration of uniform h-comb polymers in
two and three dimensions. J. Chem. Phys., 99:9170--9171.
Brooks, C. (1993). Molecuar simulations of peptide and protein unfolding: in quest
of a molten globule. Curre. Opio. Struc. Biol., 3:92--98.
Caflisch, A. and Karplus, M. (1994). Molecular dynamics simulation of protein denat-
uration: solvation of the hydrophobic cores and secondary structure of barnase.
Proc. Natl. Acad. Sci. USA, 91:1746--1750.
Caflisch, A. and Karplus, M. (1995). Acid and thermal denaturation of barnase in-
vestigated by molecular dynamics simulations. J. Mol. Biol., 252:672--708.
Chiang, C. (1996). The role of acidic amino acid residues in the structure of cardiotoxin
and it's membrane related activities. Ph.D. thesis.
Chien, K. Y., Chiang, C. M., Hseu, Y. C., Vyas, A. A., Rule, G. S., and Wu, W.
(1994). Two distinct types of cardiotoxin as revealed by the structure and activity
relationship of their interaction with zwitterionic phospholipid dispersions. J.
Biol. Chem., 269:14473--14483.
Daggett, V., Kollman, P., and Kuntz, I. (1991). A molecular dynamics simulaiton
of polyalanine: an analysis of equilibrium motions and helix-coil trasitions. Bi-
opolymers, 31:1115--1134.
Daggett, V. and Levitt, M. Realistic simulations of native-protein dynamics in solution
and beyond. Annu. Rev. Biophys. Biomol. Struct. ,volume=.
Daggett, V. and Levitt, M. (1991). A molecular dynamics simulation of the c-terminal
fragment of the l7/l12 ribosomal protein in solution. Chem. Phys., 158:501--512.
Daggett, V. and Levitt, M. (1992). Molecular dynamics simulations of helix denatur-
ation. J. Mol. Biol., 223:1121--1138.
Daggett, V. and Levitt, M. (1993). Protein unfolding pathways explored through
molecular dynamics simulations. J. Mol. Biol., 232:600--619.
Daggett, V., Li, A., Itzhaki, L., Otzen, D., and Fersht, A. (1996). Structure of the
transition state for folding of a protein derived from experiment and simulation.
J. Mol. Biol., 257:430--440.
Darden, T., York, D., and Pedersen, L. (1993). Particle mesh ewald - an n.log(n)
method for ewald sums in large systems. J. Chem. Phys., 98:10089--10092.
Diamond, R. (1974). Real-space refinement of the structure of hen egg-white lysozyme.
J. Mol. Biol., 82:371--391.
Dill, K. (1990). Dominant forces in protein folding. Biochemistry, 29:7133--7155.
Dill, K. (1993). Folding proteins: finding a needle in a haystack. Curr. Opin. Struct.
Biol., 3:99--103.
Dill, K., Bromberg, S., Yue, K., Fiebig, K., Yee, D., Thomas, P., and Chan, H. (1995).
Principles of protein folding - a perspective from simple exact models. Protein
Science, 4:561--602.
Dinner, A., Sali, A., and Karplus, M. (1996). The folding mechanism of larger model
proteins: role of native structure. Proc. Natl. Acad. Sci. USA, 93:8356--8361.
Dobson, C., Sali, A., and Karplus, M. (1998). Protien folding: A perspective from
theory and experiment. Angew. Chem. Int. Ed., 37:868--893.
Duan, Y. and Kollman, P. (1998). Pathways to a protein folding intermediate observed
in a 1-microsecond simulation in aqueous solution. Science, 282:740--744.
Duan, Y., Wilkosz, P., Crowley, M., and Rosenberg, J. (1997). Molecular dynamics
simulation study of dna dodecamer d(cgcgaattcgcg) in solution: conformation and
hydration. J. Mol. Biol., 272:4:553--572.
Dufton, M. and Hider, R. (1988). Structure and pharmacology of elapid cytotoxins.
Pharmacol Ther., 36:1--40.
Feig, M. and Pettitt, B. (1999). Modeling high-resolution hydration patterns in cor-
relation with dna sequence and conformation. J. Mol. Biol., 286:4:1075--1095.
Ferrin, T., Huang, C., Jarvis, L., and Langrige, R. (1988). The midas display system.
J. Mol. Graphics, 6:13--27.
Fersht, A. R. (1995). Optimization of rates of protein folding: The nucleation-
condensation mechanism and its implications. Proc. Natl. Acad. Sci. USA,
92:10869--10873.
Garcia, A., Hummer, G., and Soumpasis, D. (1997). Hydration of an alpha-helical
peptide: comparison of theory and molecular dynamics simulation. Proteins,
27:471--480.
Gilquin, B., Roumestand, C., Zinn-Justin, S., Menez, A., and Toma, F. (1993). Re-
fined three-dimentional solution structure of a snake cardiotoxin: analysis of the
side-chain organization suggests the existence of a possible phospholipid binding
site. Biopolymer, 33:1959--1675.
Itzhaki, L., Neira, J., Gay, J., and Fersht, A. (1995). Search for nucleation sites in
smaller fragments of chymotrypsin inhibitor 2. J. Mol. Biol., 254:289--304.
Jahnke, W., Mierke, D., Beress, L., and Kessler, H. (1994). Structure of cobra cardi-
otoxin ctxi as derived from nuclear magnetic resonance spectroscopy and distance
geometry calculations. J. Mol. Biol., 240:445--458.
Jang, J., Kumar, T., Jayaraman, G., Yang, P., and Yu, C. (1997). Comparison of the
hemolytic activity and solution structures of two snake venom cardiotoxin ana-
logues which only differ in their n-terminal amino acid. Biochemistry, 36:14635--
14641.
Jayaraman, G. (1998). Stability and ligand binding studies of cardiotoxin analogue
II from Taiwan cobra (Naja naja atra) Venom. Tsing-Hwa University, Taiwan.
Ph.D. Thesis.
Jayaraman, G., Kumar, T., Arunkumar, A. I., and Yu, C. (1996a). Trifluoroethanol
induces helical conformation in an all fi-sheet protein. Biochem. Biophys. Res.
Commun., 222:33--37.
Jayaraman, G., Kumar, T., Sivaraman, T., Lin, W., Chang, D., and Yu, C. (1996b).
Thermal denaturation of an all fi-sheet protein -- identification of a stable partially
structured intermediate at high temperature. Biol. Macromolecules, 18:303--306.
Kabsch, W. and Sander, C. (1983). Dictionary of protein secondary structure: pattern
recognition of hydrogen-bonded and geometrical features. Biopolymers, 22:2577--
2637.
Karplus, M. and Sali, A. (1995). Theoretical studies of protein folding and unfolding.
Curr. Opin. Struct. Biol., 5:58--73.
Karplus, M. and Weaver, D. (1994). Protein folding dynamics: The diffusion-collision
model and experimental data. Protein Sci., 3:650--668.
Kazmirski, S. and Daggett, V. (1998). Non-native interactions in protein folding
intermediates: molecular dynamics simulation of hen lysozyme. J. Mol. Biol.,
284:793--806.
Kim, P. and Baldwin, R. (1982). Specific intermediates in the folding reactions of small
proteins and the mechanism of protein folding. Annu. Rev. Biochem, 51:459--489.
Kumar, T., Jayaraman, G., Lee, C., Arunkumar, A., Sivaraman, T., Samuel, D.,
and Yu, C. (1997). Snake venom cardiotoxins-structure, dynamics, function and
folding. J. Biolmol. Struc. Dyna., 15:431--463.
Kumar, T., Jayaraman, G., Lee, C., Sivaraman, T., Lin, W., and Yu, C. (1995).
Identification of 'molten globule' like state in an all fi-sheet protein. Biochem.
Biophys. Res. Commun., 207:536--543.
Kumar, T., Pandian, S., Jayaraman, G., Peng, H., and Yu, C. (1999). Understanging
the structure, function and folding of cobra toxins. Proc. Natl. Sci. Counc.
ROC(A), 23:1:1--19.
Lazaridis, T. and Karplus, M. (1997). 'new view' of protein folding reconciled with
the old through multiple unfolding simulations. Science, 278:1928--1931.
Lee, C., Chang, C., Chiu, P., Tseng, T., and Lee, S. (1968). Pharmocological prop-
erties of cardiotoxin isolated from formosan cobra venom. Naunyn-Schmidebergs
Arch. Pharmak. Exp. Path., 259:360--374.
Lehninger, A., Nelson, D., and M.M.Cox (1993). Principles of Biochemistry - Second
Edition. Worth, New York.
Levinthal, C. (1968). Are there pathways for protein folding? Chim. Phys., 65:44--45.
Levitt, M. (1981). Molecular dynamics of hydrogen bonds in bovine pancreatic trypsin
inhibitor protein. Nature, 294:379--380.
Levitt, M. (1983). Molecular dynamics of native protein ii. analysis and nature of
motion. J. Mol. Biol., 168:621--657.
Li, A. and Daggett, V. (1994). Characterization of the transition state of protein
unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2. Proc. Natl.
Acad. Sci. USA, 91:10430--10434.
Li, A. and Daggett, V. (1996). Identification and characterization of the unfolding
transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations.
J. Mol. Biol., 257:412--429.
Li, A. and Daggett, V. (1998). Molecular dynamics simulation of the unfolding of
barnase: Characterization of the major intermediate. J. Mol. Biol., 275:677--694.
O'Conell, J., Bougis, P., and Wuthrich, K. (1993). Drtermination of the nuclear-
magnetic-resonance solution structure of cardiotoxin ctx iib from naja mos-
sambica mossambica. Eur. J. Biochem., 213:891--900.
Otting, G., Steinmetz, W., Bougis, P., Rochat, H., and Wuthrich, K. (1987). Sequence-
specific 1h-nmr assignments and determination of the secondary structure in
aqueous soluteion of the cardiotoxins ctxiia and ctxiib from naja mossambica
mossambica. Eur. J. Biochem., 168:609--620.
Pappu, R. and Weaver, D. (1998). The early folding kinetics of apomyoglobin. Protein
Science, 7:480--480.
Pearlman, D., Case, D., Caldwell, J., Ross, W., Cheatham, T., DeBolt, S., Ferguson,
D., Seibel, G., and Kollman, P. (1995). AMBER4.1. Univ. of Cal., San Francisco,
San Francisco.
Plotkin, S., Wang, J., and Wolynes, P. (1997). Statistical mechanics of a correlated
energy landscape model for protein folding funnels. J. Chem. Phys., 106:2932--
2948.
Prevost, M. and Ortmans, I. (1997). Refolding simulations of an isolated fragment of
barnase into a native-like beta hairpin: Evidence for compactness and hydrogen
bonding as concurrent stabilizing factors. Proteins, 29:212--227.
Prevost, M., Wodak, S., Tidor, B., and Karplus, M. (1991). Contribution of the hydro-
phobic effect to protein stability: analysis based on simulations of the ile96!ala
mutation in barnase. Proc. Natl. Acad. Sci. USA, 88:10880--10884.
Pugliese, L., Prevost, M., and Wodak, S. (1995). Unfolding simulations of the 85-102
beta-hairpin of barnase. J. Mol. Biol., 251:432--447.
Rees, B. and Bilwes, A. (1993). Three-dimensional structures of neurotoxins and
cardiotoxins. Chem. Res. Toxicol., 6:385--406.
Rees, B., Bilwes, A., Samama, J., and Moras, D. (1990). Cardiotoxin v(ii)4 from naja
mossambica mossambica. the refined crystal structure. J. Mol. Biol., 214:281--
297.
Richard, F. (1977). Areas, volumes, packing and protein structure. Ann. Rev. Biophys.
Bioeng., 6:151--176.
Rose, G. and Wolfenden, R. (1993). Hydrogen bonding, hydrophobicity, packing, and
protein folding. Ann. Rev. Biophys. Biomol. Struc., 22:381--415.
Sali, A., Shakhnovich, E., and Karplus, M. (1994). How does a protein fold? Nature,
369:248--251.
Serrano, L., Matouschek, A., and Fersht, A. (1992). The folding of an enzyme iii.
structure of the transition state for unfolding of barnase analysed by a protein
engineering procedure. J. Mol. Biol., 224:805--818.
Sharman, G. and Searle, M. (1998). Cooperative interaction between the three strands
of a designed antiparallel beta-sheet. J. Am. Chem. Soc., 120:5291--5300.
Singhal, A. K., Chien, K. Y., Wu, W., and Rule, G. S. (1993). Solution structure of
cardiotoxin v from naja naja atra. Biochemistry, 32:8036--8044.
Sivaraman, T., Kumar, T., Jayaraman, G., and Yu, C. (1997a). The mechan-
ism of 2,2,2-trichloroacetic acid-induced protein precipitation. J Protein Chem,
14:4:291--297.
Sivaraman, T., Kumar, T., and Yu, C. (1996). Destabilisation of native tertiary struc-
tural interactions is linked to helix-induction by 2,2,2-trifluoroethanol in proteins.
Biological Macromolecules, 19:235--239.
Sivaraman, T., Kumar, T. K. S., Chang, D., Lin, W., and Yu, C. (1998). Events
in the kinetic folding pathway of a small, all-fi-sheet protein. J. Biol. Chem.,
273:17:10181--10189.
Sivaraman, T., Kumar, T. K. S., Jayarman, G., Han, C. C., and Yu, C. (1997b).
Characterization of a partially structured state in an all-fi-sheet protein. Biochem.
J., 321:457--464.
Socci, N., Onuchic, J., and Wolynes, P. (1998). Protein folding mechanisms and the
multidimensional folding funnel. Proteins, 32:136--158.
Steinmetz, W., Bougis, P., Rochat, H., Redwine, D., Baraun, W., and Wuthrich, K.
(1988). 1h nuclear-magnetic-resonance studies of the three-dimensional structure
of the cardiotoxin ctxiib from naja mossambica mossambica in aqueous solu-
tion and comparison with the crystal structures of homologous toxins. Eur. J.
Biochem., 172:101--116.
Suen, J., Escobedo, F., and de Pablo, J. (1997). Monte carlo simulation of polymer
chain collaapse in an athermal solvent. J. Chem. Phys., 106:1288--1290.
Sun, Y., g. Wu, W., Chiang, C.-M., Hsin, A.-Y., and Hsiao, C.-D. (1996a). The
crystal structure of cardiotoxin v from taiwan cobra venom at 2.19 a resolution:
Role of water binding loop in the formation of membrane-binding site of p-type
cardiotoxins. J. Mol. Biol., 239:122--136.
Sun, Y., Veenstra, D., and Kollman, P. (1996b). Free energy calculations of the
mutation of ile96!ala in barnase: contributions to the difference in stability.
Protein Engineering, 9:273--281.
Surkar, N. (1947). Isolation of cardiotoxin from cobra venom (naja tripudians, mono-
cellate variety. J. Ind. Chem. Soc., 24:227--232.
van Gunsteren, W. F. and Berendsen, H. J. C. (1977). Algorithms for macromolecular
dynamics and constraint dynamics. Mol. Phys., 34:1311--1327.
Wong, C., Chen, Y.-H., Hung, M.-C., Wan, K.-T., Ho, C.-L., and Lo., T.-B. (1978).
Renaturation of a reduced taiwan cobra cardiotoxin. Biochim. Biophys. Acta,
533:105--111.
Yang, A. and Honig, B. (1995a). Free energy determinants of secondary structure
formation:i. alpha-helices. J. Mol. Biol., 252:351--365.
Yang, A. and Honig, B. (1995b). Free energy determinants of secondary structure
formation:ii. antiparallel beta-sheets. J. Mol. Biol., 252:366--376.
Yang, S. (1998). Molecular dynamics simulation of cardiotoxins. Master thesis.
Yapa, K. and Weaver, D. (1996). Protein folding dynamics: application of the
diffusion-collision model to the folding of a four-helix bundle. J. Phys. Chem.,
100:2498--2509.
Zwanzig, R. (1997). Effect of close contacts on the radius of gyration of a polymer.
J. Chem. Phys., 106:2824--2827.