近年來，蛋白質晶片儼然已成為生物檢測以及疾病診斷的重要工具，但常因
為蛋白質不適當的接合位向而使蛋白質失去功能，進而影響檢測的精確性。在本
研究中，我們提出一種將蛋白位向固定化的新方法，其中包含了兩個步驟，第一，
在遠離蛋白活性中心的地方尋找一個對接(docking)位置；第二，試著找出一個能
與此位置有很強的親和力的配體(ligand)，為了避免ligand 會與蛋白的活性中心
結合，因此希望所設定的docking 位置與活性中心附近帶有相反的電荷，又為了
增強ligand 與蛋白間的結合，於是設計的ligand 同時結合了疏水與靜電的作用力
與蛋白結合，由此可知，擬定的docking 位置附近需有疏水性的胺基酸以提供疏
水作用力，而ligand 則是透過molecular docking 的模擬所得到。
在實驗中，目標蛋白為來自於黑曲黴菌(Aspergillus niger)的葡萄糖氧化酶
(glucose oxidase，GOX)，此蛋白的活性中心以親水性胺基酸居多，因此我們以
一疏水性分子萘對GOX 作docking，藉此找出所有疏水性的區塊，再針對一結
合自由能較低的位置作性質上的分析，並發現周圍以帶正電荷的胺基酸居多，最
後根據此位置設計出有較好結合能的胺基酸LLGEG。隨後將此胜肽接枝在矽膠
體(Silica Gel，SiGel)上，並利用蛋白質的等溫吸附實驗來得到親和力的大小及活
性測試來驗證蛋白質的吸附位向。由GOX 在LLGEG-SiGel 上的等溫吸附曲線得
知GOX 與LLGEG-SiGel 的解離常數只有1.69×10-6 M。當外在離子強度下降時，
即會造成些許的GOX 因而脫附，由此可知，蛋白與ligand 間的作用，確實包含
了靜電及疏水的作用力。此外，由比活性的比較看來，位向固定化的GOX 相較
於隨機吸附於一級胺表面的GOX，比活性高了將近5 倍，因此推論GOX 可能以
活性位置曝露於外的位向吸附於LLGEG-SiGel。因此證實本研究所設計的ligand
與GOX 間具有高親和力，並且可使GOX 以合適的位向吸附於材料表面展現蛋
白質的活性，所以藉由這種研究策略可以提供一個良好的方式加強蛋白質晶片檢
測的精確性。

In the past decades, protein chips are an important tool for applying in the
examinations of bioassay and disease, but the examination efficiency of protein chips
usually decrease as immobilized protein adopting random orientation. In this study, a
new strategy for oriented immobilization of proteins was proposed. The strategy
contains two steps. The first step is to search for a docking site away from the active
site on the protein surface. The second step is trying to find a ligand that is able to
grasp the targeted site of the protein. To avoid ligand binding to the active site of
protein, the targeted docking site is selected to own opposite charges to those near the
active site. To enhance the ligand-protein binding, both hydrophobic and electrostatic
interactions need to be included. The targeted docking site should therefore contain
hydrophobic amino acids. The ligand is then selected through the help of molecular
docking simulations.
The enzyme glucose oxidase (GOX) derived from Aspergillus niger was taken
as an example for oriented immobilization. The active site of GOX is surrounded by
hydrophilic amino acids. All the possible hydrophobic sites on the surface of GOX
were evaluated by the free energy estimation through naphthalene docking. A
hydrophobic site on the opposite side of GOX’s active site was found to be positive in
net charges. A possible peptide ligand, LLGEG, was found to catch GOX by the
designated docking site. Then, the LLGEG molecules were grafted onto silica gels
and measured the affinity of GOX adsorption and the specific activity of thereby
immobilized enzymes. It was found that GOX had a dissociation constant as low as
1.69×10-6 M toward the ligand LLGEG on silica gel. The decrease in ionic strength
has little effect on desorption of GOX, which indicated the existence of hydrophobic
and electrostatic interactions between ligands and proteins. The specific activity of the
III
immobilized GOX was compared with the randomly adsorbed GOX on primary
amine containing silica gel. It was found that the orderly immobilized GOX owns a
specific activity with about five-folds as high as the one randomly adsorbed by ionic
interaction. Consequently, this new strategy for protein oriented immobilization by
designing the proper peptide ligand through the help of molecular docking is
executable.

1. Bilitewski, U., Protein-sensing assay formats and devices. Analytica Chimica Acta, 2006.
568(1-2): p. 232-247.
2. Rusmini, F., Z.Y. Zhong, and J. Feijen, Protein immobilization strategies for protein
biochips. Biomacromolecules, 2007. 8(6): p. 1775-1789.
3. Cretich, M., F. Damin, Pirri, G, Chiari, M., Protein and peptide arrays: Recent trends and
new directions. Biomolecular Engineering, 2006. 23(2-3): p. 77-88.
4. Klibanov, A. M. (1983).,Immobilized Enzymes and Cells as Practical Catalysts. Science,
1983. 219(4585): p. 722-727.
5. Silvia Ferretti, S.P., David A. Russell, Kim E. Sapsford, Self-assembled monolayers: a
versatile tool for the formulation of bio-surfaces. trends in analytical chemistry, 2000. 19:
p. 530-540.
6. Karin Busch, R.T., Single molecule research on surfaces: from analytics to construction
and back. Reviews in Molecular Biotechnology, 2001. 82: p. 3-24.
7. Jo Tominagaa, N.K., Satoshi Doia, Hirofumi Ichinoseb, Masahiro Gotoa, An enzymatic
strategy for site-specific immobilization of functional proteins using microbial
transglutaminase. Enzyme and Microbial Technology, 2004. 35: p. 613-618.
8. Cesar Mateo, G.F.n.-L., Olga Abian, Roberto Ferna´ndez-Lafuente, and and J.M. Guisa´n,
Multifunctional Epoxy Supports: A New Tool To Improve the Covalent Immobilization of
Proteins. The Promotion of Physical Adsorptions of Proteins on the Supports before Their
Covalent Linkage. Biomacromolecules, 2000. 1: p. 739-745.
9. Cesar Mateo, O.A., Roberto Fernandez-Lafuente, Jose M. Guisan, Reversible Enzyme
Immobilization via a Very Strong and Nondistorting Ionic Adsorption on Support–
55
Polyethylenimine Composites. BIOTECHNOLOGY AND BIOENGINEERING,, 2000.
68.
10. Hartmann, M., Ordered mesoporous materials for bioadsorption and biocatalysis.
Chemistry of Materials, 2005. 17(18) : p. 4577-4593.
11. Arenkov, P., A. Kukhtin, Gemmell, A., Voloshchuk, S., Chupeeva, V., Mirzabekov, A.,
Protein microchips: Use for immunoassay and enzymatic reactions. Analytical
Biochemistry, 2000. 278(2) : p. 123-131.
12. Afanassiev, V., V. Hanemann, Wolfl, S., Preparation of DNA and protein micro arrays
on glass slides coated with an agarose film. Nucleic Acids Research, 2000. 28(12) : p.
1-5.
13. Smith, C. L., J. S. Milea, Nguyen, G. H., Immobilization of nucleic acids using
biotin-strept(avidin) systems., Immobilisation of DNA on Chips Ii, 2005. 261: p. 63-90.
14. Seong, S. Y. and C. Y. Choi, Current status of protein chip development in terms of
fabrication and application. Proteomics, 2003. 3(11) : p. 2176-2189.
15. Birkert, O., H. M. Haake, Schutz, A., Mack, J., Brecht, A., Jung, G., Gauglitz, G., A
streptavidin surface on planar glass substrates for the detection of biomolecular
interaction. Analytical Biochemistry, 2000. 282(2) : p. 200-208.
16. Pavlickova, P., A. Knappik, Kambhampati, D., Ortigao, F., Hug, H., Microarray of
recombinant antibodies using a streptavidin sensor surface self-assembled onto a gold
layer. Biotechniques, 2003. 34(1) : p. 124-130.
17. Schmid, E. L., T. A. Keller, Dienes, Z., Vogel, H., Reversible oriented surface
immobilization of functional proteins on oxide surfaces. Analytical Chemistry, 1997.
69(11) : p. 1979-1985.
18. Wegner, G. J., N. J. Lee, Marriott, G., Corn, R. M., Fabrication of histidine-tagged fusion
56
protein arrays for surface plasmon resonance imaging studies of protein-protein and
protein-DNA interactions. Analytical Chemistry, 2003. 75(18) : p. 4740-4746.
19. Zhen, G. L., D. Falconnet, Kuennemann, E., Voros, J., Spencer, N. D., Textor, M.,
Zurcher, S., Nitrilotriacetic acid functionalized graft copolymers: A polymeric interface
for selective and reversible binding of histidine-tagged proteins. Advanced Functional
Materials, 2006. 16(2) : p. 243-251.
20. Hsiu-Mei Chen, W.-C.W., and Sheng-Horng Chen, A Metal-Chelating Piezoelectric
Sensor Chip for Direct Detection and Oriented Immobilization of PolyHis-Tagged
Proteins. Biotechnol. Prog., 2004. 20: p. 1237-1244.
21. Naoufel Haddour, S.C., and Chantal Gondran, Electrogeneration of a Poly(pyrrole)-NTA
Chelator Film for a ReversibleOriented Immobilization of Histidine-Tagged Proteins. J.
AM. CHEM. SOC., 2005. 127: p. 5752-5753.
22. Batalla, P., M. Fuentes, Grazu, V., Mateo, C., Fernandez-Lafuente, R., Guisan, J. M.,
Oriented covalent immobilization of antibodies on physically inert and hydrophilic
support surfaces through their glycosidic chains. Biomacromolecules, 2008. 9(2) : p.
719-723.
23. Nisnevitch, M. and M. A. Firer, The solid phase in affinity chromatography: strategies for
antibody attachment. Journal of Biochemical and Biophysical Methods, 2001. 49(1-3) : p.
467-480.
24. Phelan, M. L. and S. Nock, Generation of bioreagents for protein chips. Proteomics, 2003.
3(11) : p. 2123-2134.
25. Mathias Uhlen$QlI, B.G., Bjorn NilssonSStTeni, Gatenbeck$, LennarPt hilipsonQII, and
and M. Lindberg$, Complete Sequence of the Staphylococcal Gene EncodinPg rotein A.
THE JOURNAOFL BIOLOGICAL CHEMISTRY, 1984. 259: p. 1695-1702.
57
26. Guss, B., M. Eliasson, Olsson, A., Uhlen, M., Frej, A. K. Jornvall, H., Flock, J. I.,
Lindberg, M., Structure of the Igg-Binding Regions of Streptococcal Protein-G. Embo
Journal, 1986. 5(7) : p. 1567-1575.
27. Danczyk, R., B. Krieder, North, A., Webster, T., HogenEsch, H., Rundell, A.,
Comparison of antibody functionality using different immobilization methods.
Biotechnology and Bioengineering, 2003. 84(2) : p. 215-223.
28. Bonroy, K., F. Frederix, Reekmans, G., Dewolf, E., De Palma, R., Borghs, G., Declerck,
P., Goddeeris, B., "Comparison of random and oriented immobilisation of antibody
fragments on mixed self-assembled monolayers." Journal of Immunological Methods,
2006. 312(1-2) : p. 167-181.
29. Youngeun Kwon, Z.H., Ece Karatan, Milan Mrksich, and Brian K. Kay, Antibody Arrays
Prepared by Cutinase-Mediated Immobilization on Self-Assembled Monolayers. Anal.
Chem., 2004. 76: p. 5713-5720.
30. Seong, S. Y. and C. Y. Choi, Current status of protein chip development in terms of
fabrication and application. Proteomics, 2003. 3(11) : p. 2176-2189.
31. Anderson, G. P., M. A. Jacoby, Ligler, F. S., King, K. D., Effectiveness of protein A for
antibody immobilization for a fiber optic biosensor. Biosensors & Bioelectronics, 1997.
12(4) : 329-336.
32. Jung, Y. W., H. J. Kang, Lee, J. M., Jung, S. O., Yun, W. S., Chung, S. J., Chung, B. H.,
Controlled antibody immobilization onto immunoanalytical platforms by synthetic peptide.
Analytical Biochemistry, 2008. 374(1) : p. 99-105.
33. Hecht, H. J., H. M. Kalisz, Hendle , J., Schmid, R. D., Schomburg, D., Crystal-Structure
of Glucose-Oxidase from Aspergillus-Niger Refined at 2 .3 Angstrom Resolution. Journal
of Molecular Biology, 1993. 229(1) : p. 153-172.
58
34. Karmali, A. and P. Oliveira, Glucose 1- and 2-oxidases from fungal strains: isolation and
production of monoclonal antibodies. Journal of Biotechnology, 1999. 69(2-3) : p.
151-162.
35. Raba, J. and H. A. Mottola, Glucose-Oxidase as an Analytical Reagent. Critical Reviews
in Analytical Chemistry, 1995. 25(1) : p. 1-42.
36. Bright, H., and Appleby, M., The Ph Dependence of the Individual Step in the glucose
oxidase Reaction, J Biol Chem, 1969. 24(4) : p. 3625
37. Wohlfahrt, G., S. Witt, Hendle , J., Schomburg, D., Kalisz, H. M., Hecht, H. J., 1.8 and
1.9 angstrom resolution structures of the Penicillium amagasakiense and Aspergillus
niger glucose oxidases as a basis for modelling substrate complexes. Acta
Crystallographica Section D-Biological Crystallography, 1999. 55 : p. 969-977.
38. Bankar, S. B., M. V. Bule, Singhal, R. S., Ananthanarayan, L., Glucose oxidase - An
overview. Biotechnology Advances, 2009. 27(4) : p. 489-501.
39. J. Afseth, G. Rølla, Clinical Experiments with a Toothpaste Containing Amyloglucosidase
and Glucose Oxidase. Clinical Science, 1983. 17 : p. 472-475
40. Rasiah, I. A., K. H. Sutton, Low, F. L., Lin, H. M., Gerrard, J. A., Crosslinking of wheat
dough proteins by glucose oxidase and the resulting effects on bread and croissants. Food
Chemistry, 2005. 89(3) : p. 325-332.
41. Tzanov, T., S. A. Costa, Gubitz, G. M., Cavaco-Paulo, A., Hydrogen peroxide generation
with immobilized glucose oxidase for textile bleaching. Journal of Biotechnology, 2002.
93(1) : p. 87-94.
42. Taylor, R. D., P. J. Jewsbury, Essex, J. W., A review of protein-small molecule docking
methods. Journal of Computer-Aided Molecular Design, 2002. 16(3) : p. 151-166.