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Supplementary: I. Molecular structures of MT-2 proteins The protein metallothionein (MT-2), readily isolated from the liver and kidneys of a wide range of mammals, contains 20 cysteine residues out of total 61 amino acid residues1. MT has been well studied by a range of spectroscopic techniques and definitive information on the geometry of the metal ion binding sites has been obtained from NMR2 and X-ray-diffraction studies3. The MT molecule exhibits the unique property of binding seven metal ions in two metal clusters, named and domains. The domain of those MT-2 molecule used in this experiment contains four Cd2+ ions. The domain contains two Mn2+ and one Cd2+ ions and this metal binding cluster can also be expressed as (Mn2CdS3)3-. Figure 1 The alpha , Cd4II(SCys)11, and beta , Mn2CdII(SCys)9 domains. The seven Zn2+ ions were all replaced by two Mn2+ and five Cd 2+ ions. 1 II. Preparation of Si templates Figure 2 (a) Flow chart of the lithography, etching processes and growth of protein molecules (b) schematics of the patterned templates with nanopores. Figure 3 SEM images of patterned nanopores on the Si substrate 2 Reference 1. J.H.R. Kägi and B. Valle, J. Biol. Chem. 236, 2435 (1961). 2. D. Neuhaus, G. Wagner, M. Vašák, J.H.R. Kägi, K. Wüthrich, Eur. J. Biochem. 151, 257 (1985). 3. W.F. Furey, A.H. Robbins, L.L. Clancy, D.R. Winge, B.C. Wang and C.D. Stout, Science 231, 704 (1986). 3