PUBLISHED WORK

"Grid Workflow Software for High-Throughput Proteome Annotation Pipeline." Birnbaum, A., Hayes, J., Li, W. W., Miller, M. A., Arzberger, P.W., Bourne, P. E. & Casanova, H. Springer-Verlag GmbH Grid Computing in Life Science: First International Life Science Grid Workshop, LSGRID 2004, Kanazawa, Japan, May 31-June 1, 2004, Akihiko Konagaya, Kenji Satou eds 3370, 68 - 76 (2005).

"The Encyclopedia of Life Project: Grid Software and Deployment." W.W. Li, R.W. Byrnes, J. Hayes, V.M. Reyes, A. Birnbaum, A. Shahab, C. Mosley, D. Pekurovsky, G.B. Quinn, I.N. Shindyalov, H. Casanova, L. Ang, F. Berman, M.A. Miller, P.E. Bourne Special Issue on Grid Systems for Life Sciences. New Generation Computing, 22, 127-136 (2004).

“Crystal structure of a zinc-containing glycerol dehydrogenase (TM0423) from Thermotoga maritima at 1.5 angstrom resolution” Brinen, L. S., Canaves, J. M., Dai, X. P., Deacon, A. M., Elsliger, M. A., Eshaghi, S., Floyd, R., Godzik, A., Grittini, C., Grzechnik, S. K., Guda, C., Jaroszewski, L., Karlak, C., Klock, H. E., Koesema, E., Kovarik, J. S., Kreusch, A., Kuhn, P., Lesley, S. A., McMullan, D., McPhillips, T. M., Miller, M. A., Miller, M. D., Morse, A., Moy, K., Ouyang, J., Robb, A., Rodrigues, K., Selby, T. L., Spraggon, G., Stevens, R. C., van den Bedem, H., Velasquez, J., Vincent, J., Wang, X. H., West, B., Wolf, G., Taylor, S. S., Hodgson, K. O., Wooley, J., & Wilson, I. A. Proteins-Structure Function and Genetics 50, 371-374 (2003).

“Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 angstrom resolution” Kuhn, P., Lesley, S. A., Mathews, I. I., Canaves, J. M., Brinen, L. S., Dai, X. P., Deacon, A. M., Elsliger, M. A., Eshaghi, S., Floyd, R., Godzik, A., Grittini, C., Klock, H. E., Koesema, E. Kovarik, J. M., Kreusch, A. T., McMullan, D., McPhillips, T. M., Miller, M. A., Miller, M., Morse, A., Moy, K., Ouyang, J., Robb, A., Rodrigues, K., Selby, T. L. Spraggon, G., Stevens, R. C., Taylor, S. S., van den Bedem, H., Velasquez, J., Vincent, J., Wang, X. H., West, B., Wolf, G., Wooley, J., & Wilson, I. A. Proteins-Structure Function and Genetics 49, 142-145 (2003).

“Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline” Lesley, S. A., Kuhn, P.,Godzik, A., Deacon, A. M., Mathews, I., Kreusch, A., Spraggon, G., Klock, H. E., McMullan, D., Shin, T., Vincent, J., Robb, A., Brinen, L. S., Miller, M. D., McPhillips, T. M., Miller, M. A., Scheibe, D., Canaves, J. M., Guda, C., Jaroszewski, L., Selby, T. L., Elsliger, M. A., Wooley, J., Taylor, S. S., Hodgson, K. O., Wilson, I. A., Schultz, P. G., & Stevens, R. C. Proc. Natl Acad Sci USA. 99; 11664-11669 (2002).

"Role of the low-affinity binding site in electron transfer from cytochrome c to cytochrome c peroxidase” Mei, H. K., Geren, L.,Miller, M. A.,Durham, B., & Millett, F. Biochemistry 41, 3968-3976 (2002).

“Role of Configurational Gating in Intracomplex Electron Transfer from Cytochrome c to the Radical Cation in Cytochrome c Peroxidase." Mei, H., Wang, K., Peffer, N., Weatherly, G., Cohen, D.S., Miller, M., Pielak, G., Durham, B., Millett, F. Biochemistry 38, 6846-6854 (1999).

"Fluoride Binding in Heme Proteins: the Importance of Distal Cavity Structure" Neri, F., Kok, D, Miller, M.A., & Smulevich, G. Biochemistry 36, 8947‑8953 (1997).

"The Horse Cytochrome c/Cytochrome c Peroxidase Complex: Effect of Binding Site Mutations on the Thermodynamics of Complex Formation" Erman, J.E., Kresheck, G.C., Vitello, L.B., & Miller, M.A. Biochemistry 36, 4054‑4060 (1997).

"A Complete Mechanism for Steady‑state Oxidation of Yeast Cytochrome c by Cytochrome c Peroxidase" Miller, M.A. Biochemistry 35, 15791‑15799 (1996).

"Design of a Ruthenium‑Cytochrome c Derivative to Measure Electron Transfer to the Radical Cation and Oxyferryl Heme in Cytochrome c Peroxidase" Wang, K., Mei, H., Geren, L., Miller, M.A., Saunders, A., Wang, X., Pielak, G. J., Durham, B., & Millett, F. Biochemistry 35, 15107‑15119 (1996).

"Identifying the Physiological Electron Transfer Site of Cytochrome c Peroxidase by Structure-Based Engineering" Miller, M.A., Geren, L., Han, G.W., Saunders, A., Beasley, J., Pielak, G., Durham, B., Millett, F., & Kraut, J. Biochemistry 35, 667 ‑ 673 (1996).

"Electron Transfer Reaction Between Cytochrome c and Cytochrome c Peroxidase" Millett, F., Durham, B., Geren, L., Miller, M., & Kraut, J. J. Bioenerg. Biomemb. 27,  341 ‑351 (1995).
 
"Regulation of Interprotein Electron Transfer By Trp 191 of Cytochrome c Peroxidase" Miller, M.A., Erman, J. E., & Vitello, L.B. Biochemistry 34, 12048‑12058 (1995).

"Photooxidation of Trp 191 in Cytochrome c Peroxidase by Ruthenium‑cytochrome c Derivatives" Liu, R.‑Q., Hahm, S., Durham, B., Miller, M.A., & Millett, F. Biochemistry 34, 973‑983 (1995).

"A Cation Binding Site Stabilizes the Compound I Radical of Cytochrome c Peroxidase" Miller, M.A., Han, G.W. & Kraut, J. Proc. Nat. Acad. Sci. USA 91, 11118‑1112 (1994).

"The Crystal Structure of Oxy‑peroxidase as a Model for the Transient Enzyme:Peroxide Complex" Miller, M.A., Shaw, A., & Kraut, J. Nature Structural Biology 1, 524‑531 (1994).

"Role of Methionine 230 in Intramolecular Electron Transfer Between the Oxyferryl Heme Fe(IV) and Trp 191 in Cytochrome c Peroxidase Compound 111" Liu, R.‑Q., Hahm, S., Miller, M.A., Geren, L., Hibdon, S., Kraut, J., Durham, B., & Millett, F. Biochemistry 33, 8678‑8685 (1994).

"Interaction Domain for the Reaction of Cytochrome c with the Radical and the Oxyferryl Heme in Cytochrome c Peroxidase Compound I" Miller, M.A., Hahm, S., Liu, R.‑Q., Geren, L., Hibdon, S., Kraut, J., Durham, B., &Millett, F. Biochemistry 33, 8686‑8693 (1994).

"Reaction of Horse Cytochrome c with the Radical and the Oxyferryl Heme in Cytochrome c Peroxidase Compound I" Hahm, S., Miller, M.A., Geren, L., Kraut, J., Durham, B., & Millett, F. Biochemistry 33, 1473‑1480 (1994).

"Histidine 52 is a Critical Residue for Rapid Formation of Cytochrome c Peroxidase Compound I" Erman, J.E., Vitello, L.B., Miller, M.A., Shaw, A., Brown, K.A., & Kraut, J. Biochemistry 32, 9798‑9806 (1993).

"The Effect of Arginine 48 Replacement on the Reaction of Cytochrome c Peroxidase and Hydrogen Peroxide" Vitello, L.B., Erman, J.E., Miller, M.A., Wang, J., & Kraut, J. Biochemistry 32, 9807‑9818 (1993).

"Effect of Asp 235 ‑> Asn Substitution on the Absorption Spectrum and Hydrogen Peroxide Reactivity of Cytochrome c Peroxidase" Vitello, L.B., Erman, J.E., Miller, M.A., Mauro, J.M., & Kraut, J. Biochemistry 31, 11524‑11535 (1992).

"Active‑Site Mutations in Cytochrome c Peroxidase: A Critical Role for Histidine‑52 in the Rate of Formation of Compound I" Erman, J.E., Vitello, L.B., Miller, M.A., & Kraut, J. J. Am. Chem. Soc. 114, 6592‑6593 (1992).

"Reaction of Ferrous Cytochrome c Peroxidase with Dioxygen: Site‑Directed Mutagenesis Provides Evidence for Rapid Reduction of Dioxygen by Intramolecular Electron Transfer from the Compound I Radical Site" Miller, M.A., Bandyopadhyay, D., Mauro, J.M., Traylor, T.G., & Kraut, J. Biochemistry 31, 2789‑2797 (1992).

"Effects of Mutagenesis at Trp 191 on the Peroxide‑Dependent Oxidation of Cytochrome c by Cytochrome c Peroxidase" Miller, M.A. & Kraut, J. FASEB Journal 6, Al 17

"Conformational Change and Control of Heme Chemistry in Cytochrome c Peroxidase: Resonance Raman Evidence from Leu‑52 and Gly‑181 Mutants of Cytochrome c Peroxidase" Smulevich, G., Miller, M.A., Kraut, J., & Spiro, T.G. Biochemistry 30, 9546‑9558 (1991).

"The Compound I Radical in Site‑Directed Mutants of Cytochrome c Peroxidase as Probed by Electron Paramagnetic Resonance (EPR) and Electron Nuclear Double Resonance (ENDOR)" Fishel, L.A., Farnum, M.F., Mauro, J.M., Miller, M.A., Kraut, J., Liu, Y., Tan, X., & Scholes, C.P. Biochemistry 29,1986‑1996 (1990).

"CO Dissociation in Cytochrome c Peroxidase: Site Directed Mutagenesis Shows That Arg 48 Influences CO Dissociation Rates" Miller, M.A., Mauro, J.M., Smulevich, G., Coletta, M., Kraut, J., & Traylor, T.G. Biochemistry 29, 9978‑9988 (1990).

"CO Recombination in Cytochrome c Peroxidase: Effect of the Local Heme Environment on CO Binding Explored Through Site‑Directe Mutagenesis" Miller, M.A. Coletta, M., Mauro, J.M., Putnam, L.D., Farnum, M.F., Kraut, J., & Traylor, T.G. Biochemistry 29, 1777‑1791 (1990).

"Photodissociable Endogenous Ligand in Alkaline‑Reduced Cytochrome c Peroxidase Implicates Distal Protein Tension" Smulevich, G., Miller, M.A., Gosztola, D., & Spiro, T.G. Biochemistry 28, 9905‑9908 (1989).

"Exploring Structure‑Function Relationships in Yeast Cytochrome c Peroxidase Using Mutagenesis and Crystallography" Mauro, J.M., Miller, M.A., Edwards, S.L., Wang, J., Fishel, L.A., & Kraut, J. in Metal Ions in Biological Systems, (Helmut Sigel, ed.), vol. 25 Marcel Dekker, New York, pp 477‑503 (1989).

"Site-directed mutagenesis of yeast cytochrome c peroxidase shows Histidine 181 is not required for oxidation of ferrocytochrome c." Miller M.A., Hazzard J.T., Mauro J.M., Edwards, S.L., Simons, P.C., Tollin, G., & Kraut, J. Biochemistry 27, 9081-9088 (1988).

"Where is the radical in compound I of cytochrome c peroxidase? Clues from crystallography and mutagenesis." Edwards, S.L., Mauro, J.M.; Fishel L.A., Wang, J., Miller, M.A., Xuong N.-H., & Kraut, J. Prog. Clin. Biol. Res. 274, 463-475 (1988).

"Characterization of the pathways for phosphatidylethanolamine biosynthesis in Chinese hamster ovary mutant and parental cell lines." Miller, M.A., & Kent, C. J. Biol. Chem. 261, 9753-61 (1986).