Publications - John Philo

Publications - Philo

Philo, J. S. (2011). Limiting the sedimentation coefficient for sedimentation velocity data analysis: Partial boundary modeling and g(s( *)) approaches revisited. Anal. Biochem. 412, 189-202.

Arakawa, T., Ejima, D., Li, T., and Philo, J. S. (2010). The critical role of mobile phase composition in size exclusion chromatography of protein pharmaceuticals. J. Pharm. Sci. 99, 1674-1692.

Ogawa, H., Qiu, Y., Philo, J. S., Arakawa, T., Ogata, C. M., and Misono, K. S. (2010). Reversibly bound chloride in the atrial natriuretic peptide receptor hormone-binding domain: Possible allosteric regulation and a conserved structural motif for the chloride-binding site. Protein Sci. 19, 544-557.

Philo, J. S. and Arakawa, T. (2009). Mechanisms of protein aggregation. Curr. Pharm. Biotechnol. 10, 348-351.

Philo, J. S. (2009). A critical review of methods for size characterization of non-particulate protein aggregates. Curr. Pharm. Biotechnol. 10, 359-372.

Costantino, H. R., Culley, H., Chen, L., Morris, D., Houston, M., Roth, S., Phoenix, M. J., Foerder, C., Philo, J. S., Arakawa, T., Eidenschink, L., Andersen, N. H., Brandt, G., and Quay, S. C. (2009). Development of Calcitonin Salmon Nasal Spray: Similarity of peptide formulated in chlorobutanol compared to benzalkonium chloride as preservative. J. Pharm. Sci. 98, 3691-3706.

Arakawa, T., Philo, J. S., Ejima, D., Sato, H., and Tsumoto, K. (2007). Aggregation analysis of therapeutic proteins, part 3: Principles and optimization of field-flow fractionation (FFF). Bioprocess International 5 (10), 52-70. [PDF]

Heavner, G. A., Arakawa, T., Philo, J. S., Calmann, M. A., and Labrenz, S. (2007). Protein isolated from biopharmaceutical formulations cannot be used for comparative studies: Follow-up to "a case study using Epoetin Alfa from Epogen and EPREX". J. Pharm. Sci. 96, 3214-3225.

Arakawa, T., Philo, J. S., Ejima, D., Tsumoto, K., and Arisaka, F. (2007). Aggregation analysis of therapeutic proteins, part 2: Analytical ultracentrifugation and dynamic light scattering. Bioprocess International 5 (4), 36-47. [PDF]

Berkowitz, S. A. and Philo, J. S. (2007). Monitoring the homogeneity of adenovirus preparations (a gene therapy delivery system) using analytical ultracentrifugation. Anal. Biochem. 362, 16-37.

Ejima, D., Tsumoto, K., Fukada, H., Yumioka, R., Nagase, K., Arakawa, T., and Philo, J. S. (2007). Effects of acid exposure on the conformation, stability, and aggregation of monoclonal antibodies. Proteins 66, 954-962.

Arakawa, T., Philo, J. S., Ejima, D., Tsumoto, K., and Arisaka, F. (2006). Aggregation analysis of therapeutic proteins, part 1: General aspects and techniques for assessment. Bioprocess International 4 (10), 42-49. [PDF]

Philo JS. (2006) Is Any Measurement Method Optimal for All Aggregate Sizes and Types?. AAPS Journal. 8(3): E564-E571. [PDF]

Philo, J. S. (2006). Improved methods for fitting sedimentation coefficient distributions derived by time-derivative techniques. Anal. Biochem. 354, 238-246.

Philo, J.S. (2005). Analytical ultracentrifugation. In: Methods for Structural Analysis of Protein Pharmaceuticals. W. Jiskoot and D. Crommelin, eds. AAPS Press, pp. 379-412.

Tsumoto, K., Umetsu, M., Kumagai, I., Ejima, D., Philo, J. S., and Arakawa, T. (2004). Role of arginine in protein refolding, solubilization, and purification. Biotechnol. Prog. 20, 1301-1308.

Philo, J. S., Yang, T. H., and LaBarre, M. (2004). Re-examining the oligomerization state of macrophage migration inhibitory factor (MIF) in solution. Biophys. Chem. 108, 77-87.

Philo, J. S. (2003). Characterizing the aggregation and conformation of protein therapeutics. Amer. Biotech. Lab. 21, 22-26. [PDF]

Yokoyama, K., Ejima, D., Kita, Y., Philo, J. S., and Arakawa, T. (2003). Structure of folding intermediates at pH 4.0 and native state of microbial transglutaminase. Biosci. Biotechnol. Biochem. 67, 291-294.

Arakawa, T. and Philo, J. S. (2002). Biophysical and biochemical analysis of recombinant proteins. In: Pharmaceutical Biotechnology, 2nd edition. D. J .A. Crommelin and R. D. Sindelar, eds. Taylor & Francis, London, pp. 25-51.

Ishibashi, M., Arakawa, T., Philo, J.S., Sakashita, K., Yonezawa, Y., Tokunaga, H., and Tokunaga, M. (2002) Secondary and quaternary structural transition of the halophilic archaeon nucleoside diphosphate kinase under high- and low-salt conditions. FEMS Microbiol. Lett. 216, 235-241.

Li, T., Yamane, H., Arakawa, T., Narhi, L.O., and Philo, J.S. (2002). Effect of the intermolecular disulfide bond on the conformation and stability of glial cell line-derived neurotrophic factor. Protein Eng 15, 59-64.

Kendrick, B. S., Kerwin, B. A., Chang, B. S., and Philo, J. S. (2001). Online size-exclusion high-performance liquid chromatography light scattering and differential refractometry methods to determine degree of polymer conjugation to proteins and protein-protein or protein-ligand association States. Anal. Biochem. 299, 136-146.

Philo, J.S. (2001). Analytical ultracentrifugation. In 'The BioPharm Guide to Bioanalytical Methods' (Advanstar Communications, Cleveland OH), pp. 52-54.

Tokunaga, M., Shiraishi, Y., Odachi, M., Mizukami, M., Tokunaga, H., Philo, J. S., Arakawa, T., Ishibashi, M., Tanaka, R., and Takagi, H. (2001). Molecular cloning of groESL locus, and purification and characterization of chaperonins, GroEL and GroES, from Bacillus brevis. Biosci. Biotechnol. Biochem. 65, 1379-1387.

Arakawa, T., Philo, J. S., and Kita, Y. (2001). Kinetic and thermodynamic analysis of thermal unfolding of recombinant erythropoietin. Biosci. Biotechnol. Biochem. 65, 1321-1327.

Wen, J., Zhang, M., Horan, T.P., Philo, J.S., Li, T.S., Wypych, J., Mendiaz, E.A., Langley, K.E., Aoki, K.H., Kuwamoto, M., Kita, Y., and Arakawa, T. (2001). Copper staining method for extracting biologically active proteins from native gels. Biosci. Biotechnol. Biochem. 65, 1315-1320.

Philo, J.S. (2000). Improving sedimentation equilibrium analysis of mixed associations using numerical constraints to impose mass or signal conservation. Methods. Enzymol. 321, 100-120.

Wato, S., Kamei, K., Arakawa, T., Philo, J.S., Wen, J., Hara, S., and Yamaguchi, H. (2000). A chimera-like alpha-amylase inhibitor suggesting the evolution of Phaseolus vulgaris alpha-amylase inhibitor. J. Biochem. (Tokyo) 128, 139-144.

Philo, J.S. (2000). A method for directly fitting the time derivative of sedimentation velocity data and an alternative algorithm for calculating sedimentation coefficient distribution functions. Anal. Biochem. 179, 151-163.

Philo, J.S. (1999). Overview of the Quantitation of Protein Interactions. In Current Protocols in Protein Science, vol. 2 (John Wiley & Sons, New York), pp. 20.1.1-20.1.13.

Arakawa, T. and Philo, J. (1999). [Applications of Analytical Ultracentrifuge to Molecular Biology and Pharmaceutical Science]. Yakugaku Zasshi 119, 597-611.

Danilenko, D. N., Montestruque, S., Philo, J. S., Li, T. S., Hill, D., Speakman, J., Bahru, M., Zhang, M. S., Konishi, O., Itoh, N., Chirica, M., Delaney, J., Hernday, N., Martin, F., Hara, S., Talvenheimo, J., Narhi, L. O., and Arakawa, T. (1999). Recombinant rat fibroblast growth factor-16: Structure and biological activity. Arch. Biochem. Biophys. 361, 34-46.

Hsu, Y. R., Nybo, R., Sullivan, J. K., Costigan, V., Spahr, C. S., Wong, C., Jones, M., Pentzer, A. G., Crouse, J. A., Pacifici, R. E., Lu, H. S., Morris, C. F., and Philo, J. S. (1999). Heparin is essential for a single keratinocyte growth factor molecule to bind and form a complex with two molecules of the extracellular domain of its receptor. Biochemistry 38, 2523-2534.

Narhi, L. O., Philo, J. S., Sun, B., Chang, B. S., and Arakawa, T. (1999). Reversibility of heat-induced denaturation of the recombinant human megakaryocyte growth and development factor. Pharmaceutical Research 16, 799-807.

Li, T., Narhi, L. O., Wen, J., Philo, J. S., Sitney, K., Inoue, J., Yamamoto, T., and Arakawa, T. (1998). Interactions between NFkappaB and its inhibitor ikappaB: biophysical characterization of a NFkappaB/ikappaB-alpha complex. J. Protein Chem. 17, 757-763.

Philo, J. S. and Hensley, P. (1998). Integrating analytical ultracentrifugation with other experimental approaches: a case study on erythropoietin interactions with its receptor. Chemtracts 11, 969-979.

Rosenfeld, R. D., Zeni, L., Welcher, A. A., Narhi, L. O., Hale, C., Marasco, J., Delaney, J., Gleason, T., Philo, J. S., Katta, V., Hui, J., Baumgartner, J., Graham, M., Stark, K. L., and Karbon, W. (1998). Biochemical, biophysical, and pharmacological characterization of bacterially expressed human agouti-related protein. Biochemistry 37, 16041-16052.

Horan, T. P., Martin, F., Simonet, L., Arakawa, T., and Philo, J. S. (1997). Dimerization of granulocyte-colony stimulating factor receptor: the Ig plus CRH construct of granulocyte-colony stimulating factor receptor forms a 2:2 complex with a ligand. J. Biochem. (Tokyo) 121, 370-375.

Kolvenbach, C. G., Narhi, L. O., Philo, J. S., Li, T., Zhang, M., and Arakawa, T. (1997). Granulocyte-colony stimulating factor maintains a thermally stable, compact, partially folded structure at pH2. J.Pept.Res. 50, 310-318.

Nakaguchi, T., Arakawa, T., Philo, J. S., Wen, J., Ishimoto, M., and Yamaguchi, H. (1997). Structural characterization of an a-amylase inhibitor from a wild common bean (Phaseolus vulgaris): Insight into the common structural features of leguminous a-amylase inhibitors. J. Biochem. (Tokyo) 121, 350-354.

Narhi, L. O., Rosenfeld, R., Shimamoto, G., Lee, R., Hawkins, N., Li, T., Philo, J. S., Wen, J., and Arakawa, T. (1997). Comparison of solution properties of human and rat ciliary neurotrophic factor. J. Pept. Res. 50, 300-309.

Narhi, L. O., Aoki, K. H., Philo, J. S., and Arakawa, T. (1997). Changes in conformation and stability upon formation of complexes of erythropoietin (EPO) and soluble EPO receptor. J. Prot. Chem. 16, 213-225.

Philo, J. S. (1997). Probing receptor-ligand interactions by sedimentation equilibrium. Proceedings of SPIE 2985, 170-177.

Philo, J. S. (1997). An improved function for fitting sedimentation velocity data for low-molecular-weight solutes. Biophys. J. 72, 435-444.

Poppe, L., Brown, G. S., Philo, J. S., Nikrad, P. V., and Shah, B. H. (1997). Conformation of sLe^x tetrasaccharide, free in solution and bound to E-, P-, and L-selectin. J. Amer. Chem. Soc. 119, 1727-1736.

Wen, J., Arakawa, T., Wypych, J., Langley, K. E., Schwartz, M. G., and Philo, J. S. (1997). Chromatographic determination of extinction coefficients of non-glycosylated proteins using refractive index (RI) and UV absorbance (UV) detectors: Applications for studying protein interactions by size exclusion chromatography with light-scattering, UV, and RI detectors. In 'Techniques in Protein Chemistry VIII.' (Ed D. R. Marshak.) pp. 113-119. (Academic Press: San Diego.)

Arakawa, T., Li, T., Philo, J. S., Narhi, L. O., Horan, T. P., and Osslund, T. D. (1996). Characterization of granulocyte-colony stimulating factor: structure and interactions with its receptor. EOS J. Immunol. Immunopharmacol. 16, 35-40.

Hill, J. S., Davis, R. C., Yang, D., Wen, J., Philo, J. S., Poon, P. H., Phillips, M. L., Kempner, E. S., and Wong, H. (1996). Human hepatic lipase subunit structure determination. J. Biol. Chem. 271, 22931-22936.

Horan, T. P., Wen, J., Narhi, L. O., Parker, V., Garcia, A., Arakawa, T., and Philo, J. S. (1996). Dimerization of the extracellular domain of granulocyte-colony stimulating factor receptor by ligand binding: A monovalent ligand induces 2:2 complexes. Biochemistry 35, 4886-4896.

Kasahara, K., Hayashi, K., Arakawa, T., Philo, J. S., Wen, J., Hara, S., and Yamaguchi, H. (1996). Complete sequence, subunit structure, and complexes with pancreatic alpha-amylase of an alpha-amylase inhibitor from Phaseolus vulgaris white kidney beans. J. Biochem. (Tokyo) 120, 177-183.

Kita, Y., Tseng, J., Horan, T. P., Wen, J., Philo, J. S., Chang, D., Ratzkin, B., Pacifici, R., Brankow, D., Hu, S., Luo, Y., Wen, D., Arakawa, T., and Nicolson, M. (1996). ErbB receptor activation, cell morphology changes, and apoptosis induced by anti-Her2 monoclonal antibodies. Biochem. Biophys. Res. Commun. 226, 59-69.

Narhi, L. O., Philo, J. S., Li, T. S., Zhang, M., Samal, B., and Arakawa, T. (1996). Induction of a-helix in the b-sheet protein tumor necrosis factor-a: Acid-induced denaturation. Biochemistry 35, 11454-11460.

Narhi, L. O., Philo, J. S., Li, T. S., Zhang, M., Samal, B., and Arakawa, T. (1996). Induction of a-helix in the b-sheet protein tumor necrosis factor-a: Thermal- and trifluoroethanol-induced denaturation at neutral pH. Biochemistry 35, 11447-11453.

Philo, J. S., Wen, J., Wypych, J., Schwartz, M. G., Mendiaz, E. A., and Langley, K. E. (1996). Human stem cell factor dimer forms a complex with two molecules of the extracellular domain of its receptor, kit. J. Biol. Chem. 271, 6895-6902.

Philo, J. S., Dreyer, U., and Lary, J. W. (1996). Quaternary structure dynamics and carbon monoxide binding kinetics of hemoglobin valency hybrids. Biophys. J. 70, 1949-1965.

Philo, J. S., Aoki, K. H., Arakawa, T., Narhi, L. O., and Wen, J. (1996). Dimerization of the extracellular domain of the erythropoietin (EPO) receptor by EPO: One high-affinity and one low-affinity interaction. Biochemistry 35, 1681-1691.

Wen, J., Arakawa, T., Talvenheimo, J., Welcher, A. A., Horan, T. P., Kita, Y. A., Tseng, J., Nicolson, M., and Philo, J. S. (1996). A light scattering/size exclusion chromatography method for studying the stoichiometry of a protein-protein complex. In 'Techniques in Protein Chemistry VII.' pp. 23-31. (Academic Press: San Diego)

Wen, J., Arakawa, T., and Philo, J. S. (1996). Size-exclusion chromatography with on-line light-scattering, absorbance, and refractive index detectors for studying proteins and their interactions. Anal. Biochem. 240, 155-166.

Wen, J., Hsu, E., Kenney, W. C., Philo, J. S., Morris, C. F., and Arakawa, T. (1996). Characterization of keratinocyte growth factor binding to heparin and dextran sulfate. Arch. Biochem. Biophys. 332, 41-46.

Arakawa, T., Holst, P., Narhi, L. O., Philo, J. S., Wen, J., Prestrelski, S. J., Zhu, X. T., Rees, D. C., and Fox, G. M. (1995). The importance of Arg40 and 45 in the mitogenic activity and structural stability of basic fibroblast growth factor: Effects of acidic amino acid substitutions. Journal of Protein Chemistry 14, 263-274.

Horan, T. P., Wen, J., Arakawa, T., Liu, N., Brankow, D., Hu, S., Ratzkin, B., and Philo, J. S. (1995). Binding of Neu differentiation factor with the extracellular domain of Her2 and Her3. J. Biol. Chem. 270, 24604-24608.

Lu, H. S., Chang, D., Philo, J. S., Zhang, K., Narhi, L. O., Liu, N. L., Zhang, M., Sun, J. L., Wen, J., Yanagihara, D., Karunagaran, D., Yarden, Y., and Ratzkin, B. (1995). Studies on the structure and function of glycosylated and nonglycosylated neu differentiation factors - similarities and differences of the alpha-isoform and beta-isoform. J. Biol. Chem. 270., 4784-4791.

Arakawa, T., Haniu, M., Narhi, L. O., Miller, J. A., Talvenheimo, J., Philo, J. S., Chute, H. T., Matheson, C., Carnahan, J., Louis, J.-C., Yan, Q., Welcher, A. A., and Rosenfeld, R. (1994). Formation of heterodimers from 3 neurotrophins, nerve growth- factor, neurotrophin-3, and brain-derived neurotrophic factor. J. Biol. Chem. 269, 27833-27839.

Arakawa, T., Philo, J. S., and Kenney, W. C. (1994). Structure and solubility of interleukin-2 in sodium dodecyl sulfate. International Journal of Peptide and Protein Research 43, 583-587.

Arakawa, T., Wen, J., and Philo, J. S. (1994). Stoichiometry of heparin binding to basic fibroblast growth factor. Arch. Biochem. Biophys. 308, 267-273.

Dismukes, G. C., Zheng, M., Hutchins, R., and Philo, J. S. (1994). The inorganic biochemistry of photosynthetic water oxidation. Biochemical Society Transactions 22, 323-327.

Philo, J. S. (1994). Measuring sedimentation, diffusion, and molecular weights of small molecules by direct fitting of sedimentation velocity concentration profiles. In 'Modern analytical ultracentrifugation.' (Eds T. M. Schuster and T. M. Laue.) pp. 156-170. (Birkhauser: Boston.)

Philo, J. S., Talvenheimo, J., Wen, J., Rosenfeld, R., Welcher, A. A., and Arakawa, T. (1994). Interactions of neurotrophin-3 (NT-3), brain-derived neurotrophic factor (BDNF), and the NT-3/BDNF heterodimer with the extracellular domains of the TrkB and TrkC receptors. J. Biol. Chem. 269, 27840-27846.

Arakawa, T., Wen, J., and Philo, J. S. (1993). Densimetric determination of equilibrium binding of sucrose octasulfate with basic fibroblast growth factor. Journal of Protein Chemistry 12, 689-693.

Narhi, L. O., Rosenfeld, R., Wen, J., Arakawa, T., Prestrelski, S. J., and Philo, J. S. (1993). Acid-induced unfolding of brain-derived neurotrophic factor results in the formation of a monomeric "A state". Biochemistry 32, 10819-10825.

Philo, J. S., Rosenfeld, R., Arakawa, T., Wen, J., and Narhi, L. O. (1993). Refolding of brain-derived neurotrophic factor from guanidine hydrochloride: Kinetic trapping in a collapsed form which is incompetent for dimerization. Biochemistry 32, 10812-10818.

Rosenfeld, R., Philo, J. S., Haniu, M., Stoney, K., Rohde, M. F., Wu, G.-M., Narhi, L. O., Wong, C., Boone, T., Hawkins, N. N., Miller, J. M., and Arakawa, T. (1993). Sites of iodination in recombinant human brain-derived neurotrophic factor and its effect on neurotrophic activity. Protein Science 2, 1664-1674.

Windsor, W. T., Philo, J. S., Potschka, M., and Schuster, T. M. (1992). Kinetics of oxygen binding and subunit assembly for the hemoglobin alpha subunit. Biophysical Chemistry 43 , 61-71.

Tso, J., Sivaraja, M., Philo, J. S., and Dismukes, G. C. (1991). Ca²⁺ depletion from the photosynthetic Water Oxidizing Complex reveals photooxidation of a protein residue. Biochemistry 30, 4740-4747.

Baumgarten, M., Philo, J. S., and Dismukes, G. C. (1990). Mechanism of photoinhibition of photosynthetic water oxidation by Cl^- depletion and F^- substitution: Oxidation of a protein residue. Biochemistry 29, 10814-10822.

Baumgarten, M., Tso, J., Marino, J., Sivaraja, M., Lin, C. P., Dismukes, G. C., Sheats, J. E., Gast, P., and Philo, J. S. (1990). EPR, magnetic susceptibility, and ENDOR studies of the Water Oxidizing Complex and dimanganese models: Consequences of chloride exchange and calcium depletion. In 'Current Research in Photosynthesis, vol. 1.' (Ed M. Baltscheffsky.) pp. 953-956. (Kluwer Academic Publishers: Dordrecht, The Netherlands.)

Philo, J. S. and Lary, J. W. (1990). Kinetic investigations of the quaternary enhancement effect and alpha/beta differences in binding the last oxygen to hemoglobin tetramers and dimers. J. Biol. Chem. 265, 139-143.

Sivaraja, M., Philo, J. S., Lary, J. W., and Dismukes, G. C. (1989). Photosynthetic oxygen evolution: Changes in magnetism of the water oxidizing enzyme. J. Amer. Chem. Soc. 111, 3221-3225.

Day, E. P. and Philo, J. S. (1988). The development of the superconducting susceptometer and its biophysical applications. In 'Near zero: New frontiers of physics.' (Eds J. D. Fairbank, B. S. Deaver, C. W. F. Everitt, and P. F. Michelson.) pp. 442-455. (W. H. Freeman: New York.)

Philo, J. S., Lary, J. W., and Schuster, T. M. (1988). Quaternary interactions in hemoglobin beta subunits: Kinetics of ligand binding and self-assembly. J. Biol. Chem. 263, 682-689.

Philo, J. S. and Dreyer, U. (1985). Quaternary structure has little influence on spin-states in mixed-spin human methemoglobins. J. Biol. Chem. 263, 682-689.

Philo, J. S., Dreyer, U., and Schuster, T. M. (1984). Diamagnetism of human apo-, oxy-, and CO-hemoglobin. Biochemistry 23, 865-872.

Philo, J. S., Adams, M. L., and Schuster, T. M. (1981). Association-dependent absorption spectra of oxyhemoglobin A and its subunits. J. Biol. Chem. 256, 7917-7924.

Philo, J. S. and Fairbank, W. M. (1980). Temperature dependence of the diamagnetism of water. Journal of Chemical Physics 72, 4429-4433.

Philo, J. S. (1977). Kinetics of hemoglobin-carbon monoxide reactions measured with a superconducting magnetometer: A new method for fast reactions in solution. Proc. Nat. Acad. Sci. USA 74, 2620-2623.

Philo, J. S. and Fairbank, W. M. (1977). A high sensitivity magnetic susceptometer employing superconducting technology. Review of Scientific Instruments 48, 1529-1536.