Simulations of reversible protein aggregate and crystal structure

Biophysical Journal

Volumn 70, Issue 6, 1996, Pages 2888-2902

  Patro, Sugunakar Y ^a   Przybycien, Todd M ^a  

^a Rensselaer Polytechnic Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENTROPY; HYDROPHOBICITY; PROTEIN AGGREGATION; PROTEIN IMMOBILIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SIMULATION;

EID: 0029993064     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79859-4     Document Type: Article

References (81)

1. Bam, N. B., T. W. Randolph, and J. L. Cleland. 1995. Stability of protein formulations: investigation of surfactant effects by a novel EPR spectroscopic technique. Pharm. Res. 12:2-11.
2. Becker, G. W., R. R. Bowsher, W. C. Mackellar, M. L. Poor, P. M. Tackitt, and R. M. Riggin. 1987. Chemical, physical and biological characterization of biosynthetic human growth hormone. Biotechnol. Appl. Biochem. 9:478-487.
3. 73 Asn on the interactions of sickling hemoglobins. Biochim. Biophys. Acta. 221:373-375.
4. Brems, D. N. 1988. Solubility of different folding conformers of bovine growth hormone. Biochemistry. 27:4541-4546.
5. Brems, D. N., L. A. Alter, M. J. Beckage, R. E. Chance, R. D. DiMarchi, L. K. Green, H. B. Long, A. H. Pekar, J. E. Shields, and B. H. Frank. 1992. Altering the association properties of insulin by amino acid replacement. Protein Eng. 5:527-533.
6. Brzozowski, A. M., and S. P. Tolley. 1994. Poly(ethylene)glycol monomethyl ethers - an alternative to poly(ethylene) glycols in protein crystallization. Acta. Crystallogr. D50:466-468.
7. Carter, C. W., E. T. Baldwin, and L. Frick. 1988. Statistical design of experiments for protein crystal growth and the use of a precrystallization assay. J. Cryst. Growth. 90:60-73.
8. Casal, H. L., U. Kohler, and H. H. Manisch. 1988. Structural and conformational changes of β-lactoglobulin B: an infrared spectroscopic study of the effect of pH and temperature. Biochim. Biophys. Acta. 957:11-20.
9. Chen, T. 1992. Formulation concerns of protein drugs. Drug Dev. Ind. Pharm. 18:1311-1354.
10. Chothia, C. 1976. The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105:1-14.
11. Chothia, C. 1985. Principles that determine the structure of proteins. Annu. Rev. Biochem. 53:537-572.
12. Cleland, J. L., M. F. Powell, and S. J. Shire. 1993. The development of stable protein formulations: a close look at protein aggregation, deamidation, and oxidation. Crit. Rev. Ther. Drug Carrier Syst. 10:307-377.
13. Cleland, J. L., and D. I. C. Wang. 1993. Cosolvent effects on refolding and aggregation. In Biocatalysis Design for Stability and Specificity, ACS Symposium Series. Vol. 516. M. Himmel and G. Georgiou, editors. American Chemical Society, Washington, DC.
14. Conroy, M. J., and R. E. Lovrien. 1992. Matrix coprecipiting and cocrystallizing ligands (MCC ligands) for bioseparations. J. Cryst. Growth. 122:213-222.
15. Crosio, M., J. Janin, and M. Jullien. 1992. Crystal packing in six crystal forms of pancreatic ribonuclease. J. Mol. Biol. 228:243-251.
16. Cudney, B., S. Patel, K. Weisgraber, Y. Newhouse, and A. McPherson. 1994. Screening and optimization strategies for macromolecular crystal growth. Acta Crystallogr. D50:414-423.
17. D'Arcy, A. 1994. Crystallizing proteins - a rational approach? Acta Crystallogr. D50:469-471.
18. Dasgupta, S. 1994. Statistical analyses of nonbonded interactions at protein crystal and oligomer interfaces. Ph.D. thesis. Rensselaer Polytechnic Institute, Troy, NY.
19. De Young, L. R., A. L. Fink, and K. A. Dill. 1993a. Aggregation and denaturation of apomyoglobin in aqueous urea solutions. Biochemistry. 32:3877-3886.
20. De Young, L. R., A. L. Fink, and K. A. Dill. 1993b. Aggregation of globular proteins. Acc. Chem. Res. 26:614-620.
21. Dill, K. A. 1985. Theory for the folding and stability of globular proteins. Biochemistry. 24:1501-1509.
22. Dill, K. A., D. O. V. Alonso, and K. Hutchinson. 1989. Thermal stabilities of globular proteins. Biochemistry. 28:5439-5449.
23. Durbin, S. D., and G. Feher. 1991. Simulation of lysozyme crystal growth by the Monte Carlo method. J. Cryst. Growth. 110:41-51.
24. Feder, J. 1980. Random sequential adsorption. J. Theor. Biol. 87:237-254.
25. Fenton, W. A., Y. Kashi, K. Furtak, and A. L. Horwich. 1994. Residues in chaperonin groEL required for polypeptide binding and release. Nature. 371:614-619.
26. Fernald, R. D., and S. E. Wright. 1983. Maintenance of optical quality during crystalline lens growth. Nature. 301:618-620.
27. Fields, G. B., D. O. V. Alonso, D. Stigter, and K. A. Dill. 1992. Theory for the aggregation of proteins and copolymers. J. Phys. Chem. 96: 3974-3981.
28. Franks, F., R. H. M. Hatley, and H. L. Friedman. 1988. The thermodynamics of protein stability: cold destabilization as a general phenomenon. Biophys. Chem. 31:307-315.
29. Garavito, R. M., Z. Markovic-Housley, and J. A. Jenkins. 1986. The growth and characterization of membrane protein crystals. J. Cryst. Growth. 76:701-709.
30. Garavito, R. M., and D. Picot. 1991. Crystallization of membrane proteins: a minireview. J. Cryst. Growth. 110:89-95.
31. Goldenberg, D. P., D. H. Smith, and J. King. 1983. Genetic analysis of the folding pathway for the tailspike protein of phage P22. Proc. Natl. Acad. Sci. USA. 80:7060-7064.
32. Harvey, S. C., M. Prabhakaran, B. Mao, and J. A. McCammon. 1984. Phenylalanine transfer RNA: molecular dynamics simulation. Science. 223:1189-1191.
33. He, X. M., and D. C. Carter. 1992. Atomic structure and chemistry of human serum albumin. Nature. 358:209-215.
34. Hellebust, H., M. Murby, L. Abrahmsen, M. Uhlen, and S. O. Enfors. 1989. Different approaches to stabilize a recombinant fusion protein. Biotechnology. 7:165-168.
35. 3 at 1.8 Å resolution. J. Mol. Biol. 172:109-139.
36. Ingram, V. M. 1959. Abnormal human haemoglobins. III. The chemical difference between normal and sickle cell haemoglobins. Biochim. Biophys. Acta. 36:402-411.
37. Islam, S. A., and D. L. Weaver. 1990. Molecular interactions in protein crystals: solvent accessible surface and stability. Protein Struct. Funct. Genet. 8:1-5.
38. Kabalnov, A. S., and E. D. Shchukin. 1992. Ostwald ripening theory: applications to fluorocarbon emulsion stability. Adv. Colloid. Interface Sci. 38:69-97.
39. Kadima, W., A. McPherson, M. F. Dunn, and F. A. Jurnak. 1990. Characterization of precrystallization aggregation of canavalin by dynamic light scattering. Biophys. J. 57:125-132.
40. Kam, Z., H. B. Shore, and C. Feher. 1978. On the crystallization of proteins. J. Mol. Biol. 123:539.
41. Kane, J. F., and D. L. Hartley. 1988. Formation of recombinant protein inclusion bodies in Escherichia coli. Trends Biotechnol. 6:95-101.
42. Kauzmann, W. 1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14:1-63.
43. Lewis, U. J., E. V. Cheever, and B. K. Seavey. 1969a. Aggregate-free human growth hormone. I. Isolation by ultrafiltration. Endocrinology. 84:325-331.
44. Lewis, U. J.. D. C. Parker, M. D. Okerlund, R. M. Boyar, M. Litteria, and W. P. Vanderlaan. 1969b. Aggregate-free human growth hormone. II. Physico-chemical and biological properties. Endocrinology. 84: 332-339.
45. Liang, J. N., and X. Li. 1991. Interaction and aggregation of lens crystallins. Exp. Eye Res. 53:61-66.
46. Matthews, B. W. 1968. Solvent content of protein crystals. J. Mol. Biol. 33:491-497.
47. McElroy, H. E., G. W. Sisson, W. E. Schoetlin, R. M. Aust, and J. E. Villafranca. 1992. Studies on engineering crystallizability by mutation of surface residues of human thymidylate synthase. J. Cryst. Growth. 122:265-272.
48. McPherson, A. 1990. Current approaches to macromolecular crystallization. Eur. J. Biochem. 189:1-23.
49. Mikol, V., E. Hirsch, and R. Giege. 1990. Diagnostic of precipitant for biomacromolecule crystallization by quasi-elastic light-scattering. J. Mol. Biol. 213:187-195.
50. Miller, S., J. Janin, A. M. Lesk, and C. Chothia. 1987. Interior and surface of monomeric proteins. J. Mol. Biol. 196:641-656.
51. Mitraki, A., B. Fane, C. Haase-Pettingell, J. Sturtevant, and J. King. 1991. Global suppression of protein folding defects and inclusion body formation. Science. 253:54-58.
52. Moore, W. V., and P. Leppert. 1980. Role of aggregated human growth hormone (hGH) in development of antibodies to hGH. J. Clin. Endocrinol. 51:691-697.
53. Nozaki, Y., and C. Tanford. 1971. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. J. Biol. Chem. 246:2211-2217.
54. Pangiotopoulos, A. Z. 1987. Direct determination of phase coexistence properties of fluids by Monte Carlo simulation in a new ensemble. Mol. Phys. 61:813-826.
55. Patro, S. Y., and T. M. Przybycien. 1994. Simulations of kinetically irreversible protein aggregate structure. Biophys. J. 66:1274-1289.
56. Pattou, D., B. Maigret, M. C. Fourniezaluski, and B. P. Roques. 1991. Computational analysis of conformational behavior of cholecystokinin fragments I - Cck4, Cck5, Cck6 and Cck7 molecules. Int. J. Pept. Protein Res. 37:440-450.
57. Pauling, L., H. A. Itano, S. J. Singer, and I. C. Wells. 1949. Sickle cell anemia, a molecular disease. Science. 110:543-548.
58. Przybycien, T. M., and J. E. Bailey. 1989. Aggregation kinetics in salt-induced protein precipitation. AIChE J. 35:1779-1790.
59. Rinas, U., L. B. Tsai, D. Lyons, G. M. Fox, G. Stearns, J. Fieschko, D. Fenton, and J. E. Bailey. 1992. Cysteine to serine substitutions in basic fibroblast growth factor: effect on inclusion body formation and proteolytic susceptibility during in vitro folding. Biotechnology. 10:435-440.
60. Savitzky, A., and M. Golay. 1967. Smoothing and differentiation of data by simplified least square procedures. Anal. Chem. 36:1627-1639.
61. Schick, B., and F. Jurnak. 1994. Crystal growth and crystal improvement strategies: extension of the diffraction resolution of crystals. Acta Crystallogr. D50:563-568.
62. Sedzik, J. 1994. DESIGN: a guide to protein crystallization experiments. Arch. Biochem. Biophys. 308:342-348.
63. Sedzik, J., and D. K. Kirschner. 1992. Is myelin basic protein crystallizable? Neurochem. Res. 17:157-166.
64. Sergeev, Y. V., Y. N. Chirgadze, S. E. Mylvaganam, H. Driessen, C. Slingsby, and T. L. Blundell. 1988. Surface interactions of γ-crystallins in the crystal medium in relation to their association in the eye lens. Proteins. 4:137-147.
65. Sheriff, S., W. A. Hendrickson, R. E. Stenkamp, L. C. Sicker, and L. H. Jensen. 1985. Influence of solvent accessibility and intermolecular contacts on atomic mobilities in hemerythrins. Proc. Natl. Acad. Sci. USA. 82:1104-1107.
66. Shortle, D., H. S. Chan, and K. A. Dill. 1992. Modeling the effects of mutations on the denatured states of proteins. Protein Sci. 1:201-215.
67. Sluzky, V., A. M. Klibanov, and R. Langer. 1992. Mechanism of insulin aggregation and stabilization in agitated aqueous solutions. Biotech. Bioeng. 40:895-903.
68. St. Clair, N. L., and M. A. Navia. 1992. Cross-linked enzyme crystals as robust biocatalysts. J. Am. Chem. Soc. 114:7314.
69. Steinier, J., Y. Termonia, and J. Deltour. 1972. Comments on smoothing and differentiation of data by simplified least square procedure. Anal. Chem. 44:1906-1909.
70. Takahashi, T., S. Endo, and K. Nagayama. 1993. Stabilization of protein crystals by electrostatic interactions as revealed by a numerical approach. J. Mol. Biol. 234:421-432.
71. Tandom, S., and P. M. Horowitz. 1989. Reversible folding of rhodanese. J. Biol. Chem. 264:9859.
72. Tanford, C. 1978. The hydrophobic effect and the organization of living matter. Science. 200:1012-1018.
73. Vonck, J., and E. F. J. van Bruggen. 1990. Electron microscopy and image analysis of two-dimensional crystals and single molecules of alcohol oxidase from Hansenula polymorpha. Biochim. Biophys. Acta. 1038: 74-79.
74. Welzel, R., L. J. Perry, and C. Veilleux. 1991. Mutations in human interferon γ affecting inclusion body formation identified by a general immunochemical screen. Biotechnology. 9:731-737.
75. White, H. E., H. P. C. Driessen, C. Slingsby, D. S. Moss, and P. F. Lindley. 1989. Packing interactions in the eye lens. J. Mol. Biol. 207:217-235.
76. Wolfenden, R. 1983. Waterlogged molecules. Science. 222:1087.
77. Wolfenden, R., L. Andersson, P. M. Cullis, and C. C. B. Southgate. 1981. Affinities of amino acid side chains for solvent water. Biochemistry. 20:849-855.
78. Yeager, M. 1994. Crystallization of membrane proteins: in situ two-dimensional crystallization of a polytopic membrane protein: the cardiac gap junction channel. Acta. Crystallogr. D50:632-638.
79. Yoshikawa, S., K. Shinzawa-Itoh, H. Ueda, T. Tsukihara, Y. Fukumoto, T. Kubota, M. Kawamoto, K. Jukuyama, and H. Matsubara. 1992. Strategies for crystallization of large membrane protein complexes. J. Cryst. Growth. 122:298-302.
80. 1*. J. Biol. Chem. 247:1012-1019.
81. Yue, K., and K. A. Dill. 1992. Inverse protein folding problem: designing polymer sequences. Proc. Natl. Acad. Sci. USA. 89:4163-4167.