Abstract
The three-dimensional structure of human angiogenin has been determined by X-ray crystallography and is compared here with an earlier model which predicted its structure, based on the homology of angiogenin with bovine pancreatic ribonuclease A. Comparison of the predicted model and crystal structure shows that the active-site histidine residues and the core of the angiogenin molecule, including most of theβ-strands andα-helices, were predicted reasonably well. However, the structure of the surface loop regions and residues near the truncated C-terminus differs significantly. The C-terminal segment includes the active-site residues Asp-116, Gln-117, and Ser-118; Gln-117 in particular has been shown to be important in affecting the ribonucleolytic activity of angiogenin. Also, the orientation of one helix in the model differed from the orientation observed experimentally by about 20°, resulting in a large displacement of this chain segment. The difficulty encountered in predicting the surface loop regions has led to a new algorithm [Palmer and Scheraga (1991),J. Comput. Chem.,12, 505–526; (1992),J. Comput. Chem.,13, 329–350] for predicting the conformations of surface loops.
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Acharya, K. R., Stuart, D. I., Phillips, D. C., and Scheraga, H. A. (1990).J. Protein Chem. 9, 549–563.
Acharya, K. R., Shapiro, R., Allen, S. C., Riordan, J. F., and Vallee, B. L. (1994).Proc. Natl. Acad. Sci. USA 91, 2915–2919.
Blundell, T. L., Sibanda, B. L., and Pearl, L. (1983).Nature 304, 273–275.
Blundell, T. L., Sibanda, B. L., Sternberg, M. J. E., and Thornton, J. M. (1987).Nature 326, 347–352.
Bond, M. D., Strydom, D. J., and Vallee, B. L. (1993).Biochim. Biophys. Acta 1162, 177–186.
Borah, B., Chen, C. W., Egan, W., Miller, M., Wlodawer, A., and Cohen, J. S. (1985).Biochemistry 24, 2058–2067.
Browne, W. J., North, A. C. T., Phillips, D. C., Brew, K., Vanaman, T. C., and Hill, R. L. (1969).J. Mol. Biol. 42, 65–86.
Chothia, C., and Lesk, A. M. (1987). InCold Spring Harbor Laboratory Symposium on Quantitative Biology, Vol. 52, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp. 399–405.
Curran, T. P., Shapiro, R., and Riordan, J. F. (1993).Biochemistry 32, 2307–2313.
Farber, G. K., and Petsko, G. A. (1990).Trends Biochem. Sci. 15, 228–234.
Fett, J. W., Strydom, D. J., Lobb, R. R., Alderman, E. M., Bethune, J. L., Riordan, J. F., and Vallee, B. L. (1985).Biochemistry 24, 5480–5486.
Hallahan, T. W., Shapiro, R., and Vallee, B. L. (1991).Proc. Natl. Acad. Sci. USA 88, 2222–2226.
Hallahan, T. W., Shapiro, R., Strydom, D. J., and Vallee, B. L. (1992).Biochemistry 31, 8022–8029.
Hendrickson, W. A. (1979).Acta Crystallogr. A 35, 158–163.
Kabsch, W., and Sander, C. (1983).Biopolymers 22, 2577–2637.
Kraulis, P. J. (1991).J. Appl. Crystallogr. 24, 946–950.
Lee, F. S., and Vallee, B. L. (1989).Biochem. Biophys. Res. Commun. 161, 121–126.
Lee, F. S., Auld, D. S., and Vallee, B. L. (1989).Biochemistry 28, 219–224.
Momany, F. A., McGuire, R. F., Burgess, A. W., and Scheraga, H. A. (1975).J. Phys. Chem. 79, 2361–2381.
Némethy, G., Pottle, M. S., and Scheraga, H. A. (1983).J. Phys. Chem. 87, 1883–1887.
Némethy, G., Gibson, K. D., Palmer, K. A., Yoon, C., Paterlini, G., Zagari, A., Rumsey, S., and Scheraga, H. A. (1992).J. Phys. Chem. 96, 6472–6484.
Palmer, K. A., and Scheraga, H. A. (1991).J. Comput. Chem. 12, 505–526.
Palmer, K. A., and Scheraga, H. A. (1992).J. Comput. Chem. 13, 329–350.
Palmer, K. A., Scheraga, H. A., Riordan, J. F., and Vallee, B. L. (1986).Proc. Natl. Acad. Sci. USA 83, 1965–1969.
Richards, F. M., and Wyckoff, H. W. (1973). InAtlas of Molecular Structures in Biology. 1. Ribonuclease S (Phillips, D. C., and Richards, F. M., eds.), Clarendon, Oxford.
Rossmann, M. G., and Argos, P. (1976).J. Mol. Biol. 105, 75–95.
Rossmann, M. G., Moras, D., and Olsen, K. W. (1974).Nature 250, 194–199.
Rossmann, M. G., Liljas, A. Brändén, C.-I., and Banaszak, L. J. (1975). InThe Enzymes, Vol. 11, Academic Press, New York, pp.61–102.
Russo, N., Shapiro, R., Acharya, K. R., Riordan, J. F., and Vallee, B. L. (1994).Proc. Natl. Acad. Sci. USA 91, 2920–2924.
Shapiro, R., and Vallee, B. L. (1987).Proc. Natl. Acad. Sci. USA 84, 2238–2241.
Shapiro, R., Riordan, J. F., and Vallee, B. L. (1986).Biochemistry 25, 3527–3532.
Shapiro, R., Harper, J. W., Fox, E. A., Jansen, H.-W., Hein, F., and Uhlmann, E. (1988).Anal. Biochem. 175, 450–461.
Strydom, D. J., Fett, J. W., Lobb, R. R., Alderman, E. M., Bethune, J. L., Riordan, J. F., and Vallee, B. L. (1985).Biochemistry 24, 5486–5494.
Swenson, M. K., Burgess, A. W., and Scheraga, H. A. (1978). InFrontiers in Physico-chemical Biology (Pullman, B. ed), Academic Press, New York, pp. 115–142.
Teeter, M. M., Ma, X. Q., Rao, U., and Whitlow, M. (1990).Proteins: Structure Function Gene. 8, 118–132.
Warme, P. K., Momany, F. A., Rumball, S. V., Tuttle, R. W., and Scheraga, H. A. (1974).Biochemistry 13, 768–782.
Weber, I. T. (1990).Proteins: Structure, Function and Gene. 7, 172–184.
Weber, I. T., Miller, M., Jaskolski, M., Leis, J., Skalka, A. M., and Wlodawer, A. (1989).Science 243, 928–931.
Williams, A. F., and Barclay, A. N. (1988).Annu. Rev. Immunol. 6, 381–405.
Wlodawer, A., Bott, R., and Sjölin, L. (1982).J. Biol. Chem. 257, 1325–1332.
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Allen, S.C., Acharya, K.R., Palmer, K.A. et al. A comparison of the predicted and X-ray structures of angiogenin. Implications for further studies of model building of homologous proteins. J Protein Chem 13, 649–658 (1994). https://doi.org/10.1007/BF01890464
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DOI: https://doi.org/10.1007/BF01890464