1887

Abstract

The evolutionary relationship of retroviruses to the negative-stranded RNA virus superfamily was examined by comparing protein structures. Since protein structures are more conserved over time than primary protein sequences, three-dimensional structural comparisons permit the identification of evolutionary relationships that were previously undetected. Human immunodeficiency virus (HIV) and influenza virus were used as representatives of the virus groups, and proteins with similar functions were compared. Since M1 of influenza virus has membrane- and RNA nucleocapsid-binding activities that are functionally analogous to those of the HIV matrix and capsid proteins, the structural similarities between these proteins were determined. Sequence alignments were based on superimposition of the three-dimensional structures. Helices 2, 2′, 3 and 4 of the HIV matrix protein aligned and superimposed with the four-helix bundle of the membrane-binding N domain of M1 with a root mean square (RMS) of 3.48 Å. Helices A, B and C of the HIV N-terminal capsid protein aligned and superimposed with three helices of the four-helix bundle of the RNA-binding N domain of M1 with an RMS of 2.63 Å. The HIV Gag protein and influenza virus matrix protein may have evolved from a common ancestor protein. The similarities between influenza virus M1 and HIV matrix and capsid proteins may indicate an evolutionary link between retroviruses and negative-sense RNA viruses.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-80-4-863
1999-04-01
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/jgv/80/4/0800863a.html?itemId=/content/journal/jgv/10.1099/0022-1317-80-4-863&mimeType=html&fmt=ahah

References

  1. Aronson H. G., Royer W. E. Jr, Hendrickson W. A. 1994; Quantification of tertiary structural conservation despite primary sequence drift in the globin fold. Protein Science 3:1706–1711
    [Google Scholar]
  2. Baltimore D. 1980; Evolution of RNA viruses. Annals of the New York Academy of Sciences 80:492–497
    [Google Scholar]
  3. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. E., Brice M. D., Rodgers J. R., Kennard O., Shimanouchi R., Tasumi M. 1977; The Protein Data Bank: a computer-based archival file for macromolecular structures. Journal of Molecular Biology 12:535–542
    [Google Scholar]
  4. Binley J., Moore J. P. 1997; The viral mousetrap. Nature 387:346–347
    [Google Scholar]
  5. Bullough P. A., Hughson F. M., Skehel J. J., Wiley D. C. 1994; Structure of influenza haemagglutinin at the pH of membrane fusion. Nature 371:37–43
    [Google Scholar]
  6. Carson M. 1991; Ribbons 2.0. Journal of Applied Crystallography 24:958–961
    [Google Scholar]
  7. Chan D. C., Fass D., Berger J. M., Kim P. S. 1997; Core structure of gp41 from the HIV envelope glycoprotein. Cell 89:263–273
    [Google Scholar]
  8. Freed E. O., Englund G., Martin M. A. 1995; Role of the basic domain of human immunodeficiency virus type 1 matrix in macrophage infection. Journal of Virology 69:3949–3954
    [Google Scholar]
  9. Gamble T. R., Yoo S., Vajdos F. F., von Schwedler U. K., Worthylake D. K., Wang H., McCutcheon J. P., Sundquist W. I., Hill C. P. 1997; Structure of the carboxyl-terminal dimerization domain of the HIV-1 capsid protein. Science 278:849–853
    [Google Scholar]
  10. Gitti R. K., Lee B. M., Walker J., Summers M. F., Yoo S., Sundquist W. I. 1996; Structure of the amino-terminal core domain of the HIV-1 capsid protein. Science 273:231–235
    [Google Scholar]
  11. Hill C. P., Worthylake D., Bancroft D. P., Christensen A. M., Sundquist W. 1996; Crystal structures of the trimeric human immunodeficiency virus type 1 matrix protein: implications for membrane association and assembly. Proceedings of the National Academy of Sciences, USA 93:3099–3104
    [Google Scholar]
  12. Holm L., Sander C. 1998; Touring protein fold space with Dali/FSSP. Nucleic Acids Research 26:316–319
    [Google Scholar]
  13. Lenard J. 1996; Negative-strand virus M andretrovirus MA proteins: all in a family?. Virology 216:289–298
    [Google Scholar]
  14. Luban J., Bossolt K. L., Ranke E. K., Kalpana G. V., Goff S. P. 1993; Human immunodeficiency virus type 1 gag protein binds to cyclophilins A and B. Cell 73:1067–1078
    [Google Scholar]
  15. Matthews R. E. F. 1985; Viral taxonomy for the non-virologist. Annual Reviews of Microbiology 39:451–474
    [Google Scholar]
  16. Momany C., Kovari L. C., Prongay A. J., Keller W., Gitti R. K., Lee B. M., Gorbalenya A. E., Tong L., McClure J., Ehrlich L. S., Summers M. F., Carter C., Rossmann M. G. 1996; Crystal structure of dimeric HIV-1 capsid protein. Nature Structural Biology 3:763–770
    [Google Scholar]
  17. Nicholls A. 1992; GRASP: Graphical Representation and Analysis of Surface Properties. >Columbia University; New York, USA:
    [Google Scholar]
  18. Roa S. T., Rossmann M. G. 1973; Comparison of super-secondary structures in proteins. Journal of Molecular Biology 76:241–256
    [Google Scholar]
  19. Rossmann M. G., Argos P. 1975; A comparison of the heme binding pocket in globins and cytochrome b5. Journal of Biological Chemistry 250:7525–7532
    [Google Scholar]
  20. Rossmann M. G., Argos P. 1976; Exploring structural homology of proteins. Journal of Molecular Biology 105:75–95
    [Google Scholar]
  21. Rossmann M. G., Johnson J. E. 1989; Icosahedral RNA virus structure. Annual Review of Biochemistry 58:533–573
    [Google Scholar]
  22. Rossmann M. G., Rueckert R. R. 1987; What does the molecular structure of viruses tell us about viral functions ?. Microbiological Sciences 4:206–214
    [Google Scholar]
  23. Rozwarski D. A., Gronenborn A. M., Clore G. M., Basan J., Bohm A., Wlodawer A., Hatada M., Karpuls P. A. 1994; Structural comparisons among the short-chain helical cytokines. Structure 2:159–173
    [Google Scholar]
  24. Schultz A., Oroszlan S. 1983; In vivo modification of retroviral gag gene-encoded polyproteins by myristic acid. Journal of Virology 46:355–361
    [Google Scholar]
  25. Sha B., Luo M. 1997; Structure of a bifunctional membrane RNA binding protein, influenza virus matrix protein M1. Nature Structural Biology 4:239–244
    [Google Scholar]
  26. Weissenhorn W., Dessen A., Harrison S. C., Skehel J. J., Wiley D. C. 1997; Atomic structure of the ectodomain from HIV-1 gp41. Nature 387:426–430
    [Google Scholar]
  27. Wells J. A., Cunningham B. C., Graycar T. P., Estell D. A., Carter P. 1987; On the evolution of specificity and catalysis in subtilisin. Cold Spring Harbor Symposia on Quantitative Biology 52:647–652
    [Google Scholar]
  28. Wiegers K., Rutter G., Kottler H., Tessmer U., Hohenberg H., Krausslich H. G. 1998; Sequential steps in human immunodeficiency virus particle maturation revealed by alterations of individual Gag polyprotein cleavage sites. Journal of Virology 72:2846–2854
    [Google Scholar]
  29. Wu H., Lustbader J. W., Liu Y., Canfield R. E., Hendrickson W. A. 1994; Structure of human chorionic gonadotropin at 2.6 A resolution from MAD analysis ofthe selenomethionyl protein. Structure 2545–558
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-80-4-863
Loading
/content/journal/jgv/10.1099/0022-1317-80-4-863
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error