Modeling supra-molecular helices: Extension of the molecular surface recognition algorithm and application to the protein coat of the tobacco mosaic virus

Journal of Molecular Biology

Volumn 266, Issue 1, 1997, Pages 135-143

  Eisenstein, M ^a   Shariv, I ^a   Koren, G ^a   Friesem, A A ^a   Katchalski Katzir, E ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Geometric recognition; Helical assembly; Molecular surface complementarity; Protein protein docking; Tobacco mosaic virus

Indexed keywords

COAT PROTEIN;

ALGORITHM; ARTICLE; GEOMETRY; MODEL; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; TOBACCO MOSAIC VIRUS;

EID: 0031566966     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0773     Document Type: Article

References (11)

1. Abola E., Bernstein F. C., Bryant S. H., Koetzle T. F., Weng J. Protein Data Bank. Crystallographic Databases: Information Content, Software Systems, Scientific Applications.1987;Union of Crystallography, Bonn, Cambridge, Chester.
2. Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F., Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
3. Bloomer A. C., Champness J. N., Bricogne G., Staden R., Klug A. Protein disk of tobacco mosaic virus at 2.8 Å resolution showing the interactions within at between subunits. Nature. 276:1978;362-368.
4. Butler J. P. G., Klug A. The assembly of a virus. Sci. Amer. 239:1978;52-59.
5. Cherfils J., Janin J. Protein docking algorithms: simulating molecular recognition. Curr. Opin. Struct. Biol. 3:1993;265-269.
6. Goldstein H. Classical Mechanics. 1980;Addison-Wesley, Reading.
7. Huber R., Kukla D., Bode W., Schwager P, Bartels K., Deisenhofer J, Steingemann W. Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9 Å resolution. J. Mol. Biol. 89:1974;73-101.
8. Katchalski-Katzir E., Shariv I., Eisenstein M., Friesem A. A., Aflalo C., Vakser I. A. Molecular surface recognition: determination of geometric fit between proteins and their ligand by correlation techniques. Proc. Natl Acad. Sci. USA. 89:1992;2195-2199.
9. Namba K., Pattanayek R., Stubbs G. Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 Å resolution by X-ray fiber diffraction. J. Mol. Biol. 208:1989;307-325.
10. Sharff A. J., Rodseth L. E., Spurlino J. C., Quiocho F. A. Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis. Biochemistry. 31:1992;10657-10663.
11. Strynadka N. C. J., Eisenstein M., Katchalski-Katzir E., Shoichet B. K., Kuntz I. D., Abazyan R., Totrov M., Janin J., Cherfils J., Zimmerman F., Olson A., Duncan B., Rao M., Jackson R., Sternberg M., James M. N. G. Nature Struct. Biol. 3:1996;233-239.