Protein binding sites in nucleation complexes of alfalfa mosaic virus RNA 4.

The subgenomic coat protein messenger RNA 4 of alfalfa mosaic virus forms complexes with one and three coat protein dimers, which are designated complexes I and III, respectively. These complexes were separated, subjected to digestion with ribonuclease T1, and filtered onto Millipore filters. Phenol extracts of the filters contained specific fragments of RNA 4, which were sequenced after electrophoretic separation on nondenaturing and denaturing polyacrylamide gels. Complex I yielded only a 68-nucleotide fragment including the 3' terminus [fragment 814-881 according to the numbering of Brederode, F. Th., Koper-Zwarthoff, E. C., & Bol, J. F. (1980) Nucleic Acids Res. 8, 2213-2223]. Complex III yielded in addition to the former fragment also other, mostly extracistronic, fragments from the 3'-terminal region, as well as fragments from an intracistronic region, comprising positions 425-474, in the middle of RNA 4. The 3'-terminal region was subdivided by small gaps into three coat protein binding sites: 799-881, 759-787, and 667-753, designated sites 1, 2, and 3, respectively, and possibly representing the sites occupied by the three coat protein dimers. A similarity may exist between the secondary structure of sites 1 and 3, which both may have three hairpins, two of which flanked at their 3' side by an AUGC sequence. Furthermore, a complementarity was noted between the loop of a large hairpin which can be drawn in the intracistronic site and the upper part of one of the three hairpins in the 3'-terminal site 1. These binding features have been combined in a model structure for the complex of RNA 4 with three coat protein dimers.