Table 2.
Predicted interactions in the interfacial regions between adjacent M1 subunitsa
| Interaction | Subunits | Cα-Cα distance (Å) | Type |
|---|---|---|---|
| R76-E8 | B-D/F-H | 11.3 | wt (G88/R101/R105) |
| R76-E29 | B-D/F-H | 10.2 | wt |
| R78-E29 | B-D/F-H | 13.6 | wt |
| K98-D156 | B-D/F-H | 6.7 | wt |
| R101-E152◀ | B-D/F-H | 9.2 | wt |
| R101-D156◀ | B-D/F-H | 8.7 | wt |
| K104-E152◀ | B-D/F-H | 11.5 | wt |
| R134-E6 | B-D/F-H | 7.3 | wt |
| R134-E8 | B-D/F-H | 9.4 | wt |
| R134-E152 | B-D/F-H | 11.7 | wt |
| R88-E6 | A-D | 10.8 | G88R/R101S/R105S |
| R88-E114 | A-D | 8.5 | G88R/R101S/R105S |
| R88-E152 | A-D | 13.6 | G88R/R101S/R105S |
| K102-E44◀ | A-E/B-F | 7.7 | wt |
| R105-D38◀ | A-E/B-F | 11.0 | wt |
| R105-E40◀ | A-E/B-F | 8.4 | wt |
| R105-E44◀ | A-E/B-F | 8.4 | wt |
| E114-R27 | A-E/B-F | 13.9 | wt |
| E114-R49 | A-E/B-F | 10.4 | wt |
| D94-R72 | A-F | 6.8 | wt |
| K95-D38 | A-F | 8.8 | wt |
| K95-E40 | A-F | 10.6 | wt |
| R76-E152 | A-C/E-G | 9.6 | wt |
| R134-E152 | A-C/E-G | 7.5 | wt |
| R134-D156 | A-C/E-G | 8.1 | wt |
| D94-R127 | C-G/D-H | 9.9 | wt |
| K95-E23 | C-G/D-H | 10.3 | wt |
| K98-D30 | C-G/D-H | 8.7 | wt |
| K98-D38 | C-G/D-H | 9.1 | wt |
| R101-D38◀ | C-G/D-H | 11.5 | wt |
The dimeric (consisting of subunits A and B) crystal structure of the M1 protein (residues 1 to 164) of influenza A virus at neutral pH was retrieved from the Protein Data Bank (codes 1EA3 and 1AA7) and used to model the outer M1 layer of the virion. The molecular modeling was performed using SYBYL 8.1. The new putative M1 layer model, in which the positively and negatively charged surfaces face one another in the interfacial region between M1 subunits, was constructed by conceptually defining the M1 layer to be (locally) coincident with the x-y plane, with the z axis being normal (perpendicular to the surface of the layer). A small section of the M1 layer was generated from the dimer by first expanding in the x direction to generate a tetramer (i.e., a dimer of dimers) and then in the y direction to generate an octamer using the ZDOCK server (http://zdock.bu.edu/). Of the highest scoring M1 octamer models proposed by ZDOCK, one model (ZSCORE = 53.02), displaying excellent dimer-packing characteristics, was selected for further refinement and analysis. The distance between residues on adjacent subunits was measured between the backbone Cα atoms and not the usual hydrogen-bonded heavy atoms of the side chains, because a given side chain may interact with multiple partners, though not necessarily at the same time. Interactions involving the nuclear localization signal (NLS) motif 101RKLKR105 are indicated with a triangle (◀).