Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and Rna Binding Sites in Rev Proteins of Hiv-1 and Eiav Agree with Experimental Data

HIV-1 Rev is one of several clinically important proteins that are "experimentally recalcitrant," i.e., for which it has not been possible to obtain high resolution structural in formation. Identifying critic al functional residues in Rev is further complicated by the fact that Rev proteins have no significant sequence similarity to any protein with known structure, and that Rev sequences from different species have very little similarity to one another. Our comparison of predictions with experimental data on the Rev proteins from HIV-1 and EIAV demonstrates that sequence-based computational methods can identify residues in "recalcitrant" proteins that interact with other proteins or nucleic acids. When structural information is available for a protein of interest, enhanced prediction accuracy can be achieved (18, 29). Developing improved methods for predicting binding sites will contribute to our understanding of how proteins recognize their targets in cells and may significantly decrease the time needed to precisely map binding sites in the laboratory. The level of accuracy obtained using the sequence-based methods presented here suggests that they could expedite the design of experiments to explore the function of key regulatory proteins, even when no structural information is available, with obvious implications for developing new therapies for both genetic and infectious diseases. Acknowledgments This Research was supported in part by grants NIH, GM 066387 (VH, DD, & RLJ) and CA97936 (SC), by an ISU Center for Integrated Animal Genomics grant (DD, VH & RLJ), and by USDA Formula Funds (SC & DD). We thank Sijun Liu for technical assistance and Jeffrey Sander for useful comments.