Visualizing Lentiviral Protein 3D Structures

The HIV Databases at LANL have primarily focussed on primate lentiviral amino acid and genetic primary sequence information. There is increasing interest in the secondary and tertiary structures of lentiviral proteins as more 3D structures become available. The tools for viewing and manipulating these structures are also becoming more powerful and easier to use. Discovery of the 3D structures of proteins by X-ray crystallography and/or NMR is not easy. Many proteins are resistant to forming crystals, and NMR technology is limited to molecules with fewer atoms than the typical complete protein. Although there is no guarantee that a protein crystal is in the conformation that is biologically active in solution, many or most of the crystal structures in the protein structure database appear to be correct, given that data on biological activity of the proteins agrees with the structure. For one example, amino acids known through mutation analyses to influence the AZT resistance of the HIV-1 reverse transcriptase surround the AZT-binding site in the crystal structure. The number of crystal structures for HIV-1 proteins has grown sufficiently large that it is now difficult for the inexperienced user of the PDB database to find which of the many structures is most relevant to the user. The number of software tools available for displaying 3D structures on computers is also growing, and it is difficult for potential users to decide which tool is best suited to their needs. This paper and the corresponding web pages [A] are designed to serve as an overview and guide to this growing body of data and tools.