Tat peptide-calmodulin binding studies and bioinformatics of HIV-1 protein-calmodulin interactions.

The human immunodeficiency virus type 1 (HIV-1) genome encodes 18 proteins and 2 peptides. Four of these proteins encode high-affinity calmodulin-binding sites for which direct interactions with calmodulin have already been described. In this study, the HIV-1 proteome is queried using an algorithm that predicts calmodulin-binding sites revealing seven new putative calmodulin-binding sites including residues 34-56 of the transactivator of transcription (Tat). Tat is a 101-residue intrinsically disordered RNA-binding protein that plays a central role in the regulation of HIV-1 replication. Interactions between a Tat peptide (residues 34-56), melittin, a well-characterized calmodulin-binding peptide, and calmodulin were examined by direct binding studies, mass spectrometry, and fluorescence. The Tat peptide binds to both calcium-saturated and apo-calmodulin with a low micromolar affinity. Conformational changes induced in the Tat peptide were determined by circular dichroism, and residues in calmodulin that interact with the peptide were identified by HSQC NMR spectroscopy. Multiple interactions between HIV-1 proteins and calmodulin, a highly promiscuous signal transduction hub protein, may be an important mechanism by which the virus controls cell physiology.

High yield expression and purification of HIV-1 Tat1-72 for structural studies.

The HIV-1 transactivator of transcription (Tat) is a protein essential for virus replication. Tat is an intrinsically disordered RNA-binding protein that, in cooperation with host cell factors cyclin T1 and cyclin-dependent kinase 9, regulates transcription at the level of elongation. Tat also interacts with numerous other intracellular and extracellular proteins, and is implicated in a number of pathogenic processes. The physico-chemical properties of Tat make it a particularly challenging target for structural studies: Tat contains seven Cys residues, six of which are essential for transactivation, and is highly susceptible to oxidative cross-linking and aggregation. In addition, a basic segment (residues 48-57) gives the protein a high net positive charge of +12 at pH 7, endowing it with a high affinity for anionic polymers and surfaces. In order to study the structure of Tat, both alone and in complex with partner molecules, we have developed a system for the bacterial expression and purification of 6xHistidine-tagged and isotopically enriched (in N15 and C13) recombinant HIV-1 Tat(1-72) (BH10 isolate) that yields large amounts of protein. These preparations have facilitated the assignment of 95% of the backbone NMR resonances. Analysis by mass spectrometry and NMR demonstrate that the cysteine-rich Tat protein is unambiguously reduced, monomeric, and unfolded in aqueous solution at pH 4.

A comparative relativistic DFT and ab initio study on the structure and thermodynamics of the oxofluorides of uranium(IV), (V) and (VI).

All the possible uranium(VI, V, IV) oxides, fluorides and oxofluorides were studied theoretically by using density functional theory (DFT) in the generalised gradient approximation (GGA), and three different relativistic methods (all-electron scalar four component Dyall RESC method (AE), relativistic small-core ECPs, and zeroth order regular approximation ZORA). In order to test different correlation methods, for the two former relativistic methods hybrid DFT, and, for the AE method, MP2 molecular orbital calculations were performed as well. Single-point AE-CCSD(T) energies were calculated on MP2 geometries as well. Energies of the uranium(VI) and (V) oxofluorides dissociation, uranium(VI) fluoride hydrolysis and oxofluoride disproportionation were calculated and compared against the available experimental thermochemical data. AE-CCSD(T) energies were the closest to the experiment. For GGA DFT methods, all the relativistic methods used yield similar results. For thermochemistry, the best quantitative agreement with the experimental and CCSD(T) values for both U=O and U-F bond strengths was obtained with hybrid DFT methods, provided that a reliable basis set was used. Both the GGA DFT and MP2 MO methods show overbinding of these bonds; moreover, this overbinding was found to be not uniform but strongly dependent on the coordination environment of the uranium atom in each case. U=O vibrational frequencies given by hybrid DFT, however, are systematically overestimated, and are better reproduced by GGA DFT; MP2 values usually fall in-between. Reaction enthalpies, U=O frequencies and complex geometries given by the PBE, MPBE, BPBE, BLYP and OLYP GGA functionals are quite similar, with OLYP performing slightly better than the others but still not as good as hybrid DFT. The geometries of the molecules are found to be influenced by the following factors: the inverse transinfluence (ITI) of the oxygen ligand and, for U(V), and U(IV), the Jahn-Teller distortion.