Tissue-specific factors and glucocorticoid receptors present in nuclear extracts bind next to each other in the promoter region of mouse mammary tumor virus

Nuclear extracts from different mouse tissues have been used to study the interaction of factors with the steroid-inducible promoter of mouse mammary tumor virus. In addition to the glucocorticoid receptor that interacts with the distal region of the promoter, several tissue-specific proteins were found to bind to the 5' flanking region of the receptor-binding site and to the basal promoter region. The differences in the pattern of protection observed suggest that tissue-specific factors might co-operate with steroid receptors and result in a cell-type-dependent modulation of hormone action.     

Allosteric communication in cysteinyl tRNA synthetase: a network of direct and indirect readout

Protein structure networks are constructed for the identification of long-range signaling pathways in cysteinyl tRNA synthetase (CysRS). Molecular dynamics simulation trajectory of CysRS-ligand complexes were used to determine conformational ensembles in order to gain insight into the allosteric signaling paths. Communication paths between the anticodon binding region and the aminoacylation region have been identified. Extensive interaction between the helix bundle domain and the anticodon binding domain, resulting in structural rigidity in the presence of tRNA, has been detected. Based on the predicted model, six residues along the communication paths have been examined by mutations (single and double) and shown to mediate a coordinated coupling between anticodon recognition and activation of amino acid at the active site. This study on CysRS clearly shows that specific key residues, which are involved in communication between distal sites in allosteric proteins but may be elusive in direct structure analysis, can be identified from dynamics of protein structure networks.