DNA interactions - gene

Resource for building models for simulating intracellular molecular processes to predict the dynamic behavior of living cells. The system allows the user to define protein functions, protein-protein interactions, protein-DNA interactions, gene regulation, and other features of cellular metabolism. Dynamic changes in concentradons of proteins and other chemical compounds can also be visualized. 

Gebara, M. M., and McCarrey, J. R. (1992). Protein-DNA interactions associated with the onset of testis-specific expression of the mammalian Pgk-2 gene. Mol. Cell. Biol. 12 1422-1431. 

Solomon MJ, Larsen PL, Varshavsky A. Mapping protein-DNA interactions in vivo with formaldehyde evidence that histone H4 is retained on a highly transcribed gene. Cell 1988 17 937-947. 

Generally, between the two halves of the palindrome (or of the direct repetition) there are from one to five nucleotide spacers whose sequence varies from one gene to another. The sequence in which these nucleotides are found is irrelevant, as they do not directly participate in the dimer-DNA interaction. It is very important, however, that the number of nucleotide spacers be fixed to allow for correct binding to its corresponding receptor dimer. 

The normal form of interaction between receptor and DNA requires the hormone to have broken the native structure of the receptor and the dimer to have been formed. That is to say, the receptor-DNA interaction comes after the hormone-receptor interaction. Nevertheless, situations have been described in vitro in which the receptor is able to be previously associated to the HRE. This situation occurs in vivo for the thyroid hormone receptors, in which case it seems that the hormone-free dimer acts as an expression repressor of genes dependent on these hormones (Evans et al. 1988). The arrival of the hormone activates the dimer in situ and inverts its role as regulator. 

Giese, K., Kingsley, C., Kirshner, J.R., and Grosschedl, R. (1995) Assembly and function of a TCRu enhancer complex is dependent on LEF-l-induced DNA bending and multiple protein-protein interactions. Genes Dev. 9, 995-1008. 

Protein phosphatases 544, 646 Protein S 634 Protein sequenators 118 Protein sequences from genes 119 Protein synthesis 3, 538, 539 Protein tyrosine kinases 544 Protein-disulfide isomerase 83 Protein-DNA interactions 266 Proteinase. See Protease Proteoglycan(s) 181,182. See also Glycosami-noglycans... 

Schler, A. F., and W. J. Gehring, Direct-homeo domain-DNA interaction in the autoregulation of the fushi tarazu gene. Nature 356 804-806, 1992. 

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