[Investigation of polyamine interactions with the nuclear transcription factor NF-kappa B by computer modelling].

Computer modelling is used to study interactions between polyamines and nuclear transcription factor NF-kappa B and NF-kappa B. specific DNA complex. It is shown that polyamines can regulate interaction between NF-kappa B and the specific DNA sequence by binding to p50 subunit of NF-kappa B. A possible polyamines binding site on the surface of p50 is found. Dissociation of polyamines to p50.DNA complex is modelled. Kd of spermine, spermidine and putrescine are calculated. Conformational transition of DNA.(p50)2-->DNA.p50 + p50 is simulated. Kd of complex p50.DNA is calculated in the presence and in the absence of polyamine in the binding site on the p50. It is shown that polyamines stabilizes the inter-domain interface of p50 protein due to appearance of additional electrostatic and hydrogen bonds. Shah, Thomas and Shirahata obtained the following sequence of efficiency in facilitating NF-kappa B--DNA binding: spermine > spermidine > putrescine. The sequence of affinities of polyamines to NF-kappa B that we obtained corresponds well to the former sequence from the cited work. Our results support the hypothesis that polyamines decreases the probability of spontaneous dissociation of DNA.p50 complex.