Equal impact of diffusion and DNA binding rates on the potential spatial distribution of nuclear factor κB transcription factor inside the nucleus

There are two physical processes that influence the spatial distribution of transcription factor molecules entering the nucleus of a eukaryotic cell, the binding to genomic DNA and the diffusion throughout the nuclear volume. Comparison of the DNA-protein association rate constant and the protein diffusion constant may determine which one is the limiting factor. If the process is diffusion-limited, transcription factor molecules are captured by DNA before their even distribution in the nuclear volume. Otherwise, if the reaction rate is limiting, these molecules diffuse evenly and then find their binding sites. Using well-studied human NF-κB dimer as an example, we calculated its diffusion constant using the Debye-Smoluchowski equation. The value of diffusion constant was about 10(-15) cm(3)/s, and it was comparable to the NF-κB association rate constant for DNA binding known from previous studies. Thus, both diffusion and DNA binding play an equally important role in NF-κB spatial distribution. The importance of genome 3D-structure in gene expression regulation and possible dependence of gene expression on the local concentration of open chromatin can be hypothesized from our theoretical estimate.

Generation of new TRAIL mutants DR5-A and DR5-B with improved selectivity to death receptor 5

TRAIL (tumor necrosis factor (TNF) related apoptosis-inducing ligand) has been introduced as an extrinsic pathway inducer of apoptosis that does not have the toxicities of Fas and TNF. However, the therapeutic potential of TRAIL is limited because of many primary tumor cells are resistant to TRAIL. Despite intensive investigations, little is known in regards to the mechanisms underlying TRAIL selectivity and efficiency. A major reason likely lies in the complexity of the interaction of TRAIL with its five receptors, of which only two DR4 and DR5 are death receptors. Binding of TRAIL with decoy receptors DcR1 and DcR2 or soluble receptor osteoprotegerin (OPG) fail to induce apoptosis. Here we describe design and expression in Escherichia coli of DR5-selective TRAIL variants DR5-A and DR5-B. The measurements of dissociation constants of these mutants with all five receptors show that they practically do not interact with DR4 and DcR1 and have highly reduced affinity to DcR2 and OPG receptors. These mutants are more effective than wild type TRAIL in induction of apoptosis in different cancer cell lines. In combination with the drugs targeted to cytoskeleton (taxol, cytochalasin D) the mutants of TRAIL induced apoptosis in resistant Hela cells overexpressing Bcl-2. The novel highly selective and effective DR5-A and DR5-B TRAIL variants will be useful in studies on the role of different receptors in TRAIL-induced apoptosis in sensitive and resistant cell lines.

[Flagellar antigens of E. coli serologically interrlelated to H40, 41 and H41, 42, 43 flagellar antigens of Citrobacter. New H-antigeny E. coli i Citrobacter]

The authors confirmed the reference of the test strains H13 (P6c) and H22 (A231a) of the international collection of E. coli to Citrobacter; their antigenic formula was established. As shown, strains P6c possessed a variety of the H-antigen which was not described in Citrobacter earlier, designated as H41a, 97. Three types of flagellar antigens characterized by the presence of an interrelationship with the partial factor H41 of the flagellar Citrobacter antigens were revealed in E. coli; the partial composition of H-antigenic components common for E. coli and Citrobacter was studied. Two of three new varieties of the E. coli H-antigen revealed was characterized by a cross correlation and a relation to the standard H19 E. coli antigen. The strain with the third variety of the H-antigen was capable of forming the H-antigenic mutants which acquired the antigenic component identical to the standard H16 E. coli antigen. E. coli strain is recommended for the replacement of the strain P6c in the International collection of E. coli.