Correlation between binding rate constants and individual information of E. coli Fis binding sites

Individual protein binding sites on DNA can be measured in bits of information. This information is related to the free energy of binding by the second law of thermodynamics, but binding kinetics appear to be inaccessible from sequence information since the relative contributions of the on- and off-rates to the binding constant, and hence the free energy, are unknown. However, the on-rate could be independent of the sequence since a protein is likely to bind once it is near a site. To test this, we used surface plasmon resonance and electromobility shift assays to determine the kinetics for binding of the Fis protein to a range of naturally occurring binding sites. We observed that the logarithm of the off-rate is indeed proportional to the individual information of the binding sites, as predicted. However, the on-rate is also related to the information, but to a lesser degree. We suggest that the on-rate is mostly determined by DNA bending, which in turn is determined by the sequence information. Finally, we observed a break in the binding curve around zero bits of information. The break is expected from information theory because it represents the coding demarcation between specific and nonspecific binding.     

Fis binding in the dnaA operon promoter region.

The region between the rpmH and dnaA genes contains five promoters that divergently express the ribosomal protein L34 and the proteins of the dnaA operon, including DnaA, the beta clamp of DNA polymerase III holoenzyme, and RecF. The DNA-binding protein Fis was shown by the band shift assay to bind near the rpmHp2 and dnaAp2 promoters and by DNase I footprinting to bind to a single site in the dnaAp2 promoter overlapping the -35 and spacer sequences. There were no observable differences in Fis affinity or the angle of bending induced by Fis between methylated and unmethylated DNA fragments containing the Fis binding site in the dnaAp2 promoter. Fis directly or indirectly represses the expression of DnaA protein and the beta clamp of DNA polymerase III. A fis null mutant containing a dnaA-lacZ in-frame fusion had twofold greater beta-galactosidase activity than a fis wild-type strain, and induced expression of Fis eliminated the increase in activity of the fusion protein. A two- to threefold increase in the levels of DnaA and beta clamp proteins was found in a fis null mutant by immunoblot gel analysis.     

Molecular flip-flops formed by overlapping Fis sites

The DNA-binding protein Fis frequently uses pairs of sites 7 or 11 base pairs (bp) apart. Two overlapping Fis sites separated by 11 bp are found in the Escherichia coli origin of chromosomal replication. Only one of these sites is bound by Fis at a time, so the structure is a molecular flip–flop that could direct alternative firing of replication complexes in opposite directions. Alternatively, the flip–flop could represent part of an on–off switch for replication. Because they can be used to create precise switched states, molecular flip–flops could be used as the basis of a novel molecular computer.     

Quantitative analysis of ribosome binding sites in E.coli.

185 clones with randomized ribosome binding sites, from position -11 to 0 preceding the coding region of beta-galactosidase, were selected and sequenced. The translational yield of each clone was determined; they varied by more than 3000-fold. Multiple linear regression analysis was used to determine the contribution to translation initiation activity of each base at each position. Features known to be important for translation initiation, such as the initiation codon, the Shine/Dalgarno sequence, the identity of the base at position -3 and the occurrence of alternative ATGs, are all found to be important quantitatively for activity. No other features are found to be of general significance, although the effects of secondary structure can be seen as outliers. A comparison to a large number of natural E.coli translation initiation sites shows the information profile to be qualitatively similar although differing quantitatively. This is probably due to the selection for good translation initiation sites in the natural set compared to the low average activity of the randomized set.     

Information content of binding sites on nucleotide sequences

Repressors, polymerases, ribosomes and other macromolecules bind to specific nucleic acid sequences. They can find a binding site only if the sequence has a recognizable pattern. We define a measure of the information (R sequence) in the sequence patterns at binding sites. It allows one to investigate how information is distributed across the sites and to compare one site to another. One can also calculate the amount of information (R frequency) that would be required to locate the sites, given that they occur with some frequency in the genome. Several Escherichia coli binding sites were analyzed using these two independent empirical measurements. The two amounts of information are similar for most of the sites we analyzed. In contrast, bacteriophage T7 RNA polymerase binding sites contain about twice as much information as is necessary for recognition by the T7 polymerase, suggesting that a second protein may bind at T7 promoters. The extra information can be accounted for by a strong symmetry element found at the T7 promoters. This element may be an operator. If this model is correct, these promoters and operators do not share much information. The comparisons between R sequence and R frequency suggest that the information at binding sites is just sufficient for the sites to be distinguished from the rest of the genome.     

Mutational analysis of simian virus 40 large T antigen DNA binding sites.

We have tested the effects of various mutations within SV40 T antigen DNA recognition sites I and II on specific T antigen binding using the DNase footprint technique. In addition, the replication of plasmid DNA templates carrying these T antigen binding site mutations was monitored by Southern analysis of transfected DNA in COS cells. Deletion mapping of site I sequences defined a central core of approximately 18 bp that is both necessary and sufficient for T antigen recognition; this region contains the site I contact nucleotides that were previously mapped using methylation-interference and methylation-protection experiments. A similar deletion analysis delineated sequences that impart specificity of binding to site II. We find that T antigen is capable of specific recognition of site II in the absence of site I sequences, indicating that binding to site II in vitro is not dependent on binding of T antigen at site I. Site II binding was not diminished by small deletion or substitution mutations that perturb the 27-bp palindrome central to binding site II, whereas extensive substitution of site II sequences completely eliminated specific site II binding. Analysis of the replication in COS7 cells of plasmids that contain these mutant origins revealed that sequences both at the late side of binding site I and within the site II palindrome are crucial for viral DNA replication, but are not involved in binding T antigen.     

Sequence-dependent dynamics of TATA-Box binding sites.

We have carried out two nanosecond-length molecular dynamics simulations on a DNA oligomer, d(GCGTAAAAAAAACGC)2, which contains a weak binding site for the TATA-box binding protein. An analysis of the resulting trajectories shows that this oligomer behaves differently from a related oligomer [d(GCGTATATAAAACGC)2] studied earlier using the same protocol (Flatters, D., M. Young, D. L. Beveridge, and R. Lavery. 1997. Conformational properties of the TATA-box binding sequence of DNA. J. Biomol. Struct. & Dyn. 14:757-765), and which contains a strong binding site for the same protein. The two basepair mutations that relate these oligomers lead to significant changes in time-averaged structure and in dynamic behavior, which extend over entire length of the oligomer and appear to be compatible with the experimentally observed decrease of binding and functional activity. These results suggest that molecular dynamics simulations, taking into account explicit solvent and counterions, and avoiding the truncation of electrostatic interactions, are a powerful tool for investigating the indirect aspects of protein-nucleic acid recognition.     

Mutational analysis of the transferrin receptor reveals overlapping HFE and transferrin binding sites.

The transferrin receptor (TfR) binds two proteins critical for iron metabolism: transferrin (Tf) and HFE, the protein mutated in hereditary hemochromatosis. Previous results demonstrated that Tf and HFE compete for binding to TfR, suggesting that Tf and HFE bind to the same or an overlapping site on TfR. TfR is a homodimer that binds one Tf per polypeptide chain (2:2, TfR/Tf stoichiometry), whereas both 2:1 and 2:2 TfR/HFE stoichiometries have been observed. In order to more fully characterize the interaction between HFE and TfR, we determined the binding stoichiometry using equilibrium gel-filtration and analytical ultracentrifugation. Both techniques indicate that a 2:2 TfR/HFE complex can form at submicromolar concentrations in solution, consistent with the hypothesis that HFE competes for Tf binding to TfR by blocking the Tf binding site rather than by exerting an allosteric effect. To determine whether the Tf and HFE binding sites on TfR overlap, residues at the HFE binding site on TfR were identified from the 2.8 A resolution HFE-TfR co-crystal structure, then mutated and tested for their effects on HFE and Tf binding. The binding affinities of soluble TfR mutants for HFE and Tf were determined using a surface plasmon resonance assay. Substitutions of five TfR residues at the HFE binding site (L619A, R629A, Y643A, G647A and F650Q) resulted in significant reductions in Tf binding affinity. The findings that both HFE and Tf form 2:2 complexes with TfR and that mutations at the HFE binding site affect Tf binding support a model in which HFE and Tf compete for overlapping binding sites on TfR.     

Hydrophobic binding sites on human interferon.

Human interferon binds to a omega-carboxpentyl-agarose column at low ionic strength (0.15 M NaCl) and is still retained when the ionic strength is raised (to 1.0 M NaCl). The binding can be reversed, however, by ethylene glycol, indicating a hydrophobic interaction. The binding of human interferon to omega-aminohexyl-agarose is weak, even at a low ionic strength, and is probably exclusively electrostatic. This disparate binding behavior may be caused by the presence of a positive charge, adjacent to the hydrophobic binding site, on human interferon. The interaction of human interferon with omega-carboxypentyl-agarose is quite selective, inasmuch as the majority of proteins present in interferon preparations pass through the column unretained. Hydrophobic chromatography of human interferon may thus be useful in its purification.     

alpha-Bungarotoxin binding sites in the CNS.

The neurotoxin α-bungarotoxin (BuTX) has been extensively used as a specific and irreversible ligand to study the nicotinic acetylcholine receptor (nAChR) in skeletal muscle and electric fish. More recently it has been utilized to investigate the possibility of nAChRs in the CNS. The BuTX binding sites in the CNS have biochemical properties similar to muscle, have a distribution similar to other cholinergic markers, and have been histologically demonstrated to bind to post-synaptic membranes. But studies of ganglionic neurons, cultured sympathetic ganglion cells, and the PC 12 cell culture line have raised questions regarding the use of BuTX as a nicotinic receptor ligand in the CNS. The evidence for and against BuTX as a nicotinic receptor ligand is reviewed and discussed.     

Autoradiographic analysis of binding sites for 125I-Bolton-Hunter-substance P in the human eye.

Substance P is known to exert potent effects in peripheral tissues, and is thought to be important for ocular function. The mechanism of action of substance P in the human eye is not known. As a basis for biochemical characterization specific binding of 125I-Bolton-Hunter-substance P was demonstrated in the human eye using autoradiographic methods. Biochemical characterization on slide-mounted tissue preparations showed that binding was saturable with a KD of 0.27 +/- 0.1 nmol/l. Specific binding occurred at comparable autoradiographic densities to both human retina and choroid. Substance P and its carboxyterminal fragment, substance P(3-11), were shown to be highly potent in binding competition experiments against 125I-Bolton-Hunter-substance P. Similar concentrations of substance P(1-9), neurokinin A and neurokinin B failed to significantly alter specific binding of 125I-Bolton-Hunter-substance P. The results indicate expression of high affinity substance P binding sites in human retina and choroid.     

Lectin binding sites in Paramecium tetraurelia cells. I. Labeling analysis predominantly of secretory components

Though all three lectins tested (ConA, RCA II, WGA) bound to the entire cell membrane, none bound selectively to the docking site of secretory organelles (trichocysts); the same results were achieved with FITC-conjugates, or, on the EM level, with peroxidase- or gold-labeling. Only WGA triggered the release of trichocysts and none of the lectins tested inhibited AED-induced synchronous exocytosis. When exocytosis was triggered synchronously in the presence of any of these three lectins (FITC-conjugates), the resulting ghosts trapped the FITC-lectins and the cell surface was immediately afterwards studded with regularly spaced dots (corresponding to the ghosts located on the regularly spaced exocytosis sites). These disappeared within about 10 min from the cell surface (thus reflecting ghost internalization with a half life of 3 min) and fluorescent label was then found in approximately 6-10 vacuoles, which are several microns in diameter, stain for acid phosphatase and, on the EM level, contain numerous membrane fragments (otherwise not found in this form in digesting vacuoles). We conclude that synchronous massive exocytosis involves lysosomal breakdown rather than reutilization of internalized trichocyst membranes and that these contain lectin binding sites (given the fact free fluorescent probes did not efficiently stain ghosts). Trichocyst contents were analyzed for their lectin binding capacity in situ and on polyacrylamide gels. RCA II yielded intense staining (particularly of "tips"), while ConA (fluorescence concentrated over "bodies") and WGA yielded less staining of trichocyst contents on the light and electron microscopic level. Only ConA- and WGA-staining was inhibitable by an excess of specific sugars, while RCA II binding was not. ConA binding was also confirmed on polyacrylamide gels which also allowed us to assess the rather low degree of glycosylation (approximately 1% by comparison with known glycoprotein standards) of the main trichocyst proteins contained in their expandable "matrix". Since RCA II binding could be due to its own glycosylation residues we looked for an endogenous lectin. The conjecture was substantiated by the binding of FITC-lactose-albumin (inhibitable by a mixture of glucose-galactose). This preliminary new finding may be important for the elucidation of trichocyst function.     

ProPred: prediction of HLA-DR binding sites.

ProPred is a graphical web tool for predicting MHC class II binding regions in antigenic protein sequences. The server implement matrix based prediction algorithm, employing amino-acid/position coefficient table deduced from literature. The predicted binders can be visualized either as peaks in graphical interface or as colored residues in HTML interface. This server might be a useful tool in locating the promiscuous binding regions that can bind to several HLA-DR alleles. AVAILABILITY: The server is available at http://www.imtech.res.in/raghava/propred/ CONTACT: raghava@imtech.res.in SUPPLEMENTARY INFORMATION: http://www.imtech.res.in/raghava/propred/page3.html     

Lectin binding sites in Paramecium tetraurelia cells. II. Labeling analysis predominantly of non-secretory components

All the lectin-FITC conjugates tested (ConA, RCA II, WGA) bind to the surface of Paramecium cells. Yet only WGA yields a distinct fluorescent pattern; it contours the basis of cilia and in some cells it brilliantly stains a few neighbouring rows of the regular surface fields in the anterioventral region (a region known to contain extensive fields of linear aggregates of freeze-fracture particles and to be engaged in conjugation). Incubation in vivo with WGA-FITC resulted in the selective labeling of the cytopharyngeal region as well as of the cytoproct. On Lowicryl K4M sections, WGA-gold probes concomitantly labeled disk-shaped vesicles that are assumed in the literature to serve as shuttle vesicles between these two cell regions and, thus, to connect forming and defecating digesting vacuoles (stages DV I and DV IV). On K4M sections WGA-Au stains also most other components of the lysosomal system. Also on K4M sections RCA II-Au labeled the walls of bacteria contained in DV I and II type digesting vacuoles (but not lysosomes identified bona fide by their size and shape and by their frequent vicinity to or continuity with digesting vacuoles). The WGA data largely support previous conclusions on the possible functional connection of all these elements (DV I-IV, smaller lysosomes, disk-shaped vesicles etc.) of the lysosomal system in Paramecium, as proposed by Allen and his group on the basis of other lines of evidence. As shown in the accompanying paper, ConA-FITC stained ghosts (formed after massive trichocyst exocytosis) also abut into DV-like structures. The different results obtained with the three lectins tested reflect the complex sorting machinery contained in the elaborate lysosomal system of a Paramecium cell. In the cytosol, finally, there occurs a particularly intense staining with ConA-gold, applied to Lowicryl sections, that probably represents glycogen-like particles. The same procedure reveals some weak staining of secretory contents and of nuclear structures.