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A report is presented on the crystal structure of inactive MtrA. It is an essential gene product for the human pathogen Mycobacterium tuberculosis.

The structural features which underlie the nucleocytoplasmic transport of FABP4 is explained. FABP4 delivers specific ligands from the cytosol to the nuclesr receptor PPARgamma in the nucleus, thereby facilitating the ligation and enhancing the transcriptional activity of the receptor.

A study was conducted to explore the specificity and function of interaction between the tumor suppressor protein p53 in the yeast three-hybrid system (Y3H) and RNA. The findings prove that p53 binds RNA with little sequence specificity, RNA binding has the potential to regulate DNA binding, and RNA-p53 interactions could be regulated by acetylation of the p53 C-terminus.

The research makes use of a structure model, in addition to the various energy transfer distance measurements to study the T7 RNA polymerase, which causes bending of its promoter DNA on binding by various proteins and other complexes. The analysis proves the existence of a bent and an open model for the initiation complex of T7 and also shows that in spite of the massive changes, the DNA of the active site is very much identical in initiation as well as elongation complexes.

The study employs techniques like NMR and CD calculations to describe the three-dimensional structures of the four tandem repeats of the fibroin-modular-binding protein (FMBP-1), which act as the DNA-binding domain. The analysis shows that the binding of the full-length score and three amino acid peptide repeat leads to an increase in the [alpha]-helicity of the protein regions, which then tend to form a regular secondary structure.

A study finds out how HiNF-P is regulated during the cell-cycle and examines its stability relative to [p220.sup.NPAT] using serum-stimulated cells and cells synchronized in S-phase and in mitosis. It was observed that while HiNF-P is maintained at steady-state levels in the complete cell cycle, the proteasome pathway actively degrades both HiNF-P and [p220.sup.NPAT].

A methodology to quantify the binding of proteins to target DNA molecules based on single-molecule detection and real-time counting of individual free and bound fluorescently tagged molecules flowing past a detection device is presented. The methodology was used for measuring DNA binding by fluorescently tagged domains of four distinct transcription factors and these proteins represent different structural classes, quaternary states and relative affinities.

The effects of the turn, the hydrophobic cluster, and a disulfide cross-linker on the folding kinetics of a designed alpha-helical hairpin, Z34C, are examined using an infrared temperature-jump method in conjunction with site-specific mutagenesis. Results reveal that Z34C folds with an ultrafast rate and support a folding mechanism in which the rate-limiting step corresponds to the formation of the reverse turn.

Proline 61 A (P61A) mutation related to the factor for inversion stimulation (FIS) where a homodimeric DNA-binding protein found in enteric bacteria is presented. It confirmed the existence of thermostable dimeric intermediate of P61A FIS by glutaraldehyde cross-linking experiments at 95 degree Celsius.

Microcalorimatric and optical methods are used to study the thermodynamic properties and DNA binding ability of the N-terminal DNA binding domains of interferon regulatory factors IRF-1 (DBD1) and IRF-3 (DBD3). It is found that DBD1 has more sequence specificity than DBD3 and the strength of the DBDs' specific association with DNA is inversely related to the stability of the free DBDs.

A series of oligonucleotides containing modified purines and pyrimidines at the recognition site were prepared to probe their mechanism of selective interaction to bind to the methyl-binding domain (MBD) of the methyl-CpG-binding protein 2 (MeCP2). DNA-protein interface mediated by structured water as opposed to hydrophobic interactions elucidated the improved binding of the MBD to oligonucleotides containing several cytosine analogues

The self-assembly properties of highly purified, recombinant L4-22K protein is characterized to understand the thermodynamics of assembly of two human adenoviral (Ad) proteins, IVa2 and L4-22K. L4-22K which reversibly assembles into higher-order structures according to an indefinite, isodesmic assembly scheme could provide significant insight into the thermodynamics of assembly of L4-22K and IVa2 on the PS.

A pair of furan-based cyclic homooligopeptides is prepared to specifically target G-quadruplexes and UV melting has shown that these ligands have effectively induced G-quadruplex structures in the G-rich 22-mer c-MYC DNA sequence and have stabilized the structure. The studies have shown that the present molecules are effective in specifically binding and stabilizing quadruplexes and have provided a suitable scaffold to develop into a quadruplex-targeting therapeutic agent.

The equilibrium binding Deinococcus radiodurans single-stranded (ss) DNA binding protein (DrSSB) to ssDNA is examined for comparison with that of Escherichia coli SSB (EcoSSB). The binding enthalpy has shown a large sensitivity to NaCl concentration, similar to that seen for EcoSSB and these common features for SSB proteins having multiple DNA binding domains enable versatility of SSB function in vivo.

Two X-ray structures of chicken smooth muscle tropomyosin overlap complex are described. The interactions between the N- and C-terminal coiled coils of smooth muscle tropomyosin have displayed curvature, which has differed between the two structures and has implied flexibility in the overlap complex, at least in solution.

The properties of six individually expressed human methylated DNA binding protein 2 (MeCP2) domains spanning the entire protein were analyzed in detail to better understand their interactions with each other, with DNA, and with nucleosomal arrays. The results offer new mechanistic and biochemical insights related to the conformational modulations of intrinsically disordered MeCP2 protein, and its context-dependent in vivo roles.

Isothermal titration calorimetry was used to probe the specificity and examine the thermodynamics of single-stranded DNA binding protein (SSB) binding to two Escherichia coli proteins important for DNA replication, the x subunit of DNA polymerase III holoenzyme and the PriA helicase. The results suggested that DNA binding proteins could use the interaction of SSB with both x and PriA to gain access to ssDNA by first interacting with the SSB C-termini.

Coiled-coil arrays were used to study the interaction specificity of four viral basic-region leucine-zipper transcription factors (bZIPs) and assess their self-associations as well as heterointeractions with 33 representative human bZIPs. The new interactions detected for HBZ with MAFB, MAFG, ATF2, CEBPG, and CREBZF and MEQ with NFIL3 were confirmed in solution by circular dichroism.

The fluorescent single-stranded DNA binding protein (SSB) is used to develop the kinetic mechanism by which the protein and ssDNA associate and dissociate and understand the interaction between single-stranded DNA (ssDNA) and SSB. The complex dissociation kinetics of the fluorescent SSB*ssDNA complex is found to be greatly accelerated by the presence of free wild-type SSB.

A high-resolution NMR solution structure of recombinant ribosomal protein L14e, a component of the large ribosomal subunit in both archaea and eukaryotes is characterized to understand the classic SH3 fold structure adopted by the N-terminal 57 residues. Great similarities observed between the N-terminal sequence of L14e of any Sulfolobus protein and N-terminal sequence of Sac8b, a DNA-binding protein indicated the potential use of structure of L14e to serve as model to study other members of the L14e family, including COG2163 group, L6e and L27e.

Nuclear magnetic resonance spectroscopy and proton exchange were used to characterize two RNA-DNA hybrids from the tR2 intrinsic transcription terminator site of phage [lambda]. The results suggested for the first time that the RNA-DNA hybrid structures with the same base sequence, the opening dynamics and the stability of individual base pairs are strongly influenced by the chemical nature of each strand.

The functional significance of three conserved aromatic amino acids (Trp37, Tyr60, and Phe104) for heat shock transcription factor 1 (HSF1) trimerization is demonstrated. An intramolecular interaction between Tyr60 and [alpha]-helix 1 in the DNA-binding domain and intermolecular aromatic-aromatic interaction between the Trp37 and Phe104 facilitated the formation of intermolecular disulfide bonds, leading to the heat-induced HSF1 trimerization.

The first biochemical characterization of XPB, the largest subunit of the eukaryotic transcription factor TFIIH, which is essential for both initiation of transcription by RNA polymerase II and nucleotide excision repair (NER) from bacteria, Mycobacterium tuberculosis and Kineococcus radiotolerans is reported. The ATP hydrolytic acttivity by the bacterial XPBs is strongly dependent on both the nature of a nucleotide triphosphate and that of a divalent metal.

Several properties of Helicobacter pylori NikR (HpNikR), a nickel-responsive transcription factor were explored to understand its role in the direct or indirect internal pH-regulation in modulation of the DNA-binding activity upon exposure to acidic shock. The results obtained from the site-directed mutagenesis of HpNikR revealed that either Asp7 or Asp8 in the N-terminus of HpNikR significant for the activation of DNA binding and the viability of H. pylori.

The isothermal titration calorimetry and NMR spectroscopy were utilized to map the interaction between the transactivation domain (TAD) of p53 and the transcriptional coactivators CBP KIX domain. The KIX-binding affinity of p53 TAD was observed to be enhanced by simultaneous phosphorylation of Thr18 and Ser20.

The isothermal titration calorimetry approach is employed to explain the thermodynamics of the Jun-Fos heterodimeric transcription factor to the synthetic dsDNA oligos containing TGACTCA element. The TGACTCA cis motif is shown to play an extremely significant role in the modulation of energetics and orientation of the binding process.

The three-step mechanism that is involved in the binding and bending of the AdMLP TATA sequence (TATAAAAG) by a protein core domain is discussed. The structures and the properties of DNA bound in solution and the crystal are shown to be completely different.

A nuclear magnetic resonance (NMR) is employed to map the interaction between Bdp1 and Brf1, two of the transcription factors of TFIIIB at single-amino acid resolution, using minimal functional segments of the two proteins. The structural model derived from NMR revealed that the most important anchorage site of Brf1 is located on a convex surface of Bdp1 that encompasses helix 1 and helix 3 of its conserved SANT domain.

A biochemical study is carried out to examine the proteins containing both an A/T-rich interaction domain (ARID) and a high mobility group (HMG)-box domain from Arabidopsis thaliana. The results showed that both the ARID and the HMG-box domain contribute to the DNA interactions of ARID-HMG1 to give the protein characteristics of ARID and HMG-box proteins.

The studies of antigene locked nucleic acids (agLNAs) that reduce RNA levels of targeted genes block RNA polymerase and transcription factor association at gene promoters, and bind to chromosomal DNA are presented. The data obtained suggested that the mechanism for agLNA-mediated inhibition of gene expression involved binding of LNAs to chromosomal DNA.

A transcriptome/proteome-wide approach is used for discovering binding partners for chromogranin A (CHGA) by employing a phase display cDNA library method. The studies have shown that the trans-Golgi protein SCLIP and SCG10 has interacted with CHGA, shared partial colocalization in the Golgi apparatus and are required for typical transmitter storage and release from chromaffin cells.

A combination of Raman difference spectroscopy and gel mobility assays were used to characterize the molecular mechanisms of proteins IHF and HU of eubacteria that bind as homodimers to double-stranded DNA. The results provided insight into the differences in the structural perturbations induced by IHF and HU in common DNA substrate.

The structural changes induced into the E subunit of the human heterotetrameric negative transctription elongation factor containing a conical [beta][alpha][beta][beta][alpha][beta] RNA recognition motif (NELF-E RRM) upon RNA binding are investigated. The structural studies show that RNA binding to NELF-E RRM induces formation of a helix in the C-terminus similar to the RNA-bound to U1A RRM.

A study is conducted to examine the DNA-binding specificity and mechanisms of SIX2 and SIX6 toward the Trex/MEF3 consensus sequence and the core tetranucleotide ATTA commonly recognized by homeodomain proteins. The data result show that SIX and SIX6 differ in their DNA-binding mechanisms and in the consequences of interactions with the protein tyrosine phosphate Eyes Absent on SIX2/6-DNA-binding affinity.

A study was conducted to examine the product specificity in the catalysis reaction by SET7/9 histone lysine methyltransferase of AdoMet N-methylation of the transcriptional factor p53-Lys4-N[H.sub.2]. The results from bond-order computations suggested that the methyl transfer reaction in protein lysin methyltransferases occurs via a linear [S.sub.N]2 associative reaction with bond making of approximately 50%.

Nuclear magnetic resonance (NMR) spectroscopy is used for determining the atomic-resolution structure of [Ca.sup.2+]-bound DREAM (calsenilin/KChIP3) in solution. [Ca.sup.2+]-induced dimerization of DREAM has partially blocked the putative DNA-binding site, which has shown how [Ca.sup.2+] has abolished DREAM binding to DNA in order to activate the transcription of prodynorphin and other downstream genes in pain control.

The determination of the single-molecule kinetics of endonuclease V (endo V) in a catalytic cycle by using a substrate of deoxyinosine-containing single-strand DNA (ssDNA) revealed endo V to have two metal binding sites to regulate its enzymatic activities.

The well established inhibitory effect of HMGB-1 on repair of capsulation-damaged DNA with two modified forms of the protein, shown to blind palatinate DNA with higher affinity than the original protein in vivo acetylated HMGB-1 and HMGB-1 lacking its C-terminal domain is studied. The findings suggest that the HMGB-1 -induced inhibition of capsulation-DNA adduct repair is accomplished through the acidic domain.

The role of the ferroxidase center in iron uptake and hydrogen peroxide detoxification is investigated in Listeria innocua DNA binding protein from starved cells (LiDps). It is concluded that the behavior of the ferroxidase center variants of LiDps show that an intact ferroxidase center is not required when the bacterium is in an aerobic environment.

The chemistry of iron binding and oxidation in Listeria innocua DNA binding protein from starved cells (LiDps) is studied using H(sub 2)O(sub 2) as oxidant to further define the mechanism of iron deposition inside the protein and the role of LiDps in protecting DNA from oxidative damage. It is concluded that the reactions occur in place of undesirable odd-electron redox processes that produce hydroxyl radical.

A novel DNA-binding template for construction of new therapeutic candidates is proposed. Four bisphenylcarbazoles derivatives, derived from the combined molecular architectures of known antitumor bisphenylbenzimidazoles and anti-infectious diatonic carbazoles are designed and their interaction with DNA studied by a combination of biochemical and biophysical methods.

This study shows that the predominant form of FNR in aerobic cells is apo-FNR (cluster-less FNR) indicating that the [2Fe-2S](super 2+) cluster like the [4Fe-4S](super 2+) cluster is not stable under aerobic conditions.

A method based on quantitative analysis of nucleosome dissociation in dilution experiments that provides a simple practical measure of nucleosome stability was developed recently, and soluble conditions were found, which suggest that this approach might allow absolute equilibrium affinity of the histone chamber for DNA to be measured. The concept that nucleosome assembly/dissembly process is not strictly reversible in these solution conditions is demonstrated, and this implies that equilibrium affinities cannot be obtained from these measurements,

Cobalt is genotoxic and mutagenic at higher concentrations, and treatment of cells with cobalt generates DNA strand breaks and covalent protein-DNA complexes; however, the basis for these effects is not well understood. Since the toxic events induced by cobalt are similar to those of topoisomerase II poisons, the effect of the metal on human topoisomerase IIa was examined.

The structural gene of the putative ATP-dependent DNA ligase of Neisseria meningitidis is expressed after cloning. Protein is purified and its substrate specificity and kinetic properties are investigated. The results highlight the similarities and differences between ADL and both NAD(super +) -dependent bacterial DNA ligases and various ATP-dependent DNA ligases.

Basic leucine zipper (bZIP) transcription factors are dimeric proteins that recognize dyadic and mostly palindromic DNA sites. The kinetics of DNA recognition by unfolded monomeric and folded dimeric derivatives of GCN4 are reported using a 19 bp double-stranded DNA containing a palindromic CRE site.