Position Of Binding Site Research Articles

Determination of VH Family Usage in B-Cell Malignancies via the BIOMED-2 IGH PCR Clonality Assay.

To determine whether V H family usage in B-cell lymphoproliferative disorders can be deduced from polymerase chain reaction (PCR) product-length information obtained through the BIOMED-2 (Invivoscribe, San Diego, CA) clonality assay. We develop an algorithm that uses the sizing information of the BIOMED-2 immunoglobulin heavy chain (IGH) clonality assay to deduce V H family usage. PCR with family-specific primers on 51 clinical samples containing 54 rearranged alleles were used to validate the algorithm. The clonal PCR products in different framework reactions contain the same NDN segment (because they are from the same allele). Subtracting the size of the framework III product from the size of the framework I and II products yields the relative position of the framework primer binding sites for the V H segment used. The V H family can be assigned with these relative positions because they are V H family specific in the BIOMED-2 assay. The V H family assigned by the algorithm was concordant with family-specific PCR results for 49 (96%) of the 51 specimens. We have developed an algorithm that can correctly assign V H family usage when all three BIOMED-2 framework reactions produced clonal products. Given the wide adoption of BIOMED-2 assay, the algorithm can facilitate collection of IGH V H usage data without additional cost to the laboratories.

A drift-diffusion model for molecular motor transport in anisotropic filament bundles

In this study we consider the density of motor proteins in filament bundles with polarity graded in space. We start with a microscopic model that includes information on motor binding site positions along specific filaments and on their polarities. We assume that filament length is small compared to the characteristic length scale of the bundle polarity pattern. This leads to a separation of scales between molecular motor movement within the bundle and along single fibers which we exploit to derive a drift-diffusion equation as a first order perturbation equation. The resulting drift-diffusion model reveals that drift dominates in unidirectional bundles while diffusion dominates in isotropic bundles. In general, however, those two modes of transport are balanced according to the polarity and thickness of the filament bundle. The model makes testable predictions on the dependence of the molecular motor density on filament density and polarity.

Development of a control region-based mtDNA SNaPshot™ selection tool, integrated into a mini amplicon sequencing method

Mitochondrial DNA (mtDNA) analysis is regularly applied to forensic DNA samples with limited amounts of nuclear DNA (nDNA), such as hair shafts and bones. Generally, this mtDNA analysis involves examination of the hypervariable control region by Sanger sequencing of amplified products. When samples are severely degraded, small-sized amplicons can be applied and an earlier described mini-mtDNA method by Eichmann et al. [1] that accommodates ten mini amplicons in two multiplexes is found to be a very robust approach. However, in cases with large numbers of samples, like when searching for hairs with an mtDNA profile deviant from that of the victim, the method is time (and cost) consuming. Previously, Chemale et al. [2] described a SNaPshot™-based screening tool for a Brazilian population that uses standard-size amplicons for HVS-I and HVS-II. Here, we describe a similar tool adapted to the full control region and compatible with mini-mtDNA amplicons. Eighteen single nucleotide polymorphisms (SNPs) were selected based on their relative frequencies in a European population. They showed a high discriminatory power in a Dutch population (97.2%). The 18 SNPs are assessed in two SNaPshot™ multiplexes that pair to the two mini-mtDNA amplification multiplexes. Degenerate bases are included to limit allele dropout due to SNPs at primer binding site positions. Three SNPs provide haplogroup information. Reliability testing showed no differences with Sanger sequencing results. Since mini-mtSNaPshot screening uses only a small portion of the same PCR products used for Sanger sequencing, no additional DNA extract is consumed, which is forensically advantageous.

Point mutation of cytochrome P450 2A6 (a polymorphic variant CYP2A6.25) confers new substrate specificity towards flavonoids.

CYP2A6 is a major hepatic member of the cytochrome P450 family in humans. Much variation in CYP2A6 levels and activity can be attributed to genetic polymorphisms of this gene. CYP2A6*25 comprises an amino acid substitution, F118L. To clarify the effect of the leucine substitution at position 118 in CYP2A6.25, this variant, wild type CYP2A6 and three additional variants consisting of artificial mutations at the substrate binding site (position 481) suggested by earlier reports using random mutagenesis studies [CYP2A6.1, CYP2A6.25, CYP2A6.1(F118A), CYP2A6.1(A481G) and CYP2A6.25(A481G)], were co-expressed with NADPH-cytochrome P450 reductase in E. coli. The hydroxylase activity of these variants toward 7-ethoxycoumarin, coumarin, flavone, α-naphthoflavone, flavanone and hydroxyflavanone were examined. All the mutants had lower activities for coumarin 7-hydroxylation than the wild type. All the mutants showed higher activities for flavone and α-naphthoflavone compared with CYP2A6.1. CYP2A6.1 had the highest flavanone 2'-hydroxylase activity, whereas CYP2A6.25 had the highest 6- and 4'-hydroxylase activities. CYP2A6.1(F118A), CYP2A6.1(A481G) and CYP2A6.25(A481G) had higher flavanone 3'-hydroxylase activities than CYP2A6.1 and CYP2A6.25. Furthermore, 4'-hydroxyflavanone was metabolized by CYP2A6.25. These results indicate that the CYP2A6.25 mutation confers new substrate specificity towards flavonoids.

An enhanced protein–protein interaction based on enzymatic complex through replacement of the recognition site

Clostridium cellulovorans, produce multi-enzymatic complexes known as cellulosomes, which assemble via the interaction of a dockerin module in the cellulosomal subunit with one of the several cohesin modules in the scaffolding protein, to degrade the plant cell wall polymer. An enhanced cohesin–dockerin interaction was demonstrated by modified certain cellulosomal enzymes with altered amino acid residues at the crucial binding site, 11th and 12th positions in dockerin module. In fluorescence intensity analyses using the cellulosome-based biomarker system, the modified cellulosomal enzymes (EngE SL to AI and EngH SM to AI) showed an increased intensity (1.4- to 2.2-fold) compared with the wild-type proteins. Conversely, modified ExgS (AI to SM) exhibited a reduced intensity (0.6- to 0.7-fold) compared with the wild type. In enzyme-linked and competitive enzyme-linked interaction assays, the some modified protein (EngE SL to AI and EngH SM to AI) showed their increased binding affinity toward the cohesins (Coh2 and Coh9). Surface plasmon resonance analysis quantitatively demonstrated the binding affinity of these two modified proteins toward cohesins showed similar or higher affinity comparing with its with wild type proteins. These results suggest the replacement of amino acid residues in the certain recognition site significantly affects the binding affinity of the cohesin–dockerin interaction.

The first study about the relationship between the extractability of thiacalix[4]arene derivatives and the position of the coordination binding sites.

Three organic ionophores (2-4) based on the p-tert-butylthiacalix[4]arene backbone, blocked in the 1,3-alternate conformation, bearing two pyridyl coordinating moieties (ortho for 2, meta for 3 and para for 4), have been synthesized and characterized in the solid state. The solvent extraction experiments with the metal ions showed that the ability of these derivatives to complex with Ag(+) appeared to be largely dependent on the position of the nitrogen atoms of the pyridyl ring. Two different complexation modes have been confirmed by 1H NMR titration. Ionophore 2 armed with two pyridyl moieties, complexed with Ag(+) cation through N···Ag(+)···S interactions; however, ionophore 3 and ionophore 4 complexed with Ag(+) through metal-nitrogen (N···Ag(+)) interactions. The DFT computational studies were consistent with the experimental findings. These findings will provide us with an important rule to design an appropriate thiacalix[4]arene ionophore in the future. Another study on the possibility for application of ionophores 2-4 for the treatment of waste water containing Cr(VI) and Cr(III), showed that ionophore 3 was useful in the application of the solvent extraction method in selective treatment of waste water containing Cr(VI) and Cr(III) prior to discharge.

Location of the binding position for HBV X protein functional interaction with cytochrome C oxidase III

To identify the binding site position of the hepatitis B virus (HBV) X protein (HBx) functional interaction with the cytochrome C oxidase subunit III (COX III, a key regulator of mitochondrial function) by using a yeast two-hybrid system. Two fragments of HBx mutants (X1 1-72aa and X2 1-117aa) were amplified by PCR and inserted into the bait plasmid pAS2-1.The resultant mutant plasmids were transfected into yeast cells using the lithium acetate-method.PCR and gene sequencing were used to confirm that the mutant fragments were expressed properly in yeast cells.Western blotting was used to verify that the mutant proteins were translated accurately in the yeast cells.Filter assay was used to exclude autoactivated mutants.Hybridization in solid medium and beta-gal activity detection were used to determine the precise position of the binding site for HBx and COX III interaction. The two mutant plasmids containing HBx 1-72aa and 1-117aa respectively were successfully constructed and the mutants were both properly expressed and translated in yeast cells; no autoactivated mutants were detected throughout the experimental process.The binding site of HBx and COX III was found to be encompass the amino acids 72 through 117 of HBx. Amino acids 72 through 117 of HBx are the key domain of the HBx functional interaction With COX III; this domain may represent a useful target for molecular-based therapies to treat HBV-related diseases.

Contributions of water transfer energy to protein‐ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors

In our previous work, we proposed that desolvation and resolvation of the binding sites of proteins can serve as the slowest steps during ligand association and dissociation, respectively, and tested this hypothesis on two protein-ligand systems with known binding kinetics behavior. In the present work, we test this hypothesis on another kinetically-determined protein-ligand system-that of p38α and eight Type II BIRB 796 inhibitor analogs. The kon values among the inhibitor analogs are narrowly distributed (10⁴ ≤ kon ≤ 10⁵ M⁻¹ s⁻¹), suggesting a common rate-determining step, whereas the koff values are widely distributed (10⁻¹ ≤ koff ≤ 10⁻⁶ s⁻¹), suggesting a spectrum of rate-determining steps. We calculated the solvation properties of the DFG-out protein conformation using an explicit solvent molecular dynamics simulation and thermodynamic analysis method implemented in WaterMap to predict the enthalpic and entropic costs of water transfer to and from bulk solvent incurred upon association and dissociation of each inhibitor. The results suggest that the rate-determining step for association consists of the transfer of a common set of enthalpically favorable solvating water molecules from the binding site to bulk solvent. The rate-determining step for inhibitor dissociation consists of the transfer of water from bulk solvent to specific binding site positions that are unfavorably solvated in the apo protein, and evacuated during ligand association. Different sets of unfavorable solvation are evacuated by each ligand, and the observed dissociation barriers are qualitatively consistent with the calculated solvation free energies of those sets.

Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation

The conserved human LIN28 RNA-binding proteins function in development, maintenance of pluripotency and oncogenesis. We used PAR-CLIP and a newly developed variant of this method, iDo-PAR-CLIP, to identify LIN28B targets as well as sites bound by the individual RNA-binding domains of LIN28B in the human transcriptome at nucleotide resolution. The position of target binding sites reflected the known structural relative orientation of individual LIN28B-binding domains, validating iDo-PAR-CLIP. Our data suggest that LIN28B directly interacts with most expressed mRNAs and members of the let-7 microRNA family. The Lin28-binding motif detected in pre-let-7 was enriched in mRNA sequences bound by LIN28B. Upon LIN28B knockdown, cell proliferation and the cell cycle were strongly impaired. Quantitative shotgun proteomics of LIN28B depleted cells revealed significant reduction of protein synthesis from its RNA targets. Computational analyses provided evidence that the strength of protein synthesis reduction correlated with the location of LIN28B binding sites within target transcripts.

RSAT peak-motifs: fast extraction of transcription factor binding motifs from full-size ChIP-seq datasets

ChIP-seq has become a method of choice to study binding preferences of transcription factors, and localization of epigenetic regulatory marks at a genomic scale. There is a crucial need for specialized software tools to make sense of these data. While various programs have been developed to perform read mapping and peak calling, the subsequent steps have not yet reached proper maturation: identifying relevant transcription factor binding motifs and the precise location of their binding sites remains a bottleneck. Most existing tools present limitations on sequence size, and typically restrict motif discovery to a few hundreds peaks. We present a pipeline called peak-motifs, integrated in the Regulatory Sequence Analysis Tools1, which takes as input a set of peak sequences, discovers exceptional motifs, compares them with motif databases, predicts binding site positions, and offers different visualization interfaces. The pipeline relies on tried-and-tested algorithms whose computing time increases linearly with sequence size, ensuring scalability to massive datasets of several tens of Mb. In addition to the website, peakmotifs can be used as stand-alone application, as well as SOAP/WSDL web services. We assessed peak-motifs performances on several published datasets. In all cases, relevant motifs are disclosed. For example, we discovered individual Oct and Sox motifs in Sox2 and Oct4 peak collections, whereas the original study only found the composite Sox/Oct motif. For the generic transcriptional co-activator p300 examined in heart and midbrain, peak-motifs identified motifs bound by tissue-specific transcription factors consistent with these two tissues. In summary, peak-motifs supports time-efficient and statistically reliable analysis of complete ChIP-seq datasets, while offering an online user-friendly and well-documented interface.

Tumor Necrosis Factor α-Mediated Induction of Interleukin 17C in Human Keratinocytes Is Controlled by Nuclear Factor κB

IL-17C is a member of the IL-17 family of cytokines. The expression of IL-17C has been demonstrated to be strongly induced by TNFα in human keratinocytes, and recently the level of IL-17C was found to be increased in the inflammatory skin disease psoriasis. However, little is known about the molecular mechanisms involved in the regulation of IL-17C. Here, we show that pretreatment of cultured human keratinocytes with the inhibitor of κB kinase 2 inhibitor, SC-514, resulted in a significant reduction in both IL-17C mRNA and protein expression, indicating the significance of this pathway in the regulation of IL-17C. NF-κB binding sites were identified upstream from the IL-17C gene, and by electrophoretic mobility shift assay NF-κB was shown to bind to all three identified binding sites. Moreover, NF-κB binding to these sites was inducible by TNFα. Supershift analysis revealed binding of the NF-κB subunits p65 and p50 to all three NF-κB binding sites. To determine the contribution of NF-κB in IL-17C expression, we conducted luciferase gene reporter experiments and demonstrated that a 3204-bp promoter fragment of IL-17C containing three putative NF-κB binding sites was strongly activated by TNFα. Interestingly, mutations of the three NF-κB binding sites revealed that one specific NF-κB binding site was crucial for the TNFα-mediated IL-17C induction because mutation of this specific site completely abolished TNFα-induced IL-17C promoter activation. We conclude that the activation of NF-κB (p65/p50) is crucial for the TNFα-induced stimulation of IL-17C expression in human keratinocytes.

Glycine Hinges with Opposing Roles at the Acetylcholine Receptor-Channel Transmitter Binding Site

The nicotinic acetylcholine receptor-channel (AChR) is an allosteric protein and an important model for understanding how transmitter molecules activate synaptic receptors. The extent to which agonists activate synaptic receptor-channels depends on the intrinsic tendency of the unliganded receptor to open and the amount of agonist binding energy realized in the channel-opening process. We examined mutations of the nicotinic acetylcholine receptor transmitter binding site (alpha subunit loop B) with regard to both of these parameters. alphaG147 is an ‘activation’ hinge where backbone flexibility maintains high values for intrinsic gating, the equilibrium dissociation constant ratio of the resting conformation for agonists and net ligand binding energy. alphaG153 is a ‘deactivation’ hinge that maintains low values for these parameters. alphaW149 (between these two glycines) mainly serves to provide ligand binding energy for gating. A concerted motion of the two glycine hinges (plus other structural elements at the binding site) positions alphaW149 so that it provides physiologically-optimal binding and gating function at the nerve-muscle synapse.

Glycine Hinges with Opposing Actions at the Acetylcholine Receptor-Channel Transmitter Binding Site

The extent to which agonists activate synaptic receptor-channels depends on both the intrinsic tendency of the unliganded receptor to open and the amount of agonist binding energy realized in the channel-opening process. We examined mutations of the nicotinic acetylcholine receptor transmitter binding site (α subunit loop B) with regard to both of these parameters. αGly147 is an "activation" hinge where backbone flexibility maintains high values for intrinsic gating, the affinity of the resting conformation for agonists and net ligand binding energy. αGly153 is a "deactivation" hinge that maintains low values for these parameters. αTrp149 (between these two glycines) serves mainly to provide ligand binding energy for gating. We propose that a concerted motion of the two glycine hinges (plus other structural elements at the binding site) positions αTrp149 so that it provides physiologically optimal binding and gating function at the nerve-muscle synapse.

Adenovirus L4-22K stimulates major late transcription by a mechanism requiring the intragenic late-specific transcription factor-binding site

The adenovirus major late promoter (MLP) generates a primary transcript that undergoes a complex pattern of regulated alternative RNA splicing and polyadenylation events. The late-specific activation of the MLP requires binding of two infected-cell specific transcription factor complexes, DEF-A and DEF-B, to the so-called DE sequence located downstream of the MLP start site. Previous studies have shown that DEF-B is a homodimer of the viral IVa2 protein and suggested that DEF-A is a heterodimer of IVa2 and an unknown protein. Two proteins from the adenoviral L4 unit have been suggested as DEF-A candidates. Here we have examined L4-22K and L4-33K for possible DEF-A activity. We show that L4-22K stimulates transcription from the MLP in a DE sequence dependent manner both in vivo and in vitro, and that L4-22K binds to the DE sequence in vitro. Further, the position of the L4-22K DNA binding site in a promoter does not appear to be critical for function. Thus, tethering L4-22K either to a position upstream or downstream of the MLP start site, or upstream of a minimal E1B promoter, resulted in an activation of transcription. We also show that the viral pIX promoter is a natural target, activated by L4-22K. Collectively, our results are compatible with the hypothesis that L4-22K may be the elusive component of DEF-A that partakes in activation of the MLP.

The Transcriptional Repressor CcpN from Bacillus subtilis Uses Different Repression Mechanisms at Different Promoters

CcpN, a transcriptional repressor from Bacillus subtilis that is responsible for the carbon catabolite repression of three genes, has been characterized in detail in the past 4 years. However, nothing is known about the actual repression mechanism as yet. Here, we present a detailed study on how CcpN exerts its repression effect at its three known target promoters of the genes sr1, pckA, and gapB. Using gel shift assays under non-repressive and repressive conditions, we showed that CcpN and RNA polymerase can bind simultaneously and that CcpN does not prevent RNA polymerase (RNAP) binding to the promoter. Furthermore, we investigated the effect of CcpN on open complex formation and demonstrate that CcpN also does not act at this step of transcription initiation at the sr1 and pckA and presumably at the gapB promoter. Investigation of abortive transcript synthesis revealed that CcpN acts differently at the three promoters: At the sr1 and pckA promoter, promoter clearance is impeded by CcpN, whereas synthesis of abortive transcripts is repressed at the gapB promoter. Eventually, we demonstrated with Far Western blots and co-elution experiments that CcpN is able to interact with the RNAP alpha-subunit, which completes the picture of the requirements for the repressive action of CcpN. On the basis of the presented results, we propose a new working model for CcpN action.

Challenges of fragment screening

Fragment-based screening for lead generation has seen tremendous growth and success in the last few years. Furthermore, the careful design of fragment libraries has ensured both that the coverage of chemical space is as great as possible and also that the included fragments have desirable physical properties. This particular effort has thus enhanced the advantages of a fragment-based approach. Other technological advances and applications have increased the speed of the process, resulting in more successful case studies being presented. Nonetheless challenges still remain. Weak fragment hits are often overlooked in favor of more potent HTS hits that may have poorer physical properties and ligand efficiencies. The timelines necessary to realize success with fragment-based screens can be long relative to other lead generation approaches, since fragment hits need to be given sufficient consideration and may require more cycles for optimization. A robust system for crystallography, which can be difficult to develop, can also dramatically affect the final outcome of a fragment-based lead generation campaign by enabling the determination of high-resolution complex structures that can serve as starting points for structure-based design. Active research is helping to address these challenges. Computational approaches that can aid in the optimization process either through growing or linking of fragments continue to be developed and can play a significant role in reducing the time required for improving the potency of an initial fragment lead. Methods aimed at exploiting fragment hits for uses other than scaffold generation are also being established to take full advantage of this information as well as any associated structural information available for a project. For example, fragment hits can be merged onto an HTS scaffold during the lead optimization process. In addition, for a given target, potential pharmacophores can be derived from fragment hits and later used for virtual screening of databases to enable scaffold hopping. Fragment positioning methods such as GRID [1], MCSS [2–4], SPROUT [5], MUSIC [6], LUDI [7, 8], and Superstar [9] have been in use for over two decades now and are typically employed during the early stage of lead optimization. These methods determine energetically favorable binding site positions for various functional group types or chemical fragments based on molecular mechanics or knowledge-based potentials. ‘‘Hot spots’’ can be calculated for a wide range of functional groups in a given target binding site/region. Such target-derived pharmacophoric points can also be used to guide docking calculations to more finely sample the relevant regions of a binding site (e.g., [10, 11]) or to perform pharmacophore searches of large databases. Caveat [12] and HOOK [13] were among the first ‘‘fragment-linking’’ computational approaches developed in the early 1990s. Newer generation computational methods continue to be developed (e.g., Re-core [14], Allegrow (Boston De Novo Design, Boston, MA, 2009), Confirm [15], MED-SuMo [16], and pharmacophore modeling for scaffold replacement in MOE (Chemical Computing Group, Montreal, Canada, 2009)) and successful uses of these newer programs are being reported. Increasingly, standard molecular docking programs are being utilized to screen large databases of small molecules to created target-focused fragment sets for experimental testing either in a high-concentration biochemical assay or by biophysical means such as NMR, Biacore, mass spectrometry, or X-ray crystallography. Focused fragment sets D. Joseph-McCarthy (&) Infection Computational Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA e-mail: diane.joseph-mccarthy@astrazeneca.com

Interactions between the Yeast SM22 Homologue Scp1 and Actin Demonstrate the Importance of Actin Bundling in Endocytosis

The yeast SM22 homologue Scp1 has previously been shown to act as an actin-bundling protein in vitro. In cells, Scp1 localizes to the cortical actin patches that form as part of the invagination process during endocytosis, and its function overlaps with that of the well characterized yeast fimbrin homologue Sac6p. In this work we have used live cell imaging to demonstrate the importance of key residues in the Scp1 actin interface. We have defined two actin binding domains within Scp1 that allow the protein to both bind and bundle actin without the need for dimerization. Green fluorescent protein-tagged mutants of Scp1 also indicate that actin localization does not require the putative phosphorylation site Ser-185 to be functional. Deletion of SCP1 has few discernable effects on cell growth and morphology. However, we reveal that scp1 deletion is compensated for by up-regulation of Sac6. Furthermore, Scp1 levels are increased in the absence of sac6. The presence of compensatory pathways to up-regulate Sac6 or Scp1 levels in the absence of the other suggest that maintenance of sufficient bundling activity is critical within the cell. Analysis of cortical patch assembly and movement during endocytosis reveals a previously undetected role for Scp1 in movement of patches away from the plasma membrane. Additionally, we observe a dramatic increase in patch lifetime in a strain lacking both sac6 and scp1, demonstrating the central role played by actin-bundling proteins in the endocytic process.

Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites

One of the simplest ways to predict ligand binding sites is to identify pocket-shaped regions on the protein surface. Many programs have already been proposed to identify these pocket regions. Examination of their algorithms revealed that a pocket intrinsically has two arbitrary properties, "size" and "depth". We proposed a new definition for pockets using two explicit adjustable parameters that correspond to these two arbitrary properties. A pocket region is defined as a space into which a small probe can enter, but a large probe cannot. The radii of small and large probe spheres are the two parameters that correspond to the "size" and "depth" of the pockets, respectively. These values can be adjusted individual putative ligand molecule. To determine the optimal value of the large probe spheres radius, we generated pockets for thousands of protein structures in the database, using several size of large probe spheres, examined the correspondence of these pockets with known binding site positions. A new measure of shallowness, a minimum inaccessible radius, R(inaccess), indicated that binding sites of coenzymes are very deep, while those for adenine/guanine mononucleotide have only medium shallowness and those for short peptides and oligosaccharides are shallow. The optimal radius of large probe spheres was 3-4 A for the coenzymes, 4 A for adenine/guanine mononucleotides, and 5 A or more for peptides/oligosaccharides. Comparison of our program with two other popular pocket-finding programs showed that our program had a higher performance of detecting binding pockets, although it required more computational time.

Single nucleotide polymorphism in the promoter region of human alpha-fetoprotein (AFP) gene and its significance in hepatocellular carcinoma (HCC)

Background Variations of serum AFP levels in HCC patients and cell lines are likely due to the differential activity of enhancer/silencer elements that control AFP. To understand the potential mechanism underlying the differential expression of AFP, we have examined the sequence of the AFP promoter in HCC. Methods Direct DNA sequencing was carried out to sequence 980 bp of AFP promoter of DNA samples isolated from 83 HCC patients. Results Three novel SNPs in the promoter region of the AFP gene, which have not been previously reported, were found at positions −330, −401 and −692. The level of serum AFP was significantly higher in HCC patients with the CT genotype of 330 SNP or the AG genotype of the 401 SNP. The genotype of CG in 692 SNP was also associated with a significant elevated level of serum AFP, and further this genotype appeared to be associated with the high risk of HCC development. 401 SNP and 692 SNP were located at the positions of known binding sites for transcription factors that have a role in the production of AFP and the growth of tumors. Conclusions The novel polymorphisms identified in the promoter region of the AFP gene may be pathologically significant in HCC.

Context Specific Transcription Factor Prediction

One of the goals of systems biology is the identification of regulatory mechanisms that govern an organism's response to external stimuli. Transcription factors have been hypothesized as a major contributor to an organism's response to various outside stimuli, and a great deal of work has been done to predict the set of transcription factors which regulate a given gene. Most of the current methods seek to identify possible binding sites from genomic sequence. Initial attempts at predicting transcription factors from genomic sequences suffered from the problem of false positives. Making the problem more difficult, it has also been shown that while predicted binding sites might be false positives, they can be shown to bind to their corresponding sequences in vitro. One method for rectifying this is through the use of phylogenetic analysis in which only regions which show high evolutionary conservation are analyzed. However such an approach may be too stringent because of the level of degeneracy shown in transcription factor binding site position weight matrices. Due to the degeneracy, there may be only a few bases that need to be conserved across species. Therefore, while a sequence may not show a high level of evolutionary conservation, these sequences may still show high affinity for the same transcription factor. In predicting transcription factor binding we explore the notion that "Co-expression implies co-regulation" [Allocco et al. BMC Bioinformatics 5:18, 2004]. With multiple genes requiring similar transcription factors binding sites, there exists a basis for eliminating false positives. This method allows for the selection of transcription factors binding sites that are active under a given experimental paradigm, thereby allowing us to indirectly incorporate the effects of chromosome and recognition site presentation upon transcription factor binding prediction. Rather than having to rationalize that a few transcription factors binding sites are over-represented in a cluster of genes, one can show that a few transcription factors are active in the cluster of genes that have been grouped together. Although the method focuses on predicting experiment-specific transcription factor binding sites, it is possible that if such a methodology were used in an iterative process where different experiments were analyzed, one could obtain a comprehensive set of transcription factors binding sites which regulate the various dynamic responses shown by biological systems under a variety of conditions hence building a more comprehensive model of transcriptional regulation.