An Approximated Voxel Approach for the Identification and Modelling of Ligand-Binding Sites

Most protein-ligand interactions take place on surfaces and include but not limited to factors such as chemical composition, hydrophobicity, electronegavitiy and shape complementarity. Past studies showed that protein-protein interactions occur on comparatively fiat regions whereas protein-ligand bindings involve crevices. In the search for such sites various approaches have been designed and developed each of which is algorithmically unique. The use of grid units or voxels has been demonstrated in early studies with relatively good results obtained. We present here an approximated approach comprising of the use of voxels and computer vision methods in the search for ligand-binding areas. Each test protein is modelled and analysed in 2D with all corresponding residues graphically presented for successfully identified sites. The study was carried out on 2 sets of proteins： FK506-bound proteins and heme-bound proteins with promising results obtained for all test cases.

Increased monoamine oxidase activity and imidazoline binding sites in insulin-resistant adipocytes from obese Zucker rats

BACKGROUND Despite overt insulin resistance,adipocytes of genetically obese Zucker rats accumulate the excess of calorie intake in the form of lipids.AIM To investigate whether factors can replace or reinforce insulin lipogenic action by exploring glucose uptake activation by hydrogen peroxide,since it is produced by monoamine oxidase(MAO)and semicarbazide-sensitive amine oxidase(SSAO)in adipocytes.METHODS 3H-2-deoxyglucose uptake(2-DG)was determined in adipocytes from obese and lean rats in response to insulin or MAO and SSAO substrates such as tyramine and benzylamine.14C-tyramine oxidation and binding of imidazolinic radioligands[3H-Idazoxan,3H-(2-benzofuranyl)-2-imidazoline]were studied in adipocytes,the liver,and muscle.The influence of in vivo administration of tyramine+vanadium on glucose handling was assessed in lean and obese rats.RESULTS 2-DG uptake and lipogenesis stimulation by insulin were dampened in adipocytes from obese rats,when compared to their lean littermates.Tyramine and benzylamine activation of hexose uptake was vanadate-dependent and was also limited,while MAO was increased and SSAO decreased.These changes were adipocyte-specific and accompanied by a greater number of imidazoline I2 binding sites in the obese rat,when compared to the lean.In vitro,tyramine precluded the binding to I2 sites,while in vivo,its administration together with vanadium lowered fasting plasma levels of glucose and triacylglycerols in obese CONCLUSION The adipocytes from obese Zucker rats exhibit increased MAO activity and imidazoline binding site number.However,probably as a consequence of SSAO down-regulation,the glucose transport stimulation by tyramine is decreased as much as that of insulin in these insulin-resistant adipocytes.The adipocyte amine oxidases deserve more studies with respect to their putative contribution to the management of glucose and lipid handling.

Prediction of protein binding sites using physical and chemical descriptors and the support vector machine regression method

In this paper a new continuous variable called core-ratio is defined to describe the probability for a residue to be in a binding site, thereby replacing the previous binary description of the interface residue using 0 and 1. So we can use the support vector machine regression method to fit the core-ratio value and predict the protein binding sites. We also design a new group of physical and chemical descriptors to characterize the binding sites. The new descriptors are more effective, with an averaging procedure used. Our test shows that much better prediction results can be obtained by the support vector regression （SVR） method than by the support vector classification method.

Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat

Expression divergence caused by genetic variation and crosstalks among subgenomes of the allohexaploid bread wheat(Triticum aestivum.L.,BBAADD)is hypothesized to increase its adaptability and/or plasticity.However,the molecular basis of expression divergence remains unclear.Squamosa promoter-binding protein-like(SPL)transcription factors are critical for a wide array of biological processes.In this study,we constructed expression regulatory networks by combining DAP-seq for 40 SPLs,ATACseq,and RNA-seq.Our findings indicate that a group of low-affinity SPL binding regions(SBRs)were targeted by diverse SPLs and caused different sequence preferences around the core GTAC motif.The SBRs including the low-affinity ones are evolutionarily conserved,enriched GWAS signals related to important agricultural traits.However,those SBRs are highly diversified among the cis-regulatory regions(CREs)of syntenic genes,with less than 8%SBRs coexisting in triad genes,suggesting that CRE variations are critical for subgenome differentiations.Knocking out of Ta SPL7A/B/D and Ta SPL15A/B/D subfamily further proved that both high-and low-affinity SBRs played critical roles in the differential expression of genes regulating tiller number and spike sizes.Our results have provided baseline data for downstream networks of SPLs and wheat improvements and revealed that CRE variations are critical sources for subgenome divergence in the allohexaploid wheat.

Addition of heparin binding sites strongly increases the bone forming capabilities of BMP9 in vivo

Bone Morphogenetic proteins(BMPs)like BMP2 and BMP7 have shown great potential in the treatment of severe bone defects.In recent in vitro studies,BMP9 revealed the highest osteogenic potential compared to other BMPs,possibly due to its unique signaling pathways that differs from other osteogenic BMPs.However,in vivo the bone forming capacity of BMP9-adsorbed scaffolds is not superior to BMP2 or BMP7.In silico analysis of the BMP9 protein sequence revealed that BMP9,in contrast to other osteogenic BMPs such as BMP2,completely lacks so-called heparin binding motifs that enable extracellular matrix(ECM)interactions which in general might be essential for the BMPs’osteogenic function.Therefore,we genetically engineered a new BMP9 variant by adding BMP2-derived heparin binding motifs to the N-terminal segment of BMP9′s mature part.The resulting protein(BMP9 HB)showed higher heparin binding affinity than BMP2,similar osteogenic activity in vitro and comparable binding affinities to BMPR-II and ALK1 compared to BMP9.However,remarkable differences were observed when BMP9 HB was adsorbed to collagen scaffolds and implanted subcutaneously in the dorsum of rats,showing a consistent and significant increase in bone volume and density compared to BMP2 and BMP9.Even at 10-fold lower BMP9 HB doses bone tissue formation was observed.This innovative approach of significantly enhancing the osteogenic properties of BMP9 simply by addition of ECM binding motifs,could constitute a valuable replacement to the commonly used BMPs.The possibility to use lower protein doses demonstrates BMP9 HB’s high translational potential.

TrFAST: A Tool to Predict Signaling Pathway-specific Transcription Factor Binding Sites

Recent advances in the development of high-throughput tools have significantly revolutionized our understanding of molecular mech- anisms underlying normal and dysfunctional biological processes. Here we present a novel computational tool, transcription factor search and analysis tool （TrFAST）, which was developed for the in silico analysis of transcription factor binding sites （TFBSs） of sig- naling pathway-specific TFs. TrFAST facilitates searching as well as comparative analysis of regulatory motifs through an exact pattern matching algorithm followed by the graphical representation of matched binding sites in multiple sequences up to 50 kb in length. TrFAST is proficient in reducing the number of comparisons by the exact pattern matching strategy. In contrast to the pre-existing tools that find TFBS in a single sequence, TrFAST seeks out the desired pattern in multiple sequences simultaneously. It counts the GC con- tent within the given multiple sequence data set and assembles the combinational details of consensus sequence（s） located at these regions, thereby generating a visual display based on the abundance of unique pattern. Comparative regulatory region analysis of multi- ple orthologous sequences simultaneously enhances the features of TrFAST and provides a significant insight into study of conservation of non-coding cis-regulatory elements. TrFAST is freely available at http：//www.fi-pk.com/trfast.html.

Structure effect of nucleotides in terbium(Ⅲ)-nucleotide fluorescent reaction—-New evidence for the binding sites of terbium(Ⅲ) on nucleotides

Upon addition of Tb^(3+) to 16 nucleotides and homopolynucleotides, all of them showed a characteristic green emission from Tb^(3+), but with much different intensity, upon excitation in the aromatic region of bases. The result suggested that nucleotides with at least one carbonyl group in nucleotide bases are better enhancers to the fluorescence of Tb3+. The complexes of ATP, GDP and GTP with T5^(3+) are synthesized as two types of models. Guanine tpye nucleotides with one carbonyl group in the bases are the best enhancers, while adenine type nucleotides with no carbonyl group in the bases are poorest enhancers to the fluorescence of Tb^(3+). Comparing the IR spectra of ATP, GTP, GDP and their Tb^(3+) complexes suggested that C-6 carbonyl group in GTP and GDP may be involved in complex formation, which may be responsible for the effective energy transfer. This is further supported by comparing the UV spectra of ATP, Poly(A), GTP, and Poly(G) with their Tb^(3+) complexes in water solution.

Arabidopsis AtADF1 is Functionally Affected by Mutations on Actin Binding Sites

The plant actin depolymerizing factor （ADF） binds to both monomeric and filamentous actin, and is directly involved in the depolymerization of actin filaments. To better understand the actin binding sites of the Arabidopsis thaliana L. AtADF1, we generated mutants of AtADF1 and investigated their functions in vitro and in vivo. Analysis of mutants harboring amino acid substitutions revealed that charged residues （Arg98 and Lys100） located at the α-helix 3 and forming an actin binding site together with the N-terminus are essential for both G- and F-actin binding. The basic residues on the β-strand 5 （K82/A） and the α-helix 4 （R135/A, R137/A） form another actin binding site that is important for F-actin binding. Using transient expression of CFP-tagged AtADF1 mutant proteins in onion （Allium cepa） peel epidermal cells and transgenic Arabidopsis thaliana L. plants overexpressing these mutants, we analyzed how these mutant proteins regulate actin organization and affect seedling growth. Our results show that the ADF mutants with a lower affinity for actin filament binding can still be functional, unless the affinity for actin monomers is also affected. The G-actin binding activity of the ADF plays an essential role in actin binding, depolymerization of actin polymers, and therefore in the control of actin organization.

Systematic identification and annotation of multiple-variant compound effects at transcription factor binding sites in human genome

Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites （TFBSs） are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential ＂interference＂ among multiple variants within the same TFBS. In this study, we presented COPE-TFBS （Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site）, a novel method that considers sequence context to accurately predict variant effects on TFBSs. We systematically re-analyzed the sequencing data from both the 1000 Genomes Project and the Genotype-Tissue Expression （GTEx） Project via COPE-TFBS, and identified numbers of novel TFBSs, transformed TFBSs and discordantly annotated TFBSs resulting from multiple variants, further highlighting the necessity of sequence context in accurately annotating genetic variants.

Structure-Based Prediction of Transcription Factor Binding Sites

Transcription Factors（TFs） are a very diverse family of DNA-binding proteins that play essential roles in the regulation of gene expression through binding to specific DNA sequences. They are considered as one of the prime drug targets since mutations and aberrant TF-DNA interactions are implicated in many diseases.Identification of TF-binding sites on a genomic scale represents a critical step in delineating transcription regulatory networks and remains a major goal in genomic annotations. Recent development of experimental high-throughput technologies has provided valuable information about TF-binding sites at genome scale under various physiological and developmental conditions. Computational approaches can provide a cost-effective alternative and complement the experimental methods by using the vast quantities of available sequence or structural information. In this review we focus on structure-based prediction of transcription factor binding sites. In addition to its potential in genomescale predictions, structure-based approaches can help us better understand the TF-DNA interaction mechanisms and the evolution of transcription factors and their target binding sites. The success of structure-based methods also bears a translational impact on targeted drug design in medicine and biotechnology.

Nucleosomal Context of Binding Sites Influences Transcription Factor Binding Affinity and Gene Regulation

Transcription factor （TF） binding to its DNA target site plays an essential role in gene regulation. The location, orientation and spacing of transcription factor binding sites （TFBSs） also affect regulatory function of the TF. However, how nucleosomal context of TFBSs influences TF binding and subsequent gene regulation remains to be elucidated. Using genome-wide nucleosome positioning and TF binding data in budding yeast, we found that binding affinities of TFs to DNA tend to decrease with increasing nucleosome occupancy of the associated binding sites. We further demonstrated that nucleosomal context of binding sites is correlated with gene regulation of the corresponding TF. Nucleosome-depleted TFBSs are linked to high gene activity and low expression noise, whereas nucleosome-covered TFBSs are associated with low gene activity and high expression noise. Moreover, nucleosome-covered TFBSs tend to disrupt coexpression of the corresponding TF target genes. We conclude that nucleosomal context of binding sites influences TF binding affinity, subsequently affecting the regulation of TFs on their target genes. This emphasizes the need to include nucleosomal context of TFBSs in modeling gene regulation.

Studies of Site Specific DNA Binding of Small Peptides by Competitive Assays with Hoechst 33258

With a view to finding out precisely how small peptides recognize a particular binding site of DNA, we have accomplished DNA binding studies of two peptides, H-Tyr-Arg-OH (YR) and H-Gly-Gly-His-OH (GGH) by using measurements in comparison with the binding between DNA and Hoechst 33258. The inhibition mode by YR and GGH to DNA binding of Hoechst 33258 was analyzed by Lineweaver-Burk plot which shows the plot of typical competitive inhibition at concentration of Hoechst 33258 from 3.66 ( 10-9 mol / L to 1.09 ( 10-8 mol / L. And it is concluded that YR binds to DNA in its minor groove (AT rich regions) with a binding constant K = 1.02 ( 108 (mol / L)-1. The GGH(s specificity is reduced at high concentration because it can also bind GC base pair.

基于3A组装的多拷贝基因策略优化重组水蛭素变体Ⅲ的生产

水蛭素变体Ⅲ(Hirudin varidantⅢ,Hv3)是一种从水蛭中提取的活性成分,在预防和治疗白内障方面具有潜在作用。为了制备足量Hv3用于进一步的临床前应用研究,该研究开发了一种在谷氨酸棒杆菌(Corynebacterium glutamicum)中高效、稳定表达重组水蛭素变体Ⅲ(recombinant Hirudin varidantⅢ,Rhv3)的办法。首先,在C.glutamicum中构建含Ptac启动子和CspA信号肽的Rhv3分泌表达菌株,比较其在不同培养基中的表达情况。结果表明在BHI培养基中Rhv3活性最高,达到3.02×10^(3) ATU/L。为进一步提升Rhv3产量,通过核糖体结合位点(ribosome binding site,RBS)筛选,选用RBS1应用于Rhv3多拷贝菌株构建和表达。然后利用3A组装技术构建含不同信号肽和不同拷贝数的Rhv3分泌表达菌株进一步优化其产量。通过放大发酵培养,Rhv3产量达到1.89 g/L,活性达到10.91×10^(3) ATU/L。最后利用镍柱对Rhv3进行简单纯化,其纯度达到90%。该异源表达策略有效提高Rhv3表达量,为Rhv3的重组生产提供了一种质量可靠、低成本的表达体系。

Interactions Between Anticancer Pt(II) complexes and Human Erythrocyte Spectrin *

The interactions between human erythrocyte spectrin(SP) and Pt(II) complexes with different composition and configuration were studied by fluorescence and circular dichroism spectra. The results showed that there are 4.7×10 2 binding sites of cisplatin(CDDP) in a spectrin tetramer(SPT). Among them, about 70 sites with apparent binding constant K 1】3.47×10 6 were of highest affinity, 1.8×10 2 sites with K 2 = 3.47×10 6 were of high affinity, and other 2.2×10 2 sites with K 3 = 8.77×10 5 were of low affinity. The conformation change of spectrin, depending on the concentration of Pt(II) complex and molar ratio(R) of Pt(II) complex to spectrin, was induced by the binding of Pt(II) complexes. It indicated that the interaction of both CDDP and cis diaquodiamine platinum(DADP) with SP followed a two step first order kinetic process in the first stage (1 h), and the kinetic constants were determined. In the second stage, the induced conformation change, polymerization and depolymerization of SP were probably involved. It was noticed that in the reaction of SP and Pt(II) complexes with 1,2 cyclohexanediammine isomers as chiral carrier ligand, stereo matching played a more important role than the affinity of Pt(II) to thiol groups of SP.

Cloning and Analysis of a Disease Resistance Gene Homolog from Soybean

Conserved domains e.g. nucleotide binding site (NBS) were found in several cloned plant disease resistance genes. Based on the NBS domain, resistance gene analogs (RGAs) have been isolated previously and were used as probes to screen a soybean (Glycine max L. Merr.) cDNA library. A full-length cDNA, KR3, was obtained by screening the library and rapid amplification of cDNA ends (RACE) method. Sequence analysis revealed that the cDNA is 2 353 bp in length and the open reading frame (ORF) codes for a polypeptide of 636 amino acids with a Toll-Interleukin-1 receptor (TIR) and a NBS domain. Sequence alignment showed that it was similar to N gene of tobacco. The phylogenetic tree analysis of R proteins with NBS from higher plants was performed. The KR3 gene has low copies in soybean genome and its expression was induced by exogenous salicylic acid (SA).

Flumazenil-insensitive benzodiazepine effects in vitro and in vivo

OBJECTIVE To identify benzodi⁃azepine(BZD)effects that are insensitive to the classical BZD binding site antagonist,flumazenil.Whether the flumazenil-insensitive BZD effects have selectivity on different GABAA receptor sub⁃types was also investigated.METHODS The high-concentration effects of BZDs and their sensitivity to flumazenil were determined on recombi⁃nant synaptic(α1β2γ2,α2β2γ2,α5β2γ2)and extra-synaptic(α4β2δ)GABAA receptors using the voltage-clamp electrophysiology technique.The in vivo evaluation of flumazenil-insensitive BZD effects was conducted in mice loss of right reflex(LORR)test.RESULTS Diazepam induced a biphasic potentiation for theα1β2γ2,α2β2γ2 andα5β2γ2 receptor channels,but did not affect theα4β2δreceptor.In contrast to the nanomolar com⁃ponent of potentiation,the second potentiation elicited by micromolar diazepam was insensitive to flumazenil.Midazolam,clonazepam,and loraz⁃epam at 200μmol·L-1 exhibited similar flumaze⁃nil-insensitive effects onα1β2γ2,α2β2γ2 andα5β2γ2 receptors,whereas the potentiation induced by 200μmol·L-1 zolpidem or triazolam was abol⁃ished by flumazenil.Consistent with the in vitro results,flumazenil antagonized the zolpidem(50 mg·kg-1)-induced LORR,but not those induced by 50 mg·kg-1 diazepam or 100 mg·kg-1 midazolam.CONCLUSION The existence of non-classical BZD binding sites on certain GABAA receptor subtypes and the flumazenil-insensitive effects depend on the chemical structures of the allosteric modulators.

A combined statistical model for multiple motifs search

Transcription factor binding sites （TFBS） play key roles in genebior 6.8 wavelet expression and regulation. They are short sequence segments with definite structure and can be recognized by the corresponding transcription factors correctly. From the viewpoint of statistics, the candidates of TFBS should be quite different from the segments that are randomly combined together by nucleotide. This paper proposes a combined statistical model for finding over- represented short sequence segments in different kinds of data set. While the over-represented short sequence segment is described by position weight matrix, the nucleotide distribution at most sites of the segment should be far from the background nucleotide distribution. The central idea of this approach is to search for such kind of signals. This algorithm is tested on 3 data sets, including binding sites data set of cyclic AMP receptor protein in E.coli, PlantProm DB which is a non-redundant collection of proximal promoter sequences from different species, collection of the intergenic sequences of the whole genome of E.Coli. Even though the complexity of these three data sets is quite different, the results show that this model is rather general and sensible.

Bioinformatics Analysis of the Human TCF7L2 Gene Promoter Region

[Objectives]This study was conducted to investigate characteristics of the human TCF7 L2 gene promoter.[Methods]The 2000 bp sequence of the 5’regulatory region of the human TCF7 L2 gene was obtained from the UCSC genome database.The promoter,transcription factor binding sites,CpG islands,SNPs and so on were analyzed by a variety of online softwares.[Results]The bioinformatics analysis results showed there were at least 5 potential promoters in the positive-sense strand of the 2000 bp sequence,among which-242--192 bp,-853--803 bp might contain core promoters.A TATA box and a CpG island with a length of 499 bp were found.241,944 and 1035(positive-sense strand)transcription factor binding sites were predicted by the AliBaba2.1,PROMO and JASPAR softwares,respectively.207 common transcription factor binding sites in the conserved region of human and mouse homologous TCF7 L2 gene promoter were identified with CONREAL program,involving 66 kinds of transcription factors.Two SNPs were found in the promoter region.[Conclusions]The promoter of the human TCF7 L2 gene was analyzed by bioinformatics,and the promoter characteristics were obtained.

A NOVEL MOLECULARLY IMPRINTED POLYMER:SYNTHESIS AND ADSORPTION BEHAVIOR OF GATIFLOXACIN

A kind of molecularly imprinted polymer (MIPs) with high selectivity was prepared using methacrylic acid (MAA) as functional monomer, ethylene glycol dimethacrylate (EDMA) as crosslinker and Gatifloxacin as template. The effect of various parameters such as volume of solvent, functional monomer dosage, crosslinker dosage and polymerization time were investigated. The selective binding experiment for substrates show that the affinity and selectivity for Gatifloxacin were higher than that for blank polymer. Scatchard analysis show that the MIPs recognized template with two kinds of binding sites. The dissociation constant Kd and maximum adsorption quantity Qmax of these two kinds of binding sites were calculated: Kd1 and Qmax1 of the binding sites with high affinity were 8.67×10-4 mol/L and 28.19μmol/g, while Kd2 and Qmax2 of the binding sites with low affinity were1.05×10-3 mol/L and 33.20μmol/g respectively.

Investigation of the interaction between two phenylethanoid glycosides and bovine serum albumin by spectroscopic methods

Two phenylethanoid glycosides, acteoside and forsythoside B, were first isolated from the traditional Chinese herb Callicarpa peii H.T. Chang. The interaction between the two phenylethanoid glycosides and bovine serum albumin （BSA） was investigated by fluorescence, UV vis absorbance and circular dichroism （CD）. The results showed that the quenching mechanism in the drug-BSA binary systems was a combination of static quenching and non- radiative energy transfer. Displacement experiments confirmed that the drug bound to the site I of BSA. UVvis and CD measurements indicated that the binding of the drug to BSA induced conformational changes in BSA.