Design of novel zinc finger proteins: towards artificial control of specific gene expression

Identification of drug side effects with a path-based method

The study of drug side effects is a significant task in drug discovery. Candidate drugs with unaccepted side effects must be eliminated to prevent risks for both patients and pharmaceutical companies. Thus, all side effects for any candidate drug should be determined. However, this task, which is carried out through traditional experiments, is time-consuming and expensive. Building computational methods has been increasingly used for the identification of drug side effects. In the present study, a new path-based method was proposed to determine drug side effects. A heterogeneous network was built to perform such method, which defined drugs and side effects as nodes. For any drug and side effect, the proposed path-based method determined all paths with limited length that connects them and further evaluated the association between them based on these paths. The strong association indicates that the drug has a side effect with a high probability. By using two types of jackknife test, the method yielded good performance and was superior to some other network-based methods. Furthermore, the effects of one parameter in the method and heterogeneous network was analyzed.

Pre-dialysis serum creatinine as an independent predictor of responsiveness to zinc supplementation among patients on hemodialysis

BACKGROUND

To investigate whether pre-dialysis level of serum creatinine (SCre) could indicate the responsiveness to zinc supplementation of patients on maintenance hemodialysis (MHD).

METHODS

We retrospectively reviewed the results of our previous randomized study of 91 patients who had been on MHD and received zinc supplementation with either zinc acetate hydrate (ZAH; zinc, 50 mg/day) or polaprezinc (PPZ; zinc, 34 mg/day). A late response to zinc supplementation was defined as a serum zinc level of < 80 μg/dL three months after the study began. Patients were divided into two groups: late response (serum zinc level < 80 μg/dL) and early response (serum zinc level ≥ 80 μg/dL). Factors independently associated with a late response to zinc supplementation were determined using inverse probability of treatment weighting (IPTW) multivariate logistic analysis.

RESULTS

Of 91 patients, 86 continued to receive zinc supplementation after three months. The mean pre-dialysis SCre level was 10.0 mg/dL. The number of patients with a late response and response to zinc supplementation was 32 and 54, respectively. There was a significant negative correlation between the pre-dialysis SCre and the Δserum zinc change for 3 months. (r = - 0.284, P = 0.008). IPTW multivariate analysis showed that a pre-dialysis SCre level ≥ 10.0 mg/dL (odds ratio, 3.71; 95% confidence interval; 1.24-11.1, P = 0.022) was an independent factor associated with a late response to zinc supplementation.

CONCLUSIONS

Pre-dialysis SCre level was independently associated with responsiveness to zinc supplementation after three months in patients on MHD.

Comparison of zinc acetate hydrate and polaprezinc for zinc deficiency in patients on maintenance hemodialysis: A single-center, open-label, prospective randomized study

The efficacy and safety of zinc acetate hydrate (ZAH) for zinc supplementation in patients on maintenance hemodialysis (MHD) remains unknown. In this prospective, single-center, open-label, parallel-group trial for MHD patients with serum zinc level <70 μg/dL, we compared ZAH (zinc; 50 mg/day) and polaprezinc (PPZ; zinc; 34 mg/day) beyond 6-month administration in a 1:1 randomization manner. The ZAH and PPZ groups had 44 and 47 patients, respectively. At 3 months, the change rate of serum zinc levels in the ZAH group was significantly higher than that in the PPZ group. Three months after the study, serum copper levels significantly decreased in the ZAH group, but not in the PPZ group. No significant differences were noted in anemia management in either group. ZAH was superior to PPZ in increasing serum zinc levels. Clinicians should note the stronger decline in serum copper levels when using ZAH for MHD patients.

Effect of Zinc Supplementation on Maintenance Hemodialysis Patients: A Systematic Review and Meta-Analysis of 15 Randomized Controlled Trials

We aimed to examine the effects of zinc supplementation on nutritional status, lipid profile, and antioxidant and anti-inflammatory therapies in maintenance hemodialysis (MHD) patients. We performed a systematic review and meta-analysis of randomized, controlled clinical trials of zinc supplementation. Metaregression analyses were utilized to determine the cause of discrepancy. Begg and Egger tests were performed to assess publication bias. Subgroup analysis was utilized to investigate the effects of zinc supplementation in certain conditions. In the crude pooled results, we found that zinc supplementation resulted in higher serum zinc levels (weighted mean difference [WMD] = 28.489; P < 0.001), higher dietary protein intake (WMD = 8.012; P < 0.001), higher superoxide dismutase levels (WMD = 357.568; P = 0.001), and lower levels of C-reactive protein (WMD = −8.618; P = 0.015) and malondialdehyde (WMD = −1.275; P < 0.001). The results showed no differences in lipid profile. In the metaregression analysis, we found that serum zinc levels correlated positively with intervention time (β = 0.272; P = 0.042) and varied greatly by ethnicity (P = 0.023). Results from Begg and Egger tests showed that there was no significant bias in our meta-analysis (P > 0.1). Results of subgroup analysis supported the above results. Our analysis shows that zinc supplementation may benefit the nutritional status of MHD patients and show a time-effect relationship.

Copper(II) ion binding to cellular prion protein

Prion diseases are fatal neurodegenerative diseases thought to arise from the post-translational conversion of normal cellular prion protein to a scrapie isoform. Experimental data suggest a role for copper(II) ions in the process. An ab initio QM/MM approach and available experimental data were combined in order to identify and evaluate three potential copper(II) ion binding sites in the C-terminal portion of the normal cellular prion protein. Our results suggest that copper(II) ion binds to His 187 but not to His 140 and His 177 of the binding site in the cellular prion protein.

Alpha-helical linker of an artificial 6-zinc finger peptide contributes to selective DNA binding to a discontinuous recognition sequence

Although many zinc finger motifs have been developed to recognize specific DNA triplets, a rational way to selectively skip a particular non-recognized gap in the DNA sequence has never been established. We have now created a 6-zinc finger peptide with an alpha-helix linker, Sp1ZF6(EAAAR)4, which selectively binds to the discontinuous recognition sites in the same phase (10 bp gap) against the opposite phase (5 bp gap) of the DNA helix. The linker peptide (EAAAR)4 forms an alpha-helix structure stabilized by salt bridges, and the helical length is estimated to be about 30 A, corresponding to that of the 10 bp DNA. The gel shift assays demonstrate that Sp1ZF6(EAAAR)4 preferably binds to the 10 bp-gapped target rather than the 5 bp-gapped target. The CD spectra show that the alpha-helical content of the (EAAAR)4 linker is higher in the complex with the 10 bp-gapped target than in the complex with the 5 bp-gapped target. The present results indicate that the alpha-helical linker is suitable for binding to the recognition sites in the same phase and that the linker induces the loss of binding affinity to the recognition sites with the opposite phase. The engineering of a helix-structured linker in the 6-zinc finger peptides should be one of the most promising approaches for selectively targeting discontinuous recognition sites depending on their phase situations.

In vivo drafting of single-chain antibodies for regulatory duty on the sigma54-promoter Pu of the TOL plasmid

The identification of single-chain antibodies (scFvs) that interfere in vivo with the building of the complex that activate the prokaryotic, sigma54-dependent promoter Pu of the catabolic TOL plasmid pWW0 is reported. To this end, a phage M13 library of scFvs was raised against the cognate prokaryotic enhancer-binding activator, XylR. The scFv pool was then expressed intracellularly in a reporter Pu-lacZ strain of Escherichia coli designed to permit formation of intramolecular disulphide bonds in cytoplasmic proteins. This strain allowed the assembly of functional scFvs and the direct testing of their activity on the Pu promoter in vivo. Specifically, genetic screening for lacZ-minus colonies yielded a number of scFvs able to downregulate transcriptional output in live cells. Two antibody clones were purified and shown to inhibit the activity of the same promoter in vitro as well. These scFvs targeted the DNA-binding domain of XylR and its ATP binding site respectively. This work provides a proof of principle that mimetic regulatory factors can be derived from an antibody repertoire that specifically interact with given transcriptional activators. As assembly of initiation complexes is stimulated or inhibited by regulatory proteins we argue that anti-XylR scFvs operate as bona fide transcriptional inhibitors of the Pu promoter.

Laboratory-directed protein evolution

Systematic approaches to directed evolution of proteins have been documented since the 1970s. The ability to recruit new protein functions arises from the considerable substrate ambiguity of many proteins. The substrate ambiguity of a protein can be interpreted as the evolutionary potential that allows a protein to acquire new specificities through mutation or to regain function via mutations that differ from the original protein sequence. All organisms have evolutionarily exploited this substrate ambiguity. When exploited in a laboratory under controlled mutagenesis and selection, it enables a protein to "evolve" in desired directions. One of the most effective strategies in directed protein evolution is to gradually accumulate mutations, either sequentially or by recombination, while applying selective pressure. This is typically achieved by the generation of libraries of mutants followed by efficient screening of these libraries for targeted functions and subsequent repetition of the process using improved mutants from the previous screening. Here we review some of the successful strategies in creating protein diversity and the more recent progress in directed protein evolution in a wide range of scientific disciplines and its impacts in chemical, pharmaceutical, and agricultural sciences.

An artificial six-zinc finger peptide with polyarginine linker: Selective binding to the discontinuous DNA sequences

Artificial DNA binding peptides recognizing separated sequences would expand varieties of the target genes for desirable transcriptional control. Here we demonstrated that polyarginine linker between two 3-zinc finger domains gives DNA binding selectivity to the separated target sequences. We created a six-zinc finger peptide, Sp1ZF6(Arg)8, by connecting two DNA binding domains of transcription factor Sp1 with a bulky and cationic polyarginine linker. The DNA binding properties to continuous and discontinuous target sequences were examined and compared to those of Sp1ZF6(Gly)10 containing a flexible and neutral polyglycine linker. The dissociation constants indicate that Sp1ZF6(Arg)8 has an obvious DNA binding preference to discontinuous target sequences but not Sp1ZF6(Gly)10. Footprinting analyses also showed that Sp1ZF6(Arg)8 binds properly only to the discontinuous target sites, while Sp1ZF6(Gly)10 does not distinguish them. The results provide helpful information for linker design of future zinc finger peptides to various states of DNA as gene expression regulators.

A Novel Zinc Finger Gene ZNF468 with Two Co-Expressional Splice Variants, ZNF468.1 and ZNF468.2

A novel human zinc finger protein encoding gene ZNF468 was obtained from a fetal brain cDNA library. By BLAST-N analysis we found two different splice variants. We termed the two splice variants ZNF468.1 and ZNF468.2. By BLAST search against the human genome database, ZNF468 was mapped to 19q13.4. The ZNF468.1 cDNA has four exons, and the ZNF468.2 cDNA has one more, between the third and fourth exon. This extra exon creates a difference between the deduced protein N-termini of the two splice variants. The ZNF468.1 cDNA is 3906 bp in length, encoding a 522a a protein, and ZNF468.2 is 4024 bp, encoding a 469-aa-protein. Both proteins contain 11 C2H2-type zinc finger motifs at their C-termini. The N-terminus of the deduced protein of ZNF468.1 has a well-conserved Krüppel-associated box (KRAB) domain that consists of KRAB boxes A and B, whereas the protein of ZNF468.2 does not have the KRAB domain. Tissue distribution of the ZNF468 gene indicates that the two splice variants are widely expressed in normal human tissues, except in heart and brain, and they are also co-expressional.

Optimization of in vitro vascular cell transfection with non-viral vectors for in vivo applications

BACKGROUND

Syngeneic vascular cells are interesting tools for indirect gene therapy in the cardiovascular system. This study aims to optimize transfection conditions of primary cultures of vascular smooth muscle cells (VSMCs) using different non-viral vectors and zinc as an adjuvant and to implant these transfected cells in vivo.

METHODS

Non-liposomal cationic vectors (FuGene 6), polyethylenimines (ExGen 500), and histidylated polylysine (HPL) were used as non-viral vectors in vitro with secreted alkaline phosphatase (SEAP) as reporter gene. Transfection efficiency was compared in cultured rat, rabbit and human VSMCs and fibroblasts. Zinc chloride (ZnCl2) was added to optimize transfection of rat VSMCs in vitro which were then seeded in vivo.

RESULTS

Much higher SEAP levels were obtained in rabbit cells with FuGene 6 (p <0.0001) at day 2 than in equivalent rat and human cells. Rat VSMCs transfected in vitro with FuGene 6 and ExGen 500 expressed higher SEAP levels than with HPL. In rat VSMCs, SEAP secretion was more than doubled by addition of 250 microM ZnCl2 (p <0.0001) for all vectors. Seeding of syngeneic VSMCs transfected under optimized conditions (FuGene 6/pcDNA3-SEAP +250 microM ZnCl2) into healthy Lewis rats using various routes or into post-infarct myocardial scar resulted in a peak of SEAP expression at day 2 and detectable activity in the plasma for at least 8 days.

CONCLUSIONS

FuGene 6 is an efficient non-viral transfection reagent for gene transfer in somatic smooth muscle cells in vitro and ZnCl2 enhances its efficiency. This increased expression of the transgene product is maintained after seeding in vivo.

Synthetic zinc finger peptides: old and novel applications

In the last decade, the efforts in clarifying the interaction between zinc finger proteins and DNA targets strongly stimulated the creativity of scientists in the field of protein engineering. In particular, the versatility and the modularity of zinc finger (ZF) motives make these domains optimal building blocks for generating artificial zinc finger peptides (ZFPs). ZFPs can act as transcription modulators potentially able to control the expression of any desired gene, when fused to an appropriate effector domain. Artificial ZFPs open the possibility to re-program the expression of specific genes at will and can represent a powerful tool in basic science, biotechnology and gene therapy. In this review we will focus on old, novel and possible future applications of artificial ZFPs.Key words: synthetic zinc finger, recognition code, artificial transcription factor, chromatin modification, gene therapy.

Effects of Zn(II) Binding and Apoprotein Structural Stability on the Conformation Change of Designed Antennafinger Proteins

Ligand-induced conformation change is a general strategy for controlling protein function. In this work, we demonstrate the relationships between ligand binding and conformational stability using a previously designed protein, Ant-F, which undergoes a conformation change upon Zn(II) binding. To investigate the effect of stabilization of the apo structure on the conformation change, we also created a novel protein, Ant-F-H1, into which mutations are introduced to increase its stability over that of Ant-F. The chemical denaturation experiments clarified that apo-Ant-F-H1 is more stable than apo-Ant-F (DeltaDeltaG = -1.28 kcal/mol) and that the stability of holo-Ant-F-H1 is almost the same as that of holo-Ant-F. The Zn(II) binding assay shows that the affinity of Zn(II) for Ant-F-H1 is weaker than that for Ant-F (DeltaDeltaG = 1.40 kcal/mol). A large part of the increased value of free energy in stability corresponds to the decreased value of free energy in Zn(II) binding, indicating that the stability of the apo structure directly affects the conformation change. The denaturation experiments also reveal that Zn(II) destabilizes the conformation of both proteins. From the thermodynamic linkage, Zn(II) is thought to bind to the unfolded state with high affinity. These results suggest that the binding of Zn(II) to the unfolded state is an important factor in the conformational change as well as the stability of the apo and holo structures.

Proteomic analysis of cellular responses to low concentration N-methyl-N'-nitro-N-nitrosoguanidine in human amnion FL cells

We have shown previously that exposure to a low concentration of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) induces comprehensive changes in the protein expression profile of human amnion FL cells, including the induction, suppression, upregulation, and downregulation of various proteins. In addition, by proteomic analysis combining two-dimensional gel electrophoresis (2-DE) and mass spectrometry, some of the induced and suppressed proteins were identified. In this study, we identified an additional 18 proteins among those that were either up- or downregulated by MNNG treatment. The proteins identified were a heterogeneous group that included several zinc finger proteins, proteins involved in signal transduction, cytoskeletal proteins, cell-cycle regulation proteins, and proteins with unknown functions. The involvement of these proteins in the cellular responses to alkylating agents has not been reported before and their physiological relevance is not clear. Therefore, our findings may help better understand the global cellular stress responses to chemical carcinogens, and may lead to new studies on the functions of these MNNG-responsive proteins. Furthermore, some of these proteins may serve as biomarkers for detecting exposure of human populations to environmental carcinogens.

A novel zinc finger transcription factor with two isoforms that are differentially repressed by estrogen receptor-alpha

Estrogen receptor-alpha (ERalpha) can induce the expression of genes in response to estrogen by binding to estrogen response elements in the promoters of target genes. There is growing evidence that ERalpha can alter patterns of gene expression in response to ligand by regulating the activity of other factors through a direct protein-protein interaction. To identify other factors that are regulated by ERalpha, a yeast two-hybrid screen was performed that identified a novel Cys(2)His(2) zinc finger protein named ZER6. The ZER6 protein contains a Kruppel-associated box domain and six Cys(2)His(2) zinc fingers. Transcripts from the ZER6 gene can have alternate 5' exons and encode either a p71 or p52 isoform. The p52-ZER6 protein interacts strongly with ERalpha in the presence of 17beta-estradiol, whereas the p71-ZER6 isoform has a HUB-1 amino-terminal domain that inhibits the interaction with ERalpha. A consensus ZER6 binding element was defined using PCR-assisted binding site selection. In COS-1 cells, both the p52 and p71 isoforms can activate transcription through the ZER6 binding element; however, in the presence of ERalpha, transactivation by the p52 isoform is specifically repressed. Overexpression of the p52 isoform was able to abrogate activation by p71-ZER6. Expression of ZER6 was largely restricted to the mammary gland with a lower level of expression in the kidney. We conclude that ZER6 is a novel zinc finger transcription factor in which regulation of transcription in hormone-responsive cells can be controlled by the relative level of expression of two distinct isoforms.