1
|
Zhao D, Lu K, Liu G, Hou J, Yuan L, Ma L, Liu J, He J. PEP-FOLD design, synthesis, and characteristics of finger-like polypeptides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 224:117401. [PMID: 31394393 DOI: 10.1016/j.saa.2019.117401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Polypeptides with finger-like structures can often intercalate into the grooves of DNA, thereby affecting DNA repair or activating gene transcription, both of which are crucial for the regulation of physiological processes. Their conserved amino acid sequence and simple structure have provided useful elements for the design and assembly of functional molecules. In this paper, using the C2H2 zinc finger domain and the PEP-FOLD3 online simulation platform 11 polypeptides containing 22 amino acid residues were designed. In addition, the CD spectroscopy was combined with the fluorescence spectroscopy to study the polypeptide structures and their interaction with DNA. Results showed that although addition of zinc ions affected the polypeptide structure, particularly of the polypeptides A4, B1, and B3, zinc ion was not an essential factor for increasing polypeptide-DNA interactions. Our study revealed an increase in the interaction strength between mutated polypeptides and DNA, suggesting that mutations disrupt polypeptide structure, and polypeptides interact with DNA by groove and electrostatic binding. Mutations at the 12th and 15th amino acid residues had the greatest effect. The stronger binding between A2 or B2 and DNA indicates that the polypeptide has a spatial structure that can stably interact with DNA. The structure and characteristics of these polypeptide domains can provide information for the design and development of new polypeptide functional molecules, which could have potential significance and applications. However, this information also suggests that there are many challenges facing polypeptide design due to the synergistic effects between the side chains of amino acid residues.
Collapse
Affiliation(s)
- Dongxin Zhao
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China.
| | - Kui Lu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China; School of Chemical Engineering and Food Science, Zhengzhou Institute of Technology, Zhengzhou 450044, China
| | - Guangbin Liu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450007, China
| | - Juhong Hou
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Libo Yuan
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Li Ma
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Jie Liu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Juan He
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China
| |
Collapse
|
2
|
Han R, Wang X, Wang X, Guo Y, Li D, Li G, Wang Y, Kang X, Li Z. Chicken ZNF764L gene: mRNA expression profile, alternative splicing analysis and association analysis between first exon indel mutation and economic traits. Gene 2019; 695:92-98. [PMID: 30769141 DOI: 10.1016/j.gene.2019.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/09/2019] [Accepted: 02/01/2019] [Indexed: 01/14/2023]
Abstract
Zinc finger proteins are a class of transcription factors with finger-like domains and have diverse uses in biological processes, including development, differentiation, and metabolism. In this study, we identified the absence of the 24 bp sequence in the third exon of the zinc finger protein 764-like (ZNF764L) gene that lead to the production of two new transcripts, ZNF764L-SV1 and ZNF764L-SV2, and the sum of the expression levels of the two transcripts is approximately equal the total RNA expression level. Temporal and spatial expression showed that ZNF764L had higher expression during the embryonic stage. Moreover, the research study revealed a 22-bp indel mutation in the first exon region of ZNF764L gene. Statistically significant results (P < 0.05) were encountered for this indel for chicken growth and carcass traits, which include birth weight, chest breadth and body slanting length at 4 weeks of age and subcutaneous fat weight and others. Genetic parameter analysis showed that D is the predominant allele in the commercial chicken population. Gene expression for each genotype showed that birds carrying the II allele had a higher expression level than the other genotypes. These findings enrich the understanding of ZNF764L gene function and enhance reproduction in the chicken industry.
Collapse
Affiliation(s)
- Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiangnan Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Xinlei Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yaping Guo
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Donghua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanbin Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China.
| |
Collapse
|
3
|
Effect of Andrographolide on Gene Expression Profile and Intracellular Calcium in Primary Rat Myocardium Microvascular Endothelial Cells. J Cardiovasc Pharmacol 2017; 70:369-381. [DOI: 10.1097/fjc.0000000000000528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
4
|
Manar KK, Yadav CL, Tiwari N, Singh RK, Kumar A, Drew MGB, Singh N. Effect of functionalities on the crystal structures of new zinc(ii) dithiocarbamates: a combined anti-leishmanial and thermal decomposition study. CrystEngComm 2017. [DOI: 10.1039/c7ce00211d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
5
|
Shoukry AA, Al-Mhayawi SR. Solution Equilibria of Binary and Ternary Complexes Involving Zinc(II) with 2,6-Diaminopyridine and Various Biologically Relevant Ligands. J SOLUTION CHEM 2015. [DOI: 10.1007/s10953-015-0395-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
6
|
Bharty M, Dani R, Nath P, Bharti A, Singh N, Prakash O, Singh RK, Butcher R. Syntheses, structural and thermal studies on Zn(II) complexes of 5-aryl-1,3,4-oxadiazole-2-thione and dithiocarbamates: Antibacterial activity and DFT calculations. Polyhedron 2015. [DOI: 10.1016/j.poly.2015.05.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
7
|
Tan YS, Ooi KK, Ang KP, Akim AM, Cheah YK, Halim SNA, Seng HL, Tiekink ERT. Molecular mechanisms of apoptosis and cell selectivity of zinc dithiocarbamates functionalized with hydroxyethyl substituents. J Inorg Biochem 2015; 150:48-62. [PMID: 26086852 DOI: 10.1016/j.jinorgbio.2015.06.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 06/03/2015] [Accepted: 06/06/2015] [Indexed: 10/23/2022]
Abstract
In the solid state each of three binuclear zinc dithiocarbamates bearing hydroxyethyl groups, {Zn[S2CN(R)CH2CH2OH]2}2 for R = iPr (1), CH2CH2OH (2), and Me (3), and an all alkyl species, [Zn(S2CNEt2)2]2 (4), features a centrosymmetric {ZnSCS}2 core with a step topology; both 1 and 3 were isolated as monohydrates. All compounds were broadly cytotoxic, specifically against human cancer cell lines compared with normal cells, with greater potency than cisplatin. Notably, some selectivity were indicated with 2 being the most potent against human ovarian carcinoma cells (cisA2780), and 4 being more cytotoxic toward multidrug resistant human breast carcinoma cells (MCF-7R), human colon adenocarcinoma cells (HT-29), and human lung adenocarcinoma epithelial cells (A549). Based on human apoptosis PCR-array analysis, caspase activities, DNA fragmentation, cell apoptotic assays, intracellular reactive oxygen species (ROS) measurements and human topoisomerase I inhibition, induction of apoptosis in HT-29 cells is demonstrated via both extrinsic and intrinsic pathways. Compounds 2-4 activate the p53 gene while 1 activates both p53 and p73. Cell cycle arrest at the S and G2/M phases correlates with inhibition of HT-29 cell growth. Cell invasion is also inhibited by 1-4 which is correlated with down-regulation of NF-κB.
Collapse
Affiliation(s)
- Yee Seng Tan
- Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kah Kooi Ooi
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Kok Pian Ang
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Abdah Md Akim
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Yoke-Kqueen Cheah
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia.
| | | | - Hoi-Ling Seng
- Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Biological Sciences, Faculty of Science and Technology, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Edward R T Tiekink
- Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| |
Collapse
|
8
|
Bharati P, Bharti A, Chaudhari U, Bharty M, Kashyap S, Singh UP, Singh N. Trinuclear supramolecular Zn(II) complexes derived from N′-(pyridine carbonyl) hydrazine carboperthioates: Synthesis, structural characterization, luminescent properties and metalloaromaticity. Inorganica Chim Acta 2015. [DOI: 10.1016/j.ica.2014.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
9
|
Sandetskaya N, Naumann A, Hennig K, Kuhlmeier D. Specific enrichment of prokaryotic DNA using a recombinant DNA-binding protein. Anal Bioanal Chem 2014; 406:3755-62. [PMID: 24718438 DOI: 10.1007/s00216-014-7787-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/03/2014] [Accepted: 03/24/2014] [Indexed: 11/26/2022]
Abstract
Targeted enrichment of DNA is often necessary for its detection and characterization in complex samples. We describe the development and application of the novel molecular tool for the specific enrichment of prokaryotic DNA. A fused protein comprising the DNA-binding subunit of the bacterial topoisomerase II, gyrase, was expressed, purified, and immobilized on magnetic particles. We demonstrated the specific affinity of the immobilized protein towards bacterial DNA and investigated its efficiency in the samples with high background of eukaryotic DNA. The reported approach allowed for the selective isolation and further detection of as few as 5 pg Staphylococcus aureus DNA from the sample with 4 × 10(6)-fold surplus of human DNA. This method is a promising approach for the preparation of such type of samples, for example in molecular diagnostics of sepsis.
Collapse
Affiliation(s)
- Natalia Sandetskaya
- Nanotechnology Unit, Fraunhofer Institute for Cell Therapy and Immunology IZI, Perlickstrasse 1, 04103, Leipzig, Germany,
| | | | | | | |
Collapse
|
10
|
[Zn(phen)(O,N,O)(H2O)] and [Zn(phen)(O,N)(H2O)] with O,N,O is 2,6-dipicolinate and N,O is l-threoninate: synthesis, characterization, and biomedical properties. J Biol Inorg Chem 2012; 17:1093-105. [DOI: 10.1007/s00775-012-0923-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 07/07/2012] [Indexed: 02/02/2023]
|
11
|
Xu J, De Jong AT, Chen G, Chow HK, Damaso CO, Schwartz Mittelman A, Shin JA. Reengineering natural design by rational design and in vivo library selection: the HLH subdomain in bHLHZ proteins is a unique requirement for DNA-binding function. Protein Eng Des Sel 2010; 23:337-46. [PMID: 20086039 DOI: 10.1093/protein/gzp082] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
To explore the role of the HLH subdomain in bHLHZ proteins, we designed sets of minimalist proteins based on bHLHZ protein Max, bHLH/PAS protein Arnt and bZIP protein C/EBP. In the first, the Max bHLH and C/EBP leucine zipper were fused such that the leucine heptad repeats were not in register; therefore, the protein dimerization interface was disrupted. Max1bHLH-C/EBP showed little ability to activate transcription from the E-box (5'-CACGTG) in the yeast one-hybrid assay, and no E-box binding by quantitative fluorescence anisotropy. Max1bHLH-C/EBP's activity was significantly improved after library selection (three amino acids randomized between HLH and leucine zipper), despite the Max bHLH and C/EBP zipper still being out of register: a representative mutant gave a high nanomolar K(d) value for E-box binding. Thus, selection proved to be a powerful tool for salvaging the flawed Max1bHLH-C/EBP, although the out-of-register mutants still did not achieve the strong DNA-binding affinities displayed by their in-register counterparts. ArntbHLH-C/EBP hybrids further demonstrated the importance of maintaining register, as out-of-register mutants showed no E-box-responsive activity, whereas the in-register hybrid showed moderate activity. In another design, we eliminated the HLH altogether and fused the Max basic region to the C/EBP zipper to generate bZIP-like hybrids. Despite numerous designs and selections, these hybrids possessed no E-box-responsive activity. Finally, we tested the importance of the loop sequence in MaxbHLHZ by fluorescence and circular dichroism. In one mutant, the loop was shortened by two residues; in the other, the Lys57:DNA-backbone interaction was abolished by mutation to Gly57. Both showed markedly decreased E-box-binding relative to MaxbHLHZ. Our results suggest that, in contrast to the more rigid bZIP, the HLH is capable of significant conformational adaptation to enable gene-regulatory function and is required for protein dimerization and positioning the basic region for DNA recognition.
Collapse
Affiliation(s)
- Jing Xu
- Department of Chemistry, University of Toronto, Mississauga, ON L5L1C6, Canada
| | | | | | | | | | | | | |
Collapse
|
12
|
Seng HL, Von ST, Tan KW, Maah MJ, Ng SW, Rahman RNZRA, Caracelli I, Ng CH. Crystal structure, DNA binding studies, nucleolytic property and topoisomerase I inhibition of zinc complex with 1,10-phenanthroline and 3-methyl-picolinic acid. Biometals 2009; 23:99-118. [DOI: 10.1007/s10534-009-9271-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2009] [Accepted: 09/11/2009] [Indexed: 01/17/2023]
|
13
|
Xu J, Chen G, De Jong AT, Shahravan SH, Shin JA. Max-E47, a designed minimalist protein that targets the E-box DNA site in vivo and in vitro. J Am Chem Soc 2009; 131:7839-48. [PMID: 19449889 PMCID: PMC2734406 DOI: 10.1021/ja901306q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Max-E47 is a designed hybrid protein comprising the Max DNA-binding basic region and E47 HLH dimerization subdomain. In the yeast one-hybrid system (Y1H), Max-E47 shows strong transcriptional activation from the E-box site, 5'-CACGTG, targeted by the Myc/Max/Mad network of transcription factors; two mutants, Max-E47Y and Max-E47YF, activate more weakly from the E-box in the Y1H. Quantitative fluorescence anisotropy titrations to gain free energies of protein:DNA binding gave low nanomolar K(d) values for the native MaxbHLHZ, Max-E47, and the Y and YF mutants binding to the E-box site (14, 15, 9, and 6 nM, respectively), with no detectable binding to a nonspecific control duplex. Because these minimalist, E-box-binding hybrids have no activation domain and no interactions with the c-MycbHLHZ, as shown by the yeast two-hybrid assay, they can potentially serve as dominant-negative inhibitors that suppress activation of E-box-responsive genes targeted by transcription factors including the c-Myc/Max complex. As proof-of-principle, we used our modified Y1H, which allows direct competition between two proteins vying for a DNA target, to show that Max-E47 effectively outcompetes the native MaxbHLHZ for the E-box; weaker competition is observed from the two mutants, consistent with Y1H results. These hybrids provide a minimalist scaffold for further exploration of the relationship between protein structure and DNA-binding function and may have applications as protein therapeutics or biochemical probes capable of targeting the E-box site.
Collapse
Affiliation(s)
- Jing Xu
- Department of Chemistry, University of Toronto, Mississauga, Ontario L5L 1C6, Canada
| | | | | | | | | |
Collapse
|
14
|
Chow HK, Xu J, Shahravan SH, De Jong AT, Chen G, Shin JA. Hybrids of the bHLH and bZIP protein motifs display different DNA-binding activities in vivo vs. in vitro. PLoS One 2008; 3:e3514. [PMID: 18949049 PMCID: PMC2568859 DOI: 10.1371/journal.pone.0003514] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 10/02/2008] [Indexed: 12/18/2022] Open
Abstract
Minimalist hybrids comprising the DNA-binding domain of bHLH/PAS (basic-helix-loop-helix/Per-Arnt-Sim) protein Arnt fused to the leucine zipper (LZ) dimerization domain from bZIP (basic region-leucine zipper) protein C/EBP were designed to bind the E-box DNA site, CACGTG, targeted by bHLHZ (basic-helix-loop-helix-zipper) proteins Myc and Max, as well as the Arnt homodimer. The bHLHZ-like structure of ArntbHLH-C/EBP comprises the Arnt bHLH domain fused to the C/EBP LZ: i.e. swap of the 330 aa PAS domain for the 29 aa LZ. In the yeast one-hybrid assay (Y1H), transcriptional activation from the E-box was strong by ArntbHLH-C/EBP, and undetectable for the truncated ArntbHLH (PAS removed), as detected via readout from the HIS3 and lacZ reporters. In contrast, fluorescence anisotropy titrations showed affinities for the E-box with ArntbHLH-C/EBP and ArntbHLH comparable to other transcription factors (K(d) 148.9 nM and 40.2 nM, respectively), but only under select conditions that maintained folded protein. Although in vivo yeast results and in vitro spectroscopic studies for ArntbHLH-C/EBP targeting the E-box correlate well, the same does not hold for ArntbHLH. As circular dichroism confirms that ArntbHLH-C/EBP is a much more strongly alpha-helical structure than ArntbHLH, we conclude that the nonfunctional ArntbHLH in the Y1H must be due to misfolding, leading to the false negative that this protein is incapable of targeting the E-box. Many experiments, including protein design and selections from large libraries, depend on protein domains remaining well-behaved in the nonnative experimental environment, especially small motifs like the bHLH (60-70 aa). Interestingly, a short helical LZ can serve as a folding- and/or solubility-enhancing tag, an important device given the focus of current research on exploration of vast networks of biomolecular interactions.
Collapse
Affiliation(s)
- Hiu-Kwan Chow
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - Jing Xu
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - S. Hesam Shahravan
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - Antonia T. De Jong
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - Gang Chen
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - Jumi A. Shin
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
15
|
Vázquez O, Vázquez ME, Blanco JB, Castedo L, Mascareñas JL. Specific DNA recognition by a synthetic, monomeric Cys2His2 zinc-finger peptide conjugated to a minor-groove binder. Angew Chem Int Ed Engl 2007; 46:6886-90. [PMID: 17674388 DOI: 10.1002/anie.200702345] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Olalla Vázquez
- Department de Química Orgánica y Unidad Asociada al CSIC, Universidade de Santiago de Compostela, Facultade de Química, 15782 Santiago de Compostela, Spain
| | | | | | | | | |
Collapse
|
16
|
ZHAO DX, TENG XC, DING ZC, HUANG ZX. Expression and Purification of ZNF191(243–368) in Three Expression Systems. CHINESE J CHEM 2007. [DOI: 10.1002/cjoc.200790321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
17
|
Vázquez O, Vázquez M, Blanco J, Castedo L, Mascareñas J. Specific DNA Recognition by a Synthetic, Monomeric Cys2His2 Zinc-Finger Peptide Conjugated to a Minor-Groove Binder. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200702345] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
18
|
Zfra affects TNF-mediated cell death by interacting with death domain protein TRADD and negatively regulates the activation of NF-kappaB, JNK1, p53 and WOX1 during stress response. BMC Mol Biol 2007; 8:50. [PMID: 17567906 PMCID: PMC1904229 DOI: 10.1186/1471-2199-8-50] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Accepted: 06/13/2007] [Indexed: 01/14/2023] Open
Abstract
Background Zfra is a 31-amino-acid zinc finger-like protein, which is known to regulate cell death by tumor necrosis factor (TNF) and overexpressed TNF receptor- or Fas-associated death domain proteins (TRADD and FADD). In addition, Zfra undergoes self-association and interacts with c-Jun N-terminal kinase 1 (JNK1) in response to stress stimuli. To further delineate the functional properties of Zfra, here we investigated Zfra regulation of the activation of p53, WOX1 (WWOX or FOR), NF-κB, and JNK1 under apoptotic stress. Results Transiently overexpressed Zfra caused growth suppression and apoptotic death of many but not all types of cells. Zfra either enhanced or blocked cell death caused by TRADD, FADD, or receptor-interacting protein (RIP) in a dose-related manner. This modulation is related with Zfra binding with TRADD, NF-κB, JNK1 and WOX1, as determined by GST pull-down analysis, co-immunoprecipitation, and mapping by yeast two-hybrid analysis. Functionally, transiently overexpressed Zfra sequestered NF-κB (p65), WOX1, p53 and phospho-ERK (extracellular signal-activated kinase) in the cytoplasm, and TNF or UV light could not effectively induce nuclear translocation of these proteins. Zfra counteracted the apoptotic functions of Tyr33-phosphorylated WOX1 and Ser46-phosphorylated p53. Alteration of Ser8 to Gly abolished the apoptotic function of Zfra and its regulation of WOX1 and p53. Conclusion In response to TNF, Zfra is upregulated and modulates TNF-mediated cell death via interacting with TRADD, FADD and RIP (death-inducing signaling complex) at the receptor level, and downstream effectors NF-κB, p53, WOX1, and JNK1.
Collapse
|
19
|
Abstract
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.
Collapse
Affiliation(s)
- Ling Yuan
- Department of Plant and Soil Sciences, and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA.
| | | | | | | |
Collapse
|
20
|
Liu J, Stormo GD. Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein. BMC Bioinformatics 2005; 6:176. [PMID: 16014175 PMCID: PMC1184061 DOI: 10.1186/1471-2105-6-176] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Accepted: 07/13/2005] [Indexed: 11/26/2022] Open
Abstract
Background Recognition codes for protein-DNA interactions typically assume that the interacting positions contribute additively to the binding energy. While this is known to not be precisely true, an additive model over the DNA positions can be a good approximation, at least for some proteins. Much less information is available about whether the protein positions contribute additively to the interaction. Results Using EGR zinc finger proteins, we measure the binding affinity of six different variants of the protein to each of six different variants of the consensus binding site. Both the protein and binding site variants include single and double mutations that allow us to assess how well additive models can account for the data. For each protein and DNA alone we find that additive models are good approximations, but over the combined set of data there are context effects that limit their accuracy. However, a small modification to the purely additive model, with only three additional parameters, improves the fit significantly. Conclusion The additive model holds very well for every DNA site and every protein included in this study, but clear context dependence in the interactions was detected. A simple modification to the independent model provides a better fit to the complete data.
Collapse
Affiliation(s)
- Jiajian Liu
- Department of Genetics, Washington University School of Medicine, 660 S Euclid, Box 8232, St. Louis, MO 63110, U.S.A
| | - Gary D Stormo
- Department of Genetics, Washington University School of Medicine, 660 S Euclid, Box 8232, St. Louis, MO 63110, U.S.A
| |
Collapse
|
21
|
Synthesis and characterization of mixed ligand complexes of Zn(II) and Co(II) with amino acids: Relevance to zinc binding sites in zinc fingers. J CHEM SCI 2005. [DOI: 10.1007/bf02709293] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
22
|
Biunno I, Castiglioni B, Rogozin IB, DeBellis G, Malferrari G, Cattaneo M. Cross-species conservation of SEL1L, a human pancreas-specific expressing gene. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2003; 6:187-98. [PMID: 12143964 DOI: 10.1089/153623102760092788] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
SEL1L is a recently cloned and organ-specific expressing human gene whose function is still at an embryonic stage but displays several interesting characteristics, among which a remarkable cross-species conservation. During evolution, the gene structural complexity increased, suggesting a diversification of its function; however, several amino acid motifs remain perfectly conserved from the bacteria to the human protein. SEL1L is the human ortholog of the C. elegans gene sel-1; the latter is implicated in the negative regulation of LIN-12/GLP-1/Notch receptor proteins. These receptor proteins play fundamental roles in signal transduction pathways and are key players in cell fate determination during the development of various organs. Studies in model organisms, such as C. elegans, helped to illuminate fundamental mechanisms involved in normal cellular functions and human diseases. This paper describes the conserved nature of SEL1L across a wide range of species suggesting, that the encoded protein most likely exerts a very important biological function; it may belong to a subclass of genes considered to be "essential."
Collapse
Affiliation(s)
- Ida Biunno
- Institute for Biomedical Technologies-CNR, Segrate, Milano, Italy.
| | | | | | | | | | | |
Collapse
|
23
|
Vázquez ME, Caamaño AM, Mascareñas JL. From transcription factors to designed sequence-specific DNA-binding peptides. Chem Soc Rev 2003; 32:338-49. [PMID: 14671789 DOI: 10.1039/b206274g] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Transcription factors are DNA-binding proteins responsible for initiating the transcription of particular genes upon interacting with specific DNA sequences located at their promoter or enhancer regions. The DNA recognition process, which is extremely selective, is mediated by non-covalent interactions between appropriately arranged structural motifs of the protein and exposed surfaces of the DNA bases and backbone. The great variability in DNA recognition by transcription factors has hampered the characterization of an amino acid-base step recognition code, making it very difficult to design non-natural peptides that can mimic the DNA-binding properties of these naturally occurring counterparts. However, in recent years, several transcription factor-based miniature proteins capable of tight interaction with specific DNA sites have been successfully constructed, most of them using bottom-up synthetic approaches.
Collapse
Affiliation(s)
- M Eugenio Vázquez
- Departamento de Química Orgánica, Unidad Asociada al CSIC, Universidad de Santiago de Compostela, Santiago de Compostela, 15782, Spain.
| | | | | |
Collapse
|
24
|
Conroy AT, Sharma M, Holtz AE, Wu C, Sun Z, Weigel RJ. A novel zinc finger transcription factor with two isoforms that are differentially repressed by estrogen receptor-alpha. J Biol Chem 2002; 277:9326-34. [PMID: 11779858 DOI: 10.1074/jbc.m107702200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Andrew T Conroy
- Department of Surgery, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | | | | | | | | |
Collapse
|