Conserved motif VIII of murine DNA methyltransferase Dnmt3a is essential for methylation activity

Background

Dnmt3a is a DNA methyltransferase that establishes de novo DNA methylation in mammals. The structure of the Dnmt3a C-terminal domain is similar to the bacterial M. HhaI enzyme, a well-studied prokaryotic DNA methyltransferase. No X-ray structure is available for the complex of Dnmt3a with DNA and the mechanistic details of DNA recognition and catalysis by mammalian Dnmts are not completely understood.

Results

Mutant variants of the catalytic domain of the murine Dnmt3a carrying substitutions of highly conserved N167, R200, and R202 have been generated by site directed mutagenesis and purified. Their methylation activity, DNA binding affinity, ability to flip the target cytosine out of the DNA double helix and covalent complex formation with DNA have been examined. Substitutions of N167 lead to reduced catalytic activity and reduced base flipping. Catalytic activity, base flipping, and covalent conjugate formation were almost completely abolished for the mutant enzymes with substitutions of R200 or R202.

Conclusions

We conclude that R202 plays a similar role in catalysis in Dnmt3a-CD as R232 in M.SssI and R165 in M.HhaI, which could be positioning of the cytosine for nucleophilic attack by a conserved Cys. R200 of Dnmt3a-CD is important in both catalysis and cytosine flipping. Both conserved R200 and R202 are involved in creating and stabilizing of the transient covalent intermediate of the methylation reaction. N167 might contribute to the positioning of the residues from the motif VI, but does not play a direct role in catalysis.

     

Specificity of Dnmt1 for methylation of hemimethylated CpG sites resides in its catalytic domain

The maintenance methylation of hemimethylated CpG sites by the DNA methyltransferase Dnmt1 is the molecular basis of the inheritance of DNA methylation patterns. Based on structural data and kinetics obtained with a truncated form of Dnmt1, an autoinhibition model for the specificity of Dnmt1 was proposed in which unmethylated DNA binds to Dnmt1's CXXC domain, which prevents its methylation. We have prepared CXXC domain variants that lost DNA binding. Corresponding full-length Dnmt1 variants did not display a reduction in specificity, indicating that the autoinhibition model does not apply in full-length Dnmt1. Furthermore, we show that the Dnmt1 M1235S variant, which carries an exchange in the catalytic domain of the enzyme, has a marked reduction in specificity, indicating that the recognition of the hemimethylated state of target sites resides within the catalytic domain.     

Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor

We report the complete de novo design of a four-helix bundle protein that selectively binds the nonbiological DPP-Fe(III) metalloporphyrin cofactor (DPP-Fe(III) = 5, 15-Di[(4-carboxymethyleneoxy)phenyl]porphinato iron(III)). A tetrameric, D2-symmetric backbone scaffold was constructed to encapsulate two DPP-Fe(III) units through bis(His) coordination. The complete sequence was determined with the aid of the statistical computational design algorithm SCADS. The 34-residue peptide was chemically synthesized. UV-vis and CD spectroscopy, size-exclusion chromatography, and analytical ultracentrifugation indicated the peptide undergoes a transition from a predominantly random coil monomer to an alpha-helical tetramer upon binding DPP-Fe(III). EPR spectroscopy studies indicated the axial imidazole ligands were oriented in a perpendicular fashion, as defined by second-shell interactions that were included in the design. The 1-D 1H NMR spectrum of the assembled protein displayed features of a well-packed interior. The assembled protein possessed functional redox properties different from those of structurally similar systems containing the heme cofactor. The designed peptide demonstrated remarkable cofactor selectivity with a significantly weaker binding affinity for the natural heme cofactor. These findings open a path for the selective incorporation of more elaborate cofactors into designed scaffolds for constructing molecularly well-defined nanoscale materials.     

Redox characteristics of a de novo quinone protein

The electrochemistry of 2,6-dimethylbenzoquinone (DMBQ) has been characterized for three different systems: DMBQ freely solvated in aqueous buffer; DMBQ bound to a neutral, blocked cysteine (N-acetyl-L-cysteine methyl ester) and the resulting DMBQ-bCys compound solvated in aqueous buffer; and DMBQ bound to a small model protein denoted alpha(3)C. The goal of this study is to detect and characterize differences in the redox properties of the protein-ligated DMBQ relative to the solvated quinones. The alpha(3)C protein used here is a tryptophan-32 to cysteine-32 variant of the structurally defined alpha(3)W de novo protein (Dai et al. J. Am. Chem. Soc. 2002, 124, 10952-10953). The properties of alpha(3)C were recently described (Hay et al. Biochemistry 2005, 44, 11891-11902). DMBQ was covalently bound to bCys and alpha(3)C through a sulfur substitution reaction with the cysteine thiol. In contrast to the solvated DMBQ and DMBQ-bCys compounds, diffusion controlled electrochemistry of DMBQ-alpha(3)C showed well-behaved and fully reversible n = 2 oxidation/reduction with a peak separation of approximately 30 mV between pH 5 and 9. DMBQ-alpha(3)C could also be immobilized on a gold electrode modified with a self-assembled monolayer of 3-mercaptopropionoic acid, allowing the measurement, by cyclic voltammetry, of an apparent rate of electron transfer of 22 s(-1). The (cysteine) sulfur substitution significantly lowers one of the hydroquinone pKA's from 10.4 in DMBQ to 6.8 in DMBQ-bCys. This pKA is slightly elevated in DMBQ-alpha(3)C to 7.0 and the E1/2 at pH 7.0 is raised by 110 mV from +190 mV in DMBQ-bCys to +297 mV in DMBQ-alpha(3)C.     

Creation of a type 1 blue copper site within a de novo coiled-coil protein scaffold

Type 1 blue copper proteins uniquely coordinate Cu(2+) in a trigonal planar geometry, formed by three strong equatorial ligands, His, His, and Cys, in the protein. We designed a stable Cu(2+) coordination scaffold composed of a four-stranded α-helical coiled-coil structure. Two His residues and one Cys residue were situated to form the trigonal planar geometry and to coordinate the Cu(2+) in the hydrophobic core of the scaffold. The protein bound Cu(2+), displayed a blue color, and exhibited UV-vis spectra with a maximum of 602-616 nm, arising from the thiolate-Cu(2+) ligand to metal charge transfer, depending on the exogenous axial ligand, Cl(-) or HPO(4)(2-). The protein-Cu(2+) complex also showed unresolved small A(∥) values in the electron paramagnetic resonance (EPR) spectral analysis and a 328 mV (vs normal hydrogen electrode, NHE) redox potential with a fast electron reaction rate. The X-ray absorption spectrum revealed that the Cu(2+) coordination environment was identical to that found in natural type 1 blue copper proteins. The extended X-ray absorption fine structure (EXAFS) analysis of the protein showed two typical Cu-N(His) at around 1.9-2.0 ?, Cu-S(Cys) at 2.3 ?, and a long Cu-Cl at a 2.66 ?, which are also characteristic of the natural type 1 blue copper proteins.     

Template-directed assembly of a de novo designed protein

Many naturally occurring biomaterials are composed of laminated structures in which layers of beta-sheet proteins alternate with layers of inorganic mineral. These ordered laminates often have structural and mechanical properties that differ significantly from those of nonbiological materials. An important step in the construction of novel biomaterials is the creation of composites wherein a de novo designed protein assembles into an ordered structure. To achieve this goal, we layered a de novo protein onto the surface of highly ordered pyrolytic graphite (HOPG). The protein was derived from a combinatorial library of novel sequences designed to fold into amphiphilic beta-sheet structures. Atomic force microscopy reveals that the protein assembles on the HOPG surface into ordered fibers aligned in three orientations at 120 degrees to each other. The symmetry and extent of the ordered regions indicate that the hexagonal lattice underlying the graphite surface templates assembly of millions of protein molecules into a highly ordered structure.     

β-发夹多肽的全新设计和构象研究

引入跨股氨基酸队的方法进行β-发夹结构的设计,序列[R1G2T3F4W5V6d-P7S8V9N10Y11F12, β2] 中包含二个氨基酸对V6V9和F4Y11,并以d-P7S8作转角来稳定结构.多肽合成采用Fmoc/But固相合成方法.圆二色谱研究显示,β2在202 nm呈现正峰,在217.5 nm处呈负峰,为β转角和β折叠共同贡献的叠加,是典型的β-发夹结构圆二色谱特征.红外光谱研究进一步验证了圆二色谱的结果,表明β2在溶液中主要以β-发夹结构存在.     

Slipping of a histidine improved the peroxidase activity of a de novo designed polypeptide packing an iron porphyrin

Polypeptides with two histidines and an iron porphyrin (1H⁴⁰-7H⁴⁶) were synthesized with a variety of positions of a histidine. In 4H⁴³, histidine (H⁴³) was in the hydrophobic region of an α-helix. The other polypeptides were of slightly or substantially distorted conformation. In the pH 7.2 buffer solution, two histidines of the polypeptide coordinated the iron porphyrin regardless of their positions. Some polypeptides (1H⁴⁰, 3H⁴², and 5H⁴⁴) showed an enhanced catalytic activity in the peroxidase reaction using cumene hydroperoxide compared to that of 4H⁴³, whereas some polypeptides (2H⁴¹ and 6H⁴⁵) were ineffective catalysts. The distortion of the peptide conformation by the addition of MeOH was also effective for the peroxidase reaction.     

The de novo design of median molecules within a property range of interest

Summary In this paper an application is presented of the median molecule workflow to the de novo design of novel molecular entities with a property profile of interest. Median molecules are structures that are optimised to be similar to a set of existing molecules of interest as an approach for lead exploration and hopping. An overview of this workflow is provided together with an example of an instance using the similarity to camphor and menthol as objectives. The methodology of the experiments is defined and the workflow is applied to designing novel molecules for two physical property datasets: mean molecular polarisability and aqueous solubility. This paper concludes with a discussion of the characteristics of this method.     

Development and testing of a de novo drug-design algorithm

In this article we present an implementation of a de novo drug-design algorithm. The algorithm starts with a molecule placed in the binding site of a protein and then modifies it using a sequential growth approach. This involves successive cycles of suppression of randomly picked groups in the molecule and their replacement by other groups chosen from databanks of linear or cyclic fragments. The algorithm has been coupled with the Dynamo library which allows the simulation of macromolecules using molecular mechanical and quantum chemical methods. The main body of the article describes the methodologies we use to create, characterize and evaluate putative ligands. We also consider briefly an application of the algorithm to a protein of pharmacological interest, the neuraminidase of the influenza virus, and discuss the strengths and weaknesses of our approach.     

Kinetics of methylation of a solvatochromic vinylogous α‐pyridone in different solvents

The kinetics of the reaction with iodomethane of the solvatochromic dye 4‐[2‐(N‐methyl‐4,6‐diphenylpyridiniumyl)]phenoxide 2, generated in situ from the corresponding N‐methyl‐2,4‐diphenyl‐6‐(4‐hydroxyphenyl)pyridinium salt 4, was studied in various solvents and solvent mixtures, in search of a possible correlation between its reactivity and solvatochromism in solution. © 1999 John Wiley & Sons, Inc. Int J Chem Kinet 31: 819–825, 1999     

de novo asymmetric synthesis of daumone via a palladium-catalyzed glycosylation

The enantioselective syntheses of daumone and two analogues have been achieved in seven to eight steps. This route relies upon a diasteroselective palladium-catalyzed glycosylation reaction for the formation of the anomeric bond. The asymmetry of the sugar and aglycone portion of daumone were introduced by Noyori reduction of an acylfuran and a propargyl ketone. A highly diastereoselective epoxidation and reductive ring opening established the desired C-2 and C-4 stereochemistry of daumone. [reaction: see text]     

Trimethylsilylation and methylation of 1-hydroxybenzotriazole 3-oxide

Trimethylsilylation and methylation of 1 -hydroxybenzotriazole 3-oxide (1) proceed regioselectively and afford 1-trimethylsilyloxy- and 1-methoxybenzotriazole 3-oxides, respectively. The first compound easily undergoes fast hydrolysis and methanolysis, but does not react with nitroethane at 20 °C. A fast reversible 1,5-O,O-migration of the SiMe₃ group is observed for this compound.The authors thank V. I. Gulevskaya for DTA analysis of compound4.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2283–2285, November, 1995.The present work was supported by the Russian Foundation for Basic Research (project No. 93-03-18461).     

The inhibition of the mammalian DNA methyltransferase 3a (Dnmt3a) by dietary black tea and coffee polyphenols

Background  

Black tea is, second only to water, the most consumed beverage globally. Previously, the inhibition of DNA methyltransferase 1 was shown by dietary polyphenols and epi-gallocatechin gallate (EGCG), the main polyphenolic constituent of green tea, and 5-caffeoyl quinic acid, the main phenolic constituent of the green coffee bean.     

Structure of a de novo designed protein model of radical enzymes

The use of side chains as catalytic cofactors for protein mediated redox chemistry raises significant mechanistic issues as to how these amino acids are activated toward radical chemistry in a controlled manner. De novo protein design has been used to examine the structural basis for the creation and maintenance of a tryptophanyl radical in a three-helix bundle protein maquette. Here we report the detailed structural analysis of the protein by multidimensional NMR methods. An interesting feature of the structure is an apparent pi-cation interaction involving the sole tryptophan and a lysine side chain. Hybrid density functional calculations support the notion that this interaction raises the reduction potential of the W degrees /WH redox pair and helps explain the redox characteristics of the protein. This model protein system therefore provides a powerful model for exploring the structural basis for controlled radical chemistry in protein.     

HostDesigner: a program for the de novo structure-based design of molecular receptors with binding sites that complement metal ion guests

This paper describes a novel approach to the discovery of host structures with binding sites that complement targeted metal ion guests. This approach uses a de novo structure-based design strategy that couples molecular building algorithms with scoring functions to prioritize candidate structures. The algorithms described herein have been implemented in a program called HostDesigner, the first structure-based design software specifically created for the discovery of metal ion receptors. HostDesigner generates and evaluates millions of candidate structures within minutes, rapidly identifying three-dimensional architectures that position binding sites to provide an optimal interaction with the metal ion.     

The mitogen-activated protein kinase phosphatase-1 (MKP-1) gene is a potential methylation biomarker for malignancy of breast cancer

The mitogen-activated protein kinase (MAPK) phosphatase- 1 (MKP-1) belongs to the MAPK cascades which are central to cell proliferation and apoptosis. The carcinogenic role of MKP-1 has been reported in many types of cancer but it has rarely been investigated in breast cancer. The present study was designed to evaluate the MKP-1 mRNA expression and its possible regulation by methylation of MKP-1 promoter in the model of several breast cancer cell lines and tissues as well as controls. Our data demonstrate MKP-1 mRNA expression significantly decreased in five breast cancer cell lines compared to breast controls (P<0.01). Using the methylation-specific PCR (MSP) analysis, the unmethylated reaction (U) is dominant in both normal cell lines and benign breast tumors (100% vs. 86.2%), whereas the methylated reaction (M) is dominant in both breast cancer cell lines and invasive breast tumors (100% vs. 57.2%). In terms of methylation ratio (M/M+U), methylation level in MKP-1 promoter is significantly higher in the invasive breast tumor tissues (n = 152) than in benign breast tumor tissues (n = 29) (P<0.0001). Assessing the methylation ratio of the promoter of MKP-1 gene to diagnose the breast malignancy (invasive vs. benign), the area under the receiver- operating characteristic (ROC) curve was 0.809 (95% CI: 0.711-0.906, P<0.001). The best performance for this prediction has a sensitivity of 76.32% and a specificity of 82.76% at the cutoff value of 0.38. Taken together, we firstly demonstrated that the promoter methylation of MKP-1 gene is a potential breast cancer biomarker for breast malignancy.     

Regioselective de novo synthesis of cyanohydroxypyridines with a concerted cycloaddition mechanism

An efficient cycloaddition reaction of 1-alkoxy-1-azadienes with alpha,alpha-dicyanoalkenes is described, which gives facile access to highly substituted 3-hydroxypyridines in very good yields and with complete regiocontrol and chemoselectivity. The reaction path was investigated in detail by quantum mechanics calculations, reporting that a concerted cycloaddition mechanism and thermodynamic control synergistically contribute to the observed selectivity.