[Show abstract][Hide abstract] ABSTRACT: Z-DNA binding proteins (ZBPs) play important roles in RNA editing, innate immune response and viral infection. Structural
and biophysical studies show that ZBPs initially form an intermediate complex with B-DNA for B–Z conversion. However, a comprehensive
understanding of the mechanism of Z-DNA binding and B–Z transition is still lacking, due to the absence of structural information
on the intermediate complex. Here, we report the solution structure of the Zα domain of the ZBP-containing protein kinase
from Carassius auratus (caZαPKZ). We quantitatively determined the binding affinity of caZαPKZ for both B-DNA and Z-DNA and characterized its B–Z transition activity, which is modulated by varying the salt concentration.
Our results suggest that the intermediate complex formed by caZαPKZ and B-DNA can be used as molecular ruler, to measure the degree to which DNA transitions to the Z isoform.
Preview · Article · Jan 2016 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: Antifreeze proteins (AFPs) are found in a variety of cold-adapted (psychrophilic) organisms to promote survival at subzero temperatures by binding to ice crystals and decreasing the freezing temperature of body fluids. The type III AFPs are small globular proteins that consist of one α-helix, three 310-helices, and two β-strands. Sialic acids play important roles in a variety of biological functions, such as development, recognition, and cell adhesion and are synthesized by conserved enzymatic pathways that include sialic acid synthase (SAS). SAS consists of an N-terminal catalytic domain and a C-terminal antifreeze-like (AFL) domain, which is similar to the type III AFPs. Despite having very similar structures, AFL and the type III AFPs exhibit very different temperature-dependent stability and activity. In this study, we have performed backbone dynamics analyses of a type III AFP (HPLC12 isoform) and the AFL domain of human SAS (hAFL) at various temperatures. We also characterized the structural/dynamic properties of the ice-binding surfaces by analyzing the temperature gradient of the amide proton chemical shift and its correlation with chemical shift deviation from random coil. The dynamic properties of the two proteins were very different from each other. While HPLC12 was mostly rigid with a few residues exhibiting slow motions, hAFL showed fast internal motions at low temperature. Our results provide insight into the molecular basis of thermostability and structural flexibility in homologous psychrophilic HPLC12 and mesophilic hAFL proteins.
Preview · Article · Jan 2015 · Journal of Biomolecular NMR
[Show abstract][Hide abstract] ABSTRACT: A tetra-imidazole-appended tetrakis(p-phenylene)ethylene 1-Cu2+ ensemble was found to enhancement fluorescence upon addition of histidine, but not with any other amino acids. The 1-Cu2+ ensemble also selectively detected proteins containing histidine residues in a mixture of water and methanol (90:10, v/v%). The 1-Cu2+ ensemble-coated thin-layered chromatography (TLC) plate could also detect histidine quantitatively. Furthermore, the fluorescence emission recovery upon addition of five concentrations of His was ~80% with good linearity.
No preview · Article · Oct 2014 · Chemical Communications
[Show abstract][Hide abstract] ABSTRACT: The Zα domains of human ADAR1 (ZαADAR1) bind to Z-DNA via interaction mediated by the α3-core and β-hairpin. Five residues in the α3 helix and four residues in the β-hairpin play important roles in Zα function, forming direct or water-mediated hydrogen bonds with DNA backbone phosphates or interacting hydrophobically with DNA bases. To understand the roles of these residues during BZ transition of duplex DNA, we performed NMR experiments on complexes of various ZαADAR1 mutants with a 6-bp DNA duplex at various protein-to-DNA molar ratios. Our study suggests that single mutations at residues K169, N173, or Y177 cause unusual conformational changes in the hydrophobic faces of helices α1, α2, and α3, which dramatically decrease the Z-DNA binding affinity. 1D imino proton spectra and chemical shift perturbation showed that single mutations at residues K170, R174, T191, P192, P193, or W195 slightly affected the Z-DNA binding affinity. A hydrogen exchange study proved that the K170A- and R174A-ZαADAR1 proteins could efficiently change B-DNA to left-handed Z-DNA via an active BZ transition pathway, whereas the G2·C5 base pair was significantly destabilized compared to wild-type ZαADAR1.
No preview · Article · Jul 2014 · Archives of Biochemistry and Biophysics
[Show abstract][Hide abstract] ABSTRACT: Double-stranded ribonucleic acid-activated protein kinase (PKR) downregulates translation as a defense mechanism against viral
infection. In fish species, PKZ, a PKR-like protein kinase containing left-handed deoxyribonucleic acid (Z-DNA) binding domains,
performs a similar role in the antiviral response. To understand the role of PKZ in Z-DNA recognition and innate immune response,
we performed structural and functional studies of the Z-DNA binding domain (Zα) of PKZ from Carassius auratus (caZαPKZ). The 1.7-Å resolution crystal structure of caZαPKZ:Z-DNA revealed that caZαPKZ shares the overall fold with other Zα, but has discrete structural features that differentiate its DNA binding mode from
others. Functional analyses of caZαPKZ and its mutants revealed that caZαPKZ mediates the fastest B-to-Z transition of DNA among Zα, and the minimal interaction for Z-DNA recognition is mediated by
three backbone phosphates and six residues of caZαPKZ. Structure-based mutagenesis and B-to-Z transition assays confirmed that Lys56 located in the β-wing contributes to its fast
B-to-Z transition kinetics. Investigation of the DNA binding kinetics of caZαPKZ further revealed that the B-to-Z transition rate is positively correlated with the association rate constant. Taking these
results together, we conclude that the positive charge in the β-wing largely affects fast B-to-Z transition activity by enhancing
the DNA binding rate.
Full-text · Article · Mar 2014 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: A novel bispyrene compound was synthesized to selectively detect RNA through excimer emission "turn-on" in aqueous solution at physiological pH (7.4). The compound was used to successfully image RNA in HeLa cells.
No preview · Article · Jan 2014 · Chemical Communications
[Show abstract][Hide abstract] ABSTRACT: The TCP domain is a DNA-binding domain present in plant transcription factors and has a similar structural feature to the bHTH motif of eukaryotic transcription factors. The imino proton exchange study has been performed for the DNA duplex containing the consensus DNA-binding site for the AtTCP11 transcription factor. The first two base pairs in the consensus 5'-GTGGG-3' sequence are relatively very unstable but lead to greater stabilization of the neighboring two G C base pairs. These unique dynamic features of the five base pairs in the consensus DNA sequence might play crucial roles in the effective DNA binding of the AtTCP11 protein.
[Show abstract][Hide abstract] ABSTRACT: Endocyclic homodinuclear complexation and endo/exocyclic heteronuclear networking of calix-bis-monothiacrown-5 (L) are reported. First, dipotassium(I) and disilver(I) complexes of L were isolated and their solid state structures characterized. To probe the complexation behavior for these same systems in solution, the competition between potassium(I) and silver(I) for L was monitored by (1)H NMR. Potassium(I) showed a higher affinity to L than silver(I) both in the solid and solution states. The reaction of L with KI in the presence of HgI2 afforded a two-dimensional coordination polymer with the endocyclic dipotassium(I) complex linked by an exocyclic mercury(II) iodide cluster backbone.
No preview · Article · Aug 2013 · Inorganic Chemistry
[Show abstract][Hide abstract] ABSTRACT: Human ADAR1, which has two left-handed Z-DNA binding domains, preferentially binds Z-DNA rather than B-DNA with a high binding affinity. Z-DNA can be induced in long genomic DNA by Z-DNA binding proteins through the formation of two B-Z junctions with the extrusion of one base pair from each junction. We performed NMR experiments on complexes of Zα(ADAR1) with three DNA duplexes at a variety of protein-to-DNA molar ratios. This study confirmed that the Zα(ADAR1) first binds to an 8-bp CG-rich DNA segment via a unique conformation during B-Z transition and the neighboring AT-rich region becomes destabilized. We also found that, when DNA duplexes have only 6-bp CG-rich segment, the interaction with Zα(ADAR1) did not affect the thermal stabilities of the 6-bp CG-rich segment as well as the neighboring two A·T base pairs. These results indicate that four Zα(ADAR1) proteins interact with the 8-bp DNA sequence containing a 6-bp CG-repeat segment as well as a dinucleotide step, even though the dinucleotid step contains A∙T base pairs. Thus this study suggests that the length of the CG-rich region is more important than the specific DNA sequence for determining which base-pair is extruded from the B-Z junction structure. This study also found that the Zα(ADAR1) in complex with a 11-bp DNA duplex exhibits a Z-DNA-bound conformation distinct from that of free Zα(ADAR1) and the initial contact conformations of Zα(ADAR1) complexed with 13-bp DNA duplexes.
No preview · Article · Dec 2012 · Biophysical chemistry
[Show abstract][Hide abstract] ABSTRACT: Metabolomics is the systematic identification and quantification of all metabolites in an organism or biological sample. NMR has been used as a major application tool in plant metabolomics such as quality control, chemotaxonomy, and analysis of genetically modified plants. Herbal medicines are the important therapeutics and are used to manage common diseases such as cold, inflammation, pain, heart diseases, liver cirrhosis, diabetes and central nerve system diseases. Herb plants include various kinds of species such as geranium, mint, and thyme and so on and contain different kinds of metabolites. We performed NMR-based metabolomics study on the seven different species of herb plants using NMR experiments and OPLS-DA to understand the correlation between the classification of herb plants and their metabolite contents. This study showed clear metabolic discrimination among various herb plants. This metabolmics study found several diagnostic NMR signals which are able to be used as bio-markers for identification of the specific herb plants among various species. Clear metabolic discrimination of herb plants suggests three chemotaxonomic groups of herb species.
[Show abstract][Hide abstract] ABSTRACT: In nature, complex and well-defined structures are constructed by the self-assembly of biomolecules. It has been shown that β-peptide foldamers can mimic natural peptides and self-assemble into three dimensional molecular architectures thanks to their rigid and predictable helical conformation in solution. Using shorter foldamers, which can be prepared more easily than longer ones, to form such architectures is highly desirable, but shorter foldamers have been overlooked due to the seemingly inferior number of intramolecular hydrogen bonds to stabilize a folded state in solution. Here we report that a β-peptide tetramer, although it lacks full helical propensity in solution, does self-assemble to form well-defined microtubes with rectangular cross-section by the evaporation-induced self-assembly.
Full-text · Article · Dec 2012 · Journal of the American Chemical Society
[Show abstract][Hide abstract] ABSTRACT: The Z-DNA binding domain of human ADAR1 (Zα(ADAR1)) preferentially binds Z-DNA rather than B-DNA with high binding affinity. Here, we have carried out chemical shift perturbation and backbone dynamics studies of Zα(ADAR1) in the free form and in complex with three DNA duplexes, d(CGCGCG)(2), d(CACGTG)(2), and d(CGTACG)(2). This study reveals that Zα(ADAR1) initially binds to d(CGCGCG)(2) through the distinct conformation, especially in the unusually flexible β1-loop-α2 region, from the d(CGCGCG)(2)-(Zα(ADAR1))(2) complex. This study also suggests that Zα(ADAR1) exhibits a distinct conformational change during the B-Z transition of non-CG-repeat DNA duplexes with low binding affinities compared to the CG-repeat DNA duplex.
No preview · Article · Oct 2012 · Biochemical and Biophysical Research Communications
[Show abstract][Hide abstract] ABSTRACT: Z-DNA is produced in a long genomic DNA by Z-DNA binding proteins, through formation of two B-Z junctions with the extrusion of one base pair from each junction. To answer the question of how Z-DNA binding proteins induce B-Z transitions in CG-rich segments while maintaining the B-conformation of surrounding segments, we investigated the kinetics and thermodynamics of base-pair openings of a 13-bp DNA in complex with the Z-DNA binding protein, Zα(ADAR1). We also studied perturbations in the backbone of Zα(ADAR1) upon binding to DNA. Our study demonstrates the initial contact conformation as an intermediate structure during B-Z junction formation induced by Zα(ADAR1), in which the Zα(ADAR1) protein displays unique backbone conformational changes, but the 13-bp DNA duplex maintains the B-form helix. We also found the unique structural features of the 13-bp DNA duplex in the initial contact conformation: (i) instability of the AT-rich region II and (ii) longer lifetime for the opening state of the CG-rich region I. Our findings suggest a three-step mechanism of B-Z junction formation: (i) Zα(ADAR1) specifically interacts with a CG-rich DNA segment maintaining B-form helix via a unique conformation; (ii) the neighboring AT-rich region becomes very unstable, and the CG-rich DNA segment is easily converted to Z-DNA; and (iii) the AT-rich regions are base-paired again, and the B-Z junction structure is formed.
No preview · Article · Mar 2012 · Journal of the American Chemical Society