[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: 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: 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: 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: 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
[Show abstract][Hide abstract] ABSTRACT: P53 is the major tumor suppressor and is a transcription factor involved in various cellular metabolisms, including DNA repair, regulation of cell cycle, apoptotic cell death. 1-5 The p53 contains an N-terminal transactivation domain (amino acids 1-42), a proline-rich SH3 target-region (amino acids 60-97), a DNA-binding domain (amino acids 102-292), a tetramerization domain (amino acids 323-356) and a C-terminal regulatory domain (360-393). 6 The sequence-specific DNA binding domain (DBD) of p53 plays a critical role for the initiation of biological functions of p53 system. 1-5 Deficiency of the p53 function is mainly due to mutations which interfere with the DNA-binding ability of the protein. P53 can recognize specific DNA sequences, which is called as the p53 response element (p53RE). 7 The p53RE have two half-site palindromes and each half-site palindrome has 10 base-pair (bp) with a consensus sequence of 5'-RRRCWWGYYY-3', where W can be A or T, and R and Y is purine and pyrimidine bases, respectively. The p53-DBD binds to various p53RE variants with somewhat different binding modes. The p53-DBD had different binding affinity to a variety of p53RE substrates. However, the structural features of the p53-DNA complexes could not explain this sequence selectivity of the p53-DBD. The dynamic property of the p53RE sequences with their structural feature can provide the useful information to understand the molecular interaction between the p53 and its p53RE. NMR hydrogen exchange data provide information on the thermodynamics and kinetics for base-pair opening and represent a probe of the dynamic motion of the base pairs. Hydrogen exchange data can also be used to probe how DNA duplexes are stabilized by the intermolecular interaction with proteins. Thus, to understand the origin of the sequence selectivity of the p53, the imino proton ex-change rate constants were measured for the DNA decamer duplex containing the consensus p53RE sequence (referred as to wt p53RE, Fig. 1). To further understand the corre-lation between the base pair dynamics and the sequence selectivity of the p53, the exchange rate constants (k ex) of the imino protons for the wt p53RE duplex were compared with those of the other p53RE variants (Fig. 1).
Preview · Article · Feb 2012 · Bulletin- Korean Chemical Society