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Small-molecule compounds targeting trinucleotide repeats in DNA have considerable potential as therapeutic or diagnostic agents against many neurological diseases. NiII(Chro)2 (Chro=chromomycin A3) binds specifically to the minor groove of (CCG) n repeats in duplex DNA, with unique fluorescence features that may serve as a probe for disease detection. Crystallographic studies revealed that the specificity originates from the large-scale spatial rearrangement of the DNA structure, including extrusion of consecutive bases and backbone distortions, with a sharp bending of the duplex accompanied by conformational changes in the NiII chelate itself. The DNA deformation of CCG repeats upon binding forms a GGCC tetranucleotide tract, which is recognized by NiII(Chro)2. The extruded cytosine and last guanine nucleotides form water-mediated hydrogen bonds, which aid in ligand recognition. The recognition can be accounted for by the classic induced-fit paradigm. [ABSTRACT FROM AUTHOR]

Small-molecule compounds targeting trinucleotide repeats in DNA have considerable potential as therapeutic or diagnostic agents against many neurological diseases. NiII(Chro)2 (Chro=chromomycin A3) binds specifically to the minor groove of (CCG) n repeats in duplex DNA, with unique fluorescence features that may serve as a probe for disease detection. Crystallographic studies revealed that the specificity originates from the large-scale spatial rearrangement of the DNA structure, including extrusion of consecutive bases and backbone distortions, with a sharp bending of the duplex accompanied by conformational changes in the NiII chelate itself. The DNA deformation of CCG repeats upon binding forms a GGCC tetranucleotide tract, which is recognized by NiII(Chro)2. The extruded cytosine and last guanine nucleotides form water-mediated hydrogen bonds, which aid in ligand recognition. The recognition can be accounted for by the classic induced-fit paradigm. [ABSTRACT FROM AUTHOR]

The Staphylococcus epidermidis lipase (SeLip, GehC) can be used in flavour‐compound production via esterification in aqueous solution. This study reports the crystallization and crystallographic analysis of recombinant GehC (rGehC; Lys303–Lys688) with a molecular weight of 43 kDa. rGehC was crystallized at 293 K using PEG 10 000 as a precipitant, and a 99.9% complete native data set was collected from a cooled crystal at 77 K to a resolution of 1.9 Å with an overall Rmerge value of 7.3%. The crystals were orthorhombic and belonged to space group P212121, with unit‐cell parameters a = 42.07, b = 59.31, c = 171.30 Å, α = β = γ = 90°. Solvent‐content calculations suggest that there is likely to be one lipase subunit in the asymmetric unit. [ABSTRACT FROM AUTHOR]

The N-terminal domain of the nucleocapsid protein from Middle East respiratory syndrome coronavirus (MERS-CoV NP-NTD) contains many positively charged residues and has been identified to be responsible for RNA binding during ribonucleocapsid formation by the virus. In this study, the crystallization and crystallographic analysis of MERS-CoV NP-NTD (amino acids 39-165), with a molecular weight of 14.7 kDa, are reported. MERS-CoV NP-NTD was crystallized at 293 K using PEG 3350 as a precipitant and a 94.5% complete native data set was collected from a cooled crystal at 77 K to 2.63 Å resolution with an overall Rmerge of 9.6%. The crystals were monoclinic and belonged to space group P21, with unit-cell parameters a = 35.60, b = 109.64, c = 91.99 Å, β = 101.22°. The asymmetric unit contained four MERS-CoV NP-NTD molecules. [ABSTRACT FROM AUTHOR]

CCG triplet repeats can fold into tetraplex structures, which are associated with the expansion of (CCG) n trinucleotide sequences in certain neurological diseases. These structures are stabilized by intertwining i-motifs. However, the structural basis for tetraplex i-motif formation in CCG triplet repeats remains largely unknown. We report the first crystal structure of a CCG-repeat sequence, which shows that two dT(CCG)3A strands can associate to form a tetraplex structure with an i-motif core containing four C:C+ pairs flanked by two G:G homopurine base pairs as a structural motif. The tetraplex core is attached to a short parallel-stranded duplex. Each hairpin itself contains a central CCG loop in which the nucleotides are flipped out and stabilized by stacking interactions. The helical twists between adjacent cytosine residues of this structure in the i-motif core have an average value of 30°, which is greater than those previously reported for i-motif structures. [ABSTRACT FROM AUTHOR]

CCG triplet repeats can fold into tetraplex structures, which are associated with the expansion of (CCG) n trinucleotide sequences in certain neurological diseases. These structures are stabilized by intertwining i-motifs. However, the structural basis for tetraplex i-motif formation in CCG triplet repeats remains largely unknown. We report the first crystal structure of a CCG-repeat sequence, which shows that two dT(CCG)3A strands can associate to form a tetraplex structure with an i-motif core containing four C:C+ pairs flanked by two G:G homopurine base pairs as a structural motif. The tetraplex core is attached to a short parallel-stranded duplex. Each hairpin itself contains a central CCG loop in which the nucleotides are flipped out and stabilized by stacking interactions. The helical twists between adjacent cytosine residues of this structure in the i-motif core have an average value of 30°, which is greater than those previously reported for i-motif structures. [ABSTRACT FROM AUTHOR]

Mithramycin (Mith) forms a drug-metal complex with a 2:1 stoichiometry by chelation with a Ni(II) ion, which was determined using circular dichroism spectroscopy. Mith exhibits an increased affinity (~55 fold) for Ni(II) in the presence of DNA compared to the absence of DNA, suggesting that DNA acts as an effective template to facilitate chelation. Also, we characterized the DNA-acting properties of a Ni(II) derivative of Mith. Kinetic analysis using surface plasmon resonance and UV melting studies revealed that Ni(Mith) binds to duplex DNA with a higher affinity compared to Mg(Mith). The thermodynamic parameters revealed a higher free energy of formation for duplex DNA in the presence of Ni(Mith) compared to duplex DNA in the presence of Mg(Mith). The results of a DNA-break assay indicated that Ni(Mith) is capable of promoting one-strand cleavage of plasmid DNA in the presence of hydrogen peroxide; the DNA cleavage rate of Ni(Mith) was calculated to be 4.1 × 10 s. In cell-based experiments, Ni(Mith) exhibited a more efficient reduction of c-myc and increased cytotoxicity compared to Mith alone because of its increased DNA-binding and cleavage activity. The evidence obtained in this study suggests that the biological effects of Ni(Mith) require further investigation in the future. [ABSTRACT FROM AUTHOR]

Abstract: The coronavirus (CoV) N protein oligomerizes via its carboxyl terminus. However, the oligomerization mechanism of the C-terminal domains (CTD) of CoV N proteins remains unclear. Based on the protein disorder prediction system, a comprehensive series of HCoV-229E N protein mutants with truncated CTD was generated and systematically investigated by biophysical and biochemical analyses to clarify the role of the C-terminal tail of the HCoV-229E N protein in oligomerization. These results indicate that the last C-terminal tail plays an important role in dimer–dimer association. The C-terminal tail peptide is able to interfere with the oligomerization of the CTD of HCoV-229E N protein and performs the inhibitory effect on viral titre of HCoV-229E. This study may assist the development of anti-viral drugs against HCoV. Structured summary of protein interactions: N and C-terminal tail peptide bind by cosedimentation in solution (View interaction) N and N bind by cosedimentation in solution (View Interaction: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12) C-terminal tail peptide and N bind by fluorescence technology (View interaction) N and N bind by cross-linking study (View interaction) N and N bind by cross-linking study (View Interaction: 1, 2, 3, 4) [Copyright &y& Elsevier]

The N-terminal domain of nucleocapsid protein from human coronavirus OC43 (HCoV-OC43 N-NTD) mostly contains positively charged residues and has been identified as being responsible for RNA binding during ribonucleocapsid formation in the coronavirus. In this study, the crystallization and preliminary crystallographic analysis of HCoV-OC43 N-NTD (amino acids 58-195) with a molecular weight of 20 kDa are reported. HCoV-OC43 N-NTD was crystallized at 293 K using PEG 1500 as a precipitant and a 99.9% complete native data set was collected to 1.7 Å resolution at 100 K with an overall Rmerge of 5.0%. The crystals belonged to the hexagonal space group P65, with unit-cell parameters a = 81.57, c = 42.87 Å. Solvent-content calculations suggest that there is likely to be one subunit of N-NTD in the asymmetric unit. [ABSTRACT FROM AUTHOR]

Human coronavirus OC43 (HCoV-OC43) is one of the causes of the 'common cold' in human during seasons of cold weather. The primary function of the HCoV-OC43 nucleocapsid protein (N protein) is to recognize viral genomic RNA, which leads to ribonucleocapsid formation. Here, we characterized the stability and identified the functional regions of the recombinant HCoV-OC43 N protein. Circular dichroism and fluorescence measurements revealed that the HCoV-OC43 N protein is more highly ordered and stabler than the SARS-CoV N protein previously studied. Surface plasmon resonance (SPR) experiments showed that the affinity of HCoV-OC43 N protein for RNA was approximately fivefold higher than that of N protein for DNA. Moreover, we found that the HCoV-OC43 N protein contains three RNA-binding regions in its N-terminal region (residues 1-173) and central-linker region (residues 174-232 and 233-300). The binding affinities of the truncated N proteins and RNA follow the order: residues 1-173-residues 233-300 > residues 174-232. SPR experiments demonstrated that the C-terminal region (residues 301-448) of HCoV-OC43 N protein lacks RNA-binding activity, while crosslinking and gel filtration analyses revealed that the C-terminal region is mainly involved in the oligomerization of the HCoV-OC43 N protein. This study may benefit the understanding of the mechanism of HCoV-OC43 nucleocapsid formation. [ABSTRACT FROM AUTHOR]

Phospholipase A1 (PLA1) isolated from the black-bellied hornet ( Vespa basalis) catalyzes the hydrolysis of emulsified phospholipids in addition to the potent haemolytic activity responsible for its lethal effect. In this study, the crystallization and preliminary crystallographic analysis of PLA1 from hornet venom with a molecular weight of 32 kDa are reported. PLA1 was crystallized at 277 K using PEG 4000 as precipitant and a 96.5% complete native data set was collected from a frozen crystal to 2.5 Å resolution at 100 K with an overall Rmerge of 6.8%. The crystal belongs to the triclinic space group P1, with unit-cell parameters a = 57.2, b = 70.2, c = 81.6 Å, α = 107.0, β = 109.9, γ = 100.9°. In each asymmetric unit, three or four subunits of PLA1 are present according to the calculation of the solvent content. [ABSTRACT FROM AUTHOR]

Plant pathogens secrete proteins called effectors into the cells of their host to modulate the host immune response against colonization. Effectors can either modify or arrest host target proteins to sabotage the signaling pathway, and therefore are considered potential drug targets for crop disease control. In earlier research, the Xanthomonas type III effector XopAI was predicted to be a member of the arginine-specific mono-ADP-ribosyltransferase family. However, the crystal structure of XopAI revealed an altered active site that is unsuitable to bind the cofactor NAD+, but with the capability to capture an arginine-containing peptide from XopAI itself. The arginine peptide consists of residues 60 through 69 of XopAI, and residue 62 (R62) is key to determining the protein–peptide interaction. The crystal structure and the molecular dynamics simulation results indicate that specific arginine recognition is mediated by hydrogen bonds provided by the backbone oxygen atoms from residues W154, T155, and T156, and a salt bridge provided by the E265 sidechain. In addition, a protruding loop of XopAI adopts dynamic conformations in response to arginine peptide binding and is probably involved in target protein recognition. These data suggest that XopAI binds to its target protein by the peptide-binding ability, and therefore, it promotes disease progression. Our findings reveal an unexpected and intriguing function of XopAI and pave the way for further investigation on the role of XopAI in pathogen invasion. [ABSTRACT FROM AUTHOR]

We have reported the propensity of a DNA sequence containing CCG repeats to form a stable i-motif tetraplex structure in the absence of ligands. Here we show that an i-motif DNA sequence may transition to a base-extruded duplex structure with a GGCC tetranucleotide tract when bound to the (CoII)-mediated dimer of chromomycin A3, CoII(Chro)2. Biophysical experiments reveal that CCG trinucleotide repeats provide favorable binding sites for CoII(Chro)2. In addition, water hydration and divalent metal ion (CoII) interactions also play a crucial role in the stabilization of CCG trinucleotide repeats (TNRs). Our data furnish useful structural information for the design of novel therapeutic strategies to treat neurological diseases caused by repeat expansions. [ABSTRACT FROM AUTHOR]