• BMB Reports
• /
• v.36 no.5
• /
• pp.505-507
• /
• 2003

One of the small proteins from Helicobacter pylori, acyl carrier protein (ACP), was investigated by NMR. ACP is related to various cellular processes, especially with the biosynthesis of fatty acid. The basic NMR resonance assignment is a prerequisite for the validation of a heterologuous protein interaction with ACP in H.pylori. Here, the results of the backbone $^1H$, $^{15}N$, and $^{l3}C$ resonance assignments of the H. pylori ACP are reported using double- and triple-resonance techniques. About 97% of all of the $^1HN$, $^{15}N$, $^{13}CO$, $^{13}C{\alpha}$, and $^{13}C{\beta}$ resonances that cover 76 of the 78 non-proline residues are clarified through sequential- and specific-assignments. In addition, four helical regions were clearly identified on the basis of the resonance assignments.

• Journal of the Korean Magnetic Resonance Society
• /
• v.16 no.2
• /
• pp.172-184
• /
• 2012

The prokaryotic molecular chaperone Hsp33 achieves its holdase activity upon response to oxidative stress particularly at elevated temperature. Despite many structural studies of Hsp33, which were conducted mainly by X-ray crystallography, the actual structures of the Hsp33 in solution remains controversial. Thus, we have initiated NMR study of the reduced, inactive Hsp33 monomer and backbone NMR assignments were obtained in the present study. Based on a series of triple resonance spectra measured on a triply isotope-[$^2H/^{13}C/^{15}N$]-labeled protein, sequence-specific assignments of the backbone amide signals observed in the 2D-[$^1H/^{15}N$]TROSY spectrum could be completed up to more than 96%. However, even considering the small portion of non-assigned resonances due to the lack of sequential connectivity, we confirmed that the total number of observed signals was quite smaller than that expected from the number of amino acid residues in Hsp33. Thus, it is postulated that peculiar dynamic properties would be involved in the solution structure of the inactive Hsp33 monomer. We expect that the present assignment data would eventually provide the most fundamental and important data for the progressing studies on the 3-dimensional structure and molecular dynamics of Hsp33, which are critical for understanding its activation process.

• BMB Reports
• /
• v.38 no.5
• /
• pp.591-594
• /
• 2005

One of the small proteins from Helicobacter pylori, HP1242, was investigated by the solution nuclear magnetic resonance (NMR) spectroscopy. HP1242 is known as a 76-residue conserved hypothetical protein and its function cannot be identified based on sequence homology. Here, the results of the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments of the HP1242 are reported using double- and triple-resonance techniques. About 95% of all of the $^1HN$, $^{15}N$, $^{13}CO$, $^{13}C{\alpha}$, and $^{13}C{\beta}$ resonances that cover 75 non- Proline residues of the 76 residues are clarified through sequential- and specific- assignments. In addition, three helical regions were clearly identified on the basis of the resonance assignments.

• Molecules and Cells
• /
• v.25 no.1
• /
• pp.138-141
• /
• 2008

HP0892 (SwissProt/TrEMBL ID O25552) is a 90-residue conserved hypothetical protein from Helicobacter pylori strain 26695, with a calculated pI of 9.38 and a molecular mass of 10.41 kDa. It belongs to the Plasmid stabilization system protein family (PF05016) in the Pfam database. Proteins with sequence similarity to HP0892 exist in Vibrio choierae, Enterococcus faecalis, Campylobacter jejuni, Streptococcus pneumoniae, Haemophilus influenzae, Escherichia coli O157. Here we report the sequence-specific backbone resonance assignments of HP0892 using multidimentional heteronuclear NMR spectroscopy. About 97.0% (422/435) of the HN, N, CO, $C{\beta}$, $C{\alpha}$ resonances of 90 residues of HP0892 were assigned. On the basis of the resonance assignments, three helical regions and four strand regions were identified using the CSI program. This study is a prerequisite for calculating the solution structure of HP0892, and will be useful for studying its interaction with other molecules.

• Journal of the Korean Magnetic Resonance Society
• /
• v.20 no.4
• /
• pp.138-142
• /
• 2016

Replication Protein A (RPA) is the eukaryotic single-stranded DNA binding protein. It involves in DNA replication, repair, and damage response. Among three subunits, RPA70 has a protein-protein binding domain (RPA70N) at the N-terminal. It has known that the domain recruits several damage response proteins to the damaged site. Also, it is suggested that there are more candidates that interact with RPA70N. Even though several studies performed on the structural aspects of RPA70N and its ligand binding, the backbone assignments of RPA70N is not available in public. In this study, we present the backbone assignments of RPA70N.

• Journal of the Korean Magnetic Resonance Society
• /
• v.24 no.2
• /
• pp.38-42
• /
• 2020

WW domains are small protein modules consisting of three-stranded antiparallel β-sheet, and involved in the protein-protein interaction for various biological systems. We overexpressed and purified WW2 domain from human AIP4/Itch (a member of Nedd4 family) using a pH/temperature dependent cleavage system. The backbone assignments of WW2 domain were completed, and secondary structure was predicted. Furthermore, backbone flexibility of WW2 domain was determined by ¹H-¹⁵N heteronuclear NOE and amide hydrogen exchange experiments. The structural information would contribute to the structural determination of WW2 domain as well as the interaction study of WW2 domain with various binding partners.

• Journal of the Korean Magnetic Resonance Society
• /
• v.3 no.1
• /
• pp.12-26
• /
• 1999

The 1H NMR signals of the heme methyl, propionate and related chemical groups of cytochrome C3 from Desulfovibrio vulgaris Miyazaki F (D.v. MF) were assigned by means of 1D NOE, 2D DQFCOSY and 2D TOCSY spectra. They were consistent with the assignments of the hemes with the highest and second-lowest redox potentials reported by Gayda et al. [Reference: 15]. The heme assignments were also supported by NOE between the methyl groups of these hemes and the side chain of Val-18, All the results contradicted the heme assignments for D.v. MF cytochrome C3 made on the basis of NMR [Reference: 11]. Based on these assignments, the interaction of cytochrome C3 with ferredoxin I was investigated by NMR. The major interaction site of cytochrome C3 was identified as the heme with the highest redox potential, which is surrounded by the highest density of positive charges. The stoichiometry and association constant were two cytochrome C3 molecules per monomer of ferredoxin I and 108 M-2 (at 53 mM ionic strength and $25^{\circ}C$), respectively.

• Journal of the Korean Magnetic Resonance Society
• /
• v.13 no.2
• /
• pp.108-116
• /
• 2009

The HP0902, a homodimeric 22.1 kDa protein, has been suggested as a putative secretory protein from Helicobacter pylori, although the protein possesses no signal peptide for secretion. Since it may be associated with the virulence of the bacterium, NMR study has been initiated in terms of structural genomics. In our previous effort to assign the backbone NMR resonances, using 800MHz NMR machine at pH 7.8, the resonances from eight of the 99 residues could not be assined due to missing of the signals. In this work, to enhance the extent of assignments, a 900 MHz machine was employed and the sample pH was reduced down to 6.5. Finally, almost all signals, except for those from G9 and S24, could be clearly assigned. The determined secondary structure using the assined chemical shifts indicated that the HP0902 consists of 11 ${\beta}$-strands with no helices. In our database search result, HP0902 was predicted to interact with VacA (Vacuolating cytotoxin A), which is a representative virulence factor secreted from Helicobacter pylori. Thus, molecular interaction between HP0902 and VacA would be worthy of investigation, on the basis of the present results of NMR assignments.

• Molecules and Cells
• /
• v.24 no.3
• /
• pp.437-440
• /
• 2007

$OGL-20P^T$-358 is a novel 66 amino acid residue protein from the hyperthermophile Thermococcus thioreducens sp. nov., strain $OGL-20P^T$, which was collected from the wall of the hydrothermal black smoker in the Rainbow Vent along the mid-Atlantic ridge. This protein, which has no detectable sequence homology with proteins or domains of known function, has a calculated pI of 4.76 and a molecular mass of 8.2 kDa. We report here the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments of $OGL-20P^T$-358. Assignments are 97.5% (316/324) complete. Chemical shift index was used to determine the secondary structure of the protein, which appears to consist of primarily ${\alpha}$-helical regions. This work is the foundation for future studies to determine the three-dimensional solution structure of the protein.

• Molecules and Cells
• /
• v.20 no.3
• /
• pp.442-445
• /
• 2005

HP0894 (SwissProt/TrEMBL ID O25554) is an 88-residue conserved hypothetical protein from Helicobacter pylori strain 26695 with a calculated pI of 8.5 and a molecular weight of 10.38 kDa. Proteins with sequence similarity to HP0894 exist in Vibrio choierae, Enterococcus faecalis, Campylobacter jejuni, Streptococcus pneumoniae, Haemophilus influenzae, Escherichia coli O157, etc. Here we report the sequence-specific backbone resonance assignments of HP0894. About 97.5% (418/429) of the HN, N, CO, $C{\alpha}$, $C{\beta}$ resonances of the 88 residues of HP0894 were assigned. On the basis of these assignments, three helical regions and four strand regions were identified using the CSI program. This study is a prerequisite for calculating the solution structure of HP0894, and studying its interaction with its substrates, if any, and/or with other proteins.