• Journal of the Korean Magnetic Resonance Society
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• v.19 no.2
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• pp.83-87
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• 2015

Syndesmos, which is co-localized with syndecan-4 cytoplasmic domain ($Syn4^{cyto}$) in focal contacts, interacts with various cell adhesion adaptor proteins including $Syn4^{cyto}$ to control cell signaling. Syndesmos consists of 211 amino acids and it exists as a dimer (44kDa) in solution. Recently, we have determined the structure of syndesmos by x-ray crystallography, however, dynamics related to syndecan binding still remain elusive. In this report, we performed NMR experiments to acquire biochemical and structural information of syndesmos. Based on a series of three-dimensional triple resonance experiments on a $^{13}C/^{15}N/^2H$ labeled protein, NMR spectra were obtained with well dispersed and homogeneous NMR data. We present the sequence specific backbone assignment of syndesmos and assigned NMR data with combination structural information can be directly used for the studies on interaction with $Syn4^{cyto}$ and other binding molecules.

• Molecules and Cells
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• v.27 no.4
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• pp.493-496
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• 2009

Hypoxia-inducible factor $1{\alpha}$ ($HIF1{\alpha}$) is a transcription factor that plays a key role in the adaptation of cells to low oxygen stress and oxygen homeostasis. The oxygen-dependent degradation (ODD) domain of $HIF1{\alpha}$ responsible for the negative regulation of $HIF1{\alpha}$ in normoxia is intrinsically unfolded. Here, we carried out the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignment of a proteolysis-resistant fragment (residues 404-477) in the $HIF1{\alpha}$ ODD domain using NMR spectroscopy. About 98% (344/352) of all the $^1HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$, and $^{13}CO$ resonances were unambiguously assigned. The results will be useful for further investigation of the structural and dynamic states of the $HIF1{\alpha}$ ODD domain and its interaction with binding partners.

• Journal of the Korean Magnetic Resonance Society
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• v.28 no.2
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• pp.6-9
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• 2024

HscA is a Hsp70-type chaperone protein that plays an essential role to mediate the iron-sulfur (Fe-S) cluster biogenesis mechanism in Escherichia coli. Like other Hsp70 chaperones, HscA is composed of two domains: the nucleotide binding domain (NBD), which can hydrolyze ATP and use its chemical energy to facilitate the Fe-S cluster transfer process, and the substrate binding domain (SBD), which directly interacts with the substrate, IscU, the scaffold protein of an Fe-S cluster. In the present work, we prepared the isolated SBD construct of HscA (HscA(SBD)) and conducted the solution-state nuclear magnetic resonance (NMR) experiments to have its backbone chemical shift assignment information. Due to low spectral quality of HscA(SBD), we obtained all the NMR data from the sample containing the peptide LPPVKIHC, the HscA-interaction motif of IscU, from which the chemical shift assignment could be done successfully. We expect that this information provides an important basis to execute detailed structural characterization of HscA and appreciate its interaction with IscU.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.4
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• pp.138-142
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• 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
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• v.13 no.2
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• pp.117-125
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• 2009

HP0062 is an 86 residue hypothetical protein from Helicobacter pylori strain 26695. HP0062 was identified ESAT-6/WXG100 superfamily protein based on structure and sequence alignment and also contains leucine zipper domain sequence. Here, we report the sequence-specific backbone resonance assignment of HP0062. About 97.7% of all $^1H_N,\;^{15}N,\;^{13}C_{\alpha},\;^{13}C_{\beta}\;and\;^{13}C=O$ resonances were assigned unambiguously. We could predict the secondary structure of HP0062 by analyzing the deviation of the $^{13}C_{alpha}\;and\;^{13}C_{\beta}$ chemical shifts from their respective random coil values. Secondary structure prediction shows that HP0062 consist of two ${\alpha}$-helices. This study is a prerequisite for determining the solution structure of HP0062 and can be used for the study on interaction between HP0062 and DNA and other Helicobacter pylori proteins.

• Journal of the Korean Magnetic Resonance Society
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• v.16 no.2
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• pp.172-184
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• 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
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• v.40 no.5
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• pp.839-843
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• 2007

HP0495 (Swiss-Prot ID; Y495_HELPY) is an 86-residue hypothetical protein from Helicobacter pylori strain 26695. The function of HP0495 cannot be identified based on sequence homology, and HP0495 is included in a fairly unique sequence family. Here, we report the sequencespecific backbone resonance assignments of HP0495. About 97% of all the $^1HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$, and $^{13}CO$ resonances were assigned unambiguously. We could predict the secondary structure of HP0495, by analyzing the deviation of the $^{13}C{\alpha}$ and $^{13}C{\beta}$ shemical shifts from their respective random coil values. Secondary structure prediction shows that HP0495 consists of two $\alpha$-helices and four $\beta$-strands. This study is a prerequisite for determining the solution structure of HP0495 and investigating the protein-protein interaction between HP0495 and other Helicobacter pylori proteins.

• Journal of the Korean Magnetic Resonance Society
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• v.25 no.3
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• pp.39-44
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• 2021

The CRISPR-Cas system provides adaptive immunity for bacteria and archaea against invading phages and foreign plasmids. In the Class 1 CRISPR-Cas system, multi-subunit Cas proteins assemble with crRNA to bind to DNA targets. To disarm the bacterial defense system, bacteriophages evolved anti-CRISPR (Acr) proteins that actively inhibit the host CRISPR-Cas function. Here we report the backbone resonance assignments of AcrIF7 protein that inhibits the type I-F CRISPR-Cas system of Pseudomonas aeruginosa using triple-resonance nuclear magnetic resonance spectroscopy. We employed various computational methods to predict the structure and binding interface of AcrIF7, and assessed the model with experimental data. AcrIF7 binds to Cas8f protein via flexible loop regions to inhibit target DNA binding, suggesting that conformational heterogeneity is important for the Cas-Acr interaction.

• Journal of the Korean Magnetic Resonance Society
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• v.14 no.1
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• pp.45-54
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• 2010

HP1423 (Y1423_HELPY) is a conserved hypothetical protein from H. pylori strain 26695. However, Sequence Blast result indicates that HP1423 belongs to S4 (PF01479) superfamily. According to Pfam database, the S4 domain is a small domain consisting of 60-65 amino acid residues, that probably mediates binding to RNA. In this study, we report the sequence-specific backbone resonance assignment of HP1423, which has 84 amino acid residues. We could assign unambiguously about 88% of all $^{1}H_{N}$, $^{15}N$, $^{13}C_{\alpha}$, $^{13}C_{\beta}$ and $^{13}C=O$ resonances. We could not detect the resonances from residues 15-20, and disappearance of these peaks seems to be related with the intermediate-conformational exchange. These assigned NMR peaks of HP1423 can be used for studying the role of protein dynamics in millisecond timescale, and Protein-RNA binding.

• Journal of the Korean Magnetic Resonance Society
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• v.17 no.1
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• pp.54-58
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• 2013

SAV0506 is an 87 residue hypothetical protein from Staphylococcus aureus strain Mu50 and also predicted to have similar function to ribosome associated heat shock protein, Hsp 15. Hsp15 is thought to be involved in the repair mechanism of erroneously produced 50S ribosome subunit. In this report, we present the sequence specific backbone resonance assignment of SAV0506. About 82.5% of all resonances could be assigned unambiguously. By analyzing deviations of the $C{\alpha}$ and $C{\beta}$ chemical shift values, we could predict the secondary structure of SAV0506. This study is an essential step towards the structural characterization of SAV0506.