• Journal of the Korean Magnetic Resonance Society
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• v.15 no.1
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• pp.69-79
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• 2011

HP0827 has two RNP motif which is a very common protein domain involved in recognition of a wide range of ssRNA/DNA.We acquired 3D NMR spectra of HP0827 which shows well dispersed and homogeneous signals which allows us to assign 98% of all $^1H_N$, $^{15}N$, $^{13}C_{\alpha}$, $^{13}C_{\beta}$ and $^{13}C$=O resonances and 90% of all sidechain resonances. The sequence-specific backbone resonance assignment of HP0827 can be used to gain deeper insights into the nucleic acids binding specificity of HP0827 in the future study. Here, we report secondary structure prediction of HP0827 derived from NMR data. Additionally, ssRNA/DNA binding assay studies was also conducted. This study might provide a clue for exact function of HP0827 based on structure and sequence.

• Genomics & Informatics
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• v.20 no.4
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• pp.41.1-41.9
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• 2022

The pathogen Gallibacterium anatis has caused heavy economic losses for commercial poultry farms around the world. However, despite its importance, the functions of its hypothetical proteins (HPs) have been poorly characterized. The present study analyzed the functions and structures of HPs obtained from Gallibacterium anatis (NCTC11413) using various bioinformatics tools. Initially, all the functions of HPs were predicted using the VICMpred tool, and the physicochemical properties of the identified virulence proteins were then analyzed using Expasy's ProtParam server. A virulence protein (WP_013745346.1) that can act as a potential drug target was further analyzed for its secondary structure, followed by homology modeling and three-dimensional (3D) structure determination using the Swiss-Model and Phyre2 servers. The quality assessment and validation of the 3D model were conducted using ERRAT, Verify3D, and PROCHECK programs. The functional and phylogenetic analysis was conducted using ProFunc, STRING, KEGG servers, and MEGA software. The bioinformatics analysis revealed 201 HPs related to cellular processes (n = 119), metabolism (n = 61), virulence (n = 11), and information/storage molecules (n = 10). Among the virulence proteins, three were detected as drug targets and six as vaccine targets. The characterized virulence protein WP_013745346.1 is proven to be stable, a drug target, and an enzyme related to the citrate cycle in the present pathogen. This enzyme was also found to facilitate other metabolic pathways, the biosynthesis of secondary metabolites, and the biosynthesis of amino acids.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.2
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• pp.50-55
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• 2016

Backbone $^1H$, $^{13}C$ and $^{15}N$ resonance assignments are presented for the anticodon binding domain (residues 557-674) of human glycyl-tRNA synthetase (GRS). Role of the anticodon binding domain (ABD) of GRS as an anticancer ligand has recently been reported and its role in other diseases like Charcot-Marie-Tooth (CMT) and polymyositis have increased its interest. NMR assignments were completed using the isotope [$^{13}C/^{15}N$]-enriched protein and chemical shifts based secondary structure analysis with TALOS+ demonstrate similar secondary structure as reported in X-ray structure PDB 2ZT8, except some C-terminal residues. NMR signals from the N-terminal residues 557 to 571 and 590 to 614 showed very weak or no signals exhibiting dynamics or conformational exchange in NMR timescale.

• Proceedings of the Korean Information Science Society Conference
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• 2003.10b
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• pp.811-813
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• 2003

단백질의 기능은 단백질의 구조에 따라 결정되며, 새로운 단백질의 기능을 파악하기 위하여 이미 밝혀진 단백질의 기능과 구조를 비교하는 방법이 사용되고 있다. 단백질 구조를 비교하는 방법은 단백질 구조를 표현하는 방법에 따라 다양하게 개발되고 있으며, 보다 효과적으로 관련된 연구자들이 자신의 연구에 활용하기 위해서는 빠르고 쉽게 활용할 수 있는 인터페이스를 제공하는 도구가 필요하다. 본 논문에서는 단백질 이차구조 및 그들 사이의 관계를 이용하여 단백질 구조를 표현하는 PSAML과 이를 이용하여 표현된 단백질 구조를 비교하는 시스템인 S4E(Search Substructures of Secondary Structure Elements)에 관하여 기술한다. S4E 시스템은 단백질 이차구조와 그들 사이의 관계(각도, 거리, 길이)를 이용하여 표현된 단백질 구조를 비교하여 유사성이 높은 부분을 찾는 기능을 제공한다. 또한 S4E 시스템은 이차구조 기반의 단백질 구조 데이터베이스(PSAML 데이터베이스) 및 웹 기반 사용자 인터페이스를 제공하여 사용자가 쉽고 효과적으로 단백질 구조 비교를 할 수 있다.

• Journal of Photoscience
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• v.9 no.2
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• pp.82-85
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• 2002

33kDa extrinsic protein, an important protein in oxygenic photosynthesis, was known to have no fixed configuration in solution. At 20$\^{C}$ and pH 6, 33kDa extrinsic protein showed changes of free energy of -14.6 kJ/mor$\^$-1/ and of standard volume of -120mL/mol, respectively, with increase of hydrostatic pressure, comparatively lower than for most proteins. NBS modification of Trp241 in 33kDa extrinsic protein dramatically changes the secondary protein structure, its affinity to photosystem II as well as photosynthetic oxygen evolution. The relationship between structural change and transport of oxygen, water and proton is deserved a further study.

• Bulletin of the Korean Chemical Society
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• v.33 no.8
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• pp.2508-2512
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• 2012

Cold shock proteins (CSPs) are a family of proteins induced at low temperatures. CSPs bind to single-stranded nucleic acids through the ribonucleoprotein 1 and 2 (RNP 1 and 2) binding motifs. CSPs play an essential role in cold adaptation by regulating transcription and translation via molecular chaperones. The solution nuclear magnetic resonance (NMR) or X-ray crystal structures of several CSPs from various microorganisms have been determined, but structural characteristics of psychrophilic CSPs have not been studied. Therefore, we optimized the purification process to obtain highly pure Lm-Csp and determined the three-dimensional structure model of Lm-Csp by comparative homology modeling using MODELLER on the basis of the solution NMR structure of Bs-CspB. Lm-Csp consists of a ${\beta}$-barrel structure, which includes antiparallel ${\beta}$ strands (G4-N10, F15-I18, V26-H29, A46-D50, and P58-Q64). The template protein, Bs-CspB, shares a similar ${\beta}$ sheet structure and an identical chain fold to Lm-Csp. However, the sheets in Lm-Csp were much shorter than those of Bs-CspB. The Lm-Csp side chains, E2 and R20 form a salt bridge, thus, stabilizing the Lm-Csp structure. To evaluate the contribution of this ionic interaction as well as that of the hydrophobic patch on protein stability, we investigated the secondary structures of wild type and mutant protein (W8, F15, and R20) of Lm-Csp using circular dichroism (CD) spectroscopy. The results showed that solvent-exposed aromatic side chains as well as residues participating in ionic interactions are very important for structural stability. Further studies on the three-dimensional structure and dynamics of Lm-Csp using NMR spectroscopy are required.

• Preventive Nutrition and Food Science
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• v.7 no.2
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• pp.184-187
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• 2002

Blood products from slaughterhouses that are not hygienically prepared for disposal or food consumption pose a human health hazard. Gamma irradiation is an effective method for sterilization of blood products, but may introduce changes in the molecular characteristics of proteins. This study evaluated the effects of irradiation on animal plasma proteins. Bovine and porcine blood was obtained from a slaughterhouse and the plasma proteins purified and lyophilized. The secondary structure and molecular weight distribution of the plasma protein solutions and powders were examined after ${\gamma}$-irradiation at 1, 5, 7 and 10 kGy. Gamma-irradiation affected the molecular properties of the protein solutions, but not the protein powders. Circular dichroism and sodium dodecyl sulfate-polyacrylamide gel electrophoresis studies showed that increased doses of ${\gamma}$-irradiation decrease the ordered structure of plasma proteins in solution, and cause initial fragmentation of the polypeptide chains and subsequent aggregation.

• Preventive Nutrition and Food Science
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• v.4 no.2
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• pp.139-144
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• 1999

Lipoprotein lipase (LPL) I san enzyme that catalyzed the hydrolysis of triacylglycerols of chylomicrons and VLDL to produce 20acylglycerols and fatty acids. The enzyme, LPL, is localized on the surface of the capillary endothelium and is widely distributed in extrahepatic tissues including heart, skeletal muscle and adipose tissue. LPL has been isolated from boving milk by affinity chromatography on heparin-separose in 2 M NaCL, 5mM barbital buffer, pH 7.4. To elucidate the lipid-binding regin, LPL was digested with trypsin and then separated by gel filtration. Lipid binding region of LPL has been investigated by recombining LPL peptides with DMPC vesicles. Proteolytic LPL fragments with DMPC were reassembled and stabilized by cholate. Lipid-binding region of LPL was identified by a PTH-automated protein sequencer, as AQQHYPVSAGYTK. The analysis of the secondary structure of the lipid-binding peptides revealed a higher probability of $\alpha$-helix structure compared to the whole LPL protein. The prediction of hydrophobicity of lipid -binding region was highly hydrophobic (-1.1) compared to LPL polypetide(-0.4).

• Mass Spectrometry Letters
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• v.11 no.4
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• pp.65-70
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• 2020

Despite its great success in the field of proteomics, mass spectrometry has limited use for determining structural details of peptides, proteins, and their assemblies. Emerging ion mobility spectrometry-mass spectrometry has enabled us to explore the conformational space of protein ions in the gas phase, and further combinations with the gas-phase ion spectroscopy and the collision-induced unfolding have extended its abilities to elucidating the secondary structure and local details of conformational transitions. This review will provide a brief introduction to the combined approaches of IMS-MS with gas-phase ion infrared spectroscopy or collision-induced unfolding and their most recent results that successfully revealed higher-order structural details.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.215-220
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• 2005

Generally, enzymes in the starch biosynthesis pathway exist in many isoforms, contributing to the difficulties in the dissection of their specific roles in controlling starch properties. In this study, we present an algorithm as an alternative method to classify isoforms of starch biosynthesis enzymes based on their conserved secondary structures. Analysis of the predicted secondary structure of plant soluble starch synthase I (SSI) and soluble starch synthase II (SSII) demonstrates that these two classes of isoform can be reclassified into three subsets, SS-A, SS-B and SS-C, according to the differences in the secondary structure of the protein at C-terminus. SS-A reveals unique structural features that are conserved only in cereal plants, while those of SS-B are found in all plants and SS-C is restricted to barley. These findings enable us to increase the accuracy in the estimation of evolutionary distance between isoforms of starch synthases. Moreover, it facilitates the elucidation of correlations between the functions of each enzyme isoforms and the properties of starches. Our secondary structure analysis tool can be applicable to study the functions of other plant enzyme isoforms of economical importance.