• Genomics & Informatics
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• v.11 no.3
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• pp.155-160
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• 2013

Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural information repositories that have been published. The reliability of the torsional system, which represents the native processes of structural change in the structural analysis, was partially proven with previous structural alignment studies. Here, a web server providing structural information and analysis based on the backbone torsional representation of a protein structure is newly introduced. The web server offers functions of secondary structure database search, secondary structure calculation, and pair-wise protein structure comparison, based on a backbone torsion angle representation system. Application of the implementation in pair-wise structural alignment showed highly accurate results. The information derived from this web server might be further utilized in the field of ab initio protein structure modeling or protein homology-related analyses.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.1
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• pp.36-40
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• 2014

Predicting secondary structure of protein through assigned backbone chemical shifts has been used widely because of its convenience and flexibility. In spite of its usefulness, chemical shift based analysis has some defects including isotopic shifts and solvent interaction. Here, it is shown that corrected chemical shift analysis for secondary structure of protein. It is included chemical shift correction through consideration of deuterium isotopic effect and calculate chemical shift index using probability-based methods. Enhanced method was applied successfully to one of the proteins from Mycobacterium tuberculosis. It is suggested that correction of chemical shift analysis could increase accuracy of secondary structure prediction of protein and small molecule in solution.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• Genomics & Informatics
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• v.21 no.1
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• pp.7.1-7.11
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• 2023

The gram-positive bacterium Listeria monocytogenes is an important foodborne intracellular pathogen that is widespread in the environment. The functions of hypothetical proteins (HP) from various pathogenic bacteria have been successfully annotated using a variety of bioinformatics strategies. In this study, a HP Imo0888 (NP_464414.1) from the Listeria monocytogenes EGD-e strain was annotated using several bioinformatics tools. Various techniques, including CELLO, PSORTb, and SOSUIGramN, identified the candidate protein as cytoplasmic. Domain and motif analysis revealed that the target protein is a PemK/MazF-like toxin protein of the type II toxin-antitoxin system (TAS) which was consistent with BLASTp analysis. Through secondary structure analysis, we found the random coil to be the most frequent. The Alpha Fold 2 Protein Structure Prediction Database was used to determine the three-dimensional (3D) structure of the HP using the template structure of a type II TAS PemK/MazF family toxin protein (DB ID_AFDB: A0A4B9HQB9) with 99.1% sequence identity. Various quality evaluation tools, such as PROCHECK, ERRAT, Verify 3D, and QMEAN were used to validate the 3D structure. Following the YASARA energy minimization method, the target protein's 3D structure became more stable. The active site of the developed 3D structure was determined by the CASTp server. Most pathogens that harbor TAS create a crucial risk to human health. Our aim to annotate the HP Imo088 found in Listeria could offer a chance to understand bacterial pathogenicity and identify a number of potential targets for drug development.

• Genomics & Informatics
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• v.9 no.2
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• pp.74-78
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• 2011

Numerous restraints and simplifications have been developed for methods that anticipate protein structure to reduce the colossal magnitude of possible conformational states. In this study, we investigated if globularity is a general characteristic of proteins and whether they can be applied as a valid constraint in protein structure simulations with approximated measurements (Gb-index). Unexpectedly, most of the proteins showed strong structural globularity (i.e., mode of approximately 76% similarity to the perfect globe) with only a few percent of proteins being outliers. Small proteins tended to be significantly non-globular ($R^2$=0.79) and the minimum Gb-index showed a logarithmic increase with the increase in protein size ($R^2$=0.62), strongly implying that the non-globular characteristics might be more acceptable for smaller proteins than larger ones. The strong perfect globe-like character and the relationship between small size and the loss of globular structure of a protein may imply that living organisms have mechanisms to aid folding into the globular structure to reduce irreversible aggregation. This also implies the possible mechanisms of diseases caused by protein aggregation, including some forms of trinucleotide repeat expansion-mediated diseases.

• The KIPS Transactions:PartA
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• v.16A no.3
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• pp.153-158
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• 2009

Analysis of 3-dimensional (3D) protein structure plays an important role of structural bioinformatics. The protein structure visualization is the one of the structural bioinformatics and the most fundamental problem. As the number of known protein structure increases rapidly and the study of protein-protein interaction is prevalent, the fast visualization of large scale protein structure becomes essential. The fast protein structure visualization system we proposed is sophisticated and well designed visualization system using geometry instancing technique. Because this system is optimized for recent 3D graphics hardware using geometry instancing technique, its rendering speed is faster than other visualization tools.

• Journal of the Korean Magnetic Resonance Society
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• v.23 no.2
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• pp.56-60
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• 2019

Study on the structure and dynamics of molecules at the atomic level is of great significance for understanding their function and stability as well as roles for various chemico-physical and biological processes. $^{17}O$ NMR spectroscopy has appeared as an elegant technique for investigating of the physicochemical and structural properties of oxygen-containing compounds such as metal organic frameworks and nanosized oxides. This method has drawn much attention as it provides unique insights into the properties of targets based on atomistic information of local oxygen environments which is otherwise difficult to obtain using other methods. In this mini review, we introduce and discuss the recent study and developments of $^{17}O$ NMR techniques which are tailored for the investigation on the structure and dynamics of water and inorganic materials.

• Molecules and Cells
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• v.43 no.12
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• pp.1035-1045
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• 2020

The Drosophila genome contains four low molecular weight-protein tyrosine phosphatase (LMW-PTP) members: Primo-1, Primo-2, CG14297, and CG31469. The lack of intensive biochemical analysis has limited our understanding of these proteins. Primo-1 and CG31469 were previously classified as pseudophosphatases, but CG31469 was also suggested to be a putative protein arginine phosphatase. Herein, we present the crystal structures of CG31469 and Primo-1, which are the first Drosophila LMW-PTP structures. Structural analysis showed that the two proteins adopt the typical LMW-PTP fold and have a canonically arranged P-loop. Intriguingly, while Primo-1 is presumed to be a canonical LMW-PTP, CG31469 is unique as it contains a threonine residue at the fifth position of the P-loop motif instead of highly conserved isoleucine and a characteristically narrow active site pocket, which should facilitate the accommodation of phosphoarginine. Subsequent biochemical analysis revealed that Primo-1 and CG31469 are enzymatically active on phosphotyrosine and phosphoarginine, respectively, refuting their classification as pseudophosphatases. Collectively, we provide structural and biochemical data on two Drosophila proteins: Primo-1, the canonical LMW-PTP protein, and CG31469, the first investigated eukaryotic protein arginine phosphatase. We named CG31469 as DARP, which stands for Drosophila ARginine Phosphatase.

• KIPS Transactions on Software and Data Engineering
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• v.3 no.4
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• pp.163-168
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• 2014

In a protein molecule, ${\alpha}$-helices are important for protein structure, function, and binding to other proteins, so the analysis on the structure of helices has been researched. Since an interaction between two helices is evaluated based on their axes, massive errors in protein structure analysis would be caused if a curved or kinked long ${\alpha}$-helix is considered as a linear one. In this paper, we present an algorithm to reconstruct ${\alpha}$-helices in a protein molecule as a sequence of straight helices under given threshold.

• Genomics & Informatics
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• v.16 no.4
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• pp.23.1-23.5
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• 2018

Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonomy to be extended from in vivo and in vitro to in silico. In this study, we verified the consistency of the current International Committee on Taxonomy of Viruses taxonomy using an in silico approach, aiming to identify the specific sequence for each virus. We applied this approach to norovirus in Caliciviridae, which causes 90% of gastroenteritis cases worldwide. First, based on the dogma "protein structure determines its function," we hypothesized that the specific sequence can be identified by the specific structure. Firstly, we extracted the coding region (CDS). Secondly, the CDS protein sequences of each genus were annotated by the conserved domain database (CDD) search. Finally, the conserved domains of each genus in Caliciviridae are classified by RPS-BLAST with CDD. The analysis result is that Caliciviridae has sequences including RNA helicase in common. In case of Norovirus, Calicivirus coat protein C terminal and viral polyprotein N-terminal appears as a specific domain in Caliciviridae. It does not include in the other genera in Caliciviridae. If this method is utilized to detect specific conserved domains, it can be used as classification keywords based on protein functional structure. After determining the specific protein domains, the specific protein domain sequences would be converted to gene sequences. This sequences would be re-used one of viral bio-marks.