• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.431-436
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• 2005

Living cells are sustained not by individual activities but rather by coordinated summative efforts of different biological functional modules. While recent research works have focused largely on finding individual functional modules, this paper attempts to explore the connections or relationships between different cellular functions through cross-function domain interaction maps. Exploring such a domain interaction map can help understand the underlying inter-function communication mechanisms. To construct a cross-function domain interaction map from existing genome-wide protein-protein interaction datasets, we propose a two-step procedure. First, we infer conserved domain-domain interactions from genome-wide protein-protein interactions of yeast, worm and fly. We then build a cross-function domain interaction map that shows the connections of different functions through various conserved domain interactions. The domain interaction maps reveal that conserved domain-domain interactions can be found in most detected cross-functional relationships and a f9w domains play pivotal roles in these relationships. Another important discovery in the paper is that conserved domains correspond to highly connected protein hubs that connect different functional modules together.

• Journal of KIISE:Computing Practices and Letters
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• v.15 no.5
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• pp.375-379
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• 2009

Protein domain is the conserved unit of compact tree-dimensional structure and evolution, which carries specific function. Domains may appear in patterns in proteins, since they have been conserved through the evolution for functional formation of proteins. In this paper, we propose a formulated method for conservation analysis of domain combination based on association rule. Proposed method measures mutual dependency of domains in a combination, as well as co-occurrence frequency of them, which is conventionally used. Based on the method, we extracted conserve domain combinations in S.cerevisiae proteins and analyzed their functions based on Gene Ontology. From the results, we drew conclusions that domains in S.cerevisiae proteins form patterns whose members are highly affiliated to one another, and that extracted patterns tend to be associated with molecular function. Moreover, the results testified to proposed method superior to conventional ones for identifying domain combinations conserved for functional cooperation.

• 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.

• Journal of Industrial Technology
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• v.24 no.B
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• pp.139-142
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• 2004

To identify conserved structural or functional subunit(s) in the CP1 (editing) domains of class Ia tRNA synthetases, five available structures were compared and analyzed. Through sequence alignments of the CP1 domains, three conserved regions were found near the amino acid binding site in the editing domain. Structural overlapping of the three subunits clearly showed that there exist three common structural subunits in all of the five editing RS structures. The new alignment suggests a translocation movement of the CP1 domain caused by the binding with tRNA. Based on the experimental and modeling results, it is proposed that subunits 1 and 3 accommodate the incoming amino acid binding, while subunit 2 contributes to the interactions with the adenosine ring of the A76 to stabilize the overall tRNA binding.. Since these subunits are critical for the editing reaction, we expect that these key structures should be conserved through all class Ia editing RSs.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.33-33
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• 2003

Human DJ-1 and Escherichia coli Hsp31 belong to ThiJ/PfpI family whose members contain a conserved domain. DJ-1 is associated with autosomal recessive early-onset parkinsonism and Hsp31 is a molecular chaperone. Structural comparisons between DJ-1, Hsp31, and an archeal protease, a member of ThiJ/PfpI family, lead to the identification of the chaperons activity of DJ-1 and the proteolytic activity of Hsp31. Moreover, the comparisons provide insights into how the functional diversity is realized in proteins that share an evolutionarily conserved domain. On the basis of the chaperons activity, the possible role of DJ-1 in the pathogenesis of Parkinson's disease is discussed.

• Journal of Plant Biotechnology
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• v.49 no.1
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• pp.39-45
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• 2022

Conserved domains are defined as recurring units in molecular evolution and are commonly used to interpret the molecular function and biochemical structure of proteins. Herein, the ADP-glucose pyrophosphorylase (AGPase) amino acid sequences of three species of the Ipomoea genus [Ipomoea trifida, I. triloba, and I. batatas (L.) Lam. (sweetpotato)] were identified to investigate their physicochemical and biochemical characteristics. The molecular weight, isoelectric point, instability index, and grand average of hyropathy markedly differed among the three species. The aliphatic index values of sweetpotato AGPase proteins were higher in the small subunit than in the large subunit. The AGPase proteins from sweetpotato were found to contain an LbH_G1P_AT_C domain in the C-terminal region and various domains (NTP_transferase, ADP_Glucose_PP, or Glyco_tranf_GTA) in the N-terminal region. Conversely, most of its two relatives (I. trifida and I. triloba) were found to only contain the NTP_transferase domain in the N-terminal region. These findings suggested that these conserved domains were species-specific and related to the subunit types of AGPase proteins. The study may enable research on the AGPase-related specific characteristics of sweetpotatoes that do not exist in the other two species, such as starch metabolism and tuberization mechanism.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.11
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• pp.6803-6806
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• 2013

Background: Interferon regulatory factor 6 (IRF6) is a transcription factor with distinct and conserved DNA and protein binding domains. Mutations within the protein binding domain have been significantly observed in subjects with orofacial cleft relative to healthy controls. In addition, recent studies have identified loss of expression of IRF6 due to promoter hypermethylation in cutaneous squamous cell carcinomas. Since mutational events occurring within the conserved domains are likely to affect the function of a protein, we investigated whether regions within the IRF6 gene that encodes for the conserved protein binding domain carried mutations in oral squamous cell carcinoma (OSCC). Materials and Methods: Total chromosomal DNA extracted from 32 post surgical OSCC tissue samples were amplified using intronic primers flanking the exon 7 of IRF6 gene, which encodes for the major region of protein binding domain. The PCR amplicons from all the samples were subsequently resolved in a 1.2% agarose gel, purified and subjected to direct sequencing to screen for mutations. Results: Sequencing analysis resulted in the identification of a mutation within exon 7 of IRF6 that occurred in heterozygous condition in 9% (3/32) of OSCC samples. The wild type codon TTC at position 252 coding for phenylalanine was found to be mutated to TAC that coded for tyrosine (F252Y). Conclusions: The present study identified for the first time a novel mutation within the conserved protein binding domain of IRF6 gene in tissue samples of subjects with OSCC.

• Genomics & Informatics
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• v.10 no.1
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• pp.9-15
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• 2012

Horizontal gene transfer (HGT) is the movement of genetic material between kingdoms and is considered to play a positive role in adaptation. $Cryptosporidium$ $parvum$ is a parasitic protozoan that causes an infectious disease. Its genome sequencing reported 14 bacteria-like proteins in the nuclear genome. Among them, cgd2_1810, which has been annotated as CysQ, a sulfite synthesis pathway protein, is listed as one of the candidates of genes horizontally transferred from bacterial origin. In this report, we examined this issue using phylogenetic analysis. Our BLAST search showed that $C.$ $parvum$ CysQ protein had the highest similarity with that of proteobacteria. Analysis with NCBI's Conserved Domain Tree showed phylogenetic incongruence, in that $C.$ $parvum$ CysQ protein was located within a branch of proteobacteria in the cd01638 domain, a bacterial member of the inositol monophosphatase family. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the sulfate assimilation pathway, where CysQ plays an important role, is well conserved in most eukaryotes as well as prokaryotes. However, the Apicomplexa, including $C.$ $parvum$, largely lack orthologous genes of the pathway, suggesting its loss in those protozoan lineages. Therefore, we conclude that $C.$ $parvum$ regained cysQ from proteobacteria by HGT, although its functional role is elusive.

• Molecules and Cells
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• v.40 no.12
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• pp.954-965
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• 2017

Mammalian genomes are well established, and highly conserved regions within odorant receptors that are unique from other G-protein coupled receptors have been identified. Numerous functional studies have focused on specific conserved amino acids motifs; however, not all conserved motifs have been sufficiently characterized. Here, we identified a highly conserved 18 amino acid sequence motif within transmembrane domain seven (CAS-TM7) which was identified by aligning odorant receptor sequences. Next, we investigated the expression pattern and distribution of this conserved amino acid motif among a broad range of odorant receptors. To examine the localization of odorant receptor proteins, we used a sequence-specific peptide antibody against CAS-TM7 which is specific to odorant receptors across species. The specificity of this peptide antibody in recognizing odorant receptors has been confirmed in a heterologous in vitro system and a rat-based in vivo system. The CAS-TM7 odorant receptors localized with distinct patterns at each region of the olfactory epithelium; septum, endoturbinate and ectoturbinate. To our great interests, we found that the CAS-TM7 odorant receptors are primarily localized to the dorsal region of the olfactory bulb, coinciding with olfactory epithelium-based patterns. Also, these odorant receptors were ectopically expressed in the various non-olfactory tissues in an evolutionary constrained manner between human and rats. This study has characterized the expression patterns of odorant receptors containing particular amino acid motif in transmembrane domain 7, and which led to an intriguing possibility that the conserved motif of odorant receptors can play critical roles in other physiological functions as well as olfaction.

• Journal of Plant Biotechnology
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• v.49 no.1
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• pp.15-29
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• 2022

Cyclophilins (CYPs) are highly conserved ubiquitous proteins belong to the peptidyl prolyl cis/trans isomerase (PPIase) superfamily. These proteins are present in a wide range of organisms; they contain a highly conserved peptidyl-prolyl cis/trans isomerase domain. A comprehensive database survey identified a total of 35 genes localized in all cellular compartments of Solanum lycopersicum L., but largely in the cytosol. Sequence alignment and conserved motif analyses of the SlCYP proteins revealed a highly conserved CLD motif. Evolutionary analysis predicted the clustering of a large number of gene pairs with high sequence similarity. Expression analysis using the RNA-Seq data showed that the majority of the SlCYP genes were highly expressed in mature leaves and blooming flowers, compared with their expression in other organs. This study provides a basis for the functional characterization of individual CYP genes in the future to elucidate their role(s) in protein refolding and long-distance signaling in tomatoes and in plant biology, in general.