위암 환자의 위암조직과 위액에서 위암에 특이한 단백에 관한 연구

박경남,신창록,고재경 한양대학교 의과대학 1994 한양의대 학술지 Vol.14 No.1

In order to investigate cancer specific proteins associated with stomach cancer, proteins of stomach cancer tissue and gastric juice from patients with stomach cancer were separated by a DEAE-cellulose column chromatography, high performance liquid chromatography(HPLC) and polyacrylamide gel electrophoresis, and the results were compared with those from control tissue and gastric juice. Protein concentration of cancer tissue and gastric juice of patients with stomach cancer was significantly increased and positive rate of protein contents in stomach cancer tissue and gastric juice as a marker for stomach cancer was high, indicating the possible use of of the protein contents as a biochemical marker for the stomach cancer. Proteins in the stomach cancer tissue were separated by a DEAE cellulose column chromatography into 6 peak proteins, of which a single peak protein (peak Ⅲb) was found to be specific to the cancer and proteins in the gastric juice from patient with stomach cancer were separated into 8 peak proteins, of which three protein peaks(peak Ⅱ, Ⅲ and Ⅳb) were specific to the cancer. Peak Ⅰ and Ⅴ proteins isolated from both cancer tissue and gastric juice from patient with stomach cancer were observed to be activated, suggesting a possible role of these proteins in carcinogenesis and suppression of the stomach cancer. Isolation patterns for proteins of the stomach cancer tissue appeared to be different form those of the control tissue, showing presence of more than 8 protein bands specific to the cancer and disappearance of more than 2 protein bands specific to the cancer and disappearance of more than 2 protein bands from the stomach cancer tissue. The results indicated that changes in proteins of cancer tissue and gastric juice from patient with stomach cancer did not take place in a single protein, but did occur in multiple proteins. Qualitative changes in the proteins were variable in nature, such as presence of cancer specific proteins, disappearance of proteins from the cancer tissue and gastric juice and activiation of the proteins.

Comparison of the large-scale periplasmic proteomes of the Escherichia coli K-12 and B strains

Han, M.J.,Kim, J.Y.,Kim, J.A. Society for Bioscience and Bioengineering, Japan ; 2014 Journal of bioscience and bioengineering Vol.117 No.4

Escherichia coli typically secretes many proteins into the periplasmic space, and the periplasmic proteins have been used for the secretory production of various proteins by the biotechnology industry. However, the identity of all of the E. coli periplasmic proteins remains unknown. Here, high-resolution periplasmic proteome reference maps of the E. coli K-12 and B strains were constructed and compared. Of the 145 proteins identified by tandem mass spectrometry, 61 proteins were conserved in the two strains, whereas 11 and 12 strain-specific proteins were identified for the E. coli K-12 and B strains, respectively. In addition, 27 proteins exhibited differences in intensities greater than 2-fold between the K-12 and B strains. The periplasmic proteins MalE and OppA were the most abundant proteins in the two E. coli strains. Distinctive differences between the two strains included several proteins that were caused by genetic variations, such as CybC, FliC, FliY, KpsD, MglB, ModA, and Ybl119, hydrolytic enzymes, particularly phosphatases, glycosylases, and proteases, and many uncharacterized proteins. Compared to previous studies, the localization of many proteins, including 30 proteins for the K-12 strain and 53 proteins for the B strain, was newly identified as periplasmic. This study identifies the largest number of proteins in the E. coli periplasm as well as the dynamics of these proteins. Additionally, these findings are summarized as reference proteome maps that will be useful for studying protein secretion and may provide new strategies for the enhanced secretory production of recombinant proteins.

Purificatin and Chacterizaion of the 22-kDa Kunitze type Potato Proteinase Inhibitors

Suh, Sang-Gon,Hannapel, David J. 영남대학교 마늘연구소 2001 의성군 ·영남대학교 관 ·학협동, 협약 조인식 및 심포지움 Vol.2001 No.-

Three abundant protein of approximate molecular masses of 22,23, and 24 kilodaltons were purified from potato (Solanum tuberosum L.) tubers by DEAE cellulose and CM-52 cellulose ion exchange culumn chromatography, electroelution, and high-pressure liquid chromatography (HPLC). Antibodies specific to the gel-purified 22-kilodalton protein were prepared. Immunoblot analysis showed that the 22-, 23-, and 24- kilodalton proteins are immunologically related and that these proteins are present in tubers and as higher molecular mass farms in leaves, but not in stems, roots, and stolons. The ratios of amino acid composition were compared among the three purified protiens, and the amino-terminal amino acid sequence were determined for these three proteins. All three proteins have identical amino-terminal sequence that match the deduced amino acid sequence of an abundant tuber protein cDNA. Using a proteinase-inhibition assay, we have demonstrated that the 22-kilodalton (kDa) potato (Solanum tuberosum L.) tuber proteins are strong inhibitors of serine proteinases. Two out of three purified proteins from the 22-kDa family of potato-tuber proteins were effective inhibitors of both trypsin and chymotrypsin, while the third, with a molecular mass (Mr) of apprex.24-kDa, inhibited only trypsin activity. Comparison of the amino-acid sequence of the putative reactive sites of several proteinase inhibitors with the deduced sequence of the 22-kDa protein showed that the 22-kDa protein contained sequences potentially pessessing "double-headed" sites of inhibition, one against trypsin and another against chymotrypsin. The genes coding for the 22-kDa proteins were developmentally regulated in tubers and environmentally regulated in leaves. Wound induction of the genes coding for the 22-kDa potato-tubers proteins was detected at the RNA level. In leaves, transcripts of the 22-kDa protein family were detected 6h after wounding and were highest after 12h in locally wounded leaves. The strongest induction occurred systemically in response to mechanical wounding in non-wounded leaves. Cross-hybridization of a cDNA, p34021, which codes for the 22-kDa tuber protein, with both proteinase-inhibitor I and II cDNAs and with a second family of 20-kDa potato-tuber cDNAs showed no cross-homology. Members of this second group of 20-kDa potato-tuber proteins also exhibited wound-induction in leaves at the RNA level.

Functional annotation of uncharacterized proteins from Fusobacterium nucleatum: identification of virulence factors

Kanchan Rauthan,Saranya Joshi,Lokesh Kumar,Divya Goel,Sudhir Kumar Korea Genome Organization 2023 Genomics & informatics Vol.21 No.2

Fusobacterium nucleatum is a gram-negative bacteria associated with diverse infections like appendicitis and colorectal cancer. It mainly attacks the epithelial cells in the oral cavity and throat of the infected individual. It has a single circular genome of 2.7 Mb. Many proteins in F. nucleatum genome are listed as "Uncharacterized." Annotation of these proteins is crucial for obtaining new facts about the pathogen and deciphering the gene regulation, functions, and pathways along with discovery of novel target proteins. In the light of new genomic information, an armoury of bioinformatic tools were used for predicting the physicochemical parameters, domain and motif search, pattern search, and localization of the uncharacterized proteins. The programs such as receiver operating characteristics determine the efficacy of the databases that have been employed for prediction of different parameters at 83.6%. Functions were successfully assigned to 46 uncharacterized proteins which included enzymes, transporter proteins, membrane proteins, binding proteins, etc. Apart from the function prediction, the proteins were also subjected to string analysis to reveal the interacting partners. The annotated proteins were also put through homology-based structure prediction and modeling using Swiss PDB and Phyre2 servers. Two probable virulent factors were also identified which could be investigated further for potential drug-related studies. The assigning of functions to uncharacterized proteins has shown that some of these proteins are important for cell survival inside the host and can act as effective drug targets.

In-depth proteomic analysis of <i>Glycine max</i> seeds during controlled deterioration treatment reveals a shift in seed metabolism

Min, Cheol Woo,Lee, Seo Hyun,Cheon, Ye Eun,Han, Won Young,Ko, Jong Min,Kang, Hang Won,Kim, Yong Chul,Agrawal, Ganesh Kumar,Rakwal, Randeep,Gupta, Ravi,Kim, Sun Tae Elsevier 2017 Journal of proteomics Vol.169 No.-

<P><B>Abstract</B></P> <P>Seed aging is one of the major events, affecting the overall quality of agricultural seeds. To analyze the effect of seed aging, soybean seeds were exposed to controlled deterioration treatment (CDT) for 3 and 7days, followed by their physiological, biochemical, and proteomic analyses. Seed proteins were subjected to protamine sulfate precipitation for the enrichment of low-abundance proteins and utilized for proteome analysis. A total of 14 differential proteins were identified on 2-DE, whereas label-free quantification resulted in the identification of 1626 non-redundant proteins. Of these identified proteins, 146 showed significant changes in protein abundance, where 5 and 141 had increased and decreased abundances, respectively while 352 proteins were completely degraded during CDT. Gene ontology and KEGG analyses suggested the association of differential proteins with primary metabolism, ROS detoxification, translation elongation and initiation, protein folding, and proteolysis, where most, if not all, had decreased abundance during CDT. Western blotting confirmed reduced level of antioxidant enzymes (DHAR, APx1, MDAR, and SOD) upon CDT. This in-depth integrated study reveals a major downshift in seed metabolism upon CDT. Reported data here serve as a resource for its exploitation to metabolic engineering of seeds for multiple purposes, including increased seed viability, vigor, and quality.</P> <P><B>Biological significance</B></P> <P>Controlled deterioration treatment (CDT) is one of the major events that negatively affects the quality and nutrient composition of agricultural seeds. However, the molecular mechanism of CDT is largely unknown. A combination of gel-based and gel-free proteomic approach was utilized to investigate the effects of CDT in soybean seeds. Moreover, we utilized protamine sulfate precipitation method for enrichment of low-abundance proteins, which are generally masked due to the presence of high-abundance seed storage proteins. Reported data here serve as resource for its exploitation to metabolic engineering of seeds for multiple purposes, including increased seed viability, vigor, and quality.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Protamine sulfate precipitation was used for enrichment of low-abundance proteins. </LI> <LI> 2DE & label-free quantitative proteomic approach were used to analyze effect of CDT. </LI> <LI> Using this approach, a total of 1640 (14+1626) proteins were identified. </LI> <LI> These proteins were mainly related to the primary metabolism and ROS detoxification. </LI> <LI> Western blotting confirmed reduced level of DHAR, APx1, MDAR, and SOD upon CDT. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

ABERRANT PTROTEIN EXPRESSION IN CLONED PLACENTAE DERIVED FROM SOMATIC CELL NUCLEAR TRANSFER IN BOVINE AND MOUSE

Jin, Dong Il,Kim, Hong Rye,Park, Chang Sik,Yoon, Jong Taek,Wakayama, Teruhiko 충남대학교 형질전환복제돼지연구센터 2007 논문집 Vol. No.10

Animal cloning by somatic cell nuclear transfer has been puzzled with low success rate in which most clones die before birth and survivors frequently display abnormalities. It is speculated that proper epigenetic reprogramming is somehow defective in reconstituted embryos. Fetal growth defect after implantation is supposed to be related to placental abnormality. It is unknown whether aberrant gene expression in cloned placental causes fetal loss during pregnancy. To analyze the differential protein patterns of cloned placenta and normal placenta of mouse and bovine, 3 placentae of postnatal death just afterbirth derived from cloned Korean Native cattle and 3 normal placentae obtained by afterbirth of AI fetuses, and 3 mouse placentae derived from ES cell nuclear transfer and 3 normal placentae were used. Placental proteins were analyzed in 2-D electrophoresis with 3 replications of each sample. In case of bovine, a total of 60 spots were identified as differentially expressed proteins of which 33 spots were up-regulated proteins in cloned placentae while 27 spots were down-regulated proteins. In mouse samples, a total of 47 differentially expressed protein spots were identified of which 28 spots were up-regulated proteins and 19 spots were down-regulated proteins. Most identified proteins in this analysis appeared to be related with protein repair, cytoskeleton, signal transduction, immune system, metabolism, extracellular matrix, transcription regulation, cell structure or differentiation and ion transport. One of differentially up-regulated proteins in both mouse and bovine cloned placentae was identified as TIMP-2 protein that is related to extracellular matrix degradation and tissue remodeling processes. In cloned mouse placentae, one differentially down-regulated protein was identified as Pre-B-cell colony-enhancing factor 1(PBEF) protein that is related to inhibition of apoptosis and induction of spontaneous labor. Currently, the status of DNA methylation and histone modification of differentially expressed gene locus in cloned placenta cells is being investigated to ensure whether discrepancy of epigenetic programming in nuclear transfer causes abnormal gene expression.

Gecko proteins induce the apoptosis of bladder cancer 5637 cells by inhibiting Akt and activating the intrinsic caspase cascade

( Geun Young Kim ),( Soon Yong Park ),( Ara Jo ),( Mira Kim ),( Sun Hee Leem ),( Woo Jin Jun ),( Sang In Shim ),( Sang Chul Lee ),( Jin Woong Chung ) 생화학분자생물학회(구 한국생화학분자생물학회) 2015 BMB Reports Vol.48 No.9

Gecko proteins have long been used as anti-tumor agents in oriental medicine, without any scientific background. Although anti-tumor effects of Gecko proteins on several cancers were recently reported, their effect on bladder cancer has not been investigated. Thus, we explored the anti-tumor effect of Gecko proteins and its cellular mechanisms in human bladder cancer 5637 cells. Gecko proteins significantly reduced the viability of 5637 cells without any cytotoxic effect on normal cells. These proteins increased the Annexin-V staining and the amount of condensed chromatin, demonstrating that the Gecko proteinsinduced cell death was caused by apoptosis. Gecko proteins suppressed Akt activation, and the overexpression of constitutively active form of myristoylated Akt prevented Gecko proteins-induced death of 5637 cells. Furthermore, Gecko proteins activated caspase 9 and caspase 3/7. Taken together, our data demonstrated that Gecko proteins suppressed the Akt pathway and activated the intrinsic caspase pathway, leading to the apoptosis of bladder cancer cells. [BMB Reports 2015; 48(9): 531-536]

Selective transport of coelomic fluid protein into oocytes of a tubicolous polychaete, Pseudopotamilla occelata

LEE, YANG RIM,KIM, YONG NYUN 이화여자대학교 생명과학연구소 1993 생명과학연구논문집 Vol.4 No.-

Coelomic fluid proteins, which are expected to include vitellogenin and putative yolk proteins isolated from the oocytes, were found to be transported selectively into the oocytes of specific stages ranging from 70-170㎛ in diameter; whereas bovine serum albumin, a nonspecific protein, was not incorporated into the oocytes of any size class. Furthermore, removal of the oocyte membrane proteins with trypsin effectively retarded the transport of the coelomic fluid proteins and yolk proteins. Carbohydrate residues of the membrane proteins appear to play a significant role in transferring vitellogenin into oocytes since the transport of the coelomic fluid proteins and yolk proteins was completely blocked by saturating with Concanavalin A or by digesting with endoglycosidase F. The observations strogly suggest that the selective transport of the coelomic fluid proteins into the oocytes of specific stages is mediated by the membrane proteins, which appear to be receptors.

Sequence Analysis of Hypothetical Proteins from Helicobacter pylori 26695 to Identify Potential Virulence Factors

Ahmad Abu Turab Naqvi,Farah Anjum,Faez Iqbal Khan,Asimul Islam,Faizan Ahmad,Md. Imtaiyaz Hassan 한국유전체학회 2016 Genomics & informatics Vol.14 No.3

Helicobacter pylori is a Gram-negative bacteria that is responsible for gastritis in human. Its spiral flagellated body helps in locomotion and colonization in the host environment. It is capable of living in the highly acidic environment of the stomach with the help of acid adaptive genes. The genome of H. pylori 26695 strain contains 1,555 coding genes that encode 1,445 proteins. Out of these, 340 proteins are characterized as hypothetical proteins (HP). This study involves extensive analysis of the HPs using an established pipeline which comprises various bioinformatics tools and databases to find out probable functions of the HPs and identification of virulence factors. After extensive analysis of all the 340 HPs, we found that 104 HPs are showing characteristic similarities with the proteins with known functions. Thus, on the basis of such similarities, we assigned probable functions to 104 HPs with high confidence and precision. All the predicted HPs contain representative members of diverse functional classes of proteins such as enzymes, transporters, binding proteins, regulatory proteins, proteins involved in cellular processes and other proteins with miscellaneous functions. Therefore, we classified 104 HPs into aforementioned functional groups. During the virulence factors analysis of the HPs, we found 11 HPs are showing significant virulence. The identification of virulence proteins with the help their predicted functions may pave the way for drug target estimation and development of effective drug to counter the activity of that protein.

Inhibition of eukaryotic translation by tetratricopeptide-repeat proteins of Orientia tsutsugamushi

Sunyoung Bang,Chan-Ki Min,하나영,최명식,김익상,Yeon-Sook Kim,조남혁 한국미생물학회 2016 The journal of microbiology Vol.54 No.2

Orientia tsutsugamushi, an obligate intracellular bacterium, is the causative agent of scrub typhus. The genome of Orientia tsutsugamushi has revealed multiple ORFs encoding tetratricopeptide- repeat (TPR) proteins. The TPR protein family has been shown to be involved in a diverse spectrum of cellular functions such as cell cycle control, transcription, protein transport, and protein folding, especially in eukaryotic cells. However, little is known about the function of the TPR proteins in O. tsutsugamushi. To investigate the potential role of TPR proteins in host-pathogen interaction, two oriential TPR proteins were expressed in E. coli and applied for GSTpull down assay. DDX3, a DEAD-box containing RNA helicase, was identified as a specific eukaryotic target of the TPR proteins. Since the RNA helicase is involved in multiple RNAmodifying processes such as initiation of translation reaction, we performed in vitro translation assay in the presence of GST-TPR fusion proteins by using rabbit reticulocyte lysate system. The TPR proteins inhibited in vitro translation of a reporter luciferase in a dose dependent manner whereas the GST control proteins did not. These results suggested TPR proteins of O. tsutsugamushi might be involved in the modulation of eukarytotic translation through the interaction with DDX3 RNA helicase after secretion into host cytoplasm.