단백질체학을 활용한 신약 개발 연구

손은수,김강회,표석능,이상필,손은화 한국생체재료학회 2005 생체재료학회지 Vol.9 No.4

One of the most promising developments to come from the study of human genes and proteins has been the identification of potential new drugs for the treatment of disease. This relies on genome and proteome information to identify proteins associated with a disease, which computer software can then use as targets for new drugs. If a certain protein is implicated in a disease, the 3D structure of that protein provides the information a computer programs needs to design drugs to interfere with the action of the protein. Proteomics, the study of the proteins and protein pathways involved in disease, is a promising tool for new drug discovery, which aim to find new drugs to inactivate proteins involved in disease. As genetic differences among individuals are found, researchers will use these same techniques to develop personalized drugs that are more effective for the individual. With recent advances in the field of proteomics, microarrays(biochips), HCS(high contents screening), cGMP(current Good Manufacturing Practice) technology have readily been adapted to proteomics applications. Using this tool, global proteome analysis and protein expression profiling will thus provide new opportunities for biomarker discovery, drug target identification and disease diagnostics, as well as providing insights into disease biology. Proteomics as a whole increasingly plays an important role in the multi-step drug-development process. In this review, the current status and methods of proteomics technology and some applications are briefly described. Additionally, this review discusses some of the recent research and market trends in proteomics.

Comprehensive proteome analysis using quantitative proteomic technologies

Abu Hena Mostafa Kamal,최종순,조용구,김홍식,송범헌,이철원,우선희 한국식물생명공학회 2010 JOURNAL OF PLANT BIOTECHNOLOGY Vol.37 No.2

With the completion of genome sequencing of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. The recent techniques of proteomics have been advanced quickly so that the high-throughput and systematic analyses of cellular proteins are enabled in combination with bioinformatics tools. Furthermore, the development of proteomic techniques helps to elucidate the functions of proteins under stress or diseased condition, resulting in the discovery of biomarkers responsible for the biological stimuli. Ultimate goal of proteomics orients toward the entire proteome of life, subcellular localization, biochemical activities, and their regulation. Comprehensive analysis strategies of proteomics can be classified as three categories: (i) protein separation by 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification by either Edman sequencing or mass spectrometry (MS),and (iii) quanitation of proteome. Currently MS-based proteomics turns shiftly from qualitative proteome analysis by 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, to quantitative proteome analysis. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. The in vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes, protein-labeling tagging with isotope-coded affinity tag, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope labeled amino acid can be in vivo labeled into live culture cells through metabolic incorporation. MS-based proteomics extends to detect the phosphopeptide mapping of biologically crucial protein known as one of post-translational modification. These complementary proteomic techniques contribute to not only the understanding of basic biological function but also the application to the applied sciences for industry.

Gel-based proteomics in disease research: Is it still valuable?

Kim, Yong-In,Cho, Je-Yoel Elsevier 2019 Biochimica et biophysica acta. Proteins and proteo Vol.1867 No.1

<P><B>Abstract</B></P> <P>Gel electrophoresis had been the primary method in proteomics. In the early era of proteomics, gel electrophoresis was a dominant technique of sample preparation for mass spectrometry analysis. Particularly, two-dimensional electrophoresis provided high-resolution proteome separation, and was regarded as the standard methodology for the separation of wide-range proteomes. However, gel electrophoresis turned downwards due to the progress of other separations including liquid chromatography and ionization techniques, resulting gel-free proteomics finally becoming dominant players at present. There are numerous advantages in gel-free approach in aspects of current trends of disease research. Interestingly, gel-free approaches are still advanced, it seems that gel electrophoresis will not be disappeared. The unique features of gel electrophoresis can be complementary for gel-free and it is suitable for the new wave of top-down functional proteomics.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Throughput of gel-free proteomics is overwhelmed against gel-based proteomics. </LI> <LI> 2-DE is still a meriting technology to provide the highest resolution on protein level. </LI> <LI> Gel-based proteomics is powerful strategy for top-down proteomics. </LI> <LI> Gel-based and gel-free approaches are complementary, not alternative. </LI> </UL> </P>

Korean plant proteomics: pioneers in plant stress physiology

Youngwoo Lee,Suhyeon Bea,서상규,심이성,김선형,김상곤,강규영,김선태 한국식물생명공학회 2011 식물생명공학회지 Vol.38 No.2

Plant proteomics is the large-scale studies of proteins, particularly on their structures and functions, governed by the physiological metabolism of plant cells. With the development of techniques and strategies in proteomics,proteomics approach is moving forward in systems biology handling sophisticated components of major signaling and biochemical pathways in plants responding to their environment. In Korea, pioneers in plant proteomics are trying to catch up with global trends in plant proteomics; these researchers are not only improving existing techniques in protein extraction but also developing new techniques in proteomics context. In the hot field of abiotic and biotic stress proteomics, 29 and 9 out of 74 papers have been published during the review period from 2005 to 2010, respectively. This present review article provides an overview on the output of Korean plant proteomers while paying special attention to both abiotic and biotic stress proteomics.

Comprehensive proteome analysis using quantitative proteomic technologies

Kamal, Abu Hena Mostafa,Choi, Jong-Soon,Cho, Yong-Gu,Kim, Hong-Sig,Song, Beom-Heon,Lee, Chul-Won,Woo, Sun-Hee The Korean Society of Plant Biotechnology 2010 식물생명공학회지 Vol.37 No.2

With the completion of genome sequencing of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. The recent techniques of proteomics have been advanced quickly so that the high-throughput and systematic analyses of cellular proteins are enabled in combination with bioinformatics tools. Furthermore, the development of proteomic techniques helps to elucidate the functions of proteins under stress or diseased condition, resulting in the discovery of biomarkers responsible for the biological stimuli. Ultimate goal of proteomics orients toward the entire proteome of life, subcellular localization, biochemical activities, and their regulation. Comprehensive analysis strategies of proteomics can be classified as three categories: (i) protein separation by 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification by either Edman sequencing or mass spectrometry (MS), and (iii) quanitation of proteome. Currently MS-based proteomics turns shiftly from qualitative proteome analysis by 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, to quantitative proteome analysis. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. The in vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes, protein-labeling tagging with isotope-coded affinity tag, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope labeled amino acid can be in vivo labeled into live culture cells through metabolic incorporation. MS-based proteomics extends to detect the phosphopeptide mapping of biologically crucial protein known as one of post-translational modification. These complementary proteomic techniques contribute to not only the understanding of basic biological function but also the application to the applied sciences for industry.

Korean plant proteomics: pioneers in plant stress physiology

Lee, Young-Woo,Bea, Suh-Yeon,Seo, Sang-Gyu,Shim, Ie-Sung,Kim, Sun-Hyung,Kim, Sang-Gon,Kang, Kyu-Young,Kim, Sun-Tae The Korean Society of Plant Biotechnology 2011 식물생명공학회지 Vol.38 No.2

Plant proteomics is the large-scale studies of proteins, particularly on their structures and functions, governed by the physiological metabolism of plant cells. With the development of techniques and strategies in proteomics, proteomics approach is moving forward in systems biology handling sophisticated components of major signaling and biochemical pathways in plants responding to their environment. In Korea, pioneers in plant proteomics are trying to catch up with global trends in plant proteomics; these researchers are not only improving existing techniques in protein extraction but also developing new techniques in proteomics context. In the hot field of abiotic and biotic stress proteomics, 29 and 9 out of 74 papers have been published during the review period from 2005 to 2010, respectively. This present review article provides an overview on the output of Korean plant proteomers while paying special attention to both abiotic and biotic stress proteomics.

Genomic and Proteomic Analysis of Microbial Function in the Gastrointestinal Tract of Ruminants - Review -

White, Bryan A.,Morrison, Mark Asian Australasian Association of Animal Productio 2001 Animal Bioscience Vol.14 No.6

Rumen microbiology research has undergone several evolutionary steps: the isolation and nutritional characterization of readily cultivated microbes; followed by the cloning and sequence analysis of individual genes relevant to key digestive processes; through to the use of small subunit ribosomal RNA (SSU rRNA) sequences for a cultivation-independent examination of microbial diversity. Our knowledge of rumen microbiology has expanded as a result, but the translation of this information into productive alterations of ruminal function has been rather limited. For instance, the cloning and characterization of cellulase genes in Escherichia coli has yielded some valuable information about this complex enzyme system in ruminal bacteria. SSU rRNA analyses have also confirmed that a considerable amount of the microbial diversity in the rumen is not represented in existing culture collections. However, we still have little idea of whether the key, and potentially rate-limiting, gene products and (or) microbial interactions have been identified. Technologies allowing high throughput nucleotide and protein sequence analysis have led to the emergence of two new fields of investigation, genomics and proteomics. Both disciplines can be further subdivided into functional and comparative lines of investigation. The massive accumulation of microbial DNA and protein sequence data, including complete genome sequences, is revolutionizing the way we examine microbial physiology and diversity. We describe here some examples of our use of genomics- and proteomics-based methods, to analyze the cellulase system of Ruminococcus flavefaciens FD-1 and explore the genome of Ruminococcus albus 8. At Illinois, we are using bacterial artificial chromosome (BAC) vectors to create libraries containing large (>75 kbases), contiguous segments of DNA from R. flavefaciens FD-1. Considering that every bacterium is not a candidate for whole genome sequencing, BAC libraries offer an attractive, alternative method to perform physical and functional analyses of a bacterium's genome. Our first plan is to use these BAC clones to determine whether or not cellulases and accessory genes in R. flavefaciens exist in clusters of orthologous genes (COGs). Proteomics is also being used to complement the BAC library/DNA sequencing approach. Proteins differentially expressed in response to carbon source are being identified by 2-D SDS-PAGE, followed by in-gel-digests and peptide mass mapping by MALDI-TOF Mass Spectrometry, as well as peptide sequencing by Edman degradation. At Ohio State, we have used a combination of functional proteomics, mutational analysis and differential display RT-PCR to obtain evidence suggesting that in addition to a cellulosome-like mechanism, R. albus 8 possesses other mechanisms for adhesion to plant surfaces. Genome walking on either side of these differentially expressed transcripts has also resulted in two interesting observations: i) a relatively large number of genes with no matches in the current databases and; ii) the identification of genes with a high level of sequence identity to those identified, until now, in the archaebacteria. Genomics and proteomics will also accelerate our understanding of microbial interactions, and allow a greater degree of in situ analyses in the future. The challenge is to utilize genomics and proteomics to improve our fundamental understanding of microbial physiology, diversity and ecology, and overcome constraints to ruminal function.

Proteomics/qPCR protocol to estimate physical ages of wild male oriental fruit flies, Bactrocera dorsalis (Hendel)

Chiou Ling Chang 한국응용곤충학회 2016 Journal of Asia-Pacific Entomology Vol.19 No.2

Laboratory reared fruit flies may have different behavioral phenotypes as compared to the wild in the field. The domesticated lab setting and the absence of factors from the natural environment on lab reared insects may result in different behavioral patterns, such as the length of life cycle. This study was performed to conduct a regression analysis of the ratio of odorant binding protein 99b (OBP99b) expression from 4 to 12-d-old oriental fruit fly males, relative to 1-d-old males to estimate the physical ages of wild male fruit flies. We established two polynomial linear regression equations based on 4–12 days old lab-reared flies using proteomics and qPCR. The equations are Y = −0.7768 + 0.7205X, R2 = 0.89 (for proteomics) and Y = −0.6478 + 0.344X, R2 = 0.64 (for qPCR). We used these equations to estimate the physical ages of wild-caught male fruit flies. These results indicate that despite multiple behavioral differences between laboratory reared and field-caught flies, the physical ages of both groups are identical.We suggest proteomics and qPCR analysis of selected genes and the proteins they encode may be developed into reliable tools for determining the ages of wild-caught animals, including oriental fruit flies.

Caenorhabditis elegans proteomics comes of age

Shim, Yhong-Hee,Paik, Young-Ki WILEY-VCH Verlag 2010 Proteomics Vol.10 No.4

<P>Caenorhabditis elegans, a free-living soil nematode, is an ideal model system for studying various physiological problems relevant to human diseases. Despite its short history, C. elegans proteomics is receiving great attention in multiple research areas, including the genome annotation, major signaling pathways (e.g. TGF-β and insulin/IGF-1 signaling), verification of RNA interference-mediated gene targeting, aging, disease models, as well as peptidomic analysis of neuropeptides involved in behavior and locomotion. For example, a proteome-wide profiling of developmental and aging processes not only provides basic information necessary for constructing a molecular network, but also identifies important target proteins for chemical modulation. Although C. elegans has a simple body system and neural circuitry, it exhibits very complicated functions ranging from feeding to locomotion. Investigation of these functions through proteomic analysis of various C. elegans neuropeptides, some of which are not found in the predicted genome sequence, would open a new field of peptidomics. Given the importance of nematode infection in plants and mammalian pathogenesis pathways, proteomics could be applied to investigate the molecular mechanisms underlying plant– or animal–nematode pathogenesis and to identify novel antinematodal drugs. Thus, C. elegans proteomics, in combination of other molecular, biological and genetic techniques, would provide a versatile new tool box for the systematic analysis of gene functions throughout the entire life cycle of this nematode.</P>

프로테오믹스 연구의 최근 동향 및 전망

이도희,박성구,박병철,명평근 충남대학교 형질전환복제돼지연구센터 2007 논문집 Vol. No.10

Proteomics is the study of the "proteome" or the entire protein complement of a genome. It is now well-established that proteomics is far more complex than simply cataloguing all the proteins present in a cell or organism at a given time. Proteomics now includes not only the identification of proteins or the study of protein expression pattern but also the understanding of post-translational processing of proteins or protein-protein interaction, which often result in the alteration of protein stability, localization and/or function. Here we briefly summarize how proteomics has been evolved during the last decade and review a few crucial techniques widely used in the proteomic studies, such as 2-DE and mass spectrometry. Moreover, we discuss the applications of proteomic tools in related research areas and its potentials in drug discovery and the study of diseases.