• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2004년도 The 3rd Annual Conference for The Korean Society for Bioinformatics Association of Asian Societies for Bioinformatics 2004 Symposium
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• pp.203-209
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• 2004

Molecular docking using Lamarckian genetic algorithm of AutoDock 3.0 (AD3) was employed to understand in retrospect the selectivity of phenylaminopyrimidine (PAP) derivatives against the kinase domain c-Abl, implicated in chronic myelogenous leukemia (CML). The energetics of protein-ligand complex was scored using AD3 to identify active drug conformations while Ligplot and ligand protein contact (LPC) programs were used to probe schematic molecular recognition of the bound inhibitor to the protein. Results signify correlation between model and crystal structures of STI-571 compound or Imatinib (IM), a PAP derivative and now clinically proven for its efficacy in CML. A prospect active form Abl inhibitor scaffold from matlystatin class of compounds will be published elsewhere.

• Genomics & Informatics
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• 제4권4호
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• pp.173-181
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• 2006

Pattern finding is one of the important tasks in a protein or DNA sequence analysis. Alignment is the widely used technique for finding patterns in sequence analysis. BLAST (Basic Local Alignment Search Tool) is one of the most popularly used tools in bio-informatics to explore available DNA or protein sequence databases. BLAST may generate a huge output for a large sequence data that contains various sequence patterns. However, BLAST does not provide a tool to summarize and analyze the patterns or matched alignments in the BLAST output file. BLAST lacks of general and robust parsing tools to extract the essential information out from its output. This paper presents a pattern summary system which is a powerful and comprehensive tool for discovering pattern structures in huge amount of sequence data in the BLAST. The pattern summary system can identify clusters of patterns, extract the cluster pattern sequences from the subject database of BLAST, and display the clusters graphically to show the distribution of clusters in the subject database.

• Genomics & Informatics
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• 제6권1호
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• pp.50-53
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• 2008

We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC) model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.

• Mass Spectrometry Letters
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• 제11권4호
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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.

• 한국축산식품학회지
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• 제36권5호
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• pp.671-678
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• 2016

Fractioning and/or preheating treatment on the rheological properties of myofibrillar protein (MP) gels induced by microbial transglutaminase (MTG) has been reported that they may improve the functional properties. However, the optimum condition was varied depending on the experimental factors. This study was to evaluate the effect of red bean protein isolate (RBPI) on the rheological properties of MP gels mediated by MTG as affected by modifications (fractioning: 7S-globulin of RBPI and/or preheat treatment (pre-heating; 95℃/30 min): pre-heating RBPI or pre-heating/7S-globulin). Cooking yields (CY, %) of MP gels was increased with RBPI (p<0.05), while 7S-globulin decreased the effect of RBPI (p<0.05); however, preheating treatments did not affect the CY (p>0.05). Gel strength of MP was decreased when RBPI or 7S-globulin added, while preheat treatments compensated for the negative effects of those in MP. This effect was entirely reversed by MTG treatment. Although the major band of RBPI disappeared, the preheated 7S globulin band was remained. In scanning electron microscopic (SEM) technique, the appearance of more cross-linked structures were observed when RBPI was prepared with preheating at 95℃ to improve the protein-protein interaction during gel setting of MP mixtures. Thus, the effects of RBPI and 7S-globulin as a substrate, and water and meat binder for MTG-mediated MP gels were confirmed to improve the rheological properties. However, preheat treatment of RBPI should be optimized.

• Journal of Microbiology and Biotechnology
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• 제28권6호
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• pp.987-996
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• 2018

Bacterial programmed cell death is regulated by the toxin-antitoxin (TA) system. YhaV (toxin) and Pr1F (antitoxin) have been recently identified as a type II TA system in Escherichia coli. YhaV homologs have conserved active residues within the C-terminus, and to characterize the function of this region, we purified native YhaV protein (without denaturing) and constructed YhaV proteins of varying lengths. Here, we report a new low-temperature method of purifying native YhaV, which is notable given the existing challenges of purifying this highly toxic protein. The secondary structures and thermostability of the purified native protein were characterized and no significant structural destruction was observed, suggesting that the observed inhibition of cell growth in vivo was not the result of structural protein damage. However, it has been reported that excessive levels of protein expression may result in protein misfolding and changes in cell growth and mRNA stability. To exclude this possibility, we used an [$^{35}S$]-methionine prokaryotic cell-free protein synthesis system in vitro in the presence of purified YhaV, and two C-terminal truncated forms of this protein (YhaV-L and YhaV-S). Our results suggest that the YhaV C-terminal region is essential for mRNA interferase activity, and the W143 or H154 residues may play an analogous role to Y87 of RelE.

• Journal of Microbiology
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• 제39권3호
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• pp.149-153
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• 2001

The electron transfer reaction is one of the most essential processes of life. Not only does it provide the means of transforming solar and chemical energy into a utilizable form for all living organisms, it also extends into a range of metabolic processes that support the life of a cell. Thus, it is of great interest to understand the physical basis of the rates and reduction potentials of these reactions. To identify the major determinants of reduction potentials in redox proteins, we have chosen the simplest electron transfer protein, rubredoxin, a small (52-54 residue) iron-sulfur protein family, widely distributed in bacteria and archaea. Rubredoxins can be grouped into two classes based on the correlation of their reduction potentials with the identity of residue 44; those with Ala44 (ex: Pyrococcus furiosus) have reduction potentials that are ∼50 mV higher than those with Va144 (ex: Clostridium pasteurianum). Based on the crystal structures of rubredoxins from C. pasteurianum and P. furiosus, we propose the identity of residue 44 alone determines the reduction potential by the orientation of the electric dipole moment of the peptide bond between 43 and 44. Based on 1.5 $\AA$ resolution crystal structures and molecular dynamics simulations of oxidized and reduced rubredoxins from C. pasteurianum, the structural rearrangements upon reduction suggest specific mechanisms by which electron transfer reactions of rubredoxin should be facilitated.

• BMB Reports
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• 제52권10호
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• pp.601-606
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• 2019

Arginine methylation plays crucial roles in many cellular functions including signal transduction, RNA transcription, and regulation of gene expression. Protein arginine methyltransferase 8 (PRMT8), a unique brain-specific protein, is localized to the plasma membrane. However, the detailed molecular mechanisms underlying PRMT8 plasma membrane targeting remain unclear. Here, we demonstrate that the N-terminal 20 amino acids of PRMT8 are sufficient for plasma membrane localization and that oligomerization enhances membrane localization. The basic amino acids, combined with myristoylation within the N-terminal 20 amino acids of PRMT8, are critical for plasma membrane targeting. We also found that substituting Gly-2 with Ala [PRMT8(G2A)] or Cys-9 with Ser [PRMT8(C9S)] induces the formation of punctate structures in the cytosol or patch-like plasma membrane localization, respectively. Impairment of PRMT8 oligomerization/dimerization by C-terminal deletion induces PRMT8 mis-localization to the mitochondria, prevents the formation of punctate structures by PRMT8(G2A), and inhibits PRMT8(C9S) patch-like plasma membrane localization. Overall, these results suggest that oligomerization/dimerization plays several roles in inducing the efficient and specific plasma membrane localization of PRMT8.

• Bulletin of the Korean Chemical Society
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• 제27권3호
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• pp.389-394
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• 2006

Fragmentation efficiencies of various ‘activated-ion’ electron capture dissociation (AI-ECD) methods are compared for a model system of bovine ubiquitin 7+ cations. In AI-ECD studies, sufficient internal energy was given to protein cations prior to ECD application using IR laser radiation, collisions, blackbody radiation, or in-beam collisions, in turn. The added energy was utilized in increasing the population of the precursor ions with less intra-molecular noncovalent bonds or enhancing thermal fluctuations of the protein cations. Removal of noncovalent bonds resulted in extended structures, which are ECD friendly. Under their best conditions, a variety of activation methods showed a similar effectiveness in ECD fragmentation. In terms of the number of fragmented inter-residue bonds, IR laser/blackbody infrared radiation and ‘in-beam’ activation were almost equally efficient with ~70% sequence coverage, while collisions were less productive. In particular, ‘in-beam’ activation showed an excellent effectiveness in characterizing a pre-fractionated single kind of protein species. However, its inherent procedure did not allow for isolation of the protein cations of interest.

• 한국동물학회지
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• 제30권1호
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• pp.10-28
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• 1987

노랑초파리(Drosophila melanogaster)의 난자형성과정 중 egg chamber 이외의 조직에서 합성, 이입될 수 있는 가능성을 배제한 상태에서 egg chamber에서 일어나는 단백질 합성양상의 변화를 연구하였다. 단백질 합성률은 전반적으로 큰 변화를 보이지 않으나 난황형성, 난황막형성, 그리고 난각형성이 겹쳐 이루어지는 11-12에서는 높고, 성숙이 완료되는 단계 14에서는 낮았다. 누적 및 합성 단백질의 수와 종류가 단계에 따라 크게 변하고 있으며, 노랑초파리의 난자형성이 비록 짧은 기간동안에 이루어질지도 단계에 따라 특이한 단백질 합성 변화를 보이고 있다. 이러한 단백질의 합성은 주로 여포세포에서 이루어지는 것으로 생각되며, 노랑초파리의 난포세포의 성장 및 성숙을 위해서는 egg chamber 이외의 조직 뿐만 아니라 egg chamber 내의 세포 자체에 의한 단백질 합성이 직접적으로 관여하는 것으로 생각된다.