• Journal of Microbiology and Biotechnology
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• 제25권4호
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• pp.503-510
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• 2015

The iLOV protein belongs to a family of blue-light photoreceptor proteins containing a light-oxygen-voltage sensing domain with a noncovalently bound flavin mononucleotide (FMN) as its chromophore. Owing to advantages such as its small size, oxygen-independent nature, and pH stability, iLOV is an ideal candidate over other reporter fluorescent proteins such as GFP and DsRed. Here, for the first time, we describe the feasibility of applying LOV domain-based fluorescent iLOV as a metal sensor by measuring the fluorescence quenching of a protein with respect to the concentration of metal ions. In the present study, we demonstrated the inherent copper sensing property of the iLOV protein and identified the possible amino acids responsible for metal binding. The fluorescence quenching upon exposure to Cu²⁺ was highly sensitive and exhibited reversibility upon the addition of the metal chelator EDTA. The copper binding constant was found to be 4.72 ± 0.84 µM. In addition, Cu²⁺-bound iLOV showed high fluorescence quenching at near physiological pH. Further computational analysis yielded a better insight into understanding the possible amino acids responsible for Cu²⁺ binding with the iLOV protein.

• BMB Reports
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• 제29권6호
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• pp.513-518
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• 1996

A soluble protein from Saccharomyces cerevisiae specifically provides protection against a thiolcontaining oxidation system but not against an oxidation system without thiol. This 25-kDa protein was thus named thiol-dependent protector protein (TPP). The role of TPP in the cellular defense against oxidative stress was investigated in Escherichia coli containing an expression vector with a yeast genomic DNA fragment that encodes TPP (strain YP) and a mutant in which the catalytically essential amino acid in the active site of TPP (Cys-47) has been replaced with alanine by site-directed mutagenesis (strain YPC47A). There was a distinct difference between these two strains in regard to viability, modulation of activities of superoxide dismutase and catalase, and the oxidative damage of DNA upon exposure to menadione. These results suggest that TPP may play a direct role in the cellular defense against oxidative stress by functioning as an antioxidant protein.

• Molecules and Cells
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• 제20권1호
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• pp.112-118
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• 2005

It was previously shown that AtNAP1 is a plastidic SufB protein involved in Fe-S cluster assembly in Arabidopsis. In this study, we investigated the effects of depleting SufB protein from plant cells using virus-induced gene silencing (VIGS). VIGS of NbNAP1 encoding a Nicotiana benthamiana homolog of AtNAP1 resulted in a leaf yellowing phenotype. NbNAP1 was expressed ubiquitously in plant tissues with the highest level in roots. A GFP fusion protein of the N-terminal region (M1-V103) of NbNAP1 was targeted to chloroplasts. Depletion of NbNAP1 resulted in reduced numbers of chloroplasts of reduced size. Mitochondria also seemed to be affected. Despite the reduced number and size of the chloroplasts in the NbNAP1 VIGS lines, the expression of many nuclear genes encoding chloroplast-targeted proteins and chlorophyll biosynthesis genes remained unchanged.

• IMMUNE NETWORK
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• 제2권3호
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• pp.125-132
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• 2002

In the past, bioinformatics was often regarded as a difficult and rather remote field, practiced only by computer scientists and not a practical tool available to biologists. However, the various on-going genome projects have had a serious impact on biological sciences in various ways and now there is little doubt that bioinformatics is an essential part of the research environment, with a wealth of biological information to analyze and predict. Fully sequenced genomes made us to have additional insights into the functional properties of the encoded proteins and made it possible to develop new tools and schemes for functional biology on a proteomic scale. Among those are the yeast two-hybrid system, mass spectrometry and microarray: the technology of choice to detect protein-protein interactions. These functional insights emerge as networks of interacting proteins, also known as "pathway informatics" or "interactomics". Without exception it is no longer possible to make advances in the signaling/regulatory pathway studies without integrating information technologies with experimental technologies. In this paper, we will introduce the databases of protein interaction worldwide and discuss several challenging issues regarding the actual implementation of databases.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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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.

• 대한의용생체공학회:의공학회지
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• 제15권1호
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• pp.51-56
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• 1994

Protein adsorption on the polyurethane surface was modelled by a modified random sequential adsorption(RSA) process. In this model, polyurethane surface was modelled as a mixed domain of hydrophobic and hydrophilic parts which was implemented by a 2 dimensional $150{\times}150$ lattice in the computer. Protein adsorption was simulated using a small box which represents a particle of the protein, and polyurethane lattice by considering their hydrophobic interaction. In order to validate the model, we perfonned fibrinogen adsorption on polyurethane surface. Isotherms of the adsorbed protein were calculated and compared to the experimental data. The protein adsorption on the polyurethane surface could be well described using this computer model.

• Journal of Chest Surgery
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• 제23권6호
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• pp.1084-1089
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• 1990

Plasma protein concentration, plasma albumin concentration, hematocrit, and arterial blood gas tension were measured in 15 mongrel dogs undergoing heart transplantation with cardiopulmonary bypass. The hemodilution due to priming solution resulted in a 49% decrease in plasma protein concentration, a 57% decrease in plasma albumin concentration, a 46%a decrease in hematocrit. The measurements had returned to preperfusion values 1 hour after the end of cardiopulmonary bypass. The intraoperative changes in plasma protein and albumin concentration did not correlate with changes in alveolar-arterial oxygen tension gradients[D[A\ulcorner PO2]]. It is concluded that, in the absence of an increase in left atrial pressure, marked decrease in plasma protein concentration can be tolerated without the occurrence of pulmonary edema. And further study should be done to determine how to prepare an ideal priming solution.

• Journal of Microbiology and Biotechnology
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• 제9권5호
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• pp.562-567
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• 1999

Single-stranded DNA binding protein (SSB) is well-characterized as having a helix-destabilizing activity. The helix-destabilizing capability of SSB has been re-examined in this study. The results of restriction endonuclease protection assays and titration experiments suggest that the stimulatory effect of SSB on strand exchange acts by melting out the secondary structure which is inaccessible to RecA protein binding; however, SSB is excluded from regions of secondary structure present in native single-stranded DNA. Complexes of SSB and RecA protein are required for eliminating the secondary structure barriers under optimal conditions for strand exchange.

• 생명과학회지
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• 제6권1호
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• pp.1-5
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• 1996

Using differential hybridization, a cDNA clone was isolated fortuitously from Amaranthus viridis and sequenced. This nucleotide sequence exhibited 55.1% identity with vma6 which encodes the 36-kD subunit of the vacuolar proton transporting ATPase in Saccharmoyces cerevisiae. The predicted open reading frame encodes a protein of 221 amino acid sequence with a calculated molecular weight of 25,452 and reveals high levels of similarity with subunit D polypeptide of vacuolar H -ATP(e.g., 48.5, 52.1 and 49.3% identity to the vacuolar 36-kD chain of yeast, vacuolar 32-kD polypeptide IV of human and vacuolar 28-kD protein of bovine chromaffin granules, respectively). The hydropathy index computation revealed that this predicted protein is a peripheral protein. These results indicated that the predicted protein may play a sturctural role in the vaculor H -ATPase as does gamma subunit in V-type ATPase.

• 약학회지
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• 제48권5호
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• pp.261-265
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• 2004

In the previous report, we described the marked antitumor and immunomodulatory activities of PVp, a protein-polysaccharide fraction of a Korean wild mushroom Psathyrella velutina. In this study, a protein-polysaccharide fraction, PVMP, was prepared from the shake-cultured mycelia of the same mushroom and its immunoactivities as well as chemical compositions were investigated. At 200 $\mu\textrm{g}$/ml, PVMP weakly stimulated the BALB/c mouse splenic lymphocytes to form lymphoblasts and upregulated the expression of CD25 molecules, but failed to stimulate peritoneal macrophages. In chemical analysis these two protein-polysaccharide fractions were found to be quite different in that the carbohydrate contents of PVMP and PVP, respectively, was 85.3% and 41.2%. These results reveals that PVMP, unlike PVP, is a moderate immunostimulator on the immune system.