• Molecules and Cells
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• v.45 no.7
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• pp.444-453
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• 2022

Multivalent macromolecular interactions underlie dynamic regulation of diverse biological processes in ever-changing cellular states. These interactions often involve binding of multiple proteins to a linear lattice including intrinsically disordered proteins and the chromosomal DNA with many repeating recognition motifs. Quantitative understanding of such multivalent interactions on a linear lattice is crucial for exploring their unique regulatory potentials in the cellular processes. In this review, the distinctive molecular features of the linear lattice system are first discussed with a particular focus on the overlapping nature of potential protein binding sites within a lattice. Then, we introduce two general quantitative frameworks, combinatorial and conditional probability models, dealing with the overlap problem and relating the binding parameters to the experimentally measurable properties of the linear lattice-protein interactions. To this end, we present two specific examples where the quantitative models have been applied and further extended to provide biological insights into specific cellular processes. In the first case, the conditional probability model was extended to highlight the significant impact of nonspecific binding of transcription factors to the chromosomal DNA on gene-specific transcriptional activities. The second case presents the recently developed combinatorial models to unravel the complex organization of target protein binding sites within an intrinsically disordered region (IDR) of a nucleoporin. In particular, these models have suggested a unique function of IDRs as a molecular switch coupling distinct cellular processes. The quantitative models reviewed here are envisioned to further advance for dissection and functional studies of more complex systems including phase-separated biomolecular condensates.

• Toxicological Research
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• v.16 no.3
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• pp.221-227
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• 2000

A 6-sulfooxymethylbenzo[a]pyrene (SMBP), the ultimate metabolite of methyl-substituted benzo[a]pyrene (BP), has been found to be carcinogenic in mice. These properties may be attributable to its strong reactivity with cellular macromolecules such as DNA. However, serum and its major constituent albumin attenuated significantly the cytotoxicity and mutagenicity of 5MBP in bacterial and mammalian cell systems. This inhibitory activity of serum against 5MBP-induced cytotoxicity and mutagenicity in Chinese hamster V79 cells appears to be caused by the reduced macromolecular adducts such as DNA and proteins, but serum failed to reduce 5MBP binding to naked calf thymus DNA. A number of proteins in the serum could act as nucleophiles that are able to intercept reactive chemicals through covalent binding. Albumin present in the plasma seems to be one of major components responsible for direct binding with 5MBp, thereby reducing its reactivity to genetic materials. We here determined which fraction is preferential for 5MBP binding through fractionation of 5MBP-treated serum with ammonium sulfate. The albumin-containing fraction had slightly more affinity for 5MBP than the immunoglobulin-containing fraction. Our results indicate that the covalent modification of plasma proteins may reduce 5MBP-induced damage.

• Journal of Microbiology and Biotechnology
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• v.31 no.5
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• pp.676-685
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• 2021

RNA-binding proteins are involved in RNA metabolism and posttranscriptional regulation of various fundamental biological processes. The PUF family of RNA-binding proteins is highly conserved in eukaryotes, and its members regulate gene expression, mitochondrial biogenesis, and RNA processing. However, their biological functions in Aspergillus species remain mostly unknown in filamentous fungi. Here we have characterized the puf genes in the model organism Aspergillus nidulans. We generated deletion mutant strains for the five putative puf genes present in the A. nidulans genome and investigated their developmental phenotypes. Deletion of pufA or pufE affected fungal growth and asexual development. pufA mutants exhibited decreased production of asexual spores and reduced mRNA expression of genes regulating asexual development. The pufE deletion reduced colony growth, increased formation of asexual spores, and delayed production of sexual fruiting bodies. In addition, the absence of pufE reduced both sterigmatocystin production and the mRNA levels of genes in the sterigmatocystin cluster. Finally, pufE deletion mutants showed reduced trehalose production and lower resistance to thermal stress. Overall, these results demonstrate that PufA and PufE play roles in the development and sterigmatocystin metabolism in A. nidulans.

• Biomedical Science Letters
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• v.12 no.4
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• pp.405-411
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• 2006

Heterotrimeric GTP binding proteins (G proteins) mediate signal transduction generated by neurotransmitter and hormones. Among G-proteins, Go is classified as a member of the Go/Gi family and the most abundant heterotrimeric G protein in brain. Most of the mechanistic analyses on the activation of Go indicated its action to be mediated by the $G{\beta}{\gamma}$ dimer because downstream effectors for its ${\alpha}$ subunit have not been clearly defined. To determine the downstream effectors of alpha subunits of Go ($Go{\alpha}$), we used yeast two-hybrid system to screen $Go{\alpha}$ interacting partners in cDNA library from the human brain. A brain specific high mobility group box containing protein (BHX), A possible transcription factor, was identified as a $Go{\alpha}$ interacting protein. We confirmed interaction between $Go{\alpha}$ and BHX employing in vitro affinity binding assay. Moreover, active form of $Go{\alpha}$ preferentially interacts with BHX than inactive farm. Our findings indicate that $Go{\alpha}$ could modulate gene expression via interaction with BHX during neuronal or brain development.

• The Korean Journal of Zoology
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• v.35 no.4
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• pp.456-465
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• 1992

The 94 KDa glucose-resulsted Protein (SH 94), one of stress Proteins, is a Ca2+-binding protein in the endoplasmic reticulum (ER). In this study, the possible effect of Ca2+ on the native conformation of grp 94 was examined. When the purified grp 94 was analyzed by Sel filtration in the presence of either EGTA or CaCl2, it was eluted with apparent molecular weight (MW) of 100 KDa in both cases. When similarly analyzed with microtome or cell Ivsate, however, srp 94 was eluted with apparent IW of 200 KDa in the presence of E6TA, while with apparent MW of 100 KDa in the presence of CaCl2, indicating possible association of grp 94 with one or more other proteins in the absence of CaCl2. Consequently, immunoprecipitation with anti-grp 94 was carried out to determine which proteins specifically interact with grp 94. It is sho%un that srp 94 may interact, in a Ca2+_dependent manner. with other proteins including BiP (grp 78) which is also a stress protein in the ER.

• Biomedical Science Letters
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• v.9 no.2
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• pp.105-110
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• 2003

Ankyrins are a ubiquitously expressed family of intracellular adaptor proteins involved in targeting diverse proteins to specialized membrane domains in both the plasma membrane and the endoplasmic reticulum. Canonical ankyrins are 190-220 kDa proteins expressed in most tissues and cell types and comprise a membrane-binding domain (MBD) of 24 ANK repeats, a spectrin-binding domain, a death domain and a C-terminal domain. Rescue studies with ankyrin-B/G chimeras have identified the C-terminal domain of ankyrin-B as the defining domain in specifying ankyrin-B activity, but the function of C-terminal domain of ankyrin-B is, however, not known. We report here that the C-terminal domain of ankyrin-B is capable of interacting with the C-terminal Region of Hsp40. The Hsps are induced not only by heat shock but also by various other environmental stresses. Hsps are also expressed constitutively at normal growth temperatures and have basic and indispensable functions in the life cycle of proteins as molecular chaperones, as well as playing a role in protecting cells from the deleterious stresses. The binding sites required in the interaction between C-terminal domain of ankyrin-B and C-terminal region of Hsp40 were characterized using the yeast two-hybrid system and GST-pull down assay. The interaction between ankyrin-B and Hsp40 represents the first direct evidence of ankyrin's role as chaperones.

• Genomics & Informatics
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• v.13 no.2
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• pp.53-59
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• 2015

In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.

• Current Research on Agriculture and Life Sciences
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• v.32 no.3
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• pp.149-154
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• 2014

It is already known that adzuki beans (Vigna angularis) are able to control appetite. Therefore, this study tested the proteins isolated from adzuki beans for their protease resistance and interaction with the intestinal mucosa. The major proteins from adzuki beans were found to be resistant to the digestive enzymes pepsin and pancreatin, and were identified using 2D-SDS-polyacrylamide gel electrophoresis and mass spectrometry. The major adzuki proteins were easily fractionated by treating the soluble protein extract with 10mM $CaCl_2$, and were found to contain lactotransferrin, a homologous protein to the dynein light chain domain, proteinase inhibitor, and proteins with unknown functions. From a tissue binding assay using mouse intestinal tissue sections, the major protein fraction showed weak, yet significant and specific binding to the mucosa layer of the small intestine. Thus, the current results suggest that adzuki proteins are resistant to digestive enzymes, which enables them to survive protease digestion in the intestinal tract, plus they may interact with the intestinal mucosa layer. Therefore, the molecules responsible for controlling appetite in adzuki beans are presumably protease-resistant proteins that interact with the intestinal mucosa or delay digestion in the digestive tract.

• Journal of Plant Biotechnology
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• v.30 no.3
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• pp.281-291
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• 2003

In this review, we described the catalogues of the rice proteome which were constructed in our program, and functional characterization of some of these proteins was discussed. Mass-spectrometry is the most prevalent technique to rapidly identify a large number of proteome analysis. However, the conventional Western blotting/sequencing technique has been used in many laboratories. As a first step to efficiently construct protein cata-file in proteome analysis of major cereals, we have analyzed the N-terminal sequences of 100 rice embryo proteins and 70 wheat spike proteins separated by two-dimensional electrophoresis. Edman degradation revealed the N-terminal peptide sequences of only 31 rice proteins and 47 wheat proteins, suggesting that the rest of separated protein sports are N-terminally blocked. To efficiently determine the internal sequence of blocked proteins, we have developed a modified Cleveland peptide mapping method. Using this above method, the internal sequences of all blocked rice proteins(i, e., 69 proteins) were determined. Among these 100 rice proteins, thirty were proteins for which homologous sequence in the rice genome database could be identified. However, the rest of the proteins lacked homologous proteins. This appears to be consistent with the fact that about 45% of total rice cDNA have been deposited in the EMBL database. Also, the major proteins involved in the growth and development of rice can be identified using the proteome approach. Some of these proteins, including a calcium-binding protein that tuned out to be calreticulin, gibberellin-binding protein, which is ribulose-1.5-bisphosphate carboxylase/oxygense active in rice, and leginsulin-binding protein in soybean have functions in the signal transduction pathway. Proteomics is well suited not only to determine interaction between pairs of proteins, but also to identify multisubunit complexes. Currently, a protein-protein interaction database for plant proteins(http://genome.c.kanazawa-u.ac.jp/Y2H)could be a very useful tool for the plant research community. Also, the information thus obtained from the plant proteome would be helpful in predicting the function of the unknown proteins and would be useful be in the plant molecular breeding.

• 한국유가공학회:학술대회논문집
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• 2002.04a
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• pp.37-42
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• 2002

Lactoferrin is an iron-binding glycoprotein and its bacteriostatic and bactericidal effects on Gram-positive and Gram-negative bacteria have been well-known. However, certain kind of lactic acid bacteria are resistant against its antibacterial effects. Moreover, it is reported that lactoferrin promotes the growth of bifidobacteria by in vitro and in vivo experiments. In this experiment, lactoferrin-binding protein was found both in the membrane and cytosolic franctions of Bifidobacterium. Bifidobacterium was grown in anaerobic conditions in MRS broth containing cysteine, gathered by centrifugation and processed by sonication. The lactoferrin-binding proteins on the PVDF-membrane transferred after SDS-PAGE were detected by far-western method using biotinylated lactoferrin and streptavidin-labeled horse radish peroxidase. Observation in growth effects of lactoferrin on Bifidobacterium suggested that there is a relation between the presence of lactoferrin-binding proteins on the cells and their growth.