• Microbiology and Biotechnology Letters
• /
• v.21 no.4
• /
• pp.336-341
• /
• 1993

In metal-affinify aqueous two-phase systems, protein partitioning is affected by a variety of parameters such as pH, the number of surface-accessible histidines, and the amount and partition coefficient of metallated polythylene glyco(PEG) ligand. To enhance partitioning of proteins with surface-accessible histidines, we have synthesized and used a (Cu(II)-ininodiacetic acid)$_2$-PEG20,000($Cu(II)_2IDA_2$-PEG20,000) as well as Cu(II)IDA-PEG5,000 as an affinity ligand. The partition coefficient of $Cu(II)_2-IDA_2$-PEG20,000 in a PEG5,000/dextran two-phase system was 30.1, which corresponded to a 3.8-fold increase over that of Cu(II)IDA-PEG5,000. The partitioning experiments were performed on four proteins, horse cytochrome c, S. cerevisiae cytochrome c, horse myoglobin, and sheep myoglobin. Partitioning of proteins which convey surface-accessible histidines was enhanced dramatically by the addition of $Cu(II)_2IDA_2$-PEG20,000 ligand. These results demonstrate that enhanced partitioning of metal-binding proteins in an aqueous two -phase system can by achieved by using an appropriate metallated PEG ligand.

• Journal of the Korean Chemical Society
• /
• v.38 no.1
• /
• pp.21-25
• /
• 1994

The proton affinities of substituted imidazoles, relevant to the binding of lexitropsins that contain imidazole ring to the base pair (G-C sequence) of minor groove of DNA, are studied with the aid of EHT calculations. It is shown that proton affinity of imidazole substituted at position $\alpha$ to the basic nitrogen is slightly larger than that of imidazole substituted at N for the methylimidazole. Proton affinities of N-substituted imidazoles are found to be larger than those of imidazoles substituted at position ${\alpha}$ for a selected set of the other derivatives. As predicted the proton affinity increases when electron-donating group is attached at position N of imidazole.

• Korean Journal of Microbiology
• /
• v.14 no.4
• /
• pp.176-185
• /
• 1976

An improved procedure for the rapid purification of glucose-6-phosphate dehydrogenase from extracts of Saccharomyces cerevisiae was developed by using affinity chromatography. Among six affinty media tested, NADP$^{+}$-agarose and Affi-gel Blue were more effective than others (i.e., Affi-gel Red, AMP-agarose, ATP-agarose, and NAD$^{+}$-agarose). Conditions to desorb the enzyme bound to the affinity media were examined to increase the purity as well as yield. The best result was obtained when the column was developed with a linear gradient of KCl (0-1.0M). In case of Affi-gel Blue, introduction of NAD$^{+}$ (15mM) washing step prior to the salt gradient was most effective to remove NAD$^{+}$-binding proteins. For a large scale preparation of G-6-P dehydrogenase higher recovery was obtained by Affi-gel Blue than NADP$^{+}$-agarose, however, the purity of the enzyme was decreased by 10 times if the former was used as the affinity medium. The capacity of Affi-gel Blue for G-6-P dehydrogenase was found to be 5 times higher than that of NADP$^{+}$-agarose. Furthermore Affi-gel Blue could be reused repeatedly and its preparation is relatively easier and less expensive than NADP$^{+}$-agarose.X> +/-agarose.

• Journal of the Korean Chemical Society
• /
• v.42 no.4
• /
• pp.391-397
• /
• 1998

The geometry of furan, relevant to the binding of bis-furan lexitropsin that contains this ring to the base pair of minor groove of DNA, is optimized by semiempirical (MNDO) and ab initio (Hartree-Fock) methods. The proton affinity and electronic structure are evaluated at the 6-31G and $6-31G^{\ast}$ level of theory for the optimized geometry. The proton affinities are also studied for various substituted furans with the electrondonating and -withdrawing groups to estimate the substituent effect on the proton affinity of furans. It has been found that the electron-donating substituents increase the proton affinity of furan, whereas the electron-withdrawing substituents decrease it. This result can be explained with atomic charge and electron density at oxygen of substituted furans.

• Bulletin of the Korean Chemical Society
• /
• v.27 no.5
• /
• pp.739-743
• /
• 2006

Synthesis of cholic acid-based tripodal receptor (1) and its high chloride ion affinity in comparison with that of chenodeoxycholic acid (2) and lithocholic acid-based receptor (3) was achieved. Anion binding affinities of the receptors were evaluated $by\;^1H$ NMR and ITC titrations. Tripodal receptor 1 showed a selective affinity for $CI ^-$ over $Br ^-$, $I^-$, $H_2 PO _4\;^-$, and $CH _3 CO_2\;^-$. The selectivity of 1 for $CI ^-$ is about 3 times that of $Br ^-$, and 17 times that for $H_2 PO_4\;^-$.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.10 no.4
• /
• pp.334-340
• /
• 2005

Lectin is a cell-agglutinating and carbohydrate-binding protein present in many plants. The lectin of Canavalia ensiformis shoot with specific affinity for D-glucose was purified by affinity chromatography using Sephadex G-100, and some of its biochemical characterizations were studied. Lectin was purified 8.87-fold and exhibited final specific activity of 225.74 units/mg protein with a $2.3\%$ yield. SDS-PAGE analysis demonstrated that the purified shoot lectin exists as a tetramer of 102 kD, composed of two subunits with molecular weight of 29 and 22 kD. The purified lectin was observed to agglutinate rabbit blood cell. The optimal temperature for the activity of this lectin was $40^{\circ}C$, and this lectin was relatively stable to heat with the highest activity at $50{\~}60^{\circ}C$. The maximal activity was observed at pH 7.2.

• BMB Reports
• /
• v.41 no.3
• /
• pp.177-183
• /
• 2008

Ubiquitin is an essential, highly-conserved small regulatory protein in eukaryotic cells. It covalently modifies a wide variety of targeted proteins in the forms of monomer and polymers, altering the conformation and binding properties of the proteins and thus regulating proteasomal delivery, protein activities and localization. Mass spectrometry has emerged as an indispensable tool for in-depth characterization of protein ubiquitination. Ubiquitinated proteins in cell lysates are usually enriched by affinity chromatography and subsequently analyzed by mass spectrometry for identification and quantification. Ubiquitin-conjugated amino acid residues can be determined by unique mass shift caused by the modification. Moreover, the complex structure of polyubiquitin chains on substrates can be dissected by bottom-up and middle-down mass spectrometric approaches, revealing potential novel functions of polyubiquitin linkages. Here I review the advances and caveats of these strategies, emphasizing caution in the validation of ubiquitinated proteins and in the interpretation of raw data.

• YAKHAK HOEJI
• /
• v.52 no.1
• /
• pp.79-84
• /
• 2008

Alismatis Rhizoma has been used as diuretics and antiphlogistics in the Chinese oriental medicine. A trypsin inhibitor was isolated from Alismatis Rhizoma using DEAE ion exchange column, trypsin affinity column, and FPLC chromatography, and its activity and characteristics were studied. The purifed Alismatis Rhizoma trypsin inhibitor (ARTI) was estimated to be about 22 kDa. The sequence determination on N-terminal amino acid residues and 84 amino acid residues has been completed, yet no homology has been found with trypsin inhibitors reported at NCBI. ARTI did not show inhibitory activities on chymotrypsin and elastase, however it exhibited a significant inhibitory activity on bovine trypsin, and formed a complex with rat liver 10-formyltetrahydrofolate dehydrogenase.

• Molecules and Cells
• /
• v.27 no.1
• /
• pp.47-54
• /
• 2009

A cDNA clone for a transcript preferentially expressed during an early phase of flooding was isolated from Nicotiana tabacum. Nucleotide sequencing of the cDNA clone identified an open reading frame that has high homology to the previously reported glycine-rich RNA-binding proteins. The open reading frame consists of 157 amino acids with an N-terminal RNA-recognition motif and a C-terminal glycine-rich domain, and thus the cDNA clone was designated as Nicotiana tabaccum glycine-rich RNA-binding protein-1 (NtGRP1). Expression of NtGRP1 was upregulated under flooding stress and also increased, but at much lower levels, under conditions of cold, drought, heat, high salt content, and abscisic acid treatment. RNA homopolymer-binding assay showed that NtGRP1 binds to all the RNA homopolymers tested with a higher affinity to poly r(G) and poly r(A) than to poly r(U) and poly r(C). Nucleic acid-binding assays showed that NtGRP1 binds to ssDNA, dsDNA, and mRNA. NtGRP1 suppressed expression of the fire luciferase gene in vitro, and the suppression of luciferase gene expression could be rescued by addition of oligonucleotides. Collectively, the data suggest NtGRP1 as a negative modulator of gene expression by binding to DNA or RNA in bulk that could be advantageous for plants in a stress condition like flooding.

• Bulletin of the Korean Chemical Society
• /
• v.35 no.8
• /
• pp.2494-2504
• /
• 2014

P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.