• Bulletin of the Korean Chemical Society
• /
• v.20 no.3
• /
• pp.345-351
• /
• 1999

The structures, the energetics, and the spectra of K+(H2O)3 have been studied at HF and MP2 levels with the basis set of triple-zeta plus two sets of polarization functions (TZ2P) for water molecules. Two structures considered are 3+0 (D3), and 2+1 (C2v). The 2+1 (C2v) has two hydrogen bonds between the primary hydration and the secondary hydration shell water molecules. They have similar binding energy and enthalpy. The most stable conformation of K+(H2O)3 is entropy driven as shown in Na+(H2O)5 and in Na+(H2O)6 cases. The 3+0 (D3) conformation is the most stable at 298 K and at 1 atm, based on Gibbs free energy changes (ΔGr). The thermal contributions to the enthalpy and the Gibbs free energy are corrected for the low frequency modes. The corrected ΔGr is in good agreement with the experimental value. Vibrational frequencies of two conformations are revealed as their characteristics.

• Journal of Industrial and Engineering Chemistry
• /
• v.67
• /
• pp.293-300
• /
• 2018

Lipocalins are diverse group of small extracellular proteins found in various organisms. In this study, members of 10 non-homologous lipocalin-ligand crystal complex structures were remodeled using rigid and flexible ligand modes to validate the prediction efficiency of molecular docking simulation. The modeled ligand conformations indicated a high prediction accuracy in rigid ligand mode using cluster based analysis for most cases whereas the flexible ligand mode required further considerations such as ligand binding energy and RMSD for some cases. This in silico study is expected to serve as a platform in the screening of novel ligands against lipocalin family of proteins.

• Journal of the Korean Magnetic Resonance Society
• /
• v.26 no.2
• /
• pp.21-23
• /
• 2022

High-pressure (HP) NMR is a powerful method to elucidate various structural features of amyloidogenic proteins. Following the previous mini-review recapitulating the HP-NMR application for amyloid-β peptides of the last issue [J. H. Kim, J. Kor. Mag. Reson. Soc. 26, 17 (2022)], the recent advancements in the HP NMR application for α-synuclein (α-Syn) are briefly summarized and discussed here. Although α-Syn is a well-known intrinsically disordered protein (IDP), several studies have shown that it can also exhibit heterogeneous yet partially folded conformations, which may correlate with its amyloid-forming propensity. HP NMR has been a valuable tool for investigating the dynamic and transient structural features of α-Syn and has provided unique insights to appreciate its aggregation-prone characters.

• BMB Reports
• /
• v.55 no.9
• /
• pp.439-446
• /
• 2022

Pyridoxal 5'-phosphate (PLP)-dependent enzymes are ubiquitous, catalyzing various biochemical reactions of approximately 4% of all classified enzymatic activities. They transform amines and amino acids into important metabolites or signaling molecules and are important drug targets in many diseases. In the crystal structures of PLP-dependent enzymes, organic cofactor PLP showed diverse conformations depending on the catalytic step. The conformational change of PLP is essential in the catalytic mechanism. In the study, we review the sophisticated catalytic mechanism of PLP, especially in transaldimination reactions. Most drugs targeting PLP-dependent enzymes make a covalent bond to PLP with the transaldimination reaction. A detailed understanding of organic cofactor PLP will help develop a new drug against PLP-dependent enzymes.

• Journal of Embryo Transfer
• /
• v.31 no.3
• /
• pp.227-233
• /
• 2016

This study was conducted to analyze the effect of single nucleotide polymorphisms (SNPs) on the equine chromosomes (ECA) 3 for the body conformations of 12 month of age in Jeju crossbred (Jeju horses ${\times}$ Thoroughbred). A total of 199 Jeju crossbred horse samples were obtained from the National Institute of Subtropical Livestock Research Institute for this study. To correctly estimate the body conformations, we measured thirteen elements relevant to the body conformation such as body weight, wither height, body length for all the 199 horses at 12 month of age. Furthermore, all the horses were genotyped using four SNPs including the BIEC2-808466, BIEC2-808543, BIEC2-808967, BIEC2-809370, of which genomic coordinates range approximately from 105.1Mbp to 110 Mbp in the ECA3. For the phenotypic data sets, the average body weight was $193.7{\pm}24.5kg$ and the height was $124.5{\pm}4.0cm$. As for the genotypic data, the miner allele frequencies of the SNPs were shown to be varied from 0.01 to 0.291. Using the phenotypic and genotypic data sets, analysis of covariance was performed to find any association between those SNP genotypes and body conformations, using year of birth, month of birth, sex, and parity as the covariance components. The result showed that alternative genotypes in the BIEC2-808967 and BIEC2-809370 SNPs were significantly associated with the body length (P<0.05) and the wither height (P<0.05) respectively in the Jeju crossbred horses. Therefore, it is estimated that there are significant associations in the body conformation of 12 month of age of Jeju crossbred for those two SNPs used in this study.

• Korean Journal of Agricultural Science
• /
• v.17 no.1
• /
• pp.26-33
• /
• 1990

This study was conducted to estimate heritabilities and genetic correlations of economic traits and body conformations in Korean Native Ogol fowl. The data analyzed were the record of 450 pullets bred from 150 dams and 20 sires of the fowl obtained from June 18, 1987 to February 6, 1989. The results of this study were summarized as follows ; The estimates of heritability for body weight, egg weight and shank length from combined variance components were relatively high, ranging from 0.415 to 0.558, while those for age at first egg, egg production and breast width were moderate, ranging from 0.301 to 0.334. For genetic correlations, body weights were negatively correlated with egg production, ranging from -0.552 to -0.309, while positive correlations were found between body weight and egg weight, ranging from 0.285 to 0.380. Also, egg production was negatively correlated with egg weight, ranging from -0.383 to -0.381. The shank length showed very high positive correlations with the body weights and age at 1st egg, ranging from 0.328 to 0.843. Hence the improvement in shank length will increase the body weight as well as the age at 1st egg.

• Journal of the Korean Chemical Society
• /
• v.53 no.5
• /
• pp.521-529
• /
• 2009

Molecular structures of the various conformers for the 1,3-dimethoxy-p-tert-butylthiacalix[4] crown-5-ether (3) were optimized by using DFT B3LYP/6 - 31 + G(d,p) and mPW1PW91/6 - 31 + G(d,p) (hybrid HF-DF) calculation methods. We have analyzed the energy differences and structures of eight in/out orientations (cone_oo, cone_oi, pc_oo, pc_io, pc_oi, pc_ii, 13a_oo, 13a_io) of two methoxy groups in three major conformations (cone, partial-cone and 1,3-alternate). The 13a_oo (out-out orientation of the 1,3-alternate conformer) is calculated to be the most stable among eight different conformations of 3, and in accord with the experimental result. The ordering of relative stability resulted from the mPW1PW91/6 - 31 + G(d,p) calculation method is following: 13a_oo > 13a_io$\sim$pc_io$\sim$cone_oo > cone_oi$\sim$pc_oo$\sim$pc_oi > pc_ii.

• Bulletin of the Korean Chemical Society
• /
• v.32 no.11
• /
• pp.3979-3990
• /
• 2011

Eight ionizable nano-baskets of cone 25,26-di(carboxymethoxy)calix[4]arene-crown-3,4,5,6 were synthesized and were verified by $^1H$ and $^{13}C$ NMR spectroscopy, IR spectroscopy and elemental analysis. The competitive solvent extractions of alkali and alkaline earth metal cations were studied using such nano-baskets. The novelty of this study is including three binding units of calixarene's bowl, crown ether's ring and electron-donor ionizable moieties in a unique scaffold to assess the binding tendency towards the cations. The objective of this work is to study the extraction efficiency, selectivity and $pH_{1/2}$ of such complexes. The result of solvent extraction experiments indicated that these compounds were effective extractants of alkali and alkaline earth metal cations. Their selectivities were greatly influenced by the acidity of solution and the conformations of the calixcrown. One conformer was selective to $Na^+$ in pH ${\geq}$ 4, while the other was highly selective to $Ba^{2+}$ in pH 6 and upper.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.3
• /
• pp.770-774
• /
• 2012

Protein loops are often involved in diverse biological functions, and some functional loops show conformational changes upon ligand binding. Since this conformational change is directly related to ligand binding pose and protein function, there have been numerous attempts to predict this change accurately. In this study, we show that it is plausible to obtain meaningful ensembles of loop conformations for flexible, ligand-binding protein loops efficiently by applying a loop modeling method. The loop modeling method employs triaxial loop closure algorithm for trial conformation generation and conformational space annealing for global energy optimization. When loop modeling was performed on the framework of ligand-free structure, loop structures within $3\AA$ RMSD from the crystal loop structure for the ligand-bound state were sampled in 4 out of 6 cases. This result is encouraging considering that no information on the ligand-bound state was used during the loop modeling process. We therefore expect that the present loop modeling method will be useful for future developments of flexible protein-ligand docking methods.

• Bulletin of the Korean Chemical Society
• /
• v.31 no.2
• /
• pp.442-446
• /
• 2010

Adenosine 3',5'-cyclic monophosphate (cAMP) is a second messenger responsible for a multitude of cellular responses. In this study, we utilized $\beta$-cyclodextrin ($\beta$-CD) as an artificial receptor with a hydrophobic cavity to elucidate the inclusion kinetics of cAMP in a hydrophobic environment using the ultrasonic relaxation method. The results revealed that the interaction of cAMP with $\beta$-CD followed a single relaxation curve as a result of host-guest interactions. The inclusion of cAMP into the $\beta$-CD cavity was found to be a diffusion-controlled reaction. The dissociation of cAMP from the $\beta$-CD cavity was slower than that of adenosine 5'-monophosphate (AMP). The syn and anti glycosyl conformations of adenine nucleotides are considered to play an important role in formation of the inclusion complex. Taken together, our findings indicate that hydrophobic interactions are involved in the inclusion complex formation of cAMP with $\beta$-CD and provide insight into the interactions of cAMP with cAMP-binding proteins.