• Animal cells and systems
• /
• v.9 no.3
• /
• pp.139-144
• /
• 2005

The attractant (orange light) or repellent (white light) signal is transmitted from SRI (Sensory Rhodopsin I) via protein-protein interaction with its transducer Htrl (Halobacterial Transducer for Sensory Rhodopsin I) which in turn controls a cytoplasmic phospho-transfer pathway that modulates flagella motor switching in Halobacterium salinarum. Some mutations in both SRI and Htrl showed an unusual mutant phenotype called inverted signaling, in which the cell produces a repellent response to normally attractant light. Twelve mutations at the Glutamate 56 (E56) position in the second transmembrane helix of Htrl were introduced by site-specific random mutagenesis. Almost all E56 mutants showed orange-light inverted responses in pH and temperature-dependent manners except E56D and E56Y. Except for these two mutants, all mutants accelerated the $S_{373}$ decay compared to wild-type at $18^{\circ}C$. This supported that there is an interaction between SRI and the second transmembrane of Htrl. Also a structural model of Htrl based on the Tar crystal structure and the secondary structure prediction program proposed the E56 residue to be in the middle of the proton channel. The most important observation is that the E56 mutant provides the evidence that this residue is very sensitive for signal relay, which can be explained by the open and closed conformations of the channel (A and R conformations) in SRI, as was postulated by the unified conformational shuttling model for transport and signaling.

• Bulletin of the Korean Chemical Society
• /
• v.14 no.6
• /
• pp.713-717
• /
• 1993

The crystal structure of the potassium salt of penicillin V has been studied by the X-ray crystallographic methods. Crystal data are as follows; potassium 3,3-dimethyl-7-oxo-6-phenoxyacetoamido-4-thia-1- azabicyclo[3.2.0]-heptane-2${\alpha}$-carboxylate, $K^+{\cdot}C_{16}H_{18}N_2O_5S^-$, $M_r$= 388.5, triclinic, Pl, a= 9.371 (1), b= 12.497 (2), c= 15.313 (2) ${\AA},\;{\alpha}= 93.74\;(2),\;{\beta}=99.32\;(1),\;{\gamma}=90.17\;(1)^{\circ},\;V=1765.7\;(2)\;{\AA}^3$, Z=4, $D_m=1.461\;gcm^{-1},\;{\lambda}(Cu\;K{\alpha})=1.5418\;{\AA},\;{\mu}=40.1\;cm^{-1}$, F(000)=808, T=296 K. The structure was solved by the heavy atom and difference Fourier methods with intensity data measured on an automated four-circle diffractometer. The structure was refined by the full-matrix least-squares method to a final R= 0.081 for 3563 observed $[I_0{\geq}2{\sigam}(I_0)]$ reflections. The four independent molecules assume different overall conformations with systematically different orientations of the phenyl groups although the penam moieties have the same closed conformations. There are intramolecular hydrogen bonds between the exocyclic amide nitrogen and phenoxy oxygen atoms. The penam moiety is conformationally very restricted although the carboxyl and exocyclic amide groups apparently have certain rotational degrees of freedom but the phenyl group is flexible about the ether bond despite the presence of the intramolecular N-H${\cdots}$O hydrogen bond. There are complicated pseudo symmetric relationships in the crystal lattice. The penam moieties are related by pseudo 20.5 screw axes and the phenyl groups by pseudo centers of symmetry. The potassium ions, related by both pseudo symmetries, form an infinite zigzag planar chain parallel to the b axis. Each potassium ion is coordinated to seven oxygen atoms in a severely distorted pentagonal bipyramid configuration, forming the infinite hydrophilic channels which in turn form the molecular stacks. Between these stacks, there are only lipophilic interactions involving the phenyl groups.

• Bulletin of the Korean Chemical Society
• /
• v.21 no.3
• /
• pp.281-290
• /
• 2000

We varied recombination method of fenetic algorithm (GA), i.e., crossover step, to compare efficiency of these methods, and to find more optimum GA method. In one method (A), we select two conformations(parents) to be recombined by systematic combination of lowest energy conformations, and in the other (B), we select them in a ratio proportional to the energy of the conformation. Second variation lies in how to select crossover point. First, we select it randomly(1). Second, we select range of residues where internal energy of the molecule does not vary for more than two residues, select randomly among such regions, and we select either thr first (2a) or the second residue (2b) from the N-terminal side, or the first (2c) or the second residue (2d) from the C-terminal side in the selected region for crossover point. Third, we select longest such hregion, and select such residue(as cases 2) (3a, 3b, 3c or 3d) of the region. These methods were tested in a 2-dimensionl lattice system for 8 different sequences (the same ones used by Unger and Moult., 1993). Results show that compared to Unger and Moult's result(UM) which corresponds to B-1 case, our B-1 case performed similarly in overall. There are many cases where our new methods performed better than UM for some different sequences. When cooling factor affecting higher energy conformation to be accepted in Monte Carlo step was reduced, our B-1 and other cases performed better than UM; we found lower energy conformers, and found same energy conformers in a smaller steps. We discuss importance of cooling factor variation in Monte Carlo simulations of protein folding for different proteins. (A) method tends to find the minimum conformer faster than (B) method, and (3) method is superior or at least equal to (1) method.

• Journal of the Korean Chemical Society
• /
• v.38 no.10
• /
• pp.710-718
• /
• 1994

We suggest a statistical thermodynamic theory for the conformational transition of a synthetic alanine (Ala), ${\alpha}$-aminoisobutyric acid (Aib) alternative oligopeptide, Buo-(Ala-Aib)$_n$-oMe, where the terminal groups Buo and oMe stand for t-butoxy and methoxy, respectively. Pure Aib homo-oligomers have always been found to adopt $3_{10}$ helical conformations, while polyalanine has always $\alpha$ helical conformation. In an organic solvent (e.g. $CD_3$CN) it shows that the length for the $3_{10}$/${\alpha}$ helix transitions of Buo-(Ala-Aib)$_n$-oMe, is 8 at room temperature. In an aqueous solution oligopeptide has always coil conformation at room temperature. In an organic solution, helical structures of the oligopeptide are more stable than coil structure, so we studied the $$3_{10}/\alpha$ helix transitions, considering coiled-conformations, coiled and $3_{10}$ helical conformations, and coiled and $\alpha$ helical conformations by using the zipper model. We determined the values of parameters ($\sigma_A$, $\sigma_T$, $\xi_A$, $\xi_T$) from the relating published data; $\sigma_A$ = 0.00011, $\sigma_T$ = 0.0060, $\xi_A$ = 10.1, $\xi_T$ = 3.90. The distributions of $\alpha$ helical length can be N-2, N-3, N-4, ${\cdots}$, 3, 2, 1 (N = 2n) while those of $3_{10}$ helical length, N-1, N-2, N-3, N-4, ${\cdots}$, 3, 2, 1.

• Management Science and Financial Engineering
• /
• v.14 no.2
• /
• pp.105-118
• /
• 2008

There are many debates on the topic of the relationship between oil prices and economic growth. Through the repeated processes of conformations and contractions on the subject, two main issues are developed; one is how to define and drive oil shocks from oil prices, and the other is how to specify an econometric model to reflect the asymmetric relations between oil prices and output growth. The study, thus, introduces the unobserved component model to pick up the oil shocks and a first-order Markov switching model to reflect the asymmetric features. We finally employ unique oil shock variables from the stochastic trend components of oil prices and adapt four lags of the mean growth Markov Switching model. The results indicate that oil shocks exert more impact to recessionary state than expansionary state and the supply-side oil shocks are more persistent and significant than the demand-side shocks.

• Bulletin of the Korean Chemical Society
• /
• v.27 no.3
• /
• pp.413-418
• /
• 2006

Sodium hyaluronate (NaHA), water soluble polymer having ultra-high molecular weight, is characterized by using on-line frit inlet asymmetrical flow field-flow fractionation (FI-AFlFFF) and multiangle light scattering (MALS). This study demonstrates the capability of power programming FI-AFlFFF for the separation of NaHA and the applicability of FI-AFlFFF with MALS for the characterization of molecular weight distribution and their structural information. Since sample injection and relaxation in FI-AFlFFF are achieved by using hydrodynamic relaxation, separation of high molecular weight polymers can be achieved smoothly without halting the separation flow. Experiments are carried out with the two different NaHA products (a raw NaHA sample and a thermally degraded NaHA product) and molecular weight distribution and conformations in solution are determined. Influence of sample filtration on the change of molecular weight distribution is also discussed.

• Bulletin of the Korean Chemical Society
• /
• v.32 no.5
• /
• pp.1620-1624
• /
• 2011

Homologated analogues 3a and 3b of potent and selective A3 adenosine receptor ligands, IB-MECA and dimethyl-IB-MECA were synthesized from commercially available 1-O-acetyl-2,3,5-tri-O-benzoyl-${\beta}$-D-ribofuranose (4) via $Co_2(CO)_8$-catalyzed siloxymethylation as a key step. Unfortunately, homologated analogues 3a and 3b did not show significant binding affinities at three subtypes of adenosine receptors, indicating that free rotation, resulting from homologation, induced unfavorable interactions in the binding site of the receptor maybe due to the presence of many conformations.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.9
• /
• pp.3017-3024
• /
• 2012

The geometrical parameters, vibrational frequencies, and binding energies for $(H_2O_3)_n$ (n = 1-5) have been investigated using various quantum mechanical techniques. The possible structures of the clusters (n = 2-5) are fully optimized and the binding energies are predicted using energy differences at each optimized geometry. The harmonic vibrational frequencies are also determined and zero-point vibrational energies (ZPVEs) are considered for the better prediction of the binding energy. The best estimation of the binding energy for the dimer is 8.65 kcal/mol. For n = 2 and 3, linear structures with all trans forms of the HOOOH monomers are predicted to be the lowest conformations in energy, while the cyclic structures with all cis-HOOOH monomers are preferable structures for n = 4 and 5.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.3
• /
• pp.917-924
• /
• 2012

The conformational study of glycerol has been carried out using the M06-2X/cc-pVTZ level of theory in the gas phase and the SMD M06-2X/cc-pVTZ level of theory in water in order to understand its conformational preferences and solvation effects. Most of the preferred conformers of glycerol have two $C_5$ hydrogen bonds in the gas phase, as found by the analysis of calorimetric data. It has been known that the solvation drove the hydrogen bonds of glycerol to be weaker and its potential surface to be fatter and that glycerol exists as an ensemble of many feasible local minima in water. The calculated populations of glycerol in the gas phase and in water are consistent with the observed values, which are better than the previously calculated ones at the G2(MP2), CBS-QB3, and SM5.42 HF/6-31G(d) levels of theory.

• 한국생물공학회:학술대회논문집
• /
• 2003.10a
• /
• pp.630-633
• /
• 2003

The mussel adhesive protein Mefp-1 is a natural, strong and durable adhesive that is stable under corrosive, saline conditions. Mefp-1 is found in the marine mussel Mytilus edulis and it has a molecular weight of ca. 130,000. The primary structure is mainly composed of repeating decapetides: Ala-Lys-Pro -Ser-Tyr Hyp-Hyp-Thr-DOPA-Lys. To elucidate the mechanism by which Mefp-1 bonds to metal surfaces, we have used surface-enhanced Raman spectroscopy to study the interactions of peptides related to the Mefp-1 decapeptide repeat with gold surfaces. We have concluded that the tyrosine residue and the carboxyl terminus interact strongly with the gold surface, and that proline and hydroxyproline constrain the conformations of the peptides, thereby limiting the types of possible interactions of the functional groups with the gold surface.