• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.63-74
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• 2014

Predicting protein loop structures is an important modeling problem since protein loops are often involved in diverse biological functions by participating in enzyme active sites, ligand binding sites, etc. However, loop structure prediction is difficult even when structures of homologous proteins are known due to large sequence and structure variability among loops of homologous proteins. Therefore, an ab initio approach is necessary to solve loop modeling problems. One of the difficulties in the development of ab initio loop modeling method is to derive an accurate scoring function that closely approximates the true free energy function. In particular, entropy as well as energy contribution have to be considered adequately for loops because loops tend to be flexible compared to other parts of protein. In this study, the contribution of conformational entropy is considered in scoring loop conformations by employing "colony energy" which was previously proposed to estimate the free energy for an ensemble of conformations. Loop conformations were generated by using two EDISON_Chem programs GalaxyFill and GalaxySC, and colony energy was designed for this sampling by tuning relevant parameters. On a test set of 40 loops, the accuracy of predicted loop structure improved on average by scoring with the colony energy compared to scoring by energy alone. In addition, high correlation between colony energy and deviation from the native structure suggested that more extensive sampling can further improve the prediction accuracy. In another test on 6 ligand-binding loops that show conformational changes by ligand binding, both ligand-free and ligand-bound states could be identified by using colony energy when no information on the ligand-bound conformation is used.

• Journal of the Korean Chemical Society
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• v.21 no.3
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• pp.171-179
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• 1977

Proton magnetic resonance spectra of five glycine-containing dipeptides glycyl-L-valine, L-valyl-glycine, glycyl-DL-alanine, glycyl-DL-serine and glycyl-L-aspartic acid in $D_2O$ were investigated as a function of pH at room temperature. From the analysis of the spectra, it was found that the chemical shift of the $C_{\alpha}H,\;C_{\beta}H\;and\;C_rH$protons varies with pH as a one-step titration curve, and that the spin-spin coupling constant remains almost unchanged. Two distinct values of the chemical shift for $C_{\alpha}H,\;C_{\beta}H\;or\;C_rH$protons of constituent amino acids in dipeptide solutions indicate the existence of two magnetically non-equivalent sites in solution. From this study, the structures of the five dipeptides have been confirmed by proton magnetic resonance spectra and it has been suggested that the structural change, conformation and sequence determination can be explored for oligopeptides by an analysis of proton magnetic resonance spectra.

• Animal Bioscience
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• v.34 no.4
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• pp.489-498
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• 2021

Objective: Milk production is one of the most desirable traits in livestock. Recently, the toll-like receptor (TLR) has been identified as a candidate gene for milk traits in cows. So far, there is no information concerning the contribution of this gene in milk traits in sheep. This study was designed to investigate the TLR 4 gene polymorphisms in Barki ewes in Egypt and then correlate that with milk traits in order to identify potential single nucleotide polymorphisms (SNPs) for these traits in sheep. Methods: A part of the ovine TLR 4 gene was amplified in Barki ewes, to identify the SNPs. Consequently; Barki ewes were genotyped using polymerase chain reaction-single strand conformation polymorphism protocol. These genotypes were correlated with milk traits, which were the daily milk yield (DMY), protein percentage (PP), fat percentage (FP), lactose percentage, and total solid percentage (TSP). Results: Age and parity of the ewe had a significant effect (p<0.05 or p<0.01) on DMY, FP, and TSP. The direct sequencing identified a missense mutation located in the coding sequence of the gene (rs592076818; c.1710C>A) and was predicted to change the amino acid sequence of the resulted protein (p.Asn570Lys). The association analyses suggested a significant effect (p<0.05) of the TLR genotype on the FP and PP, while the DMY tended to be influenced as well (p = 0.07). Interestingly, the presence of the G allele tended to increase the DMY (+40.5 g/d) and significantly (p<0.05 or p<0.01) decreased the FP (-1.11%), PP (-1.21%), and TSP (-7.98%). Conclusion: The results of this study suggested the toll-like receptor 4 (TLR4) as a candidate gene to improve milk traits in sheep worldwide, which will enhance the ability to understand the genetic architecture of genes underlying SNPs that affect such traits.

• Journal of Photoscience
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• v.9 no.2
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• pp.114-117
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• 2002

Ultraviolet resonance Raman (UVRR) spectroscopy was used to elucidate the dynamic change of the protein structure of bacteriorhodopsin (BR) during the photocycle. The photointermediates minus light- adapted (LA) BR difference spectra show Trp difference signals, which are assigned to Trp189 or Trp182 on helix F by using the mutants, W182F and W189F. The Difference signals of Trp 182 indicates an increase in hydrogen bonding strength at the indole nitrogen and a large change in the side chain conformation (X$\^$2,1/ torsion angle) in the M$_1$ \longrightarrow M$_2$ transition. On the other hand, Trp189 shows an increased hydrophobic interaction. These results suggest that the tilt of helix F occurs in the M$_1$\longrightarrow M$_2$ transition. In the M$_2$ \longrightarrow N transition, the hydrophobic interaction of Trp182 decreases drastically, The decrease in hydrophobic interaction of Trp182 in the N state suggests an invasion of water molecules that promote the proton transfer from Asp96 to the Schiff base. Structural reorganization of the protein after the tilt of helix F may be important for efficient reprotonation of the Schiff base.

• Proceeding of EDISON Challenge
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• 2013.04a
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• pp.256-259
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• 2013

We investigate co-doping effects of conjugated P-N B-N with increasing of N concentration in the graphene sheets using a first principles based on the density functional theory. N doping sites of the graphene consider two possible sites (pyridinic and porphyrin-like). Energy calculation shows that additional doping of B atom in the porphyrin-like N doped graphene ($V+B-N_x$) is hard to form. At the low chemical potential of N, one N atom with additional doping in the graphene ($V+P-N_1$, $P/B-N_1$) has low formation energy on the other hand at high chemical potential of N, high concentration of N ($V+P-N_4$, $P/B-N_3$) in the graphene is governing conformation. From the results of electronic band structure calculation, it is found that $V+P-N_4$ and $P/B-N_3$ cases change the Fermi energy therefore type change is occurred. On the other hand, the cases of $V+P-N_1$ and N+B recover the electronic structure of pristine graphene.

• Proceedings of the Korean Fiber Society Conference
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• 2003.10a
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• pp.59-60
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• 2003

The undrawn monofilament of poly (trimethylene terephthalate) (PTT) was obtained by melt-spinning. After being annealed at 40 C it was analyzed by the measurements of DSC, DMA, WAXD and ATR FT-IR. Tg of PTT fiber after annealing for more than 96 hours was 20 C higher than that before annealing as determined by the DSC and DMA measurements. The WAXD analysis showed very weak diffraction peaks at 2$\theta$=17$^{\circ}$ and 2$\theta$=24$^{\circ}$ for the annealing time of more than 96 hours. The ATR FT-IR measurements made clear the conformational change of methylene chains of PTT glycol residue from random to gauche-gauche conformation.

• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.3
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• pp.205-211
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• 2005

Water-soluble polyethyleneimine (PE) derivatives containing nucleic acid bases and hydrophilic amino acids such as homoserine (Hse) and serine were prepared by the activated ester method as nucleic acid models. From spectroscopic measurements, the polymers were found to interact with DNA accompanied by an induction of conformational change. Hypochromicity in UV spectra indicated that a stable polymer complex was formed between poly (A) with PEI­Hse-Ura by complementary hydrogen bonding with equimolar nucleic base units (adenine:uracil=1:1). The induced conformation of DNA by the interaction with the polymer containing uracil and homoserine (PEI-Hse-Ura) was concluded to be a super triple helical structure. The formation of the polymer complex, DNA: PEI-Hse-Ura, was found to be affected by the presence of metal ions such as $Ca^{2+}\;and\;Cu^{2+}$.

• Journal of Korea Technical Association of The Pulp and Paper Industry
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• v.31 no.3
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• pp.10-18
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• 1999

The influence of simple electrolyte or anionic trashes on cationic starch adsorption was examined using deinked pulp and bleached thermomechniical pulp. Adsorbed amounts of cationic starches increased slightly , then decreased abruptly as the concentration of simple electrolyte increased. This phenomenon was discussed based on the compression of electrical double layer and conformation change of starch molecules. Also, the effect of the type of simple electrolytes on starch adsorption was examined and discussed. Addition of sodium slilicate increased starch adsorption since it increased surface charge density of fibers. On the other hand, addition of kraft lignin decreased cationic demand of the pulp slurries and adsorbed amounts of cationic starches. Nonionic surfactant did not show any significant effect on the cationic demand of pulp slurries. When simple electrolytes were added to the stock , grater adsorption or cationic starches was obtained with starches of lower degree of substitution . On t도 other hand, amount of adsorbed starches decreased for lower DS starches when the concentration of anionic trashes increased.

• Proceedings of the Polymer Society of Korea Conference
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• 2006.10a
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• pp.222-222
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• 2006

New types of constrained geometry complexes comprising rigid silacycloalkyl group incorporated into the bridging position between cyclopentadienyl and amido functionalities were prepared. The catalytic activities of olefin polymerization were influenced by the change of exo-cyclic ring size on bridge-head silacycloalkyl unit. It has been noted that the activities of this unique series increase with increasing size of the silacycloalkyl bridge and reach the maximum in six-membered silacyclohexyl-bridged CGC complex. It is noteworthy that conformation of silacycloalkanes gives rise to enhanced catalytic activity of the titanium center although the cyclic ring and titanium center are far remoted from each other.

• Fibers and Polymers
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• v.1 no.1
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• pp.18-24
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• 2000

The phase transformation of poly(trimethylene terephthalate) in crystalline state was simulated by atomistic modeling using molecular mechanics technique. The crystalline structure of PTT was successfully prepared using the well-defined unit cell structure of PTT and was satisfactorily verified by comparing that with the structure obtained from the x-ray diffraction experiments. The basic elastic properties were predicted in this study, showing that the crystalline structure of PTT is very pliable to the deformation at small strain. When the crystalline structure of PTT was stepwise deformed up to 50% of strain in chain direction under uniaxial extension condition, the change in dihedral angle of trimethylene unit from gg to tt conformation was accompanied with a large increase of stress, indicating that the phase transformation of PTT in crystalline state is difficult to occur.