• Macromolecular Research
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• v.8 no.5
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• pp.224-230
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• 2000

Molecular mechanics technique has been used for finding energy-minimized conformation to understand the mechanism of yielding of glassy polymers in atomistic level. As a model polymer, amor- phous isotactic polypropylene (iPP) was generated by molecular mechanics and molecular dynamics methods. The stress-strain cone was successfully obtained by using molecular mechanics technique. The torsional angle distribution showed no significant change during extension, although the torsional angles of certain bonds in polymer backbone changed more largely than other bonds. No significant change in the van der Waals interaction is observed at yielding point, whereas the torsional angle energy starts to decrease at yield strain.

• Biomolecules & Therapeutics
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• v.2 no.1
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• pp.28-33
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• 1994

In order to obtain insight into the repair mechanism of DNA containing thymine photo-dimer, the conformation of the duplex d(GCGGTTGGCG).d(CGCCAACCGC) with a thymine dimer incorporated has been studied by proton NMR. NOE data show that, although the local environment around the thymine dimer is altered, the gross structural changes are relatively small. T$_4$endonuclease V exhibited a conformational change on complex formation with DNA. This conformational change occurred around histidine 16 which was close to tyrosine 129 located in the aromatic segment (WYKYY) near the C-terminus. It is likely that the interaction between T$_4$endonuclease V and DNA is strong since the complex was not dissociated up to 1.6 M NaCl.

• Journal of the Society of Cosmetic Scientists of Korea
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• v.18 no.1
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• pp.99-132
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• 1992

Polypeptide has been used broadly as an active ingredient in cosmetics We thought it is very important to investigate the adsorption behavior of polypeptide in order to pre-estimate the effect of these polypeptides. For the study of polypeptide adsorption, we have investigated complex formation of basic homopolypeptides, poly(L-proline) Form I [PLP(I)], Form II [PLP(II)] and poly(4-hydroxy-L-proline) (PHLP) with acidic homopolypeptides, poly(L-glutamic acid) (PLGA), poly(D-glutamic acid) (PDGA) and poly(L-aspartic acid) (PLAA) through hydrogen bonding in a hydroalcoholic medium with viscometer, 1ight scatter, pH meter and circular dicroism (CD). The polypeptides used in this study have helical structure in some conditions. The result exhibited that al 1 the complexes were formed as the composition of basic/acidic homopolypeptide : L:2 irrespective of the complex systems used. A more favorable complex is formed in the PLP(II)-PLGA system than PHLP-PLGA because PLP(II) has a more flexible helical conformation, whereas PHLP has a more rigid helical conformation. The right-handed helix PLGA formed the complex favorably and quickly with the left-handed helix PLP(II), whereas the left-handed helix PDGA formed the complex favorably with the right-handed helix PLP(I). The effect of side chain of the acidic homopolypeptides on the complexation was also studied. The result showed that more favorable condition for the complexation was PLGA-PLP(II) system which has longer side chain at acidic homopolypeptide than PLAA - PLP(II). All the above facts were well supported by CD measurement for the complex systems. By the CD spectra for the complexes we could deduce the conformational change of each homopolypeptide in the complexes On the basis of the above results, we performed the adsorption test of PLP(I, II) and PHLP on the hair having a left-handed helix. The adsorption amount of each polypeptide was analyzed by HPLC. The result showed that PLP(I) was adsorbed more than PLP(II), PLP(II) was adsorbed more than PHLP on the hair. On adsorbing polypeptides having a helical structure on the hair through hydrogen bonding, it could be concluded that the helical polypeptides having the opposite directional structure to the hair are adsorbed more than those having the same directional structure with the hair and also the polypeptides having a flexible conformation are adsorbed more than those having a rigid conformation.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.770-774
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• 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
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• v.29 no.2
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• pp.408-412
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• 2008

FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1) in Arabidopsis are homologous proteins that perform opposite functions: FT is an activator of flowering, and TFL1 is a repressor. It was shown before that change of a single amino acid (His88) of TFL1 to the corresponding amino acid (Tyr) of FT is enough to convert the floral repressor to an activator. However, structural basis of the functional conversion has not been understood. In our molecular dynamics simulations on modified TFL1 proteins, a hydrogen bond present in native TFL1 between the His88 residue and a residue (Asp144) in a neighboring external loop became broken by change of His88 to Tyr. This breakage induced conformational change of the external loop whose structure was previously reported to be another key functional determinant. These findings reveal that the two important factors determining the functional specificities of the floral regulators, the key amino acid (His88) and the external loop, are correlated, and the key amino acid determines the functional specificity indirectly by affecting the conformation of the external loop.

• Bulletin of the Korean Chemical Society
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• v.30 no.7
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• pp.1452-1458
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• 2009

The change in the electronic absorption and emission energy of 7-aminocoumarin derivatives in binary solvent mixtures has been studied. The electronic transition energy along with the Stokes' shift is correlated with the orientation polarizability of the solvent as well as the empirical solvent polarity parameters $E_T$ (30). It is observed that the emission peak shift traces the change of $E_T$ (30) value very closely in binary solvent mixtures. The emission transition more strongly depends on the solvent polarity than the absorption, which indicates the dipole moment gets larger on excitation. From the dependence of the Stokes’ shift of 7-aminocoumarins with the solvent polarity parameters and the ground state dipole moment obtained by the semi-empirical calculations, the excited state dipole moment was estimated. The fluorescence lifetime change of 7-aminocoumarins in binary solvent mixtures was measured and the results are explained in terms of molecular conformation and solvent polarity. The study indicates the empirical solvent polarity $E_T$ (30) is a good measure of microscopic solvent polarity and it probes in general the non-specific solvent interactions.

• BMB Reports
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• v.29 no.6
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• pp.507-512
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• 1996

The NADPH oxidase of phagocytes catalyzes the reduction of oxygen to $O_{2}^{-}$ at the expense of NADPH The enzyme is dormant in resting neutrophils and hecomes activated on stimulation. During activation. $p47^{phox}$ (phagocyte oxidase factor), a cytosolic oxidase subunit, becomes extensively phosphorylated on a number of serines located between S303-S379. Although the biochemical role of phosphorylation is speculative, it has been suggested that phosphorylation could neutralize the strongly cationic C-terminal which may result in the change of conformation of $p47^{phox}$ and subsequent translocation of this protein and other cytosolic components to the membrane. In order to mimic the effect of phosphorylation in terms of neutralizing the positive charges, recombinant $p47^{phox}$ was treated with phenylglyoxal, which removes positive charges of arginine residues. Modification of recombinant $p47^{phox}$ resulted in the activation of oxidase in a cell-free translocation system as well as a conformational change in recombinant $p47^{phox}$ which may be responsible for the activation of the enzyme.

• Bulletin of the Korean Chemical Society
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• v.23 no.2
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• pp.330-336
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• 2002

A quantum-chemical investigation on the conformations and electronic properties of bis[2-{2-methoxy-4,6-di(t-butyl)phenyl}ethenyl]benzenes (MBPBs) as building block for ${\pi}$-conjugate polymer are performed in order to display the effects of t-butyl and methoxy group substitution and of kink(ortho and meta) linkage. The conjugation length of the polymers can be controlled by substituents and kink linkages of backbone. Structures for the molecules, o-, m-, and p-MBPBs as well as unsubstituted o-, m-, and p-DSBs were fully optimized by using semiempirical AM1, PM3 methods, and ab initio HF method with 3-21G(d) basis set. The potential energy curves with respect to the change of single torsion angle are obtained by using semiempirical methods and ab initio HF/3-21G(d) basis set. The curves are similar shape in the molecules with respect to the position of vinylene groups. It is shown that the conformations of the molecules are compromised between the steric repulsion interaction and the degree of the conjugation. Electronic properties of the molecules were obtained by applying the optimized structures and geometries to the ZINDO/S method. ZINDO/S analysis performed on the geometries obtained by AM1 method and HF/3-21G(d) level is reported. The absorption wavelength on the geometries obtained by AM1 method is much longer than that by HF/3-21G(d) level. The absorption wavelength of MBPBs are red shifted with comparison to that of corresponding DSBs in the same torsion angle because of electron donating substituents. The absorption wavelength of isomers with kink(orth and meta) linkage is shorter than that of para linkage.

• The Korean Journal of Food And Nutrition
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• v.15 no.4
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• pp.331-336
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• 2002

Conformation of soymilk protein was examined to obtain basic information for improved calcium intolerence of soymilk protein partially hydrolyzed with protease. Surface hydrophobicities of three proteins showed the order of SMP(soymilk protein) < SPI(soy protein isolate) < PT-SMP(protease treated soymilk protein). Total thiol group contents of SMP and PT-SMP were similar but larger than that of SPI. Reducing rate of disulfide bond in PT-SMP after 2-mercaptoethanol treatment was laster than that in SMP. And so, this result indicates that PT-SMP may be less compacting due to protease treatement. From circular dichroism result, PT-SMP showed different pattern from SMP and SPI suggesting change of secondary structure by hydrolysis. And analysis of heat denaturating property by DSC showed that denaturation enthalpy of three proteins were all small. Especially enthalpy of PT-SMP was least, and this result suggested that PT-SMP was denatured easily by heating due to less compacting structure.

• Polymer(Korea)
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• v.24 no.2
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• pp.182-193
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• 2000

Molar cyclization equilibrium constant (K$_{x}$) of poly(alkylene terephthalate) (PAT) cyclics was calculated by the Monte Carlo simulation on the basis of rotational isomeric state (RIS) model. The experimental $K_{x}$ of PAT cyclics, which was not clearly explained by the Jacobson-Stockmayer theory and the method of Flory, Suter, and Mutter however, was explained well by the direct computational method with the reaction radius ${\gamma}$=0.5 < ${\gamma}^{2}$> $^{1/2}$. The effect of PAT conformation on $K_{x}$ of PAT cyclics was investigated by changing its statistical weight parameters, ${\sigma}_{1}$ and ${\sigma}_{2}{\cdot}K_{x}$ of PAT cyclics obtained by the direct computation method with various radii and the radius ${\gamma}$=0.5 < ${\gamma}^{2}$> $^{1/2}$ was slightly changed with ${\sigma}_{1}$ and ${\sigma}_{2}$. Consequently, it was concluded that $K_{x}$ of PAT cyclics is strongly dependent on the configuration of each PAT and affected by the change of its conformation to some extent.