• Genomics & Informatics
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• 제11권3호
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• pp.155-160
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• 2013

Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural information repositories that have been published. The reliability of the torsional system, which represents the native processes of structural change in the structural analysis, was partially proven with previous structural alignment studies. Here, a web server providing structural information and analysis based on the backbone torsional representation of a protein structure is newly introduced. The web server offers functions of secondary structure database search, secondary structure calculation, and pair-wise protein structure comparison, based on a backbone torsion angle representation system. Application of the implementation in pair-wise structural alignment showed highly accurate results. The information derived from this web server might be further utilized in the field of ab initio protein structure modeling or protein homology-related analyses.

• BMB Reports
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• 제40권2호
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• pp.261-269
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• 2007

The structure and dynamics of a 37-residue antimicrobial peptide gaegurin 4 (GGN4) isolated from the skin of the native Korean frog, Rana rugosa, was determined in SDS micelles by NMR spectroscopy. The solution structure of the peptide in SDS micelles was determined from 352 NOE-derived distance constraints and 22 backbone torsion angle constraints. Dynamic properties for the amide backbone were characterized by $^1H-^{15}N $heteronuclear NOE experiments. The structural study revealed two amphipathic helices spanning residues 2-10 and 16-32 and that the helices were connected by a flexible loop. An intraresidue disulfide bridge was formed between residues Cys31 and Cys37 near the C-terminus. The loop region (11-15) connecting the two helices are were slightly more flexible than these helices themselves. From the fact that since there is no contact NOEs between two helices, it is implied that the GGN4 peptide shows an independent motion of both helices which has an angle of about $ 60^{\circ}-120^{\circ}$ from each other.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 1996년도 정기총회 및 학술발표회
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• pp.10-10
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• 1996

High-resolution solution conformation of a novel conotoxin, [Pro 7,13] $\alpha$A-conotoxin $P_{IVA}$, GCCGSYPNAACHPCSCKDROSYCGQ-N $H_2$, has been determined by two-dimensional $^1$H nmr methods in combination with distance geometry calculation to rmsd values of 0.90 $\AA$ and 1.16 $\AA$ for the backbone and heavy atoms, respectively. Total of 324 NOE-derived interproton distance restraints including 33 long-range NOE restraints a well as 11 $\Phi$ and 7 $\chi$$^1$ torsion angle restraints were used for computation of structures. (omitted)d)

• Bulletin of the Korean Chemical Society
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• 제23권2호
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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.

• 한국결정학회지
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• 제2권2호
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• pp.13-21
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• 1991

50% terephthaloyl chloride(TPA)와 50%(1-phenylethyl) hydroquinone(PEHQ)으로부터 합성된 열 액정폴리에스터 poly(1-phenylethyl-p-phenylene-terephthalate)의 chalk conformation 및 packing 상태를 X-선 회절법을 이용하여 해석하였다. 단위세포상수는 a=12.77 A, b=10.17 A(unlque axis), c=12.58 A (fiber axis), β=90.1°, 그리고 공간군은 P2l 이고 단사정계이며 Z:4 이었다. 미세구조는 주쇄상의 Phenyl-COO 그리고 COO-Phenyl 평면간의 그리고 주축과 측쇄간의 torsion angle 들을 중심으로 37개의 회절반점에 대해 Linked Atom Least Square(LALS) 방법을 이용하여 해석하였으며, 1-phenylethyl 치환체는 ortho-와 met a위치에 각각 확률적으로 0.5의 가중치를 부여함에 의해 구조적으로 모델링 되었다. 주쇄상의 Phenyl-COO그리고 Phenyl-COO평면간의 torsion angle은 각각 -6.1°와 65.6°로 주어졌으며 결국 주축상의 Phenol 평면들은 서로 59.5°로 엇갈려 주축을 형성하고 있음을 알 수 있었다. (단 ester, COO-, 기는 평면으로 가정되었다.)

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2003년도 정기총회 및 학술발표회
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• pp.75-75
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• 2003

We report here the results on N-acetyl-N'-dimethylamide of proline (Ac-Pro-NM $e_2$) calculated using the ab initio molecular orbital method with the self-consistent reaction field (SCRF) theory at the HF level with the 6-31+G(d) basis set to investigate the conformational preference of polyproline depending on the cis/trans peptide bonds and down/up puckerings along the backbone torsion angle $\square$ in the gas phase, chloroform, and water. In the gas phase, Ac-Pro-NM $e_2$ has seven local minima of tFd, tFu, cFd, cFu, cAu, tAu, and cAd conformations. In particular, polyproline conformations tFd, tFu, cFd, and cFu are found to be more stable than $\square$-helical conformations cAu, tAu, and cAd. In contrast, Ac-Pro-NHMe has seven local minima of tCd, tCu, cBd, cAu, tAu, cFd, and cFu conformations. Conformations tCd and tCu are found to be most stable, which is ascribed to the intramolecular hydrogen bond between C=O of acetyl group and $N^{~}$ H of N'-methyl amide group. The stability of the cFd conformation (i.e., the polyproline I structure) in chloroform is somewhat increased, relative to that in water, although tFd and tFu conformations (i.e., the polyproline II structure) are dominate both in chloroform and water. The population of backbone conformations feasible in chloroform and water is consistent with the experiments. This work is supported by a Korea Research Foundation Grant (KRF-2002-041-C00129).

• 한국자기공명학회논문지
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• 제17권1호
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• pp.11-18
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• 2013

Rapid advances of computational power and method have made it practical to apply the time-consuming calculations with all-atom force fields and sophisticated potential energies into refining NMR structure. Added to the all-atom force field, generalized-Born implicit solvent model (GBIS) contributes substantially to improving the qualities of the resulting NMR structures. GBIS approximates the effects that explicit solvents bring about even with fairly reduced computational times. Although GBIS is employed in the final stage of NMR structure calculation with experimental restraints, the effects by GBIS on structures have been reported notable. However, the detailed effect is little studied in a quantitative way. In this study, we report GBIS refinements of ubiquitin and GB1 structures by six GBIS models of AMBER package with experimental distance and backbone torsion angle restraints. Of GBIS models tested, the calculations with igb=7 option generated the closest structures to those determined by X-ray both in ubiquitin and GB1 from the viewpoints of root-mean-square deviations. Those with igb=5 yielded the second best results. Our data suggest that the degrees of improvements vary under different GBIS models and the proper selection of GBIS model can lead to better results.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2003년도 정기총회 및 학술발표회
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• pp.76-76
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• 2003

We report here the results on N-acetyl-N'-methylamide of 4-fluoroproline (Ac-Flp-NHMe) calculated using the ab initio molecular orbital method with the self-consistent reaction field (SCRF) theory at the HF level with the 6-31+G(d) basis set to investigate the stereoelectronic effects on the conformational preference of proline depending on the cis/trans peptide bonds and down/up puckerings along the backbone torsion angle $\square$ in the gas phase, chloroform, and water. In the gas phase, all potential energy surfaces for Ac-Flp-NHMe are quite similar to those of Ac-Pro-NHMe, except that up-puckered conformations are more stabilized than down-puckered ones. In chloroform and water, polyproline structures become dominant, whose populations are larger than those of Ac-Pro-NHMe. In chloroform and water, the populations of polyproline II (i.e., tF conformations) are quite similar to each other, but those of polyproline I (i.e., cF conformations) are larger by 5％ in water than in chloroform. In particular, all cis populations for Ac-Flp-NHMe in the gas phase, chloroform, and water are decreased than those of Ac-Pro-NHMe.

• 한국자기공명학회논문지
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• 제26권1호
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• pp.1-9
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• 2022

There are two distinct approaches to improving the quality of protein NMR structures during refinement: all-atom force fields and accumulated knowledge-assisted methods that include Rosetta. Mao et al. reported that, for 40 proteins, Rosetta increased the accuracies of their NMR-determined structures with respect to the X-ray crystal structures (Mao et al., J. Am. Chem. Soc. 136, 1893 (2014)). In this study, we calculated 32 structures of those studied by Mao et al. using all-atom force field and implicit solvent model, and we compared the results with those obtained from Rosetta. For a single protein, using only the experimental NOE-derived distances and backbone torsion angle restraints, 20 of the lowest energy structures were extracted as an ensemble from 100 generated structures. Restrained simulated annealing by molecular dynamics simulation searched conformational spaces with a total time step of 1-ns. The use of GPU-accelerated AMBER code allowed the calculations to be completed in hours using a single GPU computer-even for proteins larger than 20 kDa. Remarkably, statistical analyses indicated that the structures determined in this way showed overall higher accuracies to their X-ray structures compared to those refined by Rosetta (p-value < 0.01). Our data demonstrate the capability of sophisticated atomistic force fields in refining NMR structures, particularly when they are coupled with the latest GPU-based calculations. The straightforwardness of the protocol allows its use to be extended to all NMR structures.