• Applied Biological Chemistry
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• 제41권8호
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• pp.568-571
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• 1998

The conformations of human insulin precursors, proinsulin and preproinsulin, are described in terms of molecular dynamics simulations. Despite the presence of the C-peptide and/or the signal peptide, molecular dynamics calculations utilizing the hydration shell model over a period of 500 ps indicate that the native conformations of the A and B chains are well conserved in both cases. These results further support the NMR spectroscopy results that the C-peptide is relatively disordered and does not influence the overall conformation of the native structure. The robustness of the native structure as demonstrated by experiment and simulation will permit future protein engineering applications, whereby the expression or purification yields can be improved upon sequence modification of the C-peptide and/or the signal peptide.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2003년도 가을 학술발표논문집 Vol.30 No.2 (2)
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• pp.811-813
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• 2003

단백질의 기능은 단백질의 구조에 따라 결정되며, 새로운 단백질의 기능을 파악하기 위하여 이미 밝혀진 단백질의 기능과 구조를 비교하는 방법이 사용되고 있다. 단백질 구조를 비교하는 방법은 단백질 구조를 표현하는 방법에 따라 다양하게 개발되고 있으며, 보다 효과적으로 관련된 연구자들이 자신의 연구에 활용하기 위해서는 빠르고 쉽게 활용할 수 있는 인터페이스를 제공하는 도구가 필요하다. 본 논문에서는 단백질 이차구조 및 그들 사이의 관계를 이용하여 단백질 구조를 표현하는 PSAML과 이를 이용하여 표현된 단백질 구조를 비교하는 시스템인 S4E(Search Substructures of Secondary Structure Elements)에 관하여 기술한다. S4E 시스템은 단백질 이차구조와 그들 사이의 관계(각도, 거리, 길이)를 이용하여 표현된 단백질 구조를 비교하여 유사성이 높은 부분을 찾는 기능을 제공한다. 또한 S4E 시스템은 이차구조 기반의 단백질 구조 데이터베이스(PSAML 데이터베이스) 및 웹 기반 사용자 인터페이스를 제공하여 사용자가 쉽고 효과적으로 단백질 구조 비교를 할 수 있다.

• 한국수산과학회지
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• 제19권5호
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• pp.477-484
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• 1986

The interaction of myofibrillar protein with lipid or oxidized lipid was considered to be mostly contributing to the drop of digestibility of fish meat products. The digestibility of myofibrillar protein was $92.11\%$ for flounder and $88.04\%$ for hairtail fish, repectively, and as a rule it decreased as both the amount of lipid and reaction time increased. It also decreased with increase in the amount of added linoleate and oxidized linoleate. However, when the reaction continued for 6 hours or more the digestibility rather increased, which was provably due to the unfolding of protein structure. The hot air dried hairtail fish showed the lowest C-PER values among all dried fish products. The protein quality of flounder, hairtail fish and their dried ones except hot air dried ones measured by C-PER procedure were superior to that of ANRC casein. DC-PER values of all samples were greater than those of C-PER values and the greater discrepancies were noted in hairtail fish (fatty fish) products which possessed the lower in vitro protein digestibilities. Predicted diegstibilities, which were calculated using amino acid profiles, of all samples except raw ones were overestimated in comparison with in vitro protein digestibilities. From the observations so far, formation of complex of lipids and protein was thought to be the most important factor in lowering protein digestibility of the dried fish meat products.

• 대한의생명과학회지
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• 제12권4호
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• pp.443-450
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• 2006

To demonstrate their possibilities as an enhanced vaccine delivery system, protein-loaded Poly lactide glycolide copolymer (PLGA) microspheres were prepared with different physical characteristics. Ethyl acetate (EA) solvent extraction process was employed to prepare microspheres and the effects of process parameters on drug release properties were evaluated. The biodeuadability of microspheres was also evaluated by the pH change and GPC (Gel permeation chromatography). Primary IgG antibody responses in BALB/c mice were compared with protein saline solutions as negative controls and adsorbed alum suspensions as positive controls after single subcutaneous injection for in vivo studies. The microspheres showed a erosion with a highly porous structure and did not keep their spherical shape at 45 days and this result could be confirmed by GPC. In vitro release of proteinous drug showed initial burst effect in all batches of microspheres, followed by gradual release over the next 4 weeks. PLGA microspheres were degraded until 45 days and the secondary structure of OVA was not affected by the preparation method. Enzyme-linked immunosorbent assays demonstrated that the single subcutaneous administrations of OVA-loaded PLGA microspheres induced enhanced serum IgG antibody response in comparison to negative and positive controls. These results demonstrated that microspheres providing the controlled release of antigens might be useful in advanced vaccine formulations for the parenteral carrier system.

• 한국자기공명학회논문지
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• 제1권2호
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• pp.71-78
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• 1997

The magnetic anisotropy effects of peptide group in structured protein on proton chemical shift have been investigated using trialanine modeling. The structure dependent part of chemical shift of C${\alpha}$H of the second amino acid residue was assumed to come purely from the magnetic anisotropy effects of C=O and C-N bonds of peptide in the direct neighborhood and thus to be dependent on and $\psi$ angle of this dipeptide. A set of dipeptide models with different and $\psi$angles were generated and from these models the chemical shift values were calculated using known algorithm to emphasize the role of parameters used in the equation. Comparison of sets of different parameters resulted in an optimized parameters which could reproduce the statistical chemical shift values observed in proteins with respect ot the secondary conformation.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.4-4
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• 2003

A large number of in-vitro experiments on the inhibition of kinases and pretenses are reported in literature, and compiled by ProLINT database. Using this powerful wealth of knowledge, we have carried our an analysis of ligand specificity of these two classes of proteins. Each of the pretenses and kinases included in the database has been assigned a consensus ligand fragment signature, based on the available information about its interaction with different ligands. A set of 43 fragments efficiently represent every ligand. We have then organized the consensus fragment signatures for every protein in form of a cluster-tree diagram. This tree is also constructed from other sequence, structure and physical considerations. Cluster-cluster comparison between these analyzes provide a valuable information about ligand specific interactions and similarities between proteins.

• BMB Reports
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• 제44권2호
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• pp.118-122
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• 2011

Most widely used secondary structure assignment methods such as DSSP identify structural elements based on N-H and C=O hydrogen bonding patterns from X-ray or NMR-determined coordinates. Secondary structure assignment algorithms using limited $C{\alpha}$ information have been under development as well, but their accuracy is only ~80% compared to DSSP. We have hereby developed SABA (Secondary Structure Assignment Program Based on only Alpha Carbons) with ~90% accuracy. SABA defines a novel geometrical parameter, termed a pseudo center, which is the midpoint of two continuous $C{\alpha}s$. SABA is capable of identifying $\alpha$-helices, $3_{10}$-helices, and $\beta$-strands with high accuracy by using cut-off criteria on distances and dihedral angles between two or more pseudo centers. In addition to assigning secondary structures to $C{\alpha}$-only structures, algorithms using limited $C{\alpha}$ information with high accuracy have the potential to enhance the speed of calculations for high capacity structure comparison.

• Journal of Microbiology and Biotechnology
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• 제10권5호
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• pp.632-637
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• 2000

This research was undertaken to restore the biological activity of cyclodextrin glucanotransferase (CGTase) of Bacillus macerans origin expressed as inclusion bodies in recombinant Escherichia coli. The optimum concentration of urea used as a denaturant was 8 M. The supplementation of 0.5 M urea into a dialysis buffer increased the refolding efficiency by preventing any protein aggregation. The influence of the protein concentration, temperature, and pH were also investigated. The protein concentration was found to be the most important factor in the refolding efficiency. The optimum temperature was 15-$25^{\circ}C$ and the optimum pH was 6.0. The maximum specific activity of the CGTase refolded under the optimum conditions was 92.2 U/mg, corresponding to 72% of the native CGTase. A comparison of the secondary structure between the native and the refolded CGTase showed that the relative ratio of the $\alpha$-helix content in the native to the refolded CGTase was 1:0.82.

• 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.

• KSBB Journal
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• 제19권1호
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• pp.42-49
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• 2004

Racemic epoxide에 대한 입체선택적 가수분해능을 가지고 있는 곰팡이, Aspergillus niger LK로부터 epoxide hydrolase (EH, EC 3.3.2.3) 유전자의 진화적 유연관계 분석을 행하였다. A. niger LK의 EH 염기서열로부터 유추한 EH 단백질 아미노산 서열은 여러 박테리아의 EH들 및 포유동물의 microsomal EH들과 유의적인 유사성을 가지고 있었으며 a/$\beta$ hydrolase fold family에 속하였다. A. niger LK의 EH 단백질의 입체구조예측은 Protein Data Bank에 수록된 lqo7의 3D 결정구조와 90.6% identity를 가지는 것으로 나타났으며 다른 EH들의 아미노산 서열비교를 행한 결과 Asp$^{192}$ , Asp$^{348}$ 및 His$^{374}$ 이 catalytic triad를 구성하고 있는 것으로 추정되었다. 여러 생물종의 EH서열을 기능적 및 구조적 domain 서열을 기초로 하여 multiple sequence alignment를 행하고 Neighbor-Joining/UPGMA method를 이용하여 계통수를 복원한 결과 다른 생물종들의 EH와의 진화거리는 서로 1.841∼2.682로 멀었으나 EH의 기능을 가지기 위한 oxyanion hole 및 a/$\beta$ hydrolase fold family의 catalytic triad는 잘 보존되고 있어 공통조상으로부터 진화되어 왔음을 알 수 있었다.