• Genomics & Informatics
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• v.15 no.4
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• pp.142-146
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• 2017

More effective production of human insulin is important, because insulin is the main medication that is used to treat multiple types of diabetes and because many people are suffering from diabetes. The current system of insulin production is based on recombinant DNA technology, and the expression vector is composed of a preproinsulin sequence that is a fused form of an artificial leader peptide and the native proinsulin. It has been reported that the sequence of the leader peptide affects the production of insulin. To analyze how the leader peptide affects the maturation of insulin structurally, we adapted several in silico simulations using 13 artificial proinsulin sequences. Three-dimensional structures of models were predicted and compared. Although their sequences had few differences, the predicted structures were somewhat different. The structures were refined by molecular dynamics simulation, and the energy of each model was estimated. Then, protein-protein docking between the models and trypsin was carried out to compare how efficiently the protease could access the cleavage sites of the proinsulin models. The results showed some concordance with experimental results that have been reported; so, we expect our analysis will be used to predict the optimized sequence of artificial proinsulin for more effective production.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.4
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• pp.102-108
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• 2016

With the rapid increase of data on protein-protein interactions, the need for delineating the 3D structures of huge protein complexes has increased. The protocols for determining nuclear magnetic resonance (NMR) structure can be applied to modeling complex structures coupled with sparse experimental restraints. In this report, I suggest the use of multiple rigid bodies for improving the efficiency of NMR-assisted structure modeling of huge complexes using CYANA. By preparing a region of known structure as a new type of residue that has no torsion angle, one can facilitate the search of the conformational spaces. This method has a distinct advantage over the rigidification of a region with synthetic distance restraints, particularly for the calculation of huge molecules. I have demonstrated the idea with calculations of decaubiquitins that are linked via Lys6, Lys11, Lys27, Lys29, Lys33, Lys48, or Lys63, or head to tail. Here, the ubiquitin region consisting of residues 1-70 was treated as a rigid body with a new residue. The efficiency of the calculation was further demonstrated in Lys48-linked decaubiquitin with ambiguous distance restraints. The approach can be readily extended to either protein-protein complexes or large proteins consisting of several domains.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.28 no.1
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• pp.31-41
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• 2002

Proline-rich proteins (PRPs) are major components of human saliva. In order to know the biological roles of PRPs, we explored the expression pattern and functional protein structures of PRPs by the immunohistochemical and various molecular biological methods. Polyclonal antibody against human gPRP was generated from rabbit by the injection of oral exfoliated cells specially treated by urea and SDS buffer. The PRPs began to be expressed both in the acinar cells and ductal cells from the EIDS (Early Intermediate Developmental Stage) of fetal salivary glands and became intense in the salivary epithelium in the LDS (Late Developmental Stage) and adult salivary glands. The polyclonal antibody against the gPRP showed the cross-reactivity with aPRP and bPRP, these results were relevant to the high homology among subtypes of PRP. However, the simulated protein structures of PRPs showed the characteristic repetitive whorling domains except the N-terminal signal peptide. The whorling domains were also contained the multiple amino acids of glutamine and glycine, which may provide the receptor binding or cross-linking sites of PRPs.

• Journal of KIISE:Databases
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• v.34 no.5
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• pp.396-408
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• 2007

After the Human Genome Project finished the sequencing of a human DNA sequence, the concerns on protein functions are increasing. Since the structures of proteins are conserved in divergent evolution, their functions are determined by their structures rather than by their amino acid sequences. Therefore, if similarities between two protein structures are observed, we could expect them to have common biological functions. So far, a lot of researches on protein structure alignment have been performed. However, most of them use RMSD(Root Mean Square Deviation) as a similarity measure with which it is hard to judge the similarity level of two protein structures intuitively. In addition, they retrieve only one result having the highest alignment score with which it is hard to satisfy various users of different purpose. To overcome these limitations, we propose a novel protein structure alignment algorithm based on MRPD(Maximum of Residue Pair Distance) and SG (Similarity Graph). MRPD is more intuitive similarity measure by which fast tittering of unpromising pairs of protein pairs is possible, and SG is a compact representation method for multiple alignment results with which users can choose the most plausible one among various users' needs by providing multiple alignment results without compromising the time to align protein structures.

• Bulletin of the Korean Chemical Society
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• v.25 no.11
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• pp.1676-1680
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• 2004

We demonstrate that wide-angle X-ray scattering pattern from photoactive yellow protein (PYP) in solution using a high flux third generation synchrotron X-ray source reflects not only the overall structure, but also fine structures of the protein. X-ray scattering data from PYP in solution have been collected in q ranges from 0.02 ${\AA}^{-1}$ to 2.8 ${\AA}^{-1}$. These data are sensitive to the protein structure and consistent with the calculation based on known crystallographic atomic coordinates. Theoretical scattering patterns were also calculated for the intermediates during the photocycle of PYP to estimate the feasibility of time-resolved wide-angle X-ray scattering experiments on such proteins. These results demonstrate the possibility of using the wide-angle solution X-ray scattering as a quantitative monitor of photo-induced structural changes in PYP.

• Journal of the Korean Magnetic Resonance Society
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• v.5 no.1
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• pp.37-45
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• 2001

Synthetic pulmonary surfactants consisting of a mixture of phospholipids with synthetic peptides based on human surfactant-associated protein SP-B were prepared. These surfactants were analyzed f3r their secondary structures by circular dichroism (CD) spectroscopy and NMR spectroscopy. Two synthetic peptides (SP-B(3), SP-B(4)) combined with the phospholipid mixture displayed significant surfactant properties. The CD spectra showed that the u-helical propensities of the peptides in DPC micelles. In the NMR spectroscopy, the tertiary structures of SP-B(3) show that it has $\alpha$-helical structure from Gln5 to Arg13 in DPC micelle and SP-B(4) show that they have $\alpha$-helical structure from Gln5 to Leu12 in DPC micelle. Based on these structures, truncated peptides originated from SP-B protein, can be designed as effective synthetic surfactants for clinical use.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.22 no.5
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• pp.728-733
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• 2018

Deep learning has been actively studied for predicting protein secondary structure based only on the sequence information of the amino acids constituting the protein. In this paper, we compared the performances of the convolutional neural networks of various structures to predict the protein secondary structure. To investigate the optimal depth of the layer of neural network for the prediction of protein secondary structure, the performance according to the number of layers was investigated. We also applied the structure of GoogLeNet and ResNet which constitute building blocks of many image classification methods. These methods extract various features from input data, and smooth the gradient transmission in the learning process even using the deep layer. These architectures of convolutional neural networks were modified to suit the characteristics of protein data to improve performance.

• The KIPS Transactions:PartD
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• v.19D no.1
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• pp.21-28
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• 2012

Predication of protein interaction sites for monomer structures can reduce the search space for protein docking and has been regarded as very significant for predicting unknown functions of proteins from their interacting proteins whose functions are known. In the other hand, the prediction of interaction sites has been limited in crystallizing weakly interacting complexes which are transient and do not form the complexes stable enough for obtaining experimental structures by crystallization or even NMR for the most important protein-protein interactions. This work reports the calculation of 3D surface patches of complex structures and their properties and a machine learning approach to build a predictive model for the 3D surface patches in interaction and non-interaction sites using support vector machine. To overcome classification problems for class imbalanced data, we employed an under-sampling technique. 9 properties of the patches were calculated from amino acid compositions and secondary structure elements. With 10 fold cross validation, the predictive model built from SVM achieved an accuracy of 92.7% for classification of 3D patches in interaction and non-interaction sites from 147 complexes.

• Mass Spectrometry Letters
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• v.7 no.1
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• pp.16-20
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• 2016

Characterization of intact protein structures in the gas phase using electrospray ionization combined with ion mobility mass spectrometry has become an important tool of research. However, the biophysical properties that govern the structures of protein ions in the gas phase remain to be understood. Here, we investigated the impact of host-guest complexation of ubiquitin (Ubq) with macrocyclic host molecules, cucurbit[n]urils (CB[n]s, n = 6, 7), on its structure in the gas phase. We found that CB[n] complexation induces the formation of compact Ubq ions. Both CB[6] and CB[7] exhibited similar effects despite differences in their binding properties in solution. In addition, CB[n] attachment prevented Ubq from unfolding by collisional activation. Based on the experimental results, we suggest that CB[n]s prevent unfolding of Ubq during transfer to the gas phase to promote the formation of compact protein ions. Furthermore, interaction with positively charged residues per se is suggested to be the most important factor for the host-guest complexation effect.

• Food Science of Animal Resources
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• v.39 no.4
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• pp.576-584
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• 2019

This study was performed to evaluate the physicochemical properties of myofibrillar protein (MP) gels containing pork skin gelatin at different salt concentrations. MP gels were prepared to the different salt levels (0.15, 0.30, and 0.45 M) with or without 1.0% of pork skin gelatin. Cooking yield (CY), gel strength, shear stress were measured to determine the physical properties, and SDS-polyacrylamide gel electrophoresis, scanning electron microscopy, fourier transform infrared spectroscopy, sulfhydryl group and protein surface hydrophobicity was performed to figure out the structural changes among the proteins. The addition of gelatin into MP increased CYs and shear stress. MP at 0.45 M salt level had the highest CY and shear stress, as compared to MPs at lower salt concentrations. As the salt concentration of MP gels increased, the microstructure became the compact and wet structures, and decreased the amount of ${\alpha}-helix$/unordered structures and ${\beta}-sheet$. MP with gelatin showed a decreased amount of ${\alpha}-helix$/unordered structures and ${\beta}-sheet$ compared to MP without gelatin. The addition of gelatin to MP did not affect the sulfhydryl group, but the sulfhydryl group decreased as increased salt levels. MP mixtures containing gelatin showed a higher hydrophobicity value than those without gelatin, regardless of salt concentration. Based on these results, the addition of gelatin increased viscosity of raw meat batter and CY of MP gels for the application to low salt meat products.