• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.212-216
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• 2015

Oseltamivir, also known as Tamifu, is an inhibitor of neuraminidase protein which plays an essential role in proliferation and replication of influenza virus. Binding to the active site of neuraminidase, the oseltamivir prevents the protein from enzyme reaction. Conformational change of the protein(neuraminidase) should be accompanied by the enzyme reaction, but the drug inhibits the protein to deform. In this study, we examine the influence of oseltamivir on protein's conformational change in the structural and mechanical point of view. Finite element analysis of the protein can be an useful approach to investigate the influence of oseltamivir on the deformation of a protein. We suggest the finite element based protein model, and then perform the linear static analysis with the displacement loading condition based on the first two largest motion which can be obtained from the normal mode analysis. The results show that it takes more energy to change shape of the protein with an oseltamivir attached than the protein without an oseltamivir.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.265-271
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• 2004

The interaction network of protein -protein plays an important role to understand the various biological functions of cells. Currently, the high -throughput experimental techniques (two -dimensional gel electrophoresis, mass spectroscopy, yeast two -hybrid assay) provide us with the vast amount of data for protein-protein interaction at the proteome scale. In order to recognize the role of each protein in their network, the efficient bioinformatical and computational analysis methods are required. We propose a systematic and mathematical method which can analyze the protein -protein interaction network rigorously and enable us to capture the biological and physical essence of a topological character and stability of protein -protein network, and sensitivity of each protein along the biological pathway of their network. We set up a Laplacian matrix of spectral graph theory based on the protein-protein network of yeast proteome, and perform an eigenvalue analysis and apply a perturbation method on a Laplacian matrix, which result in recognizing the center of protein cluster, the identity of hub proteins around it and their relative sensitivities. Identifying the topology of protein -protein network via a Laplacian matrix, we can recognize the important relation between the biological pathway of yeast proteome and the formalism of master equation. The results of our systematic and mathematical analysis agree well with the experimental findings of yeast proteome. The biological function and meaning of each protein cluster can be explained easily. Our rigorous analysis method is robust for understanding various kinds of networks whether they are biological, social, economical...etc

• Nutrition Research and Practice
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• v.4 no.5
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• pp.375-382
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• 2010

The precise effects of protein intake on fractional synthesis rate (FSR) of muscle protein are still under debate. The sample size of these studies was small and the conclusions in young and elderly subjects were inconsistent. To assess the effect of dietary protein intake on the FSR level, we conducted a meta-analysis of controlled protein intake trials. Random-effects models were used to calculate the weighted mean differences (WMDs). Ten studies were included and effects of short-term protein intake were evaluated. In an overall pooled estimate, protein intake significantly increased the FSR (20 trials, 368 participants; WMD: 0.025%/h; 95%CI: 0.019-0.031; P < 0.0001). Meta-regression analysis suggested that the protein dose was positively related to the effect size (regression coefficient = 0.108%/h; 95%CI: 0.035, 0.182; P = 0.009). A subgroup analysis indicated that protein intake significantly increased FSR when the protein dose was ${\leq}$ 0.80 g/kg BW (16 trials, 308 participants; WMD: 0.027%/h; 95%CI: 0.019-0.031; P < 0.0001), but did not affect FSR when the protein dose was > 0.80 g/kg BW (4 trials, 60 participants; WMD: 0.016%/h; 95%CI: 0.004-0.029; P = 0.98). In conclusion, this study is the first integrated results showing that a short-term protein intake is effective at improving the FSR of muscle protein in the healthy elderly as well as young subjects. This beneficial effect seems to be dose-dependent when the dose levels of protein range from 0.08 to 0.80 g/kg BW.

• Journal of Life Science
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• v.14 no.6 s.67
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• pp.997-1002
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• 2004

This paper deals with the WASPIFA (Web-based Assistant System for Protein-protein Interaction and Function Analysis) system that can provide the comprehensive information on Protein-protein interaction and function concerned with function analysis. Different from existing systems for protein function and protein-protein interaction analysis, which provide fragmentary information restricted to specific field, our system furnishes end-user with comprehensive and synthetic information on the input sequence to be analyzed, including function and annotation information, domain information, and interaction relationship information. The synthetic information that our system contains as local databases has been extracted from many resources related to function, annotation, motif and domain by various pre-processing. Employing our system, end-users can evaluate and judge the synthetic results to do protein interaction and function analysis effectively. In addition, the WASPIFA system is equipped with automatic system management and data update function that facilitates system manager to maintain and manage it efficiently.

• BMB Reports
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• v.37 no.1
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• pp.45-52
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• 2004

The goal of interaction proteomics that studies the protein-protein interactions of all expressed proteins is to understand biological processes that are strictly regulated by these interactions. The availability of entire genome sequences of many organisms and high-throughput analysis tools has led scientists to study the entire proteome (Pandey and Mann, 2000). There are various high-throughput methods for detecting protein interactions such as yeast two-hybrid approach and mass spectrometry to produce vast amounts of data that can be utilized to decipher protein functions in complicated biological networks. In this review, we discuss recent developments in analytical methods for large-scale protein interactions and the future direction of interaction proteomics.

• Genomics & Informatics
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• v.18 no.4
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• pp.39.1-39.8
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• 2020

Alzheimer's disease (AD) is a chronic, progressive brain disorder that slowly destroys affected individuals' memory and reasoning faculties, and consequently, their ability to perform the simplest tasks. This study investigated the hub genes of AD. Proteins interact with other proteins and non-protein molecules, and these interactions play an important role in understanding protein function. Computational methods are useful for understanding biological problems, in particular, network analyses of protein-protein interactions. Through a protein network analysis, we identified the following top 10 hub genes associated with AD: PTGER3, C3AR1, NPY, ADCY2, CXCL12, CCR5, MTNR1A, CNR2, GRM2, and CXCL8. Through gene enrichment, it was identified that most gene functions could be classified as integral to the plasma membrane, G-protein coupled receptor activity, and cell communication under gene ontology, as well as involvement in signal transduction pathways. Based on the convergent functional genomics ranking, the prioritized genes were NPY, CXCL12, CCR5, and CNR2.

• Advances in nano research
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• v.13 no.5
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• pp.487-497
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• 2022

This study investigates the stability of protein tissues regarding the vibration analysis based on the classical beam theory coupled with the nonlocal elasticity theory concerning the exercise impact. As reported in the previous research, four different types of protein tissues are supposed, and the influence of sports training is investigated. The protein tissues are made of protein fibers surrounded by an elastic foundation. The exercise enhances the muscle area and plays an essential role in the stability and strength of protein and muscle tissues. The results are examined in detail to examine the impact of different parameters on the stability of nano protein fibers.

• Journal of Life Science
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• v.18 no.3
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• pp.318-322
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• 2008

This paper deals with an efficient management and automatic update sub-system for WASPIFA (Web-based Assistant System for Protein-protein Interaction and Function Analysis) system that had been developed in the past and now provides the comprehensive information on protein-protein interaction and protein function. Protein interacting data has increased exponentially, so that it costs enormous time and effort. In other words, it is actually impossible to manually update and manage an analysis system based on protein interacting data. Even though there exists a good analysis system, it could be useless if it was able to be updated timely and managed properly. Unfortunately, in most cases, biologists without professional knowledge on their analysis systems have to cope with a great difficulty in running them. In this respect, the efficient management and automatic update subsystem of protein interacting and its related data has been developed to facilitate experimental biologists as well as bioinformaticians to update and manage the WASPIFA system.

• Journal of the East Asian Society of Dietary Life
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• v.19 no.1
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• pp.45-51
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• 2009

In this study, food protein hydrolysates were prepared from six types of food protein: purified meat protein, whole egg protein, casein, isolated soy protein, concentrated rice protein, and gluten. Food proteins were hydrolyzed with pepsin and ethanol (80%)-soluble fractions of pepsin hydrolysates were employed for analysis. The products were colorless and odorless powders with low fat content and good solubility. The MW (molecular weight) of the protein hydrolysates was confirmed to be $200{\sim}1,800$ via gel filtration. Free amino acid contents accounted for less than 5% of the samples. The results of our amino acid analysis revealed that all food protein hydrolysates preserved their original amino acid compositions and nutritional values of their source proteins with highly pure oligopeptide mixtures. These results show that the food protein hydrolysates prepared in these investigations should prove excellent dietary nitrogen sources for a variety of applications.

• Advances in nano research
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• v.13 no.6
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• pp.561-574
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• 2022

The stability of protein tissues and protein fibers in the human muscle is investigated in the presented paper. The protein fibers are modeled via tube structures embedded in others proteins fibers like the elastic substrate. Physical sport and physical exercise play an important role in the stability of synthesis and strength of the protein tissues. In physical exercise, the temperature of the body increases, and this temperature change impacts the stability of the protein tissues, which is the aim of the current study. The mathematical simulation of the protein tissues is done based on the mechanical sciences, and the protein fibers are modeled via wire structures according to the high-order theory beams. The thermal stress due to the conditions of the sport is applied to the nanoscale protein fibers, then the stability regarding the frequency analysis is investigated. Finally, the impact of temperature change, physical exercise, and small-scale parameters on the stability of the protein tissues are examined in detail.