• The KIPS Transactions:PartD
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• v.12D no.1 s.97
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• pp.51-62
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• 2005

After figuring out the function of an amino acid sequence, we can infer the function of the other amino acids that have similar sequence composition. Besides, it is possible that we alter protein whose function we know, into useful protein using genetic engineering method. In this process. an original protein amino sequence produces various protein sequences that have different sequence composition. Here, a systematic technique is needed to manage protein version sequences and reference data of those sequences. Thus, in this paper we proposed a technique of managing protein version sequences based on local sequence alignment and a technique of managing protein historical reference data using Trigger This method automatically determines the similarity between an original sequence and each version sequence while the protein version sequences are stored into database. When this technique is employed, the storage space that stores protein sequences is also reduced. After storing the historical information of protein and analyzing the change of protein sequence, we expect that a new useful protein and drug are able to be discovered based on analysis of version sequence.

• International Journal of Contents
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• v.9 no.4
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• pp.11-15
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• 2013

"Protein Folding Problem" is considered to be one of the "Great Challenges of Computer Science" and prediction of disordered protein is an important part of the protein folding problem. Machine learning models can predict the disordered structure of protein based on its characteristic of "learning from examples". Among many machine learning models, we investigate the possibility of multilayer perceptron (MLP) as the predictor of protein disorder. The investigation includes a single hidden layer MLP, multi hidden layer MLP and the hierarchical structure of MLP. Also, the target node cost function which deals with imbalanced data is used as training criteria of MLPs. Based on the investigation results, we insist that MLP should have deep architectures for performance improvement of protein disorder prediction.

• BMB Reports
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• v.33 no.4
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• pp.289-293
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• 2000

Annexin I is a 37 kDa member of the annexin family of calcium-dependent phospholipid binding proteins. Annexin I plays regulatory roles in various cellular processes including cell proliferation and differentiation. Recently we found that annexin I is a heat shock protein (HSP) and displays a chaperone-like function. In this paper we investigated the function of annexin I as an ATPase using 1 to 32 amino acids deleted annexin I (${\Delta}-annexin$ I). ${\Delta}-Annexin$ I hydrolyzed ATP as determined by thin layer chromatography. The ability of ATP hydrolysis was inhibited by ADP, GTP and GDP, but not by the AMP, GMP and cAMP. In view of the ATP hydrolyzing function of HSP, the results support the function of annexin I as a HSP.

• 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.

• Korean Journal of Exercise Nutrition
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• v.23 no.2
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• pp.34-44
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• 2019

[Purpose] The composition of protein supplements, the consumption timing immediately before and after resistance exercise training (RET), and the quantity of protein supplementation may be important factors for the im-provement of muscle mass and function. Although these factors should be considered comprehensively for effective improvement of muscular function in protein supplementation, relatively few studies have focused on this area. Therefore, this study was designed to investigate whether a protein blend supplement before and after resistance exercise for 12 weeks would be effective in increasing muscular function. [Methods] In total, 18 participants were randomly assigned to a placebo (PLA) or protein blend supplement (PRO) group. All subjects followed the same training routine 3 times per week for 12 weeks, taking placebo or protein supplements immediately before and after each exercise session. The protein supplement consisted of 40 g of blend protein, including hydrolyzed whey protein. The RET consisted of lower body (barbell squat, dead lift, seated leg extension, and lying leg curl) and upper body (bench press, barbell rowing, preacher bench biceps curl, and dumbbell shoulder press) exercises. A repetition was defined as three sets of 10-12 times with 80% of one repetition maximum (1RM). [Results] Although the PRO group had a lower protein intake in terms of total food intake than the PLA group, the mean changes in muscle circumference, strength, and exercise volume increased, especially at week 12, compared to the PLA group. [Conclusion] These results suggest that the composition and timing of protein intake are more important than the total amount.

• BMB Reports
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• v.52 no.5
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• pp.304-311
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• 2019

The cytoplasmic FMR1-interacting protein family (CYFIP1 and CYFIP2) are evolutionarily conserved proteins originally identified as binding partners of the fragile X mental retardation protein (FMRP), a messenger RNA (mRNA)-binding protein whose loss causes the fragile X syndrome. Moreover, CYFIP is a key component of the heteropentameric WAVE regulatory complex (WRC), a critical regulator of neuronal actin dynamics. Therefore, CYFIP may play key roles in regulating both mRNA translation and actin polymerization, which are critically involved in proper neuronal development and function. Nevertheless, compared to CYFIP1, neuronal function and dysfunction of CYFIP2 remain largely unknown, possibly due to the relatively less well established association between CYFIP2 and brain disorders. Despite high amino acid sequence homology between CYFIP1 and CYFIP2, several in vitro and animal model studies have suggested that CYFIP2 has some unique neuronal functions distinct from those of CYFIP1. Furthermore, recent whole-exome sequencing studies identified de novo hot spot variants of CYFIP2 in patients with early infantile epileptic encephalopathy (EIEE), clearly implicating CYFIP2 dysfunction in neurological disorders. In this review, we highlight these recent investigations into the neuronal function and dysfunction of CYFIP2, and also discuss several key questions remaining about this intriguing neuronal protein.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.64 no.4
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• pp.373-383
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• 2019

The objectives of this study were to compare the protein expression patterns and degrees and identify the protein function of disomic addition lines (DAs) in Leymus racemosus, in order to improve the quality of wheat. Upon SDS-PAGE, L. racemosus showed two major protein bands whereas Chinese Spring (CS) had four major protein bands of high molecular weight. The DA(s) generally showed a similar protein expression pattern to that of CS, because 42 chromosomes were from CS and two chromosomes were from L. racemosus. However, only the L.r[J] line showed two protein bands of between 15 and 20 kDa, like L. racemosus. Image analysis based on 2-DE revealed that L.r[F] had the most upregulated protein spots, whereas L.r[N] had the least upregulated protein spots. For L.r[I], the frequency of the downregulated protein spots was higher than that of the upregulated ones. Using MALDI-TOF MS, the protein function was identified for each protein spot on the 2-DE polyacrylamide gel. The protein spots were classified into 11 groups according to protein function. Among the 11 groups, most protein spots of the DA(s) were identified as proteins related to metabolism. Additionally, unique protein spots of the DA(s) were related to abiotic stressors such as cold and heat. Those proteins are useful for improving wheat quality with resistance against abiotic stressors.

• BMB Reports
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• v.38 no.3
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• pp.266-274
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• 2005

High temperature requirement A (HtrA) and its homologues constitute the HtrA familiy proteins, a group of heat shock-induced serine proteases. Bacterial HtrA proteins perform crucial functions with regard to protein quality control in the periplasmic space, functioning as both molecular chaperones and proteases. In contrast to other bacterial quality control proteins, including ClpXP, ClpAP, and HslUV, HtrA proteins contain no regulatory components or ATP binding domains. Thus, they are commonly referred to as ATP-independent chaperone proteases. Whereas the function of ATP-dependent chaperone-proteases is regulated by ATP hydrolysis, HtrA exhibits a PDZ domain and a temperature-dependent switch mechanism, which effects the change in its function from molecular chaperone to protease. This mechanism is also related to substrate recognition and the fine control of its function. Structural and biochemical analyses of the three HtrA proteins, DegP, DegQ, and DegS, have provided us with clues as to the functional regulation of HtrA proteins, as well as their roles in protein quality control at atomic scales. The objective of this brief review is to discuss some of the recent studies which have been conducted regarding the structure and function of these HtrA proteins, and to compare their roles in the context of protein quality control.

• Journal of the Korean Magnetic Resonance Society
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• v.2 no.2
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• pp.131-140
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• 1998

The calcium-induced structural changes in the skeletal muscle regulatory protein troponin C (NTnC) involve a transition from a ‘closed’to an ‘open’structure with the concomitant exposure of a large hydrophobic interaction site for target proteins. Structural studies have served to define this conformational change and elucidate the mechanism of the linkage between calcium binding and the induced structural changes. There are now several structures of NTnC available from both NMR and X-ray crystallography. Comparison of the calcium bound structures reveals differences in the level of opening. We have considered the concept of a flexible open state of NTnC as a possible explanation for this apparent discrepancy. We also present simulations of the closed-to-open transition which are in agreement with the flexibility concept and with experimental energetics data.

• BMB Reports
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• v.31 no.6
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• pp.542-547
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• 1998

The main function of adipocytes in various species is to store nutrient energy in the form of triglycerides, and this function may he closely related with hormonal signaling through the plasma membrane of adipocytes. Using SDS-PAGE, two-dimensional gel electrophoresis, and a membrane biotinylation technique, we have identified a 55KDa protein (55K protein) from the plasma membrane fraction of adipocytes, with an isoelectric point (pI) of 8.1-8.3. However, this 55K protein was not observed with a two-dimensional gel electrophoresis carried out on plasma membrane fractions prepared from the liver, heart, and kidney tissues. An analysis of the 12 amino acids sequence at the N-terminal of the 55K protein showed that it has a similar sequence to that of bovine serum albumin.