• Journal of Computing Science and Engineering
• /
• v.11 no.4
• /
• pp.111-120
• /
• 2017

Post-translational modifications (PTMs) of proteins play substantial roles in the gene regulation of cell physiological functions and in the generation of major diseases. However, the majority of existing studies only explored a certain PTM of proteins, while very few have investigated the PTMs of two or more domains and the effects of their interactions. In this study, after collecting data regarding a large number of breast cancer-related and validated PTMs, a sequence and domain analysis of breast cancer proteins was carried out using bioinformatics methods. Then, protein-protein interaction network-related tools were applied in order to determine the crosstalks between the PTMs of the proteins. Finally, statistical and functional analyses were conducted to identify more modification sites of domains and proteins that may interact with at least two or more PTMs. In addition to exploring the associations between the interactive effects of PTMs, the present study also provides important information that would allow biologists to further explore the regulatory pathways of biological functions and related diseases.

• Applied Chemistry for Engineering
• /
• v.31 no.1
• /
• pp.49-56
• /
• 2020

In this study, surface modification of CaCO₃ nanoparticles by a silane coupling agent propyltrimethoxysilane (PTMS) was conducted and the effect of surface hydrophobicity on the stability of foam and emulsion was studied in order to test the potential applicability as a foam stabilizer or an emulsifier. The surface modification of CaCO₃ nanoparticles by PTMS was confirmed by FT-IR, DSC and TGA analysis. The atomic concentration of CaCO₃ particle surface treated by PTMS has been also identified by using XRD and XPS analyses. Both floating tests and contact angle measurements were also performed to examine the effect of PTMS concentration on the surface modification of CaCO₃ nanoparticles.

• Proceedings of the Korean Institute of Navigation and Port Research Conference
• /
• 2004.08a
• /
• pp.167-176
• /
• 2004

The authors have newly developed the “Port Traffic Management System (PTMS)”. The PTMS provides each ship with the detailed planned routes of all the ships entering/leaving the port. This system also has a function to predict the encounter situations between own ship and other ships in the future. Based on information of the present positions, speeds and planned routes of the own ship and other ships, it is possible to predict when and where the own ship will have dangerous encounters with other ships in the future. The software of PTMS was developed from 2001. Then onboard experiments using small training ships equipped with actual AIS were performed in June 2003. From the results of these onboard experiments, the usefulness of PTMS was clarified. In addition to these onboard experiments, the effectiveness of PTMS was confirmed by comprehensive simulator experiments. In the simulator experiments, captains/pilot maneuvered a training ship/container ship in congested waters using PTMS. [t was assumed that all ships have PTMS and send their planned routes. After the simulator experiments, captains/pilot suggested that it is very beneficial if the optimal route of own ship can be automatically calculated. In response to this suggestion, software to calculate the optimal route of own ship using Dynamic Programming was developed. This software calculates the minimum time route from the present position to the destination keeping the danger of collision against other ships under predetermined level. From the result of calculations for multi-encounter situations, it was confirmed that the developed software can provide safe and time-saving route.

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
• /
• 2006.04a
• /
• pp.216-219
• /
• 2006

Water retention curve (WRC), one of soil hydraulic properties, is often approximated by property-transfer models (PTMs). Using the PTMs, we can estimate the WRCs from other physical properties such as particle-size distribution (PSD). The objective of this work was to investigate the performance of two PTMs with different origins for numerical simulations on transport of Benzo[a]pyrene in a soil. To do this, we chose both PTMs with different origins, i.e., (1) the lognormal distribution model (L anti NL models), and (2) the modified $Kov\'{a}cs$ model (MK model). The MK model showed tile worse performance in estimation of the WRCs. When transport of B[a]P was simulated, the MK model predicted to move farther than the L and NL models did, indicating that transport of B[a]P in a soil can be greatly influenced by the choice of PTMs.

• MALSORI
• /
• no.50
• /
• pp.139-150
• /
• 2004

A Phonetic Tied-Mixture (PTM) model has been proposed as a way of efficient decoding in large vocabulary continuous speech recognition systems (LVCSR). It has been reported that PTM model shows better performance in decoding than triphones by sharing a set of mixture components among states of the same topological location[5]. In this paper we propose a Phonetic Tied-Mixture Syllable (PTMS) model which extends PTM technique up to syllables. The proposed PTMS model shows 13% enhancement in decoding speed than PTM. In spite of difference in context dependent modeling (PTM : cross-word context dependent modeling, PTMS : word-internal left-phone dependent modeling), the proposed model shows just less than 1% degradation in word accuracy than PTM with the same beam width. With a different beam width, it shows better word accuracy than in PTM at the same or higher speed.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2005.09a
• /
• pp.331-336
• /
• 2005

Post translational modifications (PTMs) discovery is an important problem in proteomic. In the past, people discover PTMs by Tandem Mass Spectrometer based on ‘bottom-up’ strategy. However, such strategy suffers from the problem of failing to discover all PTMs. Recently, due to the improvement in proteomic technology, Taylor et al. proposed a database software to discover PTMs with ‘topdown’ strategy by FTMS, which avoids the disadvantages of ‘bottom-up’ approach. However, their proposed algorithm runs in exponential time, requires a database of proteins, and needs prior knowledge about PTM sites. In this paper, a new algorithm is proposed which can work without a protein database and can identify modifications in polynomial time. Besides, no prior knowledge about PTM sites is needed.

• BMB Reports
• /
• v.51 no.6
• /
• pp.265-273
• /
• 2018

Tau protein is encoded in the microtubule-associated protein tau (MAPT) gene and contributes to the stability of microtubules in axons. Despite of its basic isoelectric point and high solubility, tau is often found in intraneuronal filamentous inclusions such as paired helical filaments (PHFs), which are the primary constituent of neurofibrillary tangles (NFTs). This pathological feature is the nosological entity termed "tauopathies" which notably include Alzheimer's disease (AD). A proteinaceous signature of all tauopathies is hyperphosphorylation of the accumulated tau, which has been extensively studied as a major pharmacological target for AD therapy. However, in addition to phosphorylation events, tau undergoes a number of diverse posttranslational modifications (PTMs) which appear to be controlled by complex crosstalk. It remains to be elucidated which of the PTMs or their combinations have pro-aggregation or anti-aggregation properties. In this review, we outline the consequences of and communications between several key PTMs of tau, such as acetylation, phosphorylation, and ubiquitination, focusing on their roles in aggregation and degradation. We place emphasis on the structure of tau protofilaments from the human AD brain, which may be good targets to modulate etiological PTMs which cause tau aggregation.

• Toxicological Research
• /
• v.29 no.2
• /
• pp.81-86
• /
• 2013

Toxicoproteomics integrates the proteomic knowledge into toxicology by enabling protein quantification in biofluids and tissues, thus taking toxicological research to the next level. Post-translational modification (PTM) alters the three-dimensional (3D) structure of proteins by covalently binding small molecules to them and therefore represents a major protein function diversification mechanism. Because of the crucial roles PTM plays in biological systems, the identification of novel PTMs and study of the role of PTMs are gaining much attention in proteomics research. Of the 300 known PTMs, protein acylation, including lysine formylation, acetylation, propionylation, butyrylation, malonylation, succinylation, and crotonylation, regulates the crucial functions of many eukaryotic proteins involved in cellular metabolism, cell cycle, aging, growth, angiogenesis, and cancer. Here, I reviewed recent studies regarding novel types of lysine acylation, their biological functions, and their applicationsin toxicoproteomics research.

• Proceedings of KOSOMES biannual meeting
• /
• 2001.05a
• /
• pp.105-133
• /
• 2001

World trade has been increasing continuously in total volume, on the other hand, environmental protection on sea and conservation of fishery resources has been rising up the major issue. All of the world are pushing their efforts two major purposes to the full, one is taking competitive place in marine transportation throughout the world and another Is environment protection. Pusan Port as world leading Port put its all effort in bring more ocean going vessels and securing their traffic route by providing them more information related marine traffics through PTMS in port. During two years of operation, statistics of marine traffic accidents showed that many dynamic casualties such as collisions, groundings, and rammings has been decreased. However, due to increasing cargo volume, limited water area and unpredictable weather condition, potential risks still exist high. In this paper, in order to maximize the efficiency of PTMS and reduce various risks in the future, we examine risk factors over operational results and experience, and propose reasonable operational methods of PTMS.

• Mass Spectrometry Letters
• /
• v.3 no.2
• /
• pp.39-42
• /
• 2012

Phosphorylation and glycosylation are two of the most important and widespread post-translational modifications (PTMs) in an organism. Proteomics analysis of the PTMs has been challenged by low stoichiometry of the modified proteins and suppression effects by high abundance proteins, typically no-functional house-keeping proteins. In this study, a novel method was applied for not only isolating PTM peptides from intact peptides but also concurrently characterizing of glyco- and phosphoproteome using electrostatic repulsion hydrophilic interaction chromatography (ERLIC) packed with silica coated by crosslinked polyethyleneimine. For 2 mg tryptic digest of mouse proteome of epicardial adipose tissue with fat diet, 802 N-glycosylated peptides of 316 glycoproteins and 159 phosphorylated peptides of 75 phosphoproteins were identified using HPLC chip/quadrupole time-of-flight (Q-OF) tandem mass spectrometer.