• Journal of the Korean Magnetic Resonance Society
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• v.22 no.1
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• pp.18-25
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• 2018

Replication protein A (RPA) is an essential single-stranded DNA binding protein in DNA processing. It is known that N terminal domain of RPA70 (RPA70N) recruits various protein partners including damage-response proteins such as p53, ATRIP, Rad9, and MRE11. Although the common binding residues of RPA70N were revealed, dynamic properties of the protein are not studied yet. In this study, we measured $^{15}N$ relaxation parameters ($T_1,\;T_2$ and heteronuclear NOE) of human RPA70N and analyzed them using model-free analysis. Our data showed that the two loops near the binding site experience fast time scale motion while the binding site does not. It suggests that the protein binding surface of RPA70N is mostly rigid for minimizing entropy cost of binding and the loops can experience conformational changes.

• JSTS:Journal of Semiconductor Technology and Science
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• v.7 no.3
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• pp.151-160
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• 2007

We report the label-free biomolecules detection based on nanomechanical micro cantilevers operated in dynamic mode for detection of two marker proteins (myoglobin and creatin kinase-MB (CK-MB)) of acute myocardical infarctions. When the specific binding between the antigen and its antibody occurred on the fuctionalized microcantilever surface, mechanical response (i.e. resonant frequency) of microcantilevers was changed in lower frequency range. We performed the label-free biomolecules detection of myoglobin and CK-MB antigen in the low concentration (clinical threshold concentration range) as much as 1 ng/ml from measuring the dynamic response change of micro cantilevers caused by the intermolecular force. Moreover, we estimate the surface stress on the dynamic microcantilevers generated by specific antibody-antigen binding. It is suggested that our dynamic microcantilevers may enable one to use the sensitive label-free biomolecules detection for application to the disease diagnosis system based on mechanical immuno-sensor.

• Journal of the Korean Magnetic Resonance Society
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• v.17 no.2
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• pp.76-80
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• 2013

The TCP domain is a DNA-binding domain present in plant transcription factors and has a similar structural feature to the bHTH motif of eukaryotic transcription factors. The imino proton exchange study has been performed for the DNA duplex containing the consensus DNA-binding site for the AtTCP11 transcription factor. The first two base pairs in the consensus 5'-GTGGG-3' sequence are relatively very unstable but lead to greater stabilization of the neighboring two G C base pairs. These unique dynamic features of the five base pairs in the consensus DNA sequence might play crucial roles in the effective DNA binding of the AtTCP11 protein.

• KIPS Transactions on Computer and Communication Systems
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• v.3 no.12
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• pp.455-462
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• 2014

In recent years, various services in mobile environments due to the growth of mobile devices and related techniques like wireless networks. Furthermore, as the increasing communication traffic in cellular networks has become a new significant issue, many studies for device-to-device(D2D) communication and D2D-based cooperative services have been performed recently. In this paper, we design a smart agent system for D2D-based cooperative services and propose a dynamic service binding method based on service ontology. We classify roles of mobile devices for cooperative services by defining three types of smart agents, and construct a knowledge base in order to describe properties of 'service' unit. The proposed knowledge model, D2D cooperative service ontology, can enable a autonomous cooperative services between mobile devices by binding a requested service to the appropriate member device according to the real-time context in mobile environments.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.2
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• pp.52-57
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• 2014

The TCP domain is a DNA-binding domain present in plant transcription factors and plays important roles in various biological functions. The hydrogen exchange rate constants of the imino protons were determined for the three DNA duplexes containing the DNA-binding sites for the TCP11, TCP15, and TCP20 transcription factors using NMR spectroscopy. The M11 duplex displays unique hydrogen exchange property of the five base pairs in the first binding site (5'-GTGGG-3'). However, the M15 and M20 duplexes lead to clear changes in thermal stabilities of these five base pairs. The unique dynamic features of the five base pairs in the first binding site might play crucial roles in the sequence-specific DNA binding of the class I TCP transcription factors.

• Molecules and Cells
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• v.45 no.7
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• pp.444-453
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• 2022

Multivalent macromolecular interactions underlie dynamic regulation of diverse biological processes in ever-changing cellular states. These interactions often involve binding of multiple proteins to a linear lattice including intrinsically disordered proteins and the chromosomal DNA with many repeating recognition motifs. Quantitative understanding of such multivalent interactions on a linear lattice is crucial for exploring their unique regulatory potentials in the cellular processes. In this review, the distinctive molecular features of the linear lattice system are first discussed with a particular focus on the overlapping nature of potential protein binding sites within a lattice. Then, we introduce two general quantitative frameworks, combinatorial and conditional probability models, dealing with the overlap problem and relating the binding parameters to the experimentally measurable properties of the linear lattice-protein interactions. To this end, we present two specific examples where the quantitative models have been applied and further extended to provide biological insights into specific cellular processes. In the first case, the conditional probability model was extended to highlight the significant impact of nonspecific binding of transcription factors to the chromosomal DNA on gene-specific transcriptional activities. The second case presents the recently developed combinatorial models to unravel the complex organization of target protein binding sites within an intrinsically disordered region (IDR) of a nucleoporin. In particular, these models have suggested a unique function of IDRs as a molecular switch coupling distinct cellular processes. The quantitative models reviewed here are envisioned to further advance for dissection and functional studies of more complex systems including phase-separated biomolecular condensates.

• BMB Reports
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• v.50 no.2
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• pp.55-57
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• 2017

Toll-like receptor 4 (TLR4) together with MD2, one of the key pattern recognition receptors for a pathogen-associated molecular pattern, activates innate immunity by recognizing lipopolysaccharide (LPS) of Gram-negative bacteria. Although LBP and CD14 catalyze LPS transfer to the TLR4/MD2 complex, the detail mechanisms underlying this dynamic LPS transfer remain elusive. Using negative-stain electron microscopy, we visualized the dynamic intermediate complexes during LPS transfer-LBP/LPS micelles and ternary CD14/LBP/LPS micelle complexes. We also reconstituted the entire cascade of LPS transfer to TLR4/MD2 in a total internal reflection fluorescence (TIRF) microscope for a single molecule fluorescence analysis. These analyses reveal longitudinal LBP binding to the surface of LPS micelles and multi-round binding/unbinding of CD14 to single LBP/LPS micelles via key charged residues on LBP and CD14. Finally, we reveal that a single LPS molecule bound to CD14 is transferred to TLR4/MD2 in a TLR4-dependent manner. These discoveries, which clarify the molecular mechanism of dynamic LPS transfer to TLR4/MD2 via LBP and CD14, provide novel insights into the initiation of innate immune responses.

• Journal of KIISE:Computer Systems and Theory
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• v.30 no.5_6
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• pp.307-318
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• 2003

In this paper, we design and construct a TMO object group that provides the guaranteed real-time services in the distributed object computing environments, and verify execution power of its model for the correct distributed real-time services. The TMO object group we suggested is based on TINA's object group concept. This model consists of TMO objects having real-time properties and some components that support the object management service and the real-time scheduling service in the TMO object group. Also TMO objects can be duplicated or non-duplicated on distributed systems. Our model can execute the guaranteed distributed real-time service on COTS middlewares without restricting the specially ORB or the of operating system. For achieving goals of our model. we defined the concepts of the TMO object and the structure of the TMO object group. Also we designed and implemented the functions and interactions of components in the object group. The TMO object group includes the Dynamic Binder object and the Scheduler object for supporting the object management service and the real-time scheduling service, respectively The Dynamic Binder object supports the dynamic binding service that selects the appropriate one out of the duplicated TMO objects for the clients'request. And the Scheduler object supports the real-time scheduling service that determines the priority of tasks executed by an arbitrary TMO object for the clients'service requests. And then, in order to verify the executions of our model, we implemented the Dynamic Binder object and the Scheduler object adopting the binding priority algorithm for the dynamic binding service and the EDF algorithm for the real-time scheduling service from extending the existing known algorithms. Finally, from the numerical analyzed results we are shown, we verified whether our TMO object group model could support dynamic binding service for duplicated or non-duplicated TMO objects, also real-time scheduling service for an arbitrary TMO object requested from clients.

• Textile Coloration and Finishing
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• v.5 no.3
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• pp.182-187
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• 1993

The binding isotherms of Methylene Blue with Poly(vinyl pyrrolidone) (PVP) were determined in a Mcllvaine buffer of pH 8.0 at 3$0^{\circ}C$ by a dynamic dialysis methods. The isotherms showed a partition binding which was increase linearly with the increase of free dye concentration in solution. The Scatchard plots for Poly(vinyl pyrrolidone)-Methylene Blue gave a constant value. The results were interpreted by the McGhee and von Hippel theory considering non-cooperative binding. The intrinsic binding constant k, for Poly(vinyl pyrrolidone)-Methylene Blue was 6.02$\ell$/base mol.

• Proceedings of the Korean Institute of Building Construction Conference
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• 2014.11a
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• pp.156-157
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• 2014

Inorganic binding material was made by recycled resource and its applicability as pile-filling material was examined. The result was that the material had same liquidity with the liquidity of OPC and high reactivity with site soil. According to dynamic/static loading tests by site test-construction, the inorganic binding material met both design bearing capacity and settlement. Since the inorganic binding material showed same or better performance than OPC, the utilization possibility of the inorganic binding material made of recycled resource as pile-filling material was verified.