• 한국자기공명학회논문지
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• 제21권3호
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• pp.109-113
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• 2017

The hepatitis C virus (HCV) internal ribosome entry site (IRES) is an RNA structure located in the 5'-UTR of the HCV RNA genome. The HCV IRES consists of four domains I, II, III, and IV, where domains II - IV are recognized by 40S ribosomal subunit and the domain III is bound to eukaryotic initiation factor 3 (eIF3) for translation initiation. Here, we have characterized the tertiary interaction between an L-/K- rich peptide and the HCV IRES domain IV. To probe the peptide binding interface in RNA, we synthesized $^{13}C$- and $^{15}N$-double labeled RNA and the binding site was identified by using the chemical shift perturbation (CSP) NMR methods. Our results showed that the peptide binds to the upper stem of the IRES domain IV, indicating that the tertiary interaction between the IRES domain IV and the peptide would disrupt the initiation of translation of HCV mRNA by blocking the start codon exposure. This study will provide an insight into the new peptide-based anti-viral drug design targeting HCV IRES RNA.

• Bulletin of the Korean Chemical Society
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• 제30권5호
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• pp.1043-1046
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• 2009

Human protein tyrosine kinase-6 (PTK6) is a member of the non-receptor protein tyrosine kinase family and it is found in two-thirds of all breast tumors. Very recently, we proposed that the SH3 domain of PTK6 interacts with the linker region (Linker) between the SH2 and kinase domains, proving that the interaction between SH3 domain and Linker plays an important role in auto-inhibition mechanism. Residues from 1 to 191 corresponding region of SH3-SH2-Linker (SH32L) of PTK6 was cloned into the pET32a expression vector with Tobbaco etch virus (TEV) protease enzyme site by sequence homology and 3D structural model. The purified PTK6-SH32L was determined as a monomer conformation in solution. The amide proton resonances in the $^{15}N-^{1}H$ 2D-HSQC spectrum suggest that PTK6-SH32L possesses disordered structural region of the flexible/unstructured linker region. In addition, the backbone amide proton chemical shifts of the SH3 domain in the PTK6-SH32L differ from that of the independent domain, indicating that intra-molecular interaction between SH3 and Linker in the PTK6-SH32L is present.

• 한국자기공명학회논문지
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• 제26권3호
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• pp.34-39
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• 2022

The SH3 domain found within a variety of proteins is comprised of generally 60 residues, and participated in protein-protein interactions with proline-rich motifs. Cobll1 was identified as a distinct molecular marker associated with CML progression, and PACSIN2 was discovered a novel Cobll1 binding partner through direct interaction between a SH3 domain of PACSIN2 and three proline-rich motifs of Cobll1. To understand the structural basis of interactions between PACSIN2 and Cobll1, backbone assignments of PACSIN2 SH3 domain were performed. Furthermore, three proline-rich peptides of Cobll1 were titrated to ¹⁵N-labeled PACSIN2 SH3 domain in various ratios. Our chemical shift changes data and conserved SH3 sequence alignment will be helpful to analyze fundamental molecular basis related to the interaction between PACSIN2 and Cobll1.

• 한국정보과학회논문지:컴퓨팅의 실제 및 레터
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• 제11권5호
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• pp.427-435
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• 2005

인터넷 상에 단백질 및 관련 데이터의 축적에 따라, 도메인에 기반하여 단백질의 상호작용을 계산적으로 예측하는 많은 기법들이 제안되었다. 그러나, 대부분의 기법들이 예측에서 낮은 정확도와 복수개의 단백질 쌍에 대한 상호작용 가능성들 간에 순위 정보를 제공하지 못하는 등의 한계로 인하여 실무 적용에 한계를 가지고 있다. 본 논문에서는 도메인 조합 기반 단백질 상호작용 예측 기법을 재평가하고 상호작용하는 것으로 예측되는 복수개의 단백질 쌍들에서 이들의 상호작용 가능성들 간에 순위를 부여하는 방법을 제시한다. 순위 부여 방법은 도메인 조합에 기반한 단백질 상호작용 예측 방법의 틀 내에서 확률 식을 고안하여 제시한다. 제시된 순위 부여 기법을 사용함으로써, 상호작용을 하는 것으로 예측된 단백질 쌍들간에 상호작용 가능성이 좀 더 높은 것을 구별해 낼 수 있다. 또한 순위 부여 기법의 검증 과정에서 학습에 사용된 단백질 집단의 PIP(Primary Interaction Probability)값과 일치된 PIP값을 가지는 단백질 쌍 그룹의 경우에는, 상호작용 확률과 예측 정확도 사이에 상관관계가 존재함을 확인할 수 있었다.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 1998년도 학술발표회
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• pp.12-12
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• 1998

The interaction between the N-terminal domain of enzyme I (EIN) and the histidine-containing phosphocarrier protein HPr of the Escherichia coli phosphoenolpyruvate：sugar phosphotransferase system has been investigated by Isothermal Titration Calorimetry and heteronuclear magnetic resonance spectroscopy.(omitted)

• 한국지진공학회:학술대회논문집
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• 한국지진공학회 1999년도 추계 학술발표회 논문집 Proceedings of EESK Conference-Fall
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• pp.107-112
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• 1999

This paper presents a time domain method for soil-structure interaction analysis for seismic loadings. It is based on the finite element formulation incorporating analytical frequency-dependent infinite elements for the far-field soil. The dynamic stiffness matrices of the far-field region formulated in frequency domain using the present method can be easily transformed into the corresponding matrices in time domain. Hence the response can be analytical computed in time domain. Example analysis has been carried out to verify the present method for an embedded block in a multi-layered half-space. The present methods can be easily extended to the nonlinear analysis since the response analysis is carried out in time domain.

• 한국자기학회:학술대회 개요집
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• 한국자기학회 2015년도 임시총회 및 하계학술연구발표회
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• pp.78-79
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• 2015

We investigate the switching current for various cell diameters and DM interaction. We find that the current density for switching can depend strongly on the cell size when the switching is governed by the domain wall motion. Moreover the switching current density is also strongly influenced by DM interaction. In the presentation, we will discuss the effect of domain wall formation and more various DMI constant on the switching current desity in detail.

• 한국HCI학회:학술대회논문집
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• 한국HCI학회 2009년도 학술대회
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• pp.677-684
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• 2009

다양한 센서 네트워크와 유비쿼터스 기술이 제공되는 지능형 협업 환경은 사용자를 위해 확장된 인터랙션을 제공할 수 있다. 기존의 인터랙션이 사용자와 컴퓨터 머신과의 직접적인 인터랙션이 주를 이룬 반면 새로 확장된 인터랙션은 사용자와 공간과의 인터랙션을, 실질적으로 공간을 구성하는, 관리와 제어가 가능한 구성요소와의 인터랙션을 나타낸다. 본 논문은 이러한 공간 인터랙션을 효과적으로 제공할 수 있도록 하기 위해서 공간 오브젝트를 등록, 인식하고, 특히 사용자의 의도에 맞는 태스크를 지원하기 위해 과거의 인터랙션 정보를 이용한 템플릿 기반 맵핑 알고리즘을 설계한다. 제안된 알고리즘을 이용하는 경우, 공간 오브젝트가 증가함에 따라 템플릿을 검색하여 처리하는데 드는 시스템의 비용이 어느 정도 향상되는지 실험을 통해 분석하도록 하며, 진행되는 모든 공간 인터랙션을 시각적으로 보여주기 위한 그래픽 기반의 도시 방법을 소개하고 결론을 맺는다.

• 대한의생명과학회지
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• 제9권2호
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• pp.105-110
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• 2003

Ankyrins are a ubiquitously expressed family of intracellular adaptor proteins involved in targeting diverse proteins to specialized membrane domains in both the plasma membrane and the endoplasmic reticulum. Canonical ankyrins are 190-220 kDa proteins expressed in most tissues and cell types and comprise a membrane-binding domain (MBD) of 24 ANK repeats, a spectrin-binding domain, a death domain and a C-terminal domain. Rescue studies with ankyrin-B/G chimeras have identified the C-terminal domain of ankyrin-B as the defining domain in specifying ankyrin-B activity, but the function of C-terminal domain of ankyrin-B is, however, not known. We report here that the C-terminal domain of ankyrin-B is capable of interacting with the C-terminal Region of Hsp40. The Hsps are induced not only by heat shock but also by various other environmental stresses. Hsps are also expressed constitutively at normal growth temperatures and have basic and indispensable functions in the life cycle of proteins as molecular chaperones, as well as playing a role in protecting cells from the deleterious stresses. The binding sites required in the interaction between C-terminal domain of ankyrin-B and C-terminal region of Hsp40 were characterized using the yeast two-hybrid system and GST-pull down assay. The interaction between ankyrin-B and Hsp40 represents the first direct evidence of ankyrin's role as chaperones.

• 한국전산구조공학회:학술대회논문집
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• 한국전산구조공학회 2008년도 정기 학술대회
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• pp.14-19
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• 2008

This paper presents dynamic infinite element formulations which have been developed for soil-structure interaction analysis both in frequency and in time domains by the present authors during the past twenty years. Axisymmetric, 2D and 3D layered half-space soil media were considered in the developments. The displacement shape functions of the infinite elements were established using approximate expressions of analytical solutions in frequency domain to represent the characteristics of multiple waves propagating into the unbounded outer domain of the media. The proposed infinite elements were verified using benchmark examples, which showed that the present formulations are very effective for the soil-structure interaction analysis either in frequency or in time domain. Example applications to actual interaction problems are also given to demonstrate the capability and versatility of the present methodology.