Structural basis for the regulation of eukaryotic replication licensing

Cho, Yunje 이화여자대학교 세포신호전달연구센터 2007 고사리 세포신호전달 심포지움 Vol. No.9

In eukarytic cells, origins of DNA must be licensed once per cell cycle. Inhibition of Cdt1 activity by geminin during S, G2, and M phases of the cell cycle is an important mechanism that prevents the inappropriate re-initiation of replication on already fired origin. Replication licensing requires an ordered assembly of ORC complex followed by Cdc6 and Cdt1, which in turn recruits the MCM complex to form pre-RC complex. I will describe the crystal structures of the conserved core of Cdt1(Cdt1M) bound to the central core of geminin and C-terminal part of Cdt1(Cdt1C) which is essential for the licensing. Structural studies on these licensing components suggest the mechanisms by which geminin inhibits the pre-RC formation and by which Cdt1 recruits the MCM complex to turn on the replication.

Crystal Structure of the elF4A and PDCD4 complex : insights into the inhibition of translation

Cho, Yunje 이화여자대학교 세포신호전달연구센터 2009 고사리 세포신호전달 심포지움 Vol. No.11

Initiation of mRNA translation is a rate-limiting stage of protein synthesis that must be tightly regulated in eukaryotic cell proliferation. The eukaryotic translation initiation factor 4A(eIF4A) plays a crucial role in the translation initiation by unwinding the secondary structure at the 5' untranslated region(5'UTR) and cap of messenger RNAs, thereby facilitating ribosome scanning. The tumor suppressor programmed cell death protein 4(PDCD4) is believed to control the translation by inhibiting the RNA helicase activity of eIF4A. The two MA3 domains of PDCD4, middle MA3(mMA3) and C-terminal MA3(cMA3), are responsible for the inhibitory activity of PDCD4. Here we determined the crystal structure of the human eIF4A and PDCD4 complex. The structure reveals that one molecule of PDCD4 binds to the two eIF4A molecules, and provides two different inhibition models. While the two MA3 domains of PDCD4 bind to eIF4A in one model, only the cMA3 domain interacts with eIF4A in another model. The complex structures in both models suggest that the MA3 domain(s) of PDCD4 binds perpendicular to the interface of the two domains of eIF4A, and prevents the domain closure of eIF4A and blocks RNA-binding to eIF4A, both of which are required events in the function of eIF4A helicase. We demonstrate that while the two models are functionally important, the two MA3 inhibition model is more critical in the inhibition of eIF4A activity and translation. The complex structure, together with biochemical analyses, provides insights into the inhibition mechanism of eIF4A and the initiation of eukaryotic translation by PDCD4.

단순 인체 모델과 Monte Carlo 시뮬레이션 기반의 흉부 X-ray 산란선 보정기법

조윤제(Yunje Cho),원치준(Chijun Weon),김승언(Seungeon Kim),장용진(Yongjin Chang),나종범(Jong Beom Ra) 대한전자공학회 2015 대한전자공학회 학술대회 Vol.2015 No.6

A Novel Method for Providing Precise Time Synchronization in a Distributed Control System Using Boundary Clock

Jae Hun Cho,Hoon Kim,Sihai Wang,Jaehoon Lee,Hanlim Lee,Seongtaek Hwang,Sungdae Cho,Yunje Oh,Tae-Jin Lee IEEE 2009 IEEE transactions on instrumentation and measureme Vol.58 No.8

<P>We propose and demonstrate a method to provide precise time synchronization in distributed control systems using a boundary clock scheme. The major drawback of the boundary clock scheme is the exponential accumulation of time synchronization error as the number of hops increases. To make the error accumulation linearly increase with the number of hops, we first separate the frequency compensation interval (FCI) and the offset and frequency compensation interval (OFCI) and then separately optimize each interval. To demonstrate the performance of this method, we implemented test benches using Ethernet-linked distributed control systems. We measured the peak-to-peak jitter performance along with the maximum time interval error to assess the short- and long-term stability after several hops in distributed control systems. Our method enables the peak-to-peak jitter to be maintained under 107 ns after seven hops. The experimental results show that the performance of time synchronization is dominated by fast jitter rather than frequency error and wander, and the proposed scheme can be used to improve the time synchronization performance in IEEE 1588-compliant control systems using boundary clock.</P>

Construction of Spatiotemporal Big Data Using Environmental Impact Assessment Information

Namwook Cho,Yunjee Kim,Moung-Jin Lee 대한원격탐사학회 2020 大韓遠隔探査學會誌 Vol.36 No.4

In this study, the information from environmental impact statements was converted into spatial data because environmental data from development sites are collected during the environmental impact assessment (EIA) process. Spatiotemporal big data were built from environmental spatial data for each environmental medium for 2,235 development sites during 2007-2018, available from public data portals. Comparing air-quality monitoring stations, 33,863 measurement points were constructed, which is approximately 75 times more measurement points than that 452 in Air Korea’s real-time measurement network. Here, spatiotemporal big data from 2,677,260 EIAs were constructed. In the future, such data might be used not only for EIAs but also for various spatial plans.

머클트리와 MQTT를 활용한 차량 Secure OTA protocol 연구

신윤제(Yunje Shin),강보근(Bogeun Kang),조성민(Sungmin Cho),전상훈(Sanghoon Jeon) 한국자동차공학회 2023 한국자동차공학회 학술대회 및 전시회 Vol.2023 No.11

소프트웨어 정의 차량(SDV)의 발전은 강력한 펌웨어 업데이트 방법의 필요성을 강조한다. 기존의 검증방식은 공급업체 서명, 메타데이터, 타임스탬프 등을 이용하지만 완전한 무결성을 보장하기 어렵다. 펌웨어 무결성을 보장하기 위해 여러 연구에서 도입된 블록체인의 탈중앙화 개념은 벤더사를 분산노드로 구성하며, 분산노드는 전체 네트워크에 영향을 미친다. 이를 차량 OTA(Over the Air) 업데이트에 적용하기에 안전성 측면에서 모든 노드들의 철저한 검증이 부족하다. 다른 도메인의 OTA와 달리 자동차 OTA는 성능과 안정성 모두 중요한 요소이다. 이에 본 연구에서는 IoT에서 널리 채택된 MQTT(Message Queuing Telemetry Transport) 프로토콜을 활용하여 성능을 확보하고, 블록체인 검증기술인 Merkle Tree를 통합하여 OTA의 무결성과 신뢰성을 보장하는 새로운 접근방식을 제안한다. The evolution of Software-Defined Vehicles (SDV) has emphasized the critical need for a robust firmware update method. Traditional verification methods, which rely on vendor signatures, metadata, timestamps, and similar elements, sometimes fail to ensure complete integrity. Moreover, while decentralization has been explored in various studies for firmware integrity verification through blockchain technology, it lacks comprehensive validation in the context of automotive Over-The-Air (OTA) updates. Automative OTA updates prioritize stability above all else, with performance remaining a crucial consideration. To address these challenges, we propose an innovative approach to ensure the integrity and reliability of Firmware Over the Air (FOTA) updates. Our approach utilizes the widely adopted Message Queuing Telemetry Transport (MQTT) protocol from the Internet of Things (IoT) and incorporates blockchain verification technology, specifically the Merkle Tree, to enhance trustworthiness and maintain the performance of SDV firmware updates.

Structural and functional relationships of FAN1

Jin, Hyeonseok,Cho, Yunje Elsevier 2017 DNA repair Vol.56 No.-

<P><B>Abstract</B></P> <P>FANCD2/FANCI-associated nuclease (FAN1) is a 5′ flap structure-specific endonuclease and 5′ to 3′ exonuclease. This nuclease can resolve interstrand cross-links (ICLs) independently of the Fanconi anemia (FA) pathway and controls the progression of stalled replication forks in an FA-dependent manner, thereby maintaining chromosomal stability. Several FAN1 mutations are observed in various cancers and degenerative diseases. Recently, several crystal structures of the FAN1-DNA complexes have been reported, and to date, these represent the only structures for a DNA bound ICL-repair nuclease. Puzzlingly, human FAN1 forms two different quaternary structures with different DNA binding modes, and based on these structures, two ICL-repair mechanisms have been proposed. In one mechanism, monomeric FAN1 recognizes the 5′ flap terminal phosphate via a basic pocket and successively cleaves at every third nucleotide of the DNA substrates. In the other mechanism, dimeric FAN1 scans, latches, and unwinds the postnick duplex of the substrate DNA to direct the scissile phosphodiester group to the active site. In this review, we discuss the structures, function, and proposed mechanisms of FAN1 nuclease, and provide the insights into its role in ICL repair and in processing of stalled replication forks.</P>

Crystal structure of the eIF4A-PDCD4 complex.

Chang, Jeong Ho,Cho, Yong Hyun,Sohn, Sun Young,Choi, Jung Min,Kim, Ahreum,Kim, Young Chang,Jang, Sung Key,Cho, Yunje National Academy of Sciences 2009 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.106 No.9

<P>Tumor suppressor programmed cell death protein 4 (PDCD4) inhibits the translation initiation factor eIF4A, an RNA helicase that catalyzes the unwinding of secondary structure at the 5'-untranslated region of mRNAs and controls the initiation of translation. Here, we determined the crystal structure of the human eIF4A and PDCD4 complex. The structure reveals that one molecule of PDCD4 binds to the two eIF4A molecules through the two different binding modes. While the two MA3 domains of PDCD4 bind to one eIF4A molecule, the C-terminal MA3 domain alone of the same PDCD4 also interacts with another eIF4A molecule. The eIF4A-PDCD4 complex structure suggests that the MA3 domain(s) of PDCD4 binds perpendicular to the interface of the two domains of eIF4A, preventing the domain closure of eIF4A and blocking the binding of RNA to eIF4A, both of which are required events in the function of eIF4A helicase. The structure, together with biochemical analyses, reveals insights into the inhibition mechanism of eIF4A by PDCD4 and provides a framework for designing chemicals that target eIF4A.</P>

Interactions of SV40 large T-antigen and other viral proteins with retinoblstoma tumour suppressor

Kim, Hye-yeon,Lee, Changwook,Cho, Yunje 이화여자대학교 세포신호전달연구센터 2002 고사리 세포신호전달 심포지움 Vol. No.4

The simian virus 40 large T antigen, the human papilloma virus E7 and the adenoviruse E1A are potent oncoproteins that can induce several types of tumours. One of the major functions of these oncoproteins is to interact with retinoblastoma tumor suppressor(Rb), a master switch of mammalian cell cycle, and to inactivate its function. Rb promotes cell cycle arrest by recruiting and regulating the proteins involved in transcription. The binding of viral oncoproteins to Rb disrupts the Rb-E2F complex, a central component in Rb mediated cell cycle network. The crystal structures of Rb pocket - viral oncoproeins complexes propose that the viral proteins recognizes the highly conserved region in the Rb pocket through their common motif, LxCxE, and through other unique regions within each viral protein. While the mechanism of Rb inactivation by viral proteins is not fully understood, we will present the atomic level information on the interactions of Rb pocket - viral protein complexes and discuss the insight how these proteins dissociate the E2F from Rb and how they deregulate the cell cycle.

차량 키리스 엔트리 시스템의 재전송 공격 방지를 위한 보안 메커니즘

강보근(Bogeun Kang),조성민(Sungmin Cho),신윤제(Yunje Shin),전상훈(Sanghoon Jeon) 한국자동차공학회 2023 한국자동차공학회 학술대회 및 전시회 Vol.2023 No.11

Recently, security vulnerabilities in vehicle keyless entry systems have emerged as a serious problem. In particular, a replay attack is an attack that controls a vehicle by retransmitting a command successfully performed by an attacker in the past, which can easily occur due to the RF communication characteristics of a smart key. In this paper, it is shown that a replay attack can occur in the vehicle keyless entry system, and to prevent such a replay attack, we propose a session key encryption technique based on the Diffie Hellmann protocol. The technique was configured to be compatible with the existing vehicle keyless entry system and to minimize the overhead of session key generation and encryption. In the future, the security of the vehicle keyless entry system is expected to become more important due to the popularization of autonomous vehicles, and this study is expected to contribute to strengthening the security of the vehicle keyless entry system.