Browsing by Author "Huang, Kuan-Wei"

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Identification of Inhibitors for the DEDDh Family of Exonucleases and a Unique Inhibition Mechanism by Crystal Structure Analysis of CRN-4 Bound with 2-Morpholin-4-ylethanesulfonate (MES)
(2016-09-08)
Huang, Kuan-Wei
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Hsu, Kai-Cheng
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Chu, Lee-Ya
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Yang, Jinn-Moon
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Yuan, Hanna S.
The DEDDh family of exonucleases plays essential roles in DNA and RNA metabolism in all kingdoms of life. Several viral and human, DEDDh exonucleases can serve as antiviral drug targets due to their critical roles virus replication. Here using RNase T and CRN-4 as the model systems, we identify potential inhibitors for DEDDh exonucleases. We further show that two of the inhibitors, ATA and PV6R, indeed inhibit the exonuclease activity of the viral protein NP exonuclease of Lassa fever virus in vitro. Moreover, we determine the crystal structure of CRN-4 in complex with MES that reveals a unique inhibition Mechanism, by inducing the general base His179 to shift out of the active site. Our results not only provide the structural basis for the inhibition mechanism but also suggest potential lead inhibitors for the DEDDh exonucleases that may pave the way for designing nuclease inhibitors for biochemical and biomedical applications.
Identification of inhibitors for the DEDDh family of exonucleases and a unique inhibition mechanism revealed by crystal structure analysis of CRN-4 bound with MES
(2016-01-01)
Hsiao, Yu-Yuan
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Huang, Kuan-Wei
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Hsu, Kai-Cheng
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Chu, Lee-Ya
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Yang, Jinn-Moon
MOLECULAR MECHANISMS OF TREX1 IN DNA REPAIR AND IMMUNE SILENCING
(2019-01-01)
Huang, Kuan-Wei
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Liu, Tung-Chang
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Hsiao, Yu-Yuan
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Hsaio, Yu-Yuan
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生物科技學系
New Hybrid Multiple Attribute Decision-Making Model for Improving Competence Sets: Enhancing a Company's Core Competitiveness
(2016-02-01)
Huang, Kuan-Wei
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Huang, Jen-Hung
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Tzeng, Gwo-Hshiung
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管理科學系
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科技管理研究所
New Idea of Multi-Objective Programming with Changeable Spaces for Improving the Unmanned Factory Planning
(2014-01-01)
Gwo-HshiungTzeng
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Huang, Kuan-Wei
;
Lin, Ching-Wei
;
Yuan, Benjamin J. C.
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管理科學系
Business decision-makers need various decision analyses to meet highly competitive environments. With increasing cost of intensive workforce and lowering marginal-profit products, how to break the limitation of resources and optimally reallocate all of the precious resources is the major issue to create the competitive advantages in the high-technology industry. Moreover, the second industrial upgrading has developed industrial robots in some production processes for providing more value-added production activities. Therefore, this study proposed a new idea of multi-objective programming with changeable spaces (decision space and objective space) named changeable spaces programming extending the concept of De Novo programming. The best production resources reallocation in re-designing the decision space can be considered how to improve the multi-objective of unmanned factory planning in a high-technology firm for achieving aspiration level. This method provides decision analysis planning and not only to reach ideal point but also how achieve aspiration level in resource reallocation/redesign. A numerical example illustrates how to release the trade-offs between industrial robots and a workforce subject to constrains of the wafer manufacturing and how stage by stage to improve each objective for closing aspiration level in objective space. Computational results are demonstrated supporting the proposed model is easily implemented with flexible effort in practical.
Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1
(2018-05-01)
Huang, Kuan-Wei
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Liu, Tung-Chang
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Liang, Ruei-Yue
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Chu, Lee-Ya
;
Cheng, Hiu-Lo
Three prime repair exonuciease 1 (TREX1) is an essential exonuclease in mammalian cells, and numerous in vivo and in vitro data evidenced its participation in immunity regulation and in genotoxicity remediation. In these very complicated cellular functions, the molecular mechanisms by which duplex DNA substrates are processed are mostly elusive because of the lack of structure information. Here, we report multiple crystal structures of TREX1 complexed with various substrates to provide the structure basis for overhang excision and terminal unwinding of DNA duplexes. The substrates were designed to mimic the intermediate structural DNAs involved in various repair pathways. The results showed that the Leu24Pro25-Ser26 cluster of TREX1 served to cap the nonscissile 5'-end of the DNA for precise removal of the short 3'-overhang in L- and Y-structural DNA or to wedge into the double-stranded region for further digestion along the duplex. Biochemical assays were also conducted to demonstrate that TREX1 can indeed degrade double-stranded DNA (dsDNA) to a full extent. Overall, this study provided unprecedented knowledge at the molecular level on the enzymatic substrate processing involved in prevention of immune activation and in responses to genotoxic stresses. For example, Arg128, whose mutation in TREX1 was linked to a disease state, were shown to exhibit consistent interaction patterns with the nonscissile strand in all of the structures we solved. Such structure basis is expected to play an indispensable role in elucidating the functional activities of TREX1 at the cellular level and in vivo.
Structural insights into the duplex DNA processing of TREX2
(2018-12-14)
Cheng, Hiu-Lo
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Lin, Chun-Ting
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Huang, Kuan-Wei
;
Wang, Shuying
;
Lin, Yeh-Tung
The three prime repair exonuclease 2 (TREX2) is an essential 3'- to-5' exonuclease that functions in cell proliferation, genome integrity and skin homeostasis maintenance. The abnormal expression level of TREX2 can result in broken chromosome, increased susceptibility to skin carcinogenesis and Psoriasis. However, the molecular mechanisms of how TREX2 binds and processes its natural substrates, dsDNA or chromosomal DNA, to maintain genome stability remain unclear. In this study, we present four new crystal structures: apo-TREX2, TREX2 in complex with two different dsDNA substrates, and TREX2 in complex with a processed dsDNA product. Analysis of the structures reveals that TREX2 stacks with the 5'-terminal of dsDNA by a Leu20-Pro21-Asn22 cluster for precisely trimming the 3'-overhang. In addition, TREX2 specifically interacts with the nonscissile strand of dsDNA by an alpha-helix-loop region. The unique interaction patterns of the TREX2-dsDNA complex highlight the requirement of long double-stranded region for TREX2 binding and provide evidence of the functional role of TREX2 in processing chromosomal DNA. Moreover, the non-processive property of TREX2 is elucidated by the structure of TREX2-product complex. Our work discloses the first structural basis of the molecular interactions between TREX2 and its substrates and unravels the mechanistic actions of TREX2.