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Structure-based design of a DNA repair enzyme with altered catalytic activity
Yamagata, Yuriko 전남대학교 약품개발연구소 1999 약품개발연구지 Vol.8 No.1
The integrity of the DNA is constantly challenged by a number of endogenous and environmental DNA-damaging agents. DNA glycosylases that recognize damaged bases and remove them by cleaving the N-glycosidic bond linking the base to deoxyribose are key enzymes in the base excision repair pathway. We have determined the crystal structure of E. coli 3-methyladenine DNA glycosylase II (AlkA) which removes numerous alkylated bases from DNA. The enzyme consists of three domains: one α+β fold domain with a similarity to one-half of the eukaryotic TATA box-binding protein, and two all helical domains similar to those of E. coli endonuclease III (EndoIII) with combined N-glycosylase/abasic lyase activity. The crystal structure and mutational studies reveal that the active site is logy m the cleft between the two helical domains and that Asp238 is the most likely candidate as a catalytic residue in the N-glycosylase reaction. The findings of the structural similarity between AlkA and EadoIII and marry hypothetical proteins with similar sequences to them in genomes suggested the existence of a DNA glycosylase superfamily. Recently the several proteins were characterized as DNA glycosylases. The members possess a common fold, yet as upon remarkably diverse lesions. The structure-based sequence alignment among members of the superfamily shows that the Lys residue at the corresponding position m Trp218 of AlkA (Lys120 in EadoIII) is conserved in all DNA glycosylase/lyases. It has been shown that the Lys residue plays a role of the Schiff base formation in the reaction process of AP lyase. To resolve a question if the replacement of Tip at 218 by Lys can produce the AP lyase activity in the monofunctional DNA glycosylases such as AlkA, the AP lyase activity of the W218K mutant was measured using a duplex 21mer with ^(32)P labeled AP site-containing strand. The W218K mutant has the efficient AP lyase activity with the lack of the methylated bases-spec DNA glycosylase activity. The appearance of the altered activity between the wed-type and W218K mutant proteins suggests that the active-site structures of AlkA and maybe the members of the DNA glycosylase superfamily are much tolerant of changes of enzyme activities. Such adapting active site structures may have provided an efficient means of evolving a diverse range of substrate specificities in the DNA glycosylase superfamily.
Japan’s Policy-level ODA Evaluation: Reflections by a Third-Party Academic Evaluator
Tatsufumi Yamagata 국제개발협력학회 2018 국제개발협력연구 Vol.10 No.4
Japan’s policy-level ODA (Official Development Assistance) evaluation has played a complementary role to project-level evaluations. Japan encountered policy-level challenges, mainly from the Development Assistance Committee of the OECD, beyond the level of project management. Some of the policy recommendations derived from the policy-level evaluation exercises were useful, and seriously considered for implementation by the Ministry of Foreign Affairs (MOFA) of Japan. However, there are limitations to conducting the evaluation under the current framework of the assignment, which are (1) a low level of independence and (2) few resources. Frequent interactions between stakeholder-divisions of the MOFA and the evaluation team, including comment-revision repetitions prior to finalizing a review report, risk the independence of a review. Consequently, the views of stakeholders may substantially influence the report. Second, minimal resources, in terms of money, time and personnel, are available to do the job. This resource limitation further weakens the independence of the evaluation. Together, these two aspects result in a low level of authority and little public awareness of the evaluation.
Wataru Yamagata,Toshio Fujisawa,Takashi Sasaki,Rei Ishibashi,Tomotaka Saito,Shuntaro Yoshida,Shizuka No,Kouta Inoue,Yousuke Nakai,Naoki Sasahira,Hiroyuki Isayama 대한소화기내시경학회 2023 Clinical Endoscopy Vol.56 No.5
Background/Aims: Mechanical properties (MPs) and axial and radial force (AF and RF) may influence the efficacy and complicationsof self-expandable metallic stent (SEMS) placement. We measured the MPs of various SEMSs and examined their influence on theSEMS clinical ability. Methods: We evaluated the MPs of 29 types of 10-mm SEMSs. RF was measured using a conventional measurement device. AF wasmeasured using the conventional and new methods, and the correlation between the methods was evaluated. Results: A high correlation in AFs was observed, as measured by the new and conventional manual methods. AF and RF scatterplotsdivided the SEMSs into three subgroups according to structure: hook-and-cross-type (low AF and RF), cross-type (high AF and lowRF), and laser-cut-type (intermediate AF and high RF). The hook-and-cross-type had the largest axial force zero border (>20°), followedby the laser-cut and cross types. Conclusions: MPs were related to stent structure. Hook-and-cross-type SEMSs had a low AF and high axial force zero border and wereconsidered safest because they caused minimal stress on the biliary wall. However, the increase in RF must be overcome.
An Evaluation of Burst Transfer Inferred by a High-level Synthesis Tool
Yuki Yamagata,Akira Yamawaki 대한전자공학회 2019 IEIE Transactions on Smart Processing & Computing Vol.8 No.2
High-level synthesis (HLS) is technology that automatically converts software to digital hardware. HLS has gained attention as a promising technology that can reduce the burden of hardware development. However, if a software program converted by HLS does not consider organization of the hardware, the current HLS technology cannot convert software to proper digital hardware. One of the characteristics of the hardware to be considered is burst transfer to memory access. Burst transfer attempts to speed up memory access by packing continuous data into a single address. This paper discusses a rectangle-drawing case study that demonstrates how to describe a C program so an HLS tool can infer burst transfer with an arbitrary burst length. Moreover, we consider the necessity to suppress optimization performed by the HLS tool to prevent increasing the amount of digital hardware when we implement the arbitrary burst length. Experiments clarify how performance and the hardware scale change based on the difference in the burst length and suppression of optimization.