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Hogyun Seo,Kyung-Jin Kim 한국생물공학회 2019 Biotechnology and Bioprocess Engineering Vol.24 No.1
Although enoyl-CoA hydratase/isomerase superfamily proteins are functionally diverse and extremely abundant in microbial and higher organism’s genome, they still have been elusively annotated. The genome of Cupriavidus necator H16 contains at least 54 enoyl-CoA hydratase/isomerase superfamily proteins that might influence on polyhydroxyalkanoate synthesis, but most of them are uncharacterized. Among them, we first determined crystal structure of H16_B0756 at a 2.0 Å resolution. The protein exhibits unique amino acid sequences compared to the other isoforms with identity lower than 36%. The structure of H16_B0756 forms a trimeric architecture and showed canonical disk-shape. Interestingly, H16_B0756 has only one glutamate residue at the active site while other enoyl- CoA hydratases have two nucleophilic glutamate at the catalytic site. We found that the active site conformation of H16_B0756 is quite similar to that of 1,2-epoxyphenylacetyl- CoA isomerase (PaaG) rather than those of other enoyl-CoA hydratases. In addition to the structural comparison, gene neighborhoods analysis suggested that H16_B0756 might function in the ring compound degradation.
GNU Binutils를 기반으로 한 재겨냥성 이진 유틸리티의 개발
김호균(Hogyun Kim),정지문(Jimoon Jung),이종원(Jongwon Lee),박상현(Sanghyun Park),윤종희(Jonghee Yoon),백윤흥(Yunheung Paek) 한국정보과학회 2009 정보과학회논문지 : 소프트웨어 및 응용 Vol.36 No.9
오늘날 가전 제품 시장에서 임베디드 시스템은 time-to-market 이라는 개념이 점차 중요해지고 있다. 프로세서의 개발 주기가 점차 짧아짐에 따라 소프트웨어의 개발 또한 중요하게 생각되고 있다. 그러나 새로운 프로세서에 특화된 소프트웨어 개발 도구들을 개발하는 시간은 여전히 개선되지 않고 있다. 이러한 점에서 Architecture Description Language(ADL)은 새로운 프로세서에 대한 소프트웨어 개발 도구들을 자동으로 생성하게 함으로써 개발하는 수고를 덜 수 있다. 본 논문에서는 GNU Binutils를 이용하여 각각의 프로세서에 맞는 소프트웨어 개발 도구들을 자동으로 생성하였다. 이 연구를 통하여 우리는 어셈블러나 링커와 같은 소프트웨어 개발 도구들을 쉽고 빠르게 생성할 수 있었다. In this days, the concept of time-to-market is important in embedded systems in consumer electronics. According to the short time of development period, it is also important in development of Software Development toolkits (SDKs). However, it is not improved to the development time of SDKs specialized in new processors. In this point, the Architecture Description Language (ADL) is an alternative to relieve the pain of building the SDKs as the required SDKs can be automatically generated from ADL for the processor. In this paper, we automatically generate SDKs specialized in processors using GNU Binutils. Through this research, we can more easier and faster produce the SDKs such as assembler and linker than by using handcrafted code.
Cheong, Hogyun,Kim, Jimin,Kim, Bum Jin,Kim, Eunjin,Park, Hae Yeon,Choi, Bong-Hyuk,Joo, Kye Il,Cho, Mi-La,Rhie, Jong Won,Lee, Jong In,Cha, Hyung Joon Elsevier 2019 Acta Biomaterialia: structure-property-function re Vol.90 No.-
<P><B>Abstract</B></P> <P>Limited regenerative capacity of the nervous system makes treating traumatic nerve injuries with conventional polymer-based nerve grafting a challenging task. Consequently, utilizing natural polymers and biomimetic topologies became obvious strategies for nerve conduit designs. As a bioinspired natural polymer from a marine organism, mussel adhesive proteins (MAPs) fused with biofunctional peptides from extracellular matrix (ECM) were engineered for accelerated nerve regeneration by enhancing cell adhesion, proliferation, neural differentiation, and neurite formation. To physically promote contact guidance of neural and Schwann cells and to achieve guided nerve regeneration, MAP was fabricated into an electrospun aligned nanofiber conduit by introducing synthetic polymer poly(lactic-co-glycolic acid) (PLGA) to control solubility and mechanical property. <I>In vitro</I> and <I>in vivo</I> experiments demonstrated that the multi-dimensional tactics of combining adhesiveness from MAP, integrin-mediated interaction from ECM peptides (in particular, IKVAV derived from laminin α1 chain), and contact guidance from aligned nanofibers synergistically accelerated functional nerve regeneration. Thus, MAP-based multi-dimensional approach provides new opportunities for neural regenerative applications including nerve grafting.</P> <P><B>Statement of significance</B></P> <P>Findings in neural regeneration indicate that a bioinspired polymer-based nerve conduit design should harmoniously constitute various factors, such as biocompatibility, neurotrophic molecule, biodegradability, and contact guidance. Here, we engineered three fusion proteins of mussel-derived adhesive protein with ECM-derived biofunctional peptides to simultaneously provide biocompatibility and integrin-based interactions. In addition, a fabrication of robust aligned nanofiber conduits containing the fusion proteins realized suitable biodegradability and contact guidance. Thus, our multi-dimensional strategy on conduit design provided outstanding biocompatibility, biodegradability, integrin-interaction, and contact guidance to achieve an accelerated functional nerve regeneration. We believe that our bioengineered mussel adhesive protein-based multi-dimensional strategy would offer new insights into the design of nerve tissue engineering biomaterials.</P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>
Seo, Hogyun,Kim, Kyung-Jin Elsevier 2018 Biochemical and biophysical research communication Vol.499 No.3
<P><B>Abstract</B></P> <P> <I>Streptomyces coelicolor</I> A3 contains <I>Sc5140</I>, a gene coding for poorly understood bacterial LOG-like protein. In this study, we determined the crystal structure of <I>Sc</I>5140 and found it resembles the overall structure of other type-II LOGs. In addition, <I>Sc</I>5140 exhibited phosphoribohydrolase activity against adenosine monophosphate (AMP), indicating that it had the same function as known type-II LOGs. Based on these results, we designated <I>Sc</I>5140 as <I>Sc</I>LOGII. We performed docking calculations of AMP into the <I>Sc</I>LOGII structure, which suggested the mode of binding for type-II LOG with their AMP substrate. The <I>Sc</I>LOGII structure uniquely exhibited a long tail-like structure at the N-terminus that was involved in hexamerization of the protein; the disordered N-terminal region (DNR). Truncation of DNR in <I>Sc</I>LOGII negatively affected both the phosphoribohydrolase activity and the oligomerization of the protein, suggesting that this region functioned in enzyme stabilization. However, results from truncation experiments using <I>Sc</I>LOGII and <I>Cg</I>LOGII, a type-II LOG homologue from <I>Corynebacterium glutamicum</I>, were quite different, leaving uncertainty regarding the general functions of DNR in type-II LOGs. Overall, the current structural work may help in understand the significance of type-II LOG protein at the molecular level.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Crystal structure of type-II LOG from <I>Streptomyces coelicolor</I> A3 (<I>Sc</I>LOGII) was determined. </LI> <LI> The substrate binding mode of type-II LOG is suggested by docking calculations of AMP into the <I>Sc</I>LOGII. </LI> <LI> <I>Sc</I>LOGII has a long tail-like structure at the N-terminus that is involved in hexamerization. </LI> </UL> </P>