• Bulletin of the Korean Chemical Society
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• 제30권6호
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• pp.1360-1364
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• 2009

The bacterium Sphingomonas chungbukensis DJ77 produces the extracellular polysaccharide gellan in high yield. Gellan produced by this bacterium is widely used as a gelling agent, and the enzyme UDP-glucose pyrophosphorylase (UGP) is thought to play a key role in the gellan biosynthetic pathway. The UGP gene has been successfully cloned and over-expressed in E. coli. The expressed enzyme was purified with a molecular weight of approximately 32 kDa, as determined by a SDS-polyacrylamide gel, but the enzyme appears as ca. 63 kDa on a native gel, suggesting that the enzyme is present in a homodimer. Kinetic analysis of UDP-glucose for UGP indicates $K_m$ = 1.14 mM and $V_{max}$ = 10.09 mM/min/mg at pH 8.0, which was determined to be the optimal pH for UGP catalytic activity. Amino acid sequence alignment against other bacteria suggests that the UGP contains two conserved domains: An activator binding site and a glucose-1-phosphate binding site. Site-directed mutagenesis of Lys194, located within the glucose-1-phosphate binding site, indicates that substitution of the charge-reversible residue Asp for Lys194 dramatically impairs the UGP activity, supporting the hypothesis that Lys194 plays a critical role in the catalysis.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2003년도 가을 학술발표논문집 Vol.30 No.2 (2)
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• pp.850-852
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• 2003

이 논문에서는 여러 가지 도구를 논리적인 순서로 사용함으로써 이루어지는 작업을 워크플로우로 보고, 이러한 관점에서 바이오인포매틱스 도구를 통합하는 새로운 멀티에이전트 시스템을 제안한다. 제안한 시스템은 기존의 도구를 랩퍼 에이전트로 구현하고, 에이전트간의 통신은 XML 형식의 메시지로 이루어진다. 수신 에이전트는 송신 에이전트가 전송하는 정보를 명시적으로 알리지 않고도 메시지로부터 필요한 정보를 추출할 수 있다. 제안한 시스템의 이러한 특징은 바이오인포매틱스 도구와 데이터베이스의 통합을 용이하게 한다. 또한, 제안한 시스템에서는 워크플로우를 여러 가지 제어 구조를 이용하여 정의할 수 있으며. 워크플로우 진행을 모니터링할 수 있는 기능을 제공한다. 제안한 시스템의 가용성을 보이기 위해 박테리아 Sphingomonas Chungbukensis DJ77 의 유전자 주해(gene annotation) 작업에 제안한 시스템을 적용하여 구현하고 있다.

• 한국지능시스템학회:학술대회논문집
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• 한국퍼지및지능시스템학회 2003년도 ISIS 2003
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• pp.94-97
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• 2003

Various bioinformatics tools for biological data processing have been developed and most of them are available in public. Most bioinformatics works are carried out by a composite application of those tools. Several integration approaches have been proposed for easy use of the tools. This paper proposes a new multiagent system architecture to integrate bioinformatics tools in the perspective of workflow since the composite applications of tools can be regarded as workflows. For the easy integration, the proposed architecture employs wrapper agents for existing tools, uses XML-based messages in the inter-agent communication, and agents are supposed to extract necessary information from the received messages. This allows new tools to be easily added on the integration framework. The proposed method allows various control structures in workflow definition and provides the progress monitoring capability of the on-going workflows. We implemented a prototype system of the proposed architecture for annotating the genes of a bacterium called Sphingomonas Chungbukensis DJ77.