蛋白質的接觸拓樸和動力學研究揭露蛋白-DNA接合特徵及酵素活性中心的分佈偏好
碩士 === 國立清華大學 === 生物資訊與結構生物研究所 === 102 === Effects of protein dynamics on protein-DNA binding have not been analyzed thoroughly so far. Using GNM and ANM, we well predict conformational change between DNA-free/DNA-bound forms. However, we fail to find fluctuation-magnitude-based characteristics to p...
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| Format: | Others |
| Language: | en_US |
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2014
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| Online Access: | http://ndltd.ncl.edu.tw/handle/32443487493035624011 |
| Summary: | 碩士 === 國立清華大學 === 生物資訊與結構生物研究所 === 102 === Effects of protein dynamics on protein-DNA binding have not been analyzed thoroughly so far. Using GNM and ANM, we well predict conformational change between DNA-free/DNA-bound forms. However, we fail to find fluctuation-magnitude-based characteristics to predict DNA binding sites. GNM-based Domain-planes (D-planes) derived from the unbound proteins are used to determine significant DNA-binding orientations with the results that larger than 95% of the 110 DNA molecules being dissected through by these planes. In addition, we also report that enzyme active sites are close to the D-planes such that 90% of the studied 732 active sites are located within 50% rank from the D-planes. We compare and contrast the thermodynamic aspects of ligand-protein and DNA-protein binding. This study suggests potential applications for filtering out unlikely DNA-protein docking poses obtained from docking software.
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