Substrate recognition by ribosome-inactivating protein studied by molecular modeling and molecular electrostatic potentials |
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| Institution: | 1. College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China;2. Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China;3. Fujian Province Key Laboratory for the Development of Bioactive Material from Marine Algae, Quanzhou Normal University, Quanzhou, 362000, China;4. Institute of Chinese Medical Sciences, State Key Laboratory of Quality Control in Chinese Medicine, University of Macau, Taipa, Macau, China;1. Department of Pure and Applied Physics, Faculty of Engineering Science, Kansai University, Osaka 564-8680, Japan;2. The Sonochemistry Group, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom;3. National Centre of Applied Microfluidic Chemistry, Pohang University of Science and Technology, Gyeongbuk 37673, Republic of Korea;4. Irish Water, Dublin 1, Ireland;1. State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, 570228, Hainan Province, PR China;2. Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, 570228, Hainan Province, PR China;3. Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, 570228, Hainan Province, PR China;4. College of Marine Sciences, Hainan University, Haikou, 570228, Hainan Province, PR China;1. Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China;2. Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, Wuxi, China |
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| Abstract: | A computer model of dianthin 30, a type 1 ribosome-inactivating protein (RIP), is constructed by homology modeling using two known X-ray structures; a type 1 RIP, pokeweed antiviral protein (PAP), and chain A of a type 2 RIP, ricin. The 3D structure is refined by molecular dynamics and its binding site compared with those of PAP and ricin using molecular electrostatic potential mapping. The differences in the maps obtained clearly show how, despite the similarity of the topology of the binding site, differences in electrostatic potential can account for the experimentally observed differences in substrate recognition and binding. This demonstrates the potential of these techniques for guiding further experimental analyses. |
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