Three-dimensional model and molecular dynamics simulation of the active site of the self-splicing intervening sequence of the bacteriophage T4 nrdB messenger RNA
The secondary and 3D structure of the active site of the self-splicing T4 nrdB RNA has been modeled on a graphics workstation by use of the suggested 3D arrangement of the active site of the Tetrahymena IVS [Kim, S.H., & Cech, T.R. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 8788-8792] as a guideli...
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| Veröffentlicht in: | Biochemistry (Easton) 1990-11, Vol.29 (45), p.10317-10322 |
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| container_title | Biochemistry (Easton) |
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| creator | Nilsson, Lennart Aahgren-Staalhandske, Agneta Sjoegren, Ann Sofie Hahne, Solveig Sjoeberg, Britt Marie |
| description | The secondary and 3D structure of the active site of the self-splicing T4 nrdB RNA has been modeled on a graphics workstation by use of the suggested 3D arrangement of the active site of the Tetrahymena IVS [Kim, S.H., & Cech, T.R. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 8788-8792] as a guideline. The initially obtained crude structure was then subjected to molecular mechanics energy minimization and molecular dynamics simulation to relax tensions. In this process the energy decreased considerably and gave a final structure that deviated by 3 A [root mean square (rms)] from the initial structure. The cofactor guanosine (and the competitive inhibitor arginine) was docked to a proposed [Michel, F., Hanna, M., Green, R., Bartel, D.P., & Szostak, J.W. (1989) Nature 342, 391-395] binding site, where it was found to fit rather well. A minor modification of the binding mode easily brought the O3' end of the guanosine within 2 A of the phosphodiester bond where the primary cleavage occurs. |
| doi_str_mv | 10.1021/bi00497a005 |
| format | Article |
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(1987) Proc. Natl. Acad. Sci. U.S.A. 84, 8788-8792] as a guideline. The initially obtained crude structure was then subjected to molecular mechanics energy minimization and molecular dynamics simulation to relax tensions. In this process the energy decreased considerably and gave a final structure that deviated by 3 A [root mean square (rms)] from the initial structure. The cofactor guanosine (and the competitive inhibitor arginine) was docked to a proposed [Michel, F., Hanna, M., Green, R., Bartel, D.P., & Szostak, J.W. (1989) Nature 342, 391-395] binding site, where it was found to fit rather well. 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(1987) Proc. Natl. Acad. Sci. U.S.A. 84, 8788-8792] as a guideline. The initially obtained crude structure was then subjected to molecular mechanics energy minimization and molecular dynamics simulation to relax tensions. In this process the energy decreased considerably and gave a final structure that deviated by 3 A [root mean square (rms)] from the initial structure. The cofactor guanosine (and the competitive inhibitor arginine) was docked to a proposed [Michel, F., Hanna, M., Green, R., Bartel, D.P., & Szostak, J.W. (1989) Nature 342, 391-395] binding site, where it was found to fit rather well. A minor modification of the binding mode easily brought the O3' end of the guanosine within 2 A of the phosphodiester bond where the primary cleavage occurs.</description><subject>Animals</subject><subject>Arginine - pharmacology</subject><subject>Base Sequence</subject><subject>Binding Sites - drug effects</subject><subject>Computer Simulation</subject><subject>Introns</subject><subject>Kinetics</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>Nucleic Acid Conformation</subject><subject>phage T4</subject><subject>RNA Splicing</subject><subject>RNA, Messenger - chemistry</subject><subject>RNA, Messenger - metabolism</subject><subject>Sequence Homology, Nucleic Acid</subject><subject>Stereoisomerism</subject><subject>T-Phages - genetics</subject><subject>Tetrahymena - genetics</subject><subject>Thermodynamics</subject><issn>0006-2960</issn><issn>1520-4995</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1990</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkctu1DAUhi0EKkNhxRrJK1hUATuJ7XhZKnqRqhaVQWVnOfbJjEviDD5JRR-HN8XVDCMWSKzO5f_ORfoJec3Ze85K_qENjNVaWcbEE7LgomRFrbV4ShaMMVmUWrLn5AXiXS5rpuoDclCWktdKLMiv5ToBFD4MEDGM0fZ0GD301Eafsx7c3NtE_UO0Q3BIMQy5MWWSjh2d1kCtm8I9ZGGCPy2Evitw0wcX4oqGOEG6h_iYI_yYIbo92eZpSGHcrO0K6LKmMfmPdABEiCtI9Obq-CV51tke4dUuHpKvp5-WJ-fF5fXZxcnxZWErxqaCCwGqapSrtG9V2XglNZe6a5q25W1VQlNKYRmXnudagJa1c7orfVU7q5ytDsnb7d5NGvOTOJkhoIO-txHGGU3DuNKSy_-CXGilhGQZPNqCLo2ICTqzSWGw6cFwZh6dM385l-k3u7VzO4Dfszursl5s9YAT_NzLNn03UlVKmOXnL6a5Pbtht_Kb0Zl_t-WtQ3M3zil7i_-8_Bt0fLFe</recordid><startdate>19901113</startdate><enddate>19901113</enddate><creator>Nilsson, Lennart</creator><creator>Aahgren-Staalhandske, Agneta</creator><creator>Sjoegren, Ann Sofie</creator><creator>Hahne, Solveig</creator><creator>Sjoeberg, Britt Marie</creator><general>American Chemical Society</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TM</scope><scope>7U9</scope><scope>H94</scope><scope>7X8</scope></search><sort><creationdate>19901113</creationdate><title>Three-dimensional model and molecular dynamics simulation of the active site of the self-splicing intervening sequence of the bacteriophage T4 nrdB messenger RNA</title><author>Nilsson, Lennart ; Aahgren-Staalhandske, Agneta ; Sjoegren, Ann Sofie ; Hahne, Solveig ; Sjoeberg, Britt Marie</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a300t-155e7387c39db728d769169f88bb1b32e8265a016d1b1b5e964cc9f2d34ca7ca3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1990</creationdate><topic>Animals</topic><topic>Arginine - pharmacology</topic><topic>Base Sequence</topic><topic>Binding Sites - drug effects</topic><topic>Computer Simulation</topic><topic>Introns</topic><topic>Kinetics</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>Nucleic Acid Conformation</topic><topic>phage T4</topic><topic>RNA Splicing</topic><topic>RNA, Messenger - chemistry</topic><topic>RNA, Messenger - metabolism</topic><topic>Sequence Homology, Nucleic Acid</topic><topic>Stereoisomerism</topic><topic>T-Phages - genetics</topic><topic>Tetrahymena - genetics</topic><topic>Thermodynamics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Nilsson, Lennart</creatorcontrib><creatorcontrib>Aahgren-Staalhandske, Agneta</creatorcontrib><creatorcontrib>Sjoegren, Ann Sofie</creatorcontrib><creatorcontrib>Hahne, Solveig</creatorcontrib><creatorcontrib>Sjoeberg, Britt Marie</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Biochemistry (Easton)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Nilsson, Lennart</au><au>Aahgren-Staalhandske, Agneta</au><au>Sjoegren, Ann Sofie</au><au>Hahne, Solveig</au><au>Sjoeberg, Britt Marie</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Three-dimensional model and molecular dynamics simulation of the active site of the self-splicing intervening sequence of the bacteriophage T4 nrdB messenger RNA</atitle><jtitle>Biochemistry (Easton)</jtitle><addtitle>Biochemistry</addtitle><date>1990-11-13</date><risdate>1990</risdate><volume>29</volume><issue>45</issue><spage>10317</spage><epage>10322</epage><pages>10317-10322</pages><issn>0006-2960</issn><eissn>1520-4995</eissn><abstract>The secondary and 3D structure of the active site of the self-splicing T4 nrdB RNA has been modeled on a graphics workstation by use of the suggested 3D arrangement of the active site of the Tetrahymena IVS [Kim, S.H., & Cech, T.R. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 8788-8792] as a guideline. The initially obtained crude structure was then subjected to molecular mechanics energy minimization and molecular dynamics simulation to relax tensions. In this process the energy decreased considerably and gave a final structure that deviated by 3 A [root mean square (rms)] from the initial structure. The cofactor guanosine (and the competitive inhibitor arginine) was docked to a proposed [Michel, F., Hanna, M., Green, R., Bartel, D.P., & Szostak, J.W. (1989) Nature 342, 391-395] binding site, where it was found to fit rather well. A minor modification of the binding mode easily brought the O3' end of the guanosine within 2 A of the phosphodiester bond where the primary cleavage occurs.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>2261475</pmid><doi>10.1021/bi00497a005</doi><tpages>6</tpages></addata></record> |
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| source | ACS Publications; MEDLINE |
| subjects | Animals Arginine - pharmacology Base Sequence Binding Sites - drug effects Computer Simulation Introns Kinetics Models, Molecular Molecular Sequence Data Nucleic Acid Conformation phage T4 RNA Splicing RNA, Messenger - chemistry RNA, Messenger - metabolism Sequence Homology, Nucleic Acid Stereoisomerism T-Phages - genetics Tetrahymena - genetics Thermodynamics |
| title | Three-dimensional model and molecular dynamics simulation of the active site of the self-splicing intervening sequence of the bacteriophage T4 nrdB messenger RNA |
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