Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography
The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventio...
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| Veröffentlicht in: | Proceedings of the National Academy of Sciences - PNAS 2012-09, Vol.109 (38), p.15301-15306 |
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| container_title | Proceedings of the National Academy of Sciences - PNAS |
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| creator | Chen, Julian C.-H Hanson, B. Leif Fisher, S. Zoë Langan, Paul Kovalevsky, Andrey Y |
| description | The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventional interactions are clearly defined, including a potential O─H…π interaction between a water molecule and the aromatic ring of residue Y44, as well as a number of potential C─H…O hydrogen bonds. Hydrogen bonding networks that are ambiguous in the 0.85 Å ultrahigh resolution X-ray structure can be resolved by accurate orientation of water molecules. Furthermore, the high resolution of the reported structure has allowed for the anisotropic description of 36 deuterium atoms in the protein. The visibility of hydrogen and deuterium atoms in the nuclear density maps is discussed in relation to the resolution of the neutron data. |
| doi_str_mv | 10.1073/pnas.1208341109 |
| format | Article |
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Leif ; Fisher, S. Zoë ; Langan, Paul ; Kovalevsky, Andrey Y</creator><creatorcontrib>Chen, Julian C.-H ; Hanson, B. Leif ; Fisher, S. Zoë ; Langan, Paul ; Kovalevsky, Andrey Y</creatorcontrib><description>The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventional interactions are clearly defined, including a potential O─H…π interaction between a water molecule and the aromatic ring of residue Y44, as well as a number of potential C─H…O hydrogen bonds. Hydrogen bonding networks that are ambiguous in the 0.85 Å ultrahigh resolution X-ray structure can be resolved by accurate orientation of water molecules. Furthermore, the high resolution of the reported structure has allowed for the anisotropic description of 36 deuterium atoms in the protein. The visibility of hydrogen and deuterium atoms in the nuclear density maps is discussed in relation to the resolution of the neutron data.</description><identifier>ISSN: 0027-8424</identifier><identifier>EISSN: 1091-6490</identifier><identifier>DOI: 10.1073/pnas.1208341109</identifier><identifier>PMID: 22949690</identifier><language>eng</language><publisher>United States: National Academy of Sciences</publisher><subject>Anisotropy ; aromatic compounds ; Atoms ; Atoms & subatomic particles ; Biochemistry - methods ; Biological Sciences ; Brassica - metabolism ; Crystallization ; Crystallography ; Crystallography - methods ; Crystals ; deuterium ; Deuterium - chemistry ; Hydrogen ; Hydrogen - chemistry ; Hydrogen Bonding ; Hydrogen bonds ; Isotopes ; Macromolecular Substances ; Molecular Conformation ; Molecules ; Neutron diffraction ; Neutron Diffraction - methods ; Neutrons ; Plant Proteins - chemistry ; Proteins ; Solvents ; Solvents - chemistry ; Water - chemistry ; X-radiation</subject><ispartof>Proceedings of the National Academy of Sciences - PNAS, 2012-09, Vol.109 (38), p.15301-15306</ispartof><rights>copyright © 1993-2008 National Academy of Sciences of the United States of America</rights><rights>Copyright National Academy of Sciences Sep 18, 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c558t-98b4dbf02c0ebe597b186ee313cc1271ab8c77fc47d75f4b38e706cd7e6abca3</citedby><cites>FETCH-LOGICAL-c558t-98b4dbf02c0ebe597b186ee313cc1271ab8c77fc47d75f4b38e706cd7e6abca3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://www.pnas.org/content/109/38.cover.gif</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/41706399$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/41706399$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,727,780,784,803,885,27924,27925,53791,53793,58017,58250</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22949690$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chen, Julian C.-H</creatorcontrib><creatorcontrib>Hanson, B. Leif</creatorcontrib><creatorcontrib>Fisher, S. Zoë</creatorcontrib><creatorcontrib>Langan, Paul</creatorcontrib><creatorcontrib>Kovalevsky, Andrey Y</creatorcontrib><title>Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography</title><title>Proceedings of the National Academy of Sciences - PNAS</title><addtitle>Proc Natl Acad Sci U S A</addtitle><description>The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventional interactions are clearly defined, including a potential O─H…π interaction between a water molecule and the aromatic ring of residue Y44, as well as a number of potential C─H…O hydrogen bonds. Hydrogen bonding networks that are ambiguous in the 0.85 Å ultrahigh resolution X-ray structure can be resolved by accurate orientation of water molecules. Furthermore, the high resolution of the reported structure has allowed for the anisotropic description of 36 deuterium atoms in the protein. The visibility of hydrogen and deuterium atoms in the nuclear density maps is discussed in relation to the resolution of the neutron data.</description><subject>Anisotropy</subject><subject>aromatic compounds</subject><subject>Atoms</subject><subject>Atoms & subatomic particles</subject><subject>Biochemistry - methods</subject><subject>Biological Sciences</subject><subject>Brassica - metabolism</subject><subject>Crystallization</subject><subject>Crystallography</subject><subject>Crystallography - methods</subject><subject>Crystals</subject><subject>deuterium</subject><subject>Deuterium - chemistry</subject><subject>Hydrogen</subject><subject>Hydrogen - chemistry</subject><subject>Hydrogen Bonding</subject><subject>Hydrogen bonds</subject><subject>Isotopes</subject><subject>Macromolecular Substances</subject><subject>Molecular Conformation</subject><subject>Molecules</subject><subject>Neutron diffraction</subject><subject>Neutron Diffraction - methods</subject><subject>Neutrons</subject><subject>Plant Proteins - chemistry</subject><subject>Proteins</subject><subject>Solvents</subject><subject>Solvents - chemistry</subject><subject>Water - chemistry</subject><subject>X-radiation</subject><issn>0027-8424</issn><issn>1091-6490</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpdkctv1DAQxiMEotvCmRNgqRcuacePJM4FCZWnVIkD5Ww5jpN4ldjBdirlv8fpLlvgMnOY33zz-LLsFYYrDBW9nq0MV5gApwxjqJ9kuxRxXrIanmY7AFLlnBF2lp2HsAeAuuDwPDsjpGZ1WcMuWz4ar1VErgna38tonEWuQ8Paetdri2R0E2pXKyejApK2RcZG7aXayICaFS1j9HIw_YC8Dm5cHiSsXqJPefYuamOR8muIchxd7-U8rC-yZ50cg355zBfZ3edPdzdf89vvX77dfLjNVVHwmNe8YW3TAVGgG13UVYN5qTXFVClMKiwbrqqqU6xqq6JjDeW6glK1lS5loyS9yN4fZOelmXSrtE2rjmL2ZpJ-FU4a8W_FmkH07l5QVnBKaBJ4dxTw7teiQxSTCUqPo7TaLUFgYJiSkpQ8oZf_oXu3eJuue6AIJqyERF0fKOVdCF53p2UwiM1RsTkqHh1NHW_-vuHE_7EwAegIbJ2PcrWgXOCCAk7I6wOyD9H5E8Nw-hattxlvD_VOOiF7b4L4-YMALgEwSUMY_Q2dI76P</recordid><startdate>20120918</startdate><enddate>20120918</enddate><creator>Chen, Julian C.-H</creator><creator>Hanson, B. 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Zoë ; Langan, Paul ; Kovalevsky, Andrey Y</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c558t-98b4dbf02c0ebe597b186ee313cc1271ab8c77fc47d75f4b38e706cd7e6abca3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Anisotropy</topic><topic>aromatic compounds</topic><topic>Atoms</topic><topic>Atoms & subatomic particles</topic><topic>Biochemistry - methods</topic><topic>Biological Sciences</topic><topic>Brassica - metabolism</topic><topic>Crystallization</topic><topic>Crystallography</topic><topic>Crystallography - methods</topic><topic>Crystals</topic><topic>deuterium</topic><topic>Deuterium - chemistry</topic><topic>Hydrogen</topic><topic>Hydrogen - chemistry</topic><topic>Hydrogen Bonding</topic><topic>Hydrogen bonds</topic><topic>Isotopes</topic><topic>Macromolecular Substances</topic><topic>Molecular Conformation</topic><topic>Molecules</topic><topic>Neutron diffraction</topic><topic>Neutron Diffraction - methods</topic><topic>Neutrons</topic><topic>Plant Proteins - chemistry</topic><topic>Proteins</topic><topic>Solvents</topic><topic>Solvents - chemistry</topic><topic>Water - chemistry</topic><topic>X-radiation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chen, Julian C.-H</creatorcontrib><creatorcontrib>Hanson, B. 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Leif</au><au>Fisher, S. Zoë</au><au>Langan, Paul</au><au>Kovalevsky, Andrey Y</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography</atitle><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle><addtitle>Proc Natl Acad Sci U S A</addtitle><date>2012-09-18</date><risdate>2012</risdate><volume>109</volume><issue>38</issue><spage>15301</spage><epage>15306</epage><pages>15301-15306</pages><issn>0027-8424</issn><eissn>1091-6490</eissn><abstract>The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventional interactions are clearly defined, including a potential O─H…π interaction between a water molecule and the aromatic ring of residue Y44, as well as a number of potential C─H…O hydrogen bonds. Hydrogen bonding networks that are ambiguous in the 0.85 Å ultrahigh resolution X-ray structure can be resolved by accurate orientation of water molecules. Furthermore, the high resolution of the reported structure has allowed for the anisotropic description of 36 deuterium atoms in the protein. The visibility of hydrogen and deuterium atoms in the nuclear density maps is discussed in relation to the resolution of the neutron data.</abstract><cop>United States</cop><pub>National Academy of Sciences</pub><pmid>22949690</pmid><doi>10.1073/pnas.1208341109</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Anisotropy aromatic compounds Atoms Atoms & subatomic particles Biochemistry - methods Biological Sciences Brassica - metabolism Crystallization Crystallography Crystallography - methods Crystals deuterium Deuterium - chemistry Hydrogen Hydrogen - chemistry Hydrogen Bonding Hydrogen bonds Isotopes Macromolecular Substances Molecular Conformation Molecules Neutron diffraction Neutron Diffraction - methods Neutrons Plant Proteins - chemistry Proteins Solvents Solvents - chemistry Water - chemistry X-radiation |
| title | Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography |
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