X-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy
X-ray absorption spectroscopy is exquisitely sensitive to the coordination geometry of an absorbing atom and therefore allows bond distances and angles of the surrounding atomic cluster to be measured with atomic resolution. By contrast, the accuracy and resolution of metalloprotein active sites obt...
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ftpubmed:oai:pubmedcentral.nih.gov:1851025 2023-05-15T18:26:40+02:00 X-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy Arcovito, Alessandro Benfatto, Maurizio Cianci, Michele Hasnain, S. Samar Nienhaus, Karin Nienhaus, G. Ulrich Savino, Carmelinda Strange, Richard W. Vallone, Beatrice Della Longa, Stefano 2007-04-10 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851025 http://www.ncbi.nlm.nih.gov/pubmed/17404234 https://doi.org/10.1073/pnas.0608411104 en eng National Academy of Sciences http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851025 http://www.ncbi.nlm.nih.gov/pubmed/17404234 http://dx.doi.org/10.1073/pnas.0608411104 © 2007 by The National Academy of Sciences of the USA Biological Sciences Text 2007 ftpubmed https://doi.org/10.1073/pnas.0608411104 2013-08-31T20:03:53Z X-ray absorption spectroscopy is exquisitely sensitive to the coordination geometry of an absorbing atom and therefore allows bond distances and angles of the surrounding atomic cluster to be measured with atomic resolution. By contrast, the accuracy and resolution of metalloprotein active sites obtainable from x-ray crystallography are often insufficient to analyze the electronic properties of the metals that are essential for their biological functions. Here, we demonstrate that the combination of both methods on the same metalloprotein single crystal yields a structural model of the protein with exceptional active-site resolution. To this end, we have collected an x-ray diffraction data set to 1.4-Å resolution and Fe K-edge polarized x-ray absorption near edge structure (XANES) spectra on the same cyanomet sperm whale myoglobin crystal. The XANES spectra were quantitatively analyzed by using a method based on the multiple scattering approach, which yielded Fe-heme structural parameters with ±(0.02–0.07)-Å accuracy on the atomic distances and ±7° on the Fe–CN angle. These XANES-derived parameters were subsequently used as restraints in the crystal structure refinement. By combining XANES and x-ray diffraction, we have obtained an cyanomet sperm whale myoglobin structural model with a higher precision of the bond lengths and angles at the active site than would have been possible with crystallographic analysis alone. Text Sperm whale PubMed Central (PMC) Proceedings of the National Academy of Sciences 104 15 6211 6216 |
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Biological Sciences Arcovito, Alessandro Benfatto, Maurizio Cianci, Michele Hasnain, S. Samar Nienhaus, Karin Nienhaus, G. Ulrich Savino, Carmelinda Strange, Richard W. Vallone, Beatrice Della Longa, Stefano X-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy |
topic_facet |
Biological Sciences |
description |
X-ray absorption spectroscopy is exquisitely sensitive to the coordination geometry of an absorbing atom and therefore allows bond distances and angles of the surrounding atomic cluster to be measured with atomic resolution. By contrast, the accuracy and resolution of metalloprotein active sites obtainable from x-ray crystallography are often insufficient to analyze the electronic properties of the metals that are essential for their biological functions. Here, we demonstrate that the combination of both methods on the same metalloprotein single crystal yields a structural model of the protein with exceptional active-site resolution. To this end, we have collected an x-ray diffraction data set to 1.4-Å resolution and Fe K-edge polarized x-ray absorption near edge structure (XANES) spectra on the same cyanomet sperm whale myoglobin crystal. The XANES spectra were quantitatively analyzed by using a method based on the multiple scattering approach, which yielded Fe-heme structural parameters with ±(0.02–0.07)-Å accuracy on the atomic distances and ±7° on the Fe–CN angle. These XANES-derived parameters were subsequently used as restraints in the crystal structure refinement. By combining XANES and x-ray diffraction, we have obtained an cyanomet sperm whale myoglobin structural model with a higher precision of the bond lengths and angles at the active site than would have been possible with crystallographic analysis alone. |
format |
Text |
author |
Arcovito, Alessandro Benfatto, Maurizio Cianci, Michele Hasnain, S. Samar Nienhaus, Karin Nienhaus, G. Ulrich Savino, Carmelinda Strange, Richard W. Vallone, Beatrice Della Longa, Stefano |
author_facet |
Arcovito, Alessandro Benfatto, Maurizio Cianci, Michele Hasnain, S. Samar Nienhaus, Karin Nienhaus, G. Ulrich Savino, Carmelinda Strange, Richard W. Vallone, Beatrice Della Longa, Stefano |
author_sort |
Arcovito, Alessandro |
title |
X-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy |
title_short |
X-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy |
title_full |
X-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy |
title_fullStr |
X-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy |
title_full_unstemmed |
X-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy |
title_sort |
x-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy |
publisher |
National Academy of Sciences |
publishDate |
2007 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851025 http://www.ncbi.nlm.nih.gov/pubmed/17404234 https://doi.org/10.1073/pnas.0608411104 |
genre |
Sperm whale |
genre_facet |
Sperm whale |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851025 http://www.ncbi.nlm.nih.gov/pubmed/17404234 http://dx.doi.org/10.1073/pnas.0608411104 |
op_rights |
© 2007 by The National Academy of Sciences of the USA |
op_doi |
https://doi.org/10.1073/pnas.0608411104 |
container_title |
Proceedings of the National Academy of Sciences |
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104 |
container_issue |
15 |
container_start_page |
6211 |
op_container_end_page |
6216 |
_version_ |
1766208640914554880 |