Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin
We present a detailed analysis of the X-ray absorption near-edge structure (XANES) data on the Fe K-edge of CO Myoglobin based on a combined procedure of Molecular Dynamics (MD) calculations and MXAN (Minuit XANes) data analysis that we call D-MXAN. The ability of performing quantitative XANES data...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
AIP Publishing LLC and ACA
2018-09-01
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| Series: | Structural Dynamics |
| Online Access: | http://dx.doi.org/10.1063/1.5031806 |
| _version_ | 1811211526438125568 |
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| author | Giovanni Chillemi Massimiliano Anselmi Nico Sanna Cristiano Padrin Lodovico Balducci Marco Cammarata Elisabetta Pace Majed Chergui Maurizio Benfatto |
| author_facet | Giovanni Chillemi Massimiliano Anselmi Nico Sanna Cristiano Padrin Lodovico Balducci Marco Cammarata Elisabetta Pace Majed Chergui Maurizio Benfatto |
| author_sort | Giovanni Chillemi |
| collection | DOAJ |
| description | We present a detailed analysis of the X-ray absorption near-edge structure (XANES) data on the Fe K-edge of CO Myoglobin based on a combined procedure of Molecular Dynamics (MD) calculations and MXAN (Minuit XANes) data analysis that we call D-MXAN. The ability of performing quantitative XANES data analysis allows us to refine classical force field MD parameters, thus obtaining a reliable tool for the atomic investigation of this important model system for biological macromolecules. The iterative procedure here applied corrects the greatest part of the structural discrepancy between classical MD sampling and experimental determinations. Our procedure, moreover, is able to discriminate between different heme conformational basins visited during the MD simulation, thus demonstrating the necessity of a sampling on the order of tens of nanoseconds, even for an application such X-ray absorption spectroscopy data analysis. |
| first_indexed | 2024-04-12T05:15:34Z |
| format | Article |
| id | doaj.art-1580f2d0a3124dfbaca32874ba0d8544 |
| institution | Directory Open Access Journal |
| issn | 2329-7778 |
| language | English |
| last_indexed | 2024-04-12T05:15:34Z |
| publishDate | 2018-09-01 |
| publisher | AIP Publishing LLC and ACA |
| record_format | Article |
| series | Structural Dynamics |
| spelling | doaj.art-1580f2d0a3124dfbaca32874ba0d85442022-12-22T03:46:38ZengAIP Publishing LLC and ACAStructural Dynamics2329-77782018-09-0155054101054101-1210.1063/1.5031806003804SDYDynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobinGiovanni Chillemi0Massimiliano Anselmi1Nico Sanna2Cristiano Padrin3Lodovico Balducci4Marco Cammarata5Elisabetta Pace6Majed Chergui7Maurizio Benfatto8 CINECA, SuperComputing Applications and Innovation Department, Via dei Tizii 6, 00185 Roma, Italy Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany CINECA, SuperComputing Applications and Innovation Department, Via dei Tizii 6, 00185 Roma, Italy CINECA, SuperComputing Applications and Innovation Department, Via dei Tizii 6, 00185 Roma, Italy Université de Rennes 1, CNRS, Univ. Bretagne Loire, Institut de Physique de Rennes, UMR 6251, Rennes F-35042, France Université de Rennes 1, CNRS, Univ. Bretagne Loire, Institut de Physique de Rennes, UMR 6251, Rennes F-35042, France Laboratori Nazionali di Frascati, INFN- Via E. Fermi 44, 00044 Frascati, Italy Lab. of Ultrafast Spectroscopy (LSU) and Lausanne Centre for Ultrafast Science (LACUS), Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, Station 6, CH-1015 Lausanne, Switzerland Laboratori Nazionali di Frascati, INFN- Via E. Fermi 44, 00044 Frascati, ItalyWe present a detailed analysis of the X-ray absorption near-edge structure (XANES) data on the Fe K-edge of CO Myoglobin based on a combined procedure of Molecular Dynamics (MD) calculations and MXAN (Minuit XANes) data analysis that we call D-MXAN. The ability of performing quantitative XANES data analysis allows us to refine classical force field MD parameters, thus obtaining a reliable tool for the atomic investigation of this important model system for biological macromolecules. The iterative procedure here applied corrects the greatest part of the structural discrepancy between classical MD sampling and experimental determinations. Our procedure, moreover, is able to discriminate between different heme conformational basins visited during the MD simulation, thus demonstrating the necessity of a sampling on the order of tens of nanoseconds, even for an application such X-ray absorption spectroscopy data analysis.http://dx.doi.org/10.1063/1.5031806 |
| spellingShingle | Giovanni Chillemi Massimiliano Anselmi Nico Sanna Cristiano Padrin Lodovico Balducci Marco Cammarata Elisabetta Pace Majed Chergui Maurizio Benfatto Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin Structural Dynamics |
| title | Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin |
| title_full | Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin |
| title_fullStr | Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin |
| title_full_unstemmed | Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin |
| title_short | Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin |
| title_sort | dynamic multiple scattering treatment of x ray absorption parameterization of a new molecular dynamics force field for myoglobin |
| url | http://dx.doi.org/10.1063/1.5031806 |
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