Dynamical Resolution of QM/MM Near-UV Circular Dichroism Spectra of Low-Symmetry Systems
Near-UV circular dichroism (CD) spectroscopy is a widely used method that provides, among others, information about the tertiary structure of biomolecular systems such as proteins, RNA, or DNA. Experimental near-UV CD spectra of proteins reflect the CD signals averaged over the many conformations th...
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| Format: | Article |
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MDPI AG
2025-04-01
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| Series: | Chemistry |
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| Online Access: | https://www.mdpi.com/2624-8549/7/2/63 |
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| author | Jérémy Morere Tanguy Leyder Catherine Michaux Claude Millot Emmanuelle Bignon Thibaud Etienne |
| author_facet | Jérémy Morere Tanguy Leyder Catherine Michaux Claude Millot Emmanuelle Bignon Thibaud Etienne |
| author_sort | Jérémy Morere |
| collection | DOAJ |
| description | Near-UV circular dichroism (CD) spectroscopy is a widely used method that provides, among others, information about the tertiary structure of biomolecular systems such as proteins, RNA, or DNA. Experimental near-UV CD spectra of proteins reflect the CD signals averaged over the many conformations that these systems can adopt. Theoretical approaches have been developed to predict such spectroscopic properties and link modeled conformations of complex biosystems to easily accessible experimental data, without having the resort to costly structural biology techniques. However, these predictions are mostly generated on the basis of a single experimental structure, missing the dynamic information reflecting the protein conformational variability. Here, we describe a complete reformulation of the theoretical foundations behind the prediction of CD spectra. We propose a QM/MM-based automated pipeline that generates an average near-UV CD spectrum from a given MD ensemble in a fast manner based on these theoretical considerations and further test it on protein systems. This pipeline has been implemented in an open-source program called DichroProt. |
| format | Article |
| id | doaj-art-a0170e248c7643edb94e6b1ccba6b914 |
| institution | OA Journals |
| issn | 2624-8549 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Chemistry |
| spelling | doaj-art-a0170e248c7643edb94e6b1ccba6b9142025-08-20T02:17:14ZengMDPI AGChemistry2624-85492025-04-01726310.3390/chemistry7020063Dynamical Resolution of QM/MM Near-UV Circular Dichroism Spectra of Low-Symmetry SystemsJérémy Morere0Tanguy Leyder1Catherine Michaux2Claude Millot3Emmanuelle Bignon4Thibaud Etienne5Université de Lorraine, CNRS, LPCT, F-54000 Nancy, FranceLaboratoire de Chimie Physique des Biomolécules (CPB), Chemistry Department, Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000 Namur, BelgiumLaboratoire de Chimie Physique des Biomolécules (CPB), Chemistry Department, Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), 5000 Namur, BelgiumUniversité de Lorraine, CNRS, LPCT, F-54000 Nancy, FranceUniversité de Lorraine, CNRS, LPCT, F-54000 Nancy, FranceUniversité de Lorraine, CNRS, LPCT, F-54000 Nancy, FranceNear-UV circular dichroism (CD) spectroscopy is a widely used method that provides, among others, information about the tertiary structure of biomolecular systems such as proteins, RNA, or DNA. Experimental near-UV CD spectra of proteins reflect the CD signals averaged over the many conformations that these systems can adopt. Theoretical approaches have been developed to predict such spectroscopic properties and link modeled conformations of complex biosystems to easily accessible experimental data, without having the resort to costly structural biology techniques. However, these predictions are mostly generated on the basis of a single experimental structure, missing the dynamic information reflecting the protein conformational variability. Here, we describe a complete reformulation of the theoretical foundations behind the prediction of CD spectra. We propose a QM/MM-based automated pipeline that generates an average near-UV CD spectrum from a given MD ensemble in a fast manner based on these theoretical considerations and further test it on protein systems. This pipeline has been implemented in an open-source program called DichroProt.https://www.mdpi.com/2624-8549/7/2/63electronic circular dichroismmulti-scale excited state calculationsmatrix methodfirst-order perturbation theory |
| spellingShingle | Jérémy Morere Tanguy Leyder Catherine Michaux Claude Millot Emmanuelle Bignon Thibaud Etienne Dynamical Resolution of QM/MM Near-UV Circular Dichroism Spectra of Low-Symmetry Systems Chemistry electronic circular dichroism multi-scale excited state calculations matrix method first-order perturbation theory |
| title | Dynamical Resolution of QM/MM Near-UV Circular Dichroism Spectra of Low-Symmetry Systems |
| title_full | Dynamical Resolution of QM/MM Near-UV Circular Dichroism Spectra of Low-Symmetry Systems |
| title_fullStr | Dynamical Resolution of QM/MM Near-UV Circular Dichroism Spectra of Low-Symmetry Systems |
| title_full_unstemmed | Dynamical Resolution of QM/MM Near-UV Circular Dichroism Spectra of Low-Symmetry Systems |
| title_short | Dynamical Resolution of QM/MM Near-UV Circular Dichroism Spectra of Low-Symmetry Systems |
| title_sort | dynamical resolution of qm mm near uv circular dichroism spectra of low symmetry systems |
| topic | electronic circular dichroism multi-scale excited state calculations matrix method first-order perturbation theory |
| url | https://www.mdpi.com/2624-8549/7/2/63 |
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