Molecular structure refinement based on residual dipolar couplings: a comparison of the molecular rotational-sampling method with the alignment-tensor approach
In NMR experiments, residual dipolar couplings (RDCs) in a molecule can be measured by averaging the dipolar couplings (DCs) over the rotational motion of a molecule in an environment that induces a slight anisotropic orientation distribution of the molecule. Since the shape of the anisotropic distr...
| Main Authors: | , , , , , |
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| Format: | Journal article |
| Language: | English |
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American Chemical Society
2024
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| _version_ | 1811139725951500288 |
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| author | Pechlaner, M van Gunsteren, WF Smith, LJ Stankiewicz, B Wirz, LN Hansen, N |
| author_facet | Pechlaner, M van Gunsteren, WF Smith, LJ Stankiewicz, B Wirz, LN Hansen, N |
| author_sort | Pechlaner, M |
| collection | OXFORD |
| description | In NMR experiments, residual dipolar couplings (RDCs) in a molecule can be measured by averaging the dipolar couplings (DCs) over the rotational motion of a molecule in an environment that induces a slight anisotropic orientation distribution of the molecule. Since the shape of the anisotropic distribution cannot be measured, it is standard practice to use a particular orientation distribution of the molecule with respect to the magnetic field, in the form of a so-called alignment tensor (AT), to calculate RDC-values for the molecule. Since the same alignment tensor is commonly used to calculate the different RDCs of a molecule, this approach rests on the assumption that the rotational motion of the molecule is decoupled from its internal motions and that the molecule is rigid. The validity of these two assumptions is investigated for a small, simple molecule, using a relatively rigid atomic interaction function or force field and a more flexible one. By simulating the molecule using an orientation-biasing force an anisotropic rotational distribution can be generated, for which RDCs can be obtained. Using these RDCs as target RDCs when applying one of the two approaches of structure refinement based on RDCs, it can be investigated how well the target RDCs are approximated in the RDC restraining and whether the corresponding nonuniform orientation distribution is reproduced. For the relatively rigid version of the molecule, the AT approach reproduces the target RDC-values, although the nonuniform orientation distribution of the angle θ<sub><i>ab,H</i></sub> between the vector <i>r⃗</i><sub><i>ab</i></sub> connecting two atoms <i>a</i> and <i>b</i> in the molecule and the vector representing the direction of the magnetic field <i>H⃗</i> as generated in the orientation-biasing simulation cannot be reproduced in the AT RDC-restraining simulation. For the relatively flexible version of the molecule, the AT approach fails to reproduce both the target RDC values and the nonuniform orientation distribution. For biomolecules with flexible parts, the application of the AT approach is thus not recommended. Instead, a method based on sampling of the rotational and internal degrees of freedom of the molecule should be applied in molecular structure determination or refinement based on measured RDCs. |
| first_indexed | 2024-09-25T04:10:40Z |
| format | Journal article |
| id | oxford-uuid:825b1144-2d0a-494e-b8ef-7ea4d27332ec |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-09-25T04:10:40Z |
| publishDate | 2024 |
| publisher | American Chemical Society |
| record_format | dspace |
| spelling | oxford-uuid:825b1144-2d0a-494e-b8ef-7ea4d27332ec2024-06-21T12:57:42ZMolecular structure refinement based on residual dipolar couplings: a comparison of the molecular rotational-sampling method with the alignment-tensor approachJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:825b1144-2d0a-494e-b8ef-7ea4d27332ecEnglishSymplectic ElementsAmerican Chemical Society2024Pechlaner, Mvan Gunsteren, WFSmith, LJStankiewicz, BWirz, LNHansen, NIn NMR experiments, residual dipolar couplings (RDCs) in a molecule can be measured by averaging the dipolar couplings (DCs) over the rotational motion of a molecule in an environment that induces a slight anisotropic orientation distribution of the molecule. Since the shape of the anisotropic distribution cannot be measured, it is standard practice to use a particular orientation distribution of the molecule with respect to the magnetic field, in the form of a so-called alignment tensor (AT), to calculate RDC-values for the molecule. Since the same alignment tensor is commonly used to calculate the different RDCs of a molecule, this approach rests on the assumption that the rotational motion of the molecule is decoupled from its internal motions and that the molecule is rigid. The validity of these two assumptions is investigated for a small, simple molecule, using a relatively rigid atomic interaction function or force field and a more flexible one. By simulating the molecule using an orientation-biasing force an anisotropic rotational distribution can be generated, for which RDCs can be obtained. Using these RDCs as target RDCs when applying one of the two approaches of structure refinement based on RDCs, it can be investigated how well the target RDCs are approximated in the RDC restraining and whether the corresponding nonuniform orientation distribution is reproduced. For the relatively rigid version of the molecule, the AT approach reproduces the target RDC-values, although the nonuniform orientation distribution of the angle θ<sub><i>ab,H</i></sub> between the vector <i>r⃗</i><sub><i>ab</i></sub> connecting two atoms <i>a</i> and <i>b</i> in the molecule and the vector representing the direction of the magnetic field <i>H⃗</i> as generated in the orientation-biasing simulation cannot be reproduced in the AT RDC-restraining simulation. For the relatively flexible version of the molecule, the AT approach fails to reproduce both the target RDC values and the nonuniform orientation distribution. For biomolecules with flexible parts, the application of the AT approach is thus not recommended. Instead, a method based on sampling of the rotational and internal degrees of freedom of the molecule should be applied in molecular structure determination or refinement based on measured RDCs. |
| spellingShingle | Pechlaner, M van Gunsteren, WF Smith, LJ Stankiewicz, B Wirz, LN Hansen, N Molecular structure refinement based on residual dipolar couplings: a comparison of the molecular rotational-sampling method with the alignment-tensor approach |
| title | Molecular structure refinement based on residual dipolar couplings: a comparison of the molecular rotational-sampling method with the alignment-tensor approach |
| title_full | Molecular structure refinement based on residual dipolar couplings: a comparison of the molecular rotational-sampling method with the alignment-tensor approach |
| title_fullStr | Molecular structure refinement based on residual dipolar couplings: a comparison of the molecular rotational-sampling method with the alignment-tensor approach |
| title_full_unstemmed | Molecular structure refinement based on residual dipolar couplings: a comparison of the molecular rotational-sampling method with the alignment-tensor approach |
| title_short | Molecular structure refinement based on residual dipolar couplings: a comparison of the molecular rotational-sampling method with the alignment-tensor approach |
| title_sort | molecular structure refinement based on residual dipolar couplings a comparison of the molecular rotational sampling method with the alignment tensor approach |
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