AlphaFold2-generated conformations overlap well with crystal structures of the open and closed state of GLIC.
<p>(A, B) Overlay of experimentally determined crystal structures in (A) the closed state (PDB ID 4NPQ) and (B) the open state (PDB ID 4HFI) with the corresponding prediction (visualized using VMD [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1013187#pcbi....
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2025
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| _version_ | 1852018918021922816 |
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| author | Samuel Eriksson Lidbrink (21616146) |
| author2 | Rebecca J. Howard (14670459) Nandan Haloi (14670453) Erik Lindahl (10338) |
| author2_role | author author author |
| author_facet | Samuel Eriksson Lidbrink (21616146) Rebecca J. Howard (14670459) Nandan Haloi (14670453) Erik Lindahl (10338) |
| author_role | author |
| dc.creator.none.fl_str_mv | Samuel Eriksson Lidbrink (21616146) Rebecca J. Howard (14670459) Nandan Haloi (14670453) Erik Lindahl (10338) |
| dc.date.none.fl_str_mv | 2025-06-27T17:57:25Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pcbi.1013187.g004 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/AlphaFold2-generated_conformations_overlap_well_with_crystal_structures_of_the_open_and_closed_state_of_GLIC_/29428908 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biophysics Biochemistry Computational Biology Biological Sciences not elsewhere classified Chemical Sciences not elsewhere classified Physical Sciences not elsewhere classified markov state models machine learning algorithms also accurately sample sample multiple conformations open upon activation landscape requires understanding transition pathway resolved identify apparent closed angle neutron scattering protein &# 8217 alphafold </ p target environmental conditions activating conditions respectively weighted conformational ensemble combine af sampling angle scattering curves angle scattering target conditions activating conditions conformational landscape conformational ensemble stable conformations extensive sampling particular conditions transition pathways transition occurs predicted closed closed channels open states xlink "> without using structural information several strategies rigid proteins projects onto predicted basins membrane protein magnitude faster efficient way complete characterization |
| dc.title.none.fl_str_mv | AlphaFold2-generated conformations overlap well with crystal structures of the open and closed state of GLIC. |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p>(A, B) Overlay of experimentally determined crystal structures in (A) the closed state (PDB ID 4NPQ) and (B) the open state (PDB ID 4HFI) with the corresponding prediction (visualized using VMD [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1013187#pcbi.1013187.ref042" target="_blank">42</a>]). The structures were aligned to minimize the RMSD of all C atoms in both the predicted and corresponding crystal structures. The pore hydration profiles for the predicted structures (calculated using HOLE [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1013187#pcbi.1013187.ref043" target="_blank">43</a>]) are also shown, with cyan and orange signifying wide (radius > 2.3 Å) and narrow (radius < 2.3 Å) parts of the pore, respectively. (C) Distance between the centers of mass of the pore and that of the upper part of the pore lining M2 helix (M2 spread) for AF-generated conformations ranging from closed-like (in red) to open-like (in blue). (D) The corresponding values for the predictions and the crystal structures as well as the density of states for all AF-generated conformations with an average pLDDT score above 75. (E, F) Upper spread of the extracellular domain (ECD), depicted as in panels C and D, respectively.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_2e1e0604ca85cce94de2e5ec0b45ea4f |
| identifier_str_mv | 10.1371/journal.pcbi.1013187.g004 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/29428908 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | AlphaFold2-generated conformations overlap well with crystal structures of the open and closed state of GLIC.Samuel Eriksson Lidbrink (21616146)Rebecca J. Howard (14670459)Nandan Haloi (14670453)Erik Lindahl (10338)BiophysicsBiochemistryComputational BiologyBiological Sciences not elsewhere classifiedChemical Sciences not elsewhere classifiedPhysical Sciences not elsewhere classifiedmarkov state modelsmachine learning algorithmsalso accurately samplesample multiple conformationsopen upon activationlandscape requires understandingtransition pathway resolvedidentify apparent closedangle neutron scatteringprotein &# 8217alphafold </ ptarget environmental conditionsactivating conditions respectivelyweighted conformational ensemblecombine af samplingangle scattering curvesangle scatteringtarget conditionsactivating conditionsconformational landscapeconformational ensemblestable conformationsextensive samplingparticular conditionstransition pathwaystransition occurspredicted closedclosed channelsopen statesxlink ">without usingstructural informationseveral strategiesrigid proteinsprojects ontopredicted basinsmembrane proteinmagnitude fasterefficient waycomplete characterization<p>(A, B) Overlay of experimentally determined crystal structures in (A) the closed state (PDB ID 4NPQ) and (B) the open state (PDB ID 4HFI) with the corresponding prediction (visualized using VMD [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1013187#pcbi.1013187.ref042" target="_blank">42</a>]). The structures were aligned to minimize the RMSD of all C atoms in both the predicted and corresponding crystal structures. The pore hydration profiles for the predicted structures (calculated using HOLE [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1013187#pcbi.1013187.ref043" target="_blank">43</a>]) are also shown, with cyan and orange signifying wide (radius > 2.3 Å) and narrow (radius < 2.3 Å) parts of the pore, respectively. (C) Distance between the centers of mass of the pore and that of the upper part of the pore lining M2 helix (M2 spread) for AF-generated conformations ranging from closed-like (in red) to open-like (in blue). (D) The corresponding values for the predictions and the crystal structures as well as the density of states for all AF-generated conformations with an average pLDDT score above 75. (E, F) Upper spread of the extracellular domain (ECD), depicted as in panels C and D, respectively.</p>2025-06-27T17:57:25ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1371/journal.pcbi.1013187.g004https://figshare.com/articles/figure/AlphaFold2-generated_conformations_overlap_well_with_crystal_structures_of_the_open_and_closed_state_of_GLIC_/29428908CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/294289082025-06-27T17:57:25Z |
| spellingShingle | AlphaFold2-generated conformations overlap well with crystal structures of the open and closed state of GLIC. Samuel Eriksson Lidbrink (21616146) Biophysics Biochemistry Computational Biology Biological Sciences not elsewhere classified Chemical Sciences not elsewhere classified Physical Sciences not elsewhere classified markov state models machine learning algorithms also accurately sample sample multiple conformations open upon activation landscape requires understanding transition pathway resolved identify apparent closed angle neutron scattering protein &# 8217 alphafold </ p target environmental conditions activating conditions respectively weighted conformational ensemble combine af sampling angle scattering curves angle scattering target conditions activating conditions conformational landscape conformational ensemble stable conformations extensive sampling particular conditions transition pathways transition occurs predicted closed closed channels open states xlink "> without using structural information several strategies rigid proteins projects onto predicted basins membrane protein magnitude faster efficient way complete characterization |
| status_str | publishedVersion |
| title | AlphaFold2-generated conformations overlap well with crystal structures of the open and closed state of GLIC. |
| title_full | AlphaFold2-generated conformations overlap well with crystal structures of the open and closed state of GLIC. |
| title_fullStr | AlphaFold2-generated conformations overlap well with crystal structures of the open and closed state of GLIC. |
| title_full_unstemmed | AlphaFold2-generated conformations overlap well with crystal structures of the open and closed state of GLIC. |
| title_short | AlphaFold2-generated conformations overlap well with crystal structures of the open and closed state of GLIC. |
| title_sort | AlphaFold2-generated conformations overlap well with crystal structures of the open and closed state of GLIC. |
| topic | Biophysics Biochemistry Computational Biology Biological Sciences not elsewhere classified Chemical Sciences not elsewhere classified Physical Sciences not elsewhere classified markov state models machine learning algorithms also accurately sample sample multiple conformations open upon activation landscape requires understanding transition pathway resolved identify apparent closed angle neutron scattering protein &# 8217 alphafold </ p target environmental conditions activating conditions respectively weighted conformational ensemble combine af sampling angle scattering curves angle scattering target conditions activating conditions conformational landscape conformational ensemble stable conformations extensive sampling particular conditions transition pathways transition occurs predicted closed closed channels open states xlink "> without using structural information several strategies rigid proteins projects onto predicted basins membrane protein magnitude faster efficient way complete characterization |