Journal: Communications Biology

Article Title: Dynamic pre-structuration of lipid nanodomain-segregating remorin proteins

doi: 10.1038/s42003-024-07330-y

Figure Lengend Snippet: a Structural bundle of ten NMR structures. N- and C-terminal endings are indicated on the structures. b Secondary structure propensity of REM-CA structures simulated with atomistic molecular dynamics simulations using the AMOEBA forcefield over 1 μs. The color code for structural motifs is indicated aside (RC random coil). Indicated below is a cartoon of the secondary structure as determined by AF2 performed on the respective REM-CA, CcpNMR analysis , and CNS structure calculation . c Examples for the RMSD of the NMR structures and the RMSF of MD simulations are shown for the REM-CA of AtREM6.2, AtREM6.3, and AtREM6.5 (complete analysis is provided in Supplementary Fig. 4 and ).

Article Snippet: Adaptive sampling MD simulations using the AMOEBA forcefield have the advantage to, respectively, optimally sample the conformational space through sequentially sampling the previously calculated conformational space, and to most accurately represent atomic charges and polarity with respect to other available forcefields (M&M subsection: Molecular dynamics simulation using the polarizable force field AMOEBA and Adaptive sampling).

Techniques:

Journal: Communications Biology

Article Title: Dynamic pre-structuration of lipid nanodomain-segregating remorin proteins

doi: 10.1038/s42003-024-07330-y

Figure Lengend Snippet: a Structural bundles of ten NMR structures for StREM1.3 171-198 , StREM 160-198 , and StREM 150-198 . The N-terminal ending is indicated on the structures. b Structure propensity of REM-CA structures simulated with atomistic molecular dynamics simulations using the AMOEBA forcefield over 1 μs (see also ). The color code for structural motifs is as in Fig. . Indicated below is a cartoon of the secondary structure as determined by AF2 performed on the respective REM-CA, CcpNMR analysis , and CNS structure calculation , as well as the RMSD (blue) of the NMR structures and the RMSF (red) of MD simulations.

Article Snippet: Adaptive sampling MD simulations using the AMOEBA forcefield have the advantage to, respectively, optimally sample the conformational space through sequentially sampling the previously calculated conformational space, and to most accurately represent atomic charges and polarity with respect to other available forcefields (M&M subsection: Molecular dynamics simulation using the polarizable force field AMOEBA and Adaptive sampling).

Techniques:

Journal: Communications Biology

Article Title: Dynamic pre-structuration of lipid nanodomain-segregating remorin proteins

doi: 10.1038/s42003-024-07330-y

Figure Lengend Snippet: a Intermolecular contact map of Cα of monomer 1 and all atoms of monomer 2 (range 3–10 Å) of the structures adopted throughout the 1 μs atomistic MD simulation based on the Amber forcefield , indicated aside are the conserved Motifs 1 and 2 (residue-specific molecular contacts detailed in Supplementary Fig. ). The blue scale is decoded in the right-hand panel. b AF2-predicted dimeric coiled-coil structures at the beginning (green) and at the end (blue) of 1 μs atomistic MD simulation. c Distance plot of the Cα-Cα contacts over 1 μs atomistic MD simulation of three selected residues of StREM 67-198 (right panel), highlighted on the structure in the left panel (Leu126 monomer_1 -Leu155 monomer_2 , Leu137 monomer_1 -Leu137 monomer_2 , and Leu155 monomer_1 -Leu126 monomer_2 ).

Article Snippet: Adaptive sampling MD simulations using the AMOEBA forcefield have the advantage to, respectively, optimally sample the conformational space through sequentially sampling the previously calculated conformational space, and to most accurately represent atomic charges and polarity with respect to other available forcefields (M&M subsection: Molecular dynamics simulation using the polarizable force field AMOEBA and Adaptive sampling).

Techniques: Residue