Supplementary Material
Conformational Flexibility of the Leucine Binding Protein Examined by Protein Domain Coarse-Grained Molecular Dynamics

Iwona Siuda,1Lea Thøgersen1,2,*

1Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, Bioinformatics Research Centre, Aarhus University, C. F. Møllers Alle 8, DK-8000 Aarhus C, Denmark
2CLC bio, Silkeborgvej 2, DK-8000 Aarhus C, Denmark

* Corresponding author email:

Atom type / Atom name / Charge
amber99_39 / N / -0.066
amber99_17 / H1 / 0.238
amber99_17 / H2 / 0.238
amber99_17 / H3 / 0.238
amber99_11 / CA / -0.218
amber99_28 / HA / 0.128
amber99_11 / CB / -0.173
amber99_18 / HB1 / 0.125
amber99_18 / HB2 / 0.125
amber99_11 / CG / -0.121
amber99_18 / HG / 0.093
amber99_11 / CD1 / -0.213
amber99_18 / HD11 / 0.075
amber99_18 / HD12 / 0.075
amber99_18 / HD13 / 0.075
amber99_11 / CD2 / -0.213
amber99_18 / HD21 / 0.075
amber99_18 / HD22 / 0.075
amber99_18 / HD23 / 0.075
amber99_2 / C / 0.354
amber99_45 / OC1 / -0.492
amber99_45 / OC2 / -0.492

Table S1Atomic charges for the zwitter-ionic leucine ligand generated using Antechamber

KS / kJ/(mol∙nm2)
Rc/Å / 50 / 500 / 5000
8 / 0.50 / 0.63 / 0.65
9 / 0.53 / 0.65 / 0.67
10 / 0.55 / 0.67 / 0.68

Table S2 RMSIP values for simulations of the closed conformation of LBP with ligand, quantifying the essential subspace overlap between the AA simulation and the ELNEDIN simulations varying the cut-off distance, RC, and spring force constant, KS. Obtained from the last 80 ns of “real” time of simulation

KS / kJ/(mol∙nm2)
Rc/Å / 50 / 500 / 5000
8 / 0.60 / 0.69 / 0.74
9 / 0.61 / 0.74 / 0.74
10 / 0.68 / 0.75 / 0.75

Table S3 RMSIP values for simulations of the open conformation of LBP, quantifying the essential subspace overlap between the AA simulation and the ELNEDIN simulations varying the cut-off distance, RC, and spring force constant, KS. Obtained from the last 80 ns of “real” time of simulation

Closed / Open
Rc/Å / ELNEDIN / domELNEDIN / ELNEDIN / domELNEDIN
8 / 0.63 / 0.63 / 0.69 / 0.70
9 / 0.65 / 0.70 / 0.74 / 0.73

Table S4 RMSIP values for simulations of the closed conformation of LBP with ligand and the open conformation of LBP, quantifying the essential subspace overlap between the AA simulation and the ELNEDIN or domELNEDIN simulations. In all cases a force constant for the elastic network of 500 kJ/(mol∙nm2) was used, and the cut-off distance, RC, was varied as given in the table. Obtained from the last 80 ns of “real” time of simulation

Fig.S1The protocol flow for setting up and running simulations using the domELNEDIN approach. Applications and scripts are shown as square boxes with the name in bold and comments or descriptions in plain text. File name examples are given in italic writing

Fig.S2RMSD as a function of simulation time for ELNEDIN simulations of the closed conformation of LBP with ligand (red line).Nine different ENs were tested, varying the cut-off distance RC (Å) ϵ {8, 9, 10} and spring force constant KS (kJ·mol-1·nm-2) ϵ {50, 500, 5000}. Plots include results from the AA simulation (black line) for comparison

Fig.S3RMSD per residuefor the ELNEDIN simulations of the closed conformation of LBP with ligand (red line).Obtained from thelast 80 ns of “real” time of simulation.Nine different ENs were tested, varying the cut-off distance RC (Å) ϵ {8, 9, 10} and spring force constant KS (kJ·mol-1·nm-2) ϵ {50, 500, 5000}. Plots include results fromthe AA simulation (black line) for comparison

Fig.S4RMSF per residuefor the ELNEDIN simulations of the closed conformation of LBP with ligand (red line).Obtained from the last 80 ns of “real” time of simulation.Nine different ENs were tested, varying the cut-off distance RC (Å) ϵ {8, 9, 10} and spring force constant KS (kJ·mol-1·nm-2) ϵ {50, 500, 5000}. Plots include results from theAA simulation(black line) for comparison

Fig. S5RMSD as a function of simulation time forthe ELNEDIN simulations of the open conformation of LBP without ligand (red line).Nine different ENs were tested, varying the cut-off distance RC (Å) ϵ {8, 9, 10} and spring force constant KS (kJ·mol-1·nm-2) ϵ {50, 500, 5000}. Plots include results from the AA simulation (black line) for comparison

Fig. S6RMSD per residuefor the ELNEDIN simulations of the open conformation of LBP without ligand (red line).Obtained from the last 80 ns of “real” time of simulation.Nine different ENs were tested, varying the cut-off distance RC (Å) ϵ {8, 9, 10} and spring force constant KS (kJ·mol-1·nm-2) ϵ {50, 500, 5000}. Plots include results from theAA simulation(black line) for comparison

Fig. S7RMSF per residuefor the ELNEDIN simulations of the open conformation of LBP without ligand (red line).Obtained from the last 80 ns of “real” time of simulation.Nine different ENs were tested, varying the cut-off distance RC (Å) ϵ {8, 9, 10} and spring force constant KS (kJ·mol-1·nm-2) ϵ {50, 500, 5000}. Plots include results from theAA simulation(black line) for comparison

Fig. S8RMSD as a function of simulation time and RMSF and RMSD per residuefor the last 80 ns of simulation obtained from AA (black line) and80 ns of “real” time of simulation obtained from domELNEDIN simulations (red line) of the closed conformation of LBP with ligand (a) and the open conformation without ligand (b). The force constant parameter, KS, of the EN is in all cases 500 kJ·mol-1·nm-2and the cut-off, RC, is either 8 Å or 9 Å as indicated on the figure

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