Molecular dynamics simulations of highly crowded ... AWS
Supporting Information for:
Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other Casey T. Andrews, and Adrian H. Elcock* Department of Biochemistry, University of Iowa, Iowa City, IA 52242 e-mail: [email protected]
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Supporting Figure Legends Figure S1
Views of the glycine systems; clockwise from top-left: 50, 100, 200 and 300 mg/ml. Glycine molecules are shown as van der Waals spheres; water molecules as licorice bonds. This figure was prepared with VMD version 1.9.1.1
Figure S2
Graph showing density versus solute concentration for all four amino acids simulated using all eight combinations of force field and water model: glycine (blue circle), valine (green square), phenylalanine (yellow upward triangle), asparagine (red downward triangle). Lines show fits of the data to quadratic functions; in all cases, error bars are expected to be smaller than the symbol sizes. Symbols colored white are for conditions in which dielectric constant calculations (Figure S6) gave results that were clear outliers from the expected trends; since such results suggest aggregation (consistent with the results shown in Figure S9), these data points have been omitted from the fits.
Figure S3
Bar chart comparing the scaled density increments obtained from simulations – using each force field and water model combination – with experiment. Density increments were calculated using only data from simulations performed up to 50 mg/ml solute concentration.
Figure S4
Graph showing viscosity versus solute concentration for all four amino acids simulated using all eight combinations of force field and water model: glycine (blue circle), valine (green square), phenylalanine (yellow upward triangle), asparagine (red downward triangle). Lines show fits of the data to quadratic functions; error bars show the standard deviation obtained from ten independent measurements of the viscosity (see text). Symbols colored white are for conditions in which dielectric constant calculations (Figure S6) gave results that were clear outliers from the expected trends; since such results suggest 2
aggregation (consistent with the results shown in Figure S9), these data points have been omitted from the fits. Figure S5
Bar chart comparing the scaled viscosity increments obtained from simulations – using each force field and water model combination – with experiment. Viscosity increments were calculated using only data from simulations performed up to 50 mg/ml solute concentration.
Figure S6
Graph showing dielectric constant versus solute concentration for all four amino acids simulated using all eight combinations of force field and water model: glycine (blue circle), valine (green square), phenylalanine (yellow upward triangle), asparagine (red downward triangle). Lines show fits of the data to quadratic functions; error bars show the standard deviation obtained from ten independent measurements of the dielectric constant (see text). Symbols colored white are clear outliers from the expected trends; since such results suggest aggregation (consistent with the results shown in Figure S9), these data points have been omitted from the fits.
Figure S7
Bar chart comparing the scaled dielectric increments obtained from simulations – using each force field and water model combination – with experiment. Dielectric increments were calculated using only data from simulations performed up to 50 mg/ml solute concentration.
Figure S8
Plot of scaled dielectric increments obtained from simulations of concentrated solutions with the average dipole moment of a single molecule simulated with the same force field and water model combination. Results are shown for all nonOPLS-AA/L force fields; error bars indicate the standard deviation of the solute dipole moments calculated for a single molecule during a 10 ns MD simulation. Shown at bottom right is a histogram of the solute dipole moments calculated for 3
a single asparagine molecule in a simulation performed with Amber ff99SBILDN and the TIP4P-Ew water model; similar histograms were obtained for the other force field and water model combinations. Figure S9
Plots show the fraction of solute molecules that are members of clusters of various sizes at each of the following solute concentrations: 50 (blue), 100 (green), 200 (yellow) and 300 mg/ml (red) for all four amino acids. The panels marked ‘ideal’ (top row) shows the distribution of cluster sizes obtained when solute molecules are randomly placed within the simulation box (see text).
Figure S10
Plots show the radial distribution function (RDF) for the intermolecular interactions of the carboxylate oxygens and the amino nitrogen for glycine (left) and for valine (right); for each molecule pair only the closest distance between either carboxyl oxygen and the amino nitrogen is used in the calculation of the RDF. Results are shown for each of the following solute concentrations: 50 (blue), 100 (green), 200 (yellow) and 300 mg/ml (red). Insets show close-up views of the first peak in the RDF. Note that the glycine RDFs were calculated at higher resolution in order to determine whether there was any shift in the position of the first peak with respect to increasing solute concentration.
Figure S11
Plots show the RDF for the intermolecular interactions of the carboxylate oxygens and the amino nitrogen for phenylalanine (left) and for asparagine (right); for each molecule pair only the closest distance between either carboxyl oxygen and the amino nitrogen is used in the calculation of the RDF. Results are shown for each of the following solute concentrations: 50 (blue), 100 (green), 200 (yellow) and 300 mg/ml (red). Insets show close-up views of the first peak in the RDF.
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Figure S12
Plot of the height of the first peak in the glycine salt bridge RDF versus the distance at which the peak occurs for all force field and water combinations: Amber ff99SB-ILDN + TIP3P (blue circle), Amber ff99SB-ILDN + TIP4P-Ew (blue triangle), Amber ff99SB-ILDN + SPC/E (blue square), CHARMM27 + TIP3P (green circle), GROMOS 53A6 + SPC (red circle), OPLS-AA/L + TIP3P (yellow circle), OPLS-AA/L + TIP4P (yellow triangle), OPLS-AA/L + TIP5P (yellow square). Note that the y-axis is plotted on a logarithmic scale.
Figure S13
Plots show the RDF for the intermolecular interactions of valine sidechains; for each molecule pair only the closest distance between any pair of sidechain heavy atoms was used in the calculation of the RDF. Results are shown for each of the following solute concentrations: 50 (blue), 100 (green), 200 (yellow) and 300 mg/ml (red). Insets show close-up views of the first peak in the RDF.
Figure S14
Plots show the effective G for the intermolecular interactions of valine sidechains relative to the values obtained from simulations performed at 50 mg/ml. Results are shown for each of the following force field and water model combinations: Amber ff99SB-ILDN + TIP3P (blue circle), Amber ff99SB-ILDN + TIP4P-Ew (blue triangle), Amber ff99SB-ILDN + SPC/E (blue square), CHARMM27 + TIP3P (green circle), GROMOS 53A6 + SPC (red circle).
Figure S15
Plots show the RDF for the intermolecular interactions of phenylalanine sidechains; for each molecule pair only the closest distance between any pair of sidechain heavy atoms is used in the calculation of the RDF. Results are shown for each of the following solute concentrations: 50 (blue), 100 (green), 200 (yellow) and 300 mg/ml (red). Insets show close-up views of the first peak in the RDF.
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Figure S16
Plots show the effective G for the intermolecular interactions of phenylalanine sidechains relative to the values obtained from simulations performed at 50 mg/ml. Results are shown for each of the following force field and water model combinations: Amber ff99SB-ILDN + TIP3P (blue circle), Amber ff99SB-ILDN + TIP4P-Ew (blue triangle), Amber ff99SB-ILDN + SPC/E (blue square), CHARMM27 + TIP3P (green circle), GROMOS 53A6 + SPC (red circle).
Figure S17
Plots show the effective G for the intermolecular interactions of asparagine sidechains relative to the values obtained from simulations performed at 50 mg/ml. Results are shown for each of the following force field and water model combinations: Amber ff99SB-ILDN + TIP3P (blue circle), Amber ff99SB-ILDN + TIP4P-Ew (blue triangle), Amber ff99SB-ILDN + SPC/E (blue square), CHARMM27 + TIP3P (green circle), GROMOS 53A6 + SPC (red circle).
Supporting References 1.
Humphrey, W., Dalke, A., and K. Schulten. VMD – Visual Molecular Dynamics. J. Molec. Graph. 1996, 14, 33-38
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Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other Casey T. Andrews, and Adrian H. Elcock* Department of Biochemistry, University of Iowa, Iowa City, IA 52242 e-mail: [email protected]
1
Supporting Figure Legends Figure S1
Views of the glycine systems; clockwise from top-left: 50, 100, 200 and 300 mg/ml. Glycine molecules are shown as van der Waals spheres; water molecules as licorice bonds. This figure was prepared with VMD version 1.9.1.1
Figure S2
Graph showing density versus solute concentration for all four amino acids simulated using all eight combinations of force field and water model: glycine (blue circle), valine (green square), phenylalanine (yellow upward triangle), asparagine (red downward triangle). Lines show fits of the data to quadratic functions; in all cases, error bars are expected to be smaller than the symbol sizes. Symbols colored white are for conditions in which dielectric constant calculations (Figure S6) gave results that were clear outliers from the expected trends; since such results suggest aggregation (consistent with the results shown in Figure S9), these data points have been omitted from the fits.
Figure S3
Bar chart comparing the scaled density increments obtained from simulations – using each force field and water model combination – with experiment. Density increments were calculated using only data from simulations performed up to 50 mg/ml solute concentration.
Figure S4
Graph showing viscosity versus solute concentration for all four amino acids simulated using all eight combinations of force field and water model: glycine (blue circle), valine (green square), phenylalanine (yellow upward triangle), asparagine (red downward triangle). Lines show fits of the data to quadratic functions; error bars show the standard deviation obtained from ten independent measurements of the viscosity (see text). Symbols colored white are for conditions in which dielectric constant calculations (Figure S6) gave results that were clear outliers from the expected trends; since such results suggest 2
aggregation (consistent with the results shown in Figure S9), these data points have been omitted from the fits. Figure S5
Bar chart comparing the scaled viscosity increments obtained from simulations – using each force field and water model combination – with experiment. Viscosity increments were calculated using only data from simulations performed up to 50 mg/ml solute concentration.
Figure S6
Graph showing dielectric constant versus solute concentration for all four amino acids simulated using all eight combinations of force field and water model: glycine (blue circle), valine (green square), phenylalanine (yellow upward triangle), asparagine (red downward triangle). Lines show fits of the data to quadratic functions; error bars show the standard deviation obtained from ten independent measurements of the dielectric constant (see text). Symbols colored white are clear outliers from the expected trends; since such results suggest aggregation (consistent with the results shown in Figure S9), these data points have been omitted from the fits.
Figure S7
Bar chart comparing the scaled dielectric increments obtained from simulations – using each force field and water model combination – with experiment. Dielectric increments were calculated using only data from simulations performed up to 50 mg/ml solute concentration.
Figure S8
Plot of scaled dielectric increments obtained from simulations of concentrated solutions with the average dipole moment of a single molecule simulated with the same force field and water model combination. Results are shown for all nonOPLS-AA/L force fields; error bars indicate the standard deviation of the solute dipole moments calculated for a single molecule during a 10 ns MD simulation. Shown at bottom right is a histogram of the solute dipole moments calculated for 3
a single asparagine molecule in a simulation performed with Amber ff99SBILDN and the TIP4P-Ew water model; similar histograms were obtained for the other force field and water model combinations. Figure S9
Plots show the fraction of solute molecules that are members of clusters of various sizes at each of the following solute concentrations: 50 (blue), 100 (green), 200 (yellow) and 300 mg/ml (red) for all four amino acids. The panels marked ‘ideal’ (top row) shows the distribution of cluster sizes obtained when solute molecules are randomly placed within the simulation box (see text).
Figure S10
Plots show the radial distribution function (RDF) for the intermolecular interactions of the carboxylate oxygens and the amino nitrogen for glycine (left) and for valine (right); for each molecule pair only the closest distance between either carboxyl oxygen and the amino nitrogen is used in the calculation of the RDF. Results are shown for each of the following solute concentrations: 50 (blue), 100 (green), 200 (yellow) and 300 mg/ml (red). Insets show close-up views of the first peak in the RDF. Note that the glycine RDFs were calculated at higher resolution in order to determine whether there was any shift in the position of the first peak with respect to increasing solute concentration.
Figure S11
Plots show the RDF for the intermolecular interactions of the carboxylate oxygens and the amino nitrogen for phenylalanine (left) and for asparagine (right); for each molecule pair only the closest distance between either carboxyl oxygen and the amino nitrogen is used in the calculation of the RDF. Results are shown for each of the following solute concentrations: 50 (blue), 100 (green), 200 (yellow) and 300 mg/ml (red). Insets show close-up views of the first peak in the RDF.
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Figure S12
Plot of the height of the first peak in the glycine salt bridge RDF versus the distance at which the peak occurs for all force field and water combinations: Amber ff99SB-ILDN + TIP3P (blue circle), Amber ff99SB-ILDN + TIP4P-Ew (blue triangle), Amber ff99SB-ILDN + SPC/E (blue square), CHARMM27 + TIP3P (green circle), GROMOS 53A6 + SPC (red circle), OPLS-AA/L + TIP3P (yellow circle), OPLS-AA/L + TIP4P (yellow triangle), OPLS-AA/L + TIP5P (yellow square). Note that the y-axis is plotted on a logarithmic scale.
Figure S13
Plots show the RDF for the intermolecular interactions of valine sidechains; for each molecule pair only the closest distance between any pair of sidechain heavy atoms was used in the calculation of the RDF. Results are shown for each of the following solute concentrations: 50 (blue), 100 (green), 200 (yellow) and 300 mg/ml (red). Insets show close-up views of the first peak in the RDF.
Figure S14
Plots show the effective G for the intermolecular interactions of valine sidechains relative to the values obtained from simulations performed at 50 mg/ml. Results are shown for each of the following force field and water model combinations: Amber ff99SB-ILDN + TIP3P (blue circle), Amber ff99SB-ILDN + TIP4P-Ew (blue triangle), Amber ff99SB-ILDN + SPC/E (blue square), CHARMM27 + TIP3P (green circle), GROMOS 53A6 + SPC (red circle).
Figure S15
Plots show the RDF for the intermolecular interactions of phenylalanine sidechains; for each molecule pair only the closest distance between any pair of sidechain heavy atoms is used in the calculation of the RDF. Results are shown for each of the following solute concentrations: 50 (blue), 100 (green), 200 (yellow) and 300 mg/ml (red). Insets show close-up views of the first peak in the RDF.
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Figure S16
Plots show the effective G for the intermolecular interactions of phenylalanine sidechains relative to the values obtained from simulations performed at 50 mg/ml. Results are shown for each of the following force field and water model combinations: Amber ff99SB-ILDN + TIP3P (blue circle), Amber ff99SB-ILDN + TIP4P-Ew (blue triangle), Amber ff99SB-ILDN + SPC/E (blue square), CHARMM27 + TIP3P (green circle), GROMOS 53A6 + SPC (red circle).
Figure S17
Plots show the effective G for the intermolecular interactions of asparagine sidechains relative to the values obtained from simulations performed at 50 mg/ml. Results are shown for each of the following force field and water model combinations: Amber ff99SB-ILDN + TIP3P (blue circle), Amber ff99SB-ILDN + TIP4P-Ew (blue triangle), Amber ff99SB-ILDN + SPC/E (blue square), CHARMM27 + TIP3P (green circle), GROMOS 53A6 + SPC (red circle).
Supporting References 1.
Humphrey, W., Dalke, A., and K. Schulten. VMD – Visual Molecular Dynamics. J. Molec. Graph. 1996, 14, 33-38
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