52 research outputs found
Atomic charges in the ionizable residues in the protonated/deprotonated states.
<p>Dummy hydrogen atoms with zero charge are added in the deprotonated states.</p
The titration curves of the 9 ionizable groups of EPG as functions of pH values obtained from the VMMS–1 simulations.
<p>The titration curves of the 9 ionizable groups of EPG as functions of pH values obtained from the VMMS–1 simulations.</p
State molar fractions of the heptapeptide, Ace-SDNKTYG-NME, during constant pH VMMS simulations.
<p>pH values are labeled in each panel. All states have an initial molar fraction of 0.125.</p
The molar fractions of deprotonated states during the VMMS–1 simulations of the heptapeptide.
<p>The molar fractions of deprotonated states during the VMMS–1 simulations of the heptapeptide.</p
State equilibrium is represented as a virtual mixture of multiple states (VMMS).
<p>In a solution shown in the center, all states equilibrate with each other and exist by state molar fractions, <i>x</i><sub>1</sub>, <i>x</i><sub>2</sub>,⋯, <i>x</i><sub><i>n</i></sub>. In VMMS, every state is explicitly represented by an all-atom subsystem. Each state has its own solvent environment and solvent can be either implicit or explicit. All subsystems form a virtual ideal solution to equilibrate with each other.</p
Energy distributions of the ASP model compound with the GB implicit solvation model in different states.
<p>The solid lines are the protonated state (state 0, black) and deprotonated state (state 1, red). The red dotted lines with filled symbols are in the V<sub>0</sub> (square) state and V<sub>1</sub> (circle) state. The green dotted lines with open symbols are the reweighted results in the V<sub>0</sub> (square) and V<sub>1</sub> (circle) states.</p
Energy distributions of the model HOH solution in the canonical ensemble and in the VMMS ensemble.
<p>The black lines are the LD simulation results for state 0 (solid) and state 1 (dashed). The red lines with squares are the VMMS simulation results for state V<sub>0</sub> (filled) and state V<sub>1</sub> (open). The green lines with circles are the reweighted VMMS simulation results for state V<sub>0</sub> (filled) and state V<sub>1</sub>(open).</p
pKa of the ionizable residues in the heptapeptide from the VMMS simulations and other studies.
<p>pKa of the ionizable residues in the heptapeptide from the VMMS simulations and other studies.</p
The pKa of K66 and conformational properties of SNase Δ+PHS/V66K during the VMMS simulation.
<p>The pKa of K66 and conformational properties of SNase Δ+PHS/V66K during the VMMS simulation.</p
The molar fractions of deprotonated states for the 9 ionizable groups of EPG during the VMMS–1 simulations.
<p>The molar fractions of deprotonated states for the 9 ionizable groups of EPG during the VMMS–1 simulations.</p
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