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With the dramatic increases in computational power, computer simulations become increasingly valuable for understanding protein function, and for providing details from the atomistic level to large-scale conformational changes. Nonetheless, biomolecular systems are still too complex to be fully modeled at an atomistic level. Instead, we need methods that allow simulations done on different length and time scales to be combined. For example, using all-atom simulations is impractical in studying non-specific protein-protein self-assembly, since the simulations would be excessively time-consuming. To study such systems, Brownian dynamics simulations with coarse-grained models has been used to model the overall motions generated by less specific interactions, e.g. hydrophobic interactions and steric clashes. These large-scale simulations can efficiently provide possible configurations of the system, which can then be mapped to the atomistic level for fine-grained analysis. A few study cases are shown here:
- Large-scale HIV-1 protease internal motions and gating effects using Brownian Dynamic simulations in a coarse-grained model
A coarse-gained model has been applied the HIV-1 protease to study the flap motions of the protein, which serve as a “gate” to modulate protein-ligand association rate constants. I implemented a flexible force field into the UHBD package, and studied the internal dynamics of the wild-type and mutant HIV-1 proteases, as well as the interactions between the protease and drugs. My simulations show that these loops or “flaps” open and close slowly on the timescale of diffusional displacements of the drug molecules. Thus the results allow us to apply an analytic theory for “gated” diffusion-controlled reactions to rationalize the relative binding rates for different protease mutants that have different gating timescales. The predicted gated association rate constants for mutant proteases are in reasonable agreements with experimental data. This new method can model the protein dynamics near the binding site that may change due to mutation, thus it is useful to predict the changes of the “gated” association rate constants of mutants when experimental data are not available. Also, in the study of the internal motion of HIV-1 proteases, the method can provide a greater understanding of drug-resistance of the protease mutants [8].
Figure 1, Left: In our coarse grained model, each bead represents a residue and the mutated residues are marked by enlarged spheres. Right: An open (blue) and closed (green) conformation of the wild-type HIV-1 protease from my the Brownian dynamics simulations.
- Multi-scale Simulations of Ligands Binding to HIV-1 Protease
Multiscale simulations (coarse-grained Brownian dynamics simulations and
all-atom molecular dynamics simulations in implicit solvent)
were applied to reveal the binding processes of ligands as they
enter the binding site of the HIV-1 protease. The initial structures
used for the molecular dynamics simulations were generated based on
the Brownian dynamics trajectories, and this is the first molecular
dynamics simulation of modeling the association of a ligand with the
protease. We found that a protease substrate successfully binds to
the protein when the flaps are fully open. Surprisingly, a smaller
cyclic urea inhibitor (XK263) can reach the binding site when the
flaps are not fully open. However, if the flaps are nearly closed,
the inhibitor must rearrange or binding can fail because the
inhibitor cannot attain proper conformations to enter the binding
site. Both the peptide substrate and XK263 can also affect the
protein's internal motion, which may help the flaps to open.
Simulations allows us to efficiently study the ligand binding
processes and may help those who study drug discovery to find
optimal association pathways and to design those ligands with the
best binding kinetics.
Left: ligand XK263 binding pathways from a molecular dynamics simulation. Complex conformations superimposed using Bio3D package; only one protein conformation is shown. Right: XK263 conformations superimposed by cyclic urea. Silver: Snapshot taken from simulation time 0 ps; Blue: 10 ps; Black: after 50 ps. Note that the flaps did not open during this binding process.
Movie: Transition of the peptide substrate from an unbound to a final bound state. The total simulation length in this run was 2 us. The protein and the substrate are coarse-grained bead representation. Colors: blue - monomer A; red - monomer B; yellow - peptide substrate.
- Dynamics of the Acetylcholinesterase Tetramer (with Dr. Alemayehu "Alex" Gorfe)
Acetylcholinesterase rapidly hydrolyzes the neurotransmitter acetylcholine in cholinergic synapses, including the neuromuscular junction. The tetramer is the most important functional form of the enzyme. Two low-resolution crystal structures have been solved. One is compact with two of its four peripheral anionic sites (PAS) sterically blocked by complementary subunits. The other is a loose tetramer with all four subunits accessible to solvent. These structures lacked the C-terminal amphipathic t-peptide (WAT domain) that interacts with the proline-rich attachment domain (PRAD). A complete tetramer model (AChEt) was built based on the structure of the PRAD/WAT complex and the compact tetramer. Normal mode analysis suggested that AChEt could exist in multiple conformations with subunits fluctuating relative to one another. Here, a multiscale simulation involving all-atom molecular dynamics and Cα-based coarse-grained Brownian dynamics simulations was carried out to investigate the large scale inter-subunit dynamics in AChEt. We sampled the ns-μs time scale motions and found that the tetramer indeed constitutes a dynamic assembly of monomers. The inter-subunit fluctuation is correlated with the occlusion of the PAS. Such motions of the subunits "gate" ligand-protein association. The gates are open more than 80% of the time on average, which suggests a small reduction of ligand-protein binding. These results are consistent with experiments, which suggest that binding of a substrate to the PAS is only somewhat hindered by the association of the subunits.
The model-built acetylcholinesterase tetrameric structure (AChEt, left) and its schematic representation (right) showing subunits A (black), B (red), C (green), D (blue). The ColQ onto which the WAT domains (residue 544-583) wrap around is in purple. Note the nearly symmetric arrangement of the monomers in this model. The three peripheral anionic site residues (Tyr72, Trp286, and Tyr341) are shown in yellow van der Waals spheres.
- The Influence of Macromolecular Crowding on Protein Internal Motion (with David Minh)
High macromolecular concentrations, or crowded conditions, have been seen to affect the equilibrium and rates of many molecular processes, including diffusion, association and dissociation, protein folding, and stability. Coarse-grained Brownian dynamics simulations have been used to study crowding effects on the protein dynamics. The HIV-1 protease has been studied, as the opening and closing of the flaps is thought to be involved in substrate/inhibitor binding and the enzymatic mechanism (Figure 1). My analyses of HIV-1 protease ligand binding kinetics indicate that they are strongly influenced by the fraction of time that the flaps are open. Our simulations show that at high crowder packing, the open fraction dropped significantly, with an order of magnitude change in the percentage of open conformations. Our results suggest that macromolecular crowding may play a significant role in the activity of HIV-1 protease.
HIV-1 protease in the presence of crowder molecules