Equilibration of experimentally determined protein structures for molecular dynamics simulation

Abstract

Preceding molecular dynamics simulations of biomolecular interactions, the molecule of interest is often equilibrated with respect to an initial configuration. This so-called equilibration stage is required because the input structure is typically not within the equilibrium phase space of the simulation conditions, particularly in systems as complex as proteins, which can lead to artifactual trajectories of protein dynamics. The time at which nonequilibrium effects from the initial configuration are minimized-what we will call the equilibration time-marks the beginning of equilibrium phase-space exploration. Note that the identification of this time does not imply exploration of the entire equilibrium phase space. We have found that current equilibration methodologies contain ambiguities that lead to uncertainty in determining the end of the equilibration stage of the trajectory. This results in equilibration times that are either too long, resulting in wasted computational resources, or too short, resulting in the simulation of molecular trajectories that do not accurately represent the physical system. We outline and demonstrate a protocol for identifying the equilibration time that is based on the physical model of Normal Mode Analysis. We attain the computational efficiency required of large-protein simulations via a stretched exponential approximation that enables an analytically tractable and physically meaningful form of the root-mean-square deviation of atoms comprising the protein. We find that the fitting parameters (which correspond to physical properties of the protein) fluctuate initially but then stabilize for increased simulation time, independently of the simulation duration or sampling frequency. We define the end of the equilibration stage--and thus the equilibration time--as the point in the simulation when these parameters attain constant values. Compared to existing methods, our approach provides the objective identification of the time at which the simulated biomolecule has entered an energetic basin. For the representative protein considered, bovine pancreatic trypsin inhibitor, existing methods indicate a range of 0.2-10 ns of simulation until a local minimum is attained. Our approach identifies a substantially narrower range of 4.5-5.5 ns , which will lead to a much more objective choice of equilibration time.

Chemomechanics of complex materials: challenges and opportunities in predictive kinetic timescales

“…This configuration was not strictly equilibrated in terms of representing the global minimum of the protein structure, of course; instead, it was chosen at a timepoint in the trajectory which we deemed to be sufficient to enter an energetic minimum in the admittedly rough energy landscape (20 ns), according to our protocol for objectively choosing an initial configuration of proteins as we outlined in Ref. [41]. We then conducted SMD simulations (Fig.…”

Modeling and simulation of chemomechanics at the cell-matrix interface

“…22,24 Improvements in computational resources have since allowed for longer and more accurate simulations of this system. 24,38 SMD has also been used to study the unbinding of the hormone retinoic acid from its receptor, and results suggest that multiple un/binding pathways exist. 39 SMD has also elucidated mechanisms for the binding of retinal to bacterio-opsin, which is an important step in the formation of bacteriorhodopsin.…”

“…Using the protocol developed in ref. 38, we determined that the complex had equilibrated within 15 ns. The equilibrated trajectory (t > 15 ns) was used for further analysis.…”

“…41,42 For our studies of ligand-receptor chemomechanics, we first consider the biotin-streptavidin complex to test the effect of initial bound configuration and ECM stiffness on unbinding. Biotinstreptavidin is a ligand-receptor system that has been very well characterized both experimentally and computationally, 22,38,[43][44][45][46][47][48][49][50][51] making this complex an ideal model system for fundamental ligandreceptor studies. Here, we use the biotin-streptavidin results to inform our design of a study for the integrin-RGD complex that is more relevant to cell-substrata adhesion.…”

“…The biotin-streptavidin tetramer (PDB ID 1STP 50 ) was simulated using the GROMACS molecular dynamics package, version 3.3 60,61 as described previously. 38 Briefly, the protein was solvated with ions added to provide charge neutrality and to mimic physiological conditions. After steepest descents minimization, unconstrained molecular dynamics simulation over 100 ns was performed to equilibrate the system.…”