An experimentally guided umbrella sampling protocol for biomolecules.
We present a simple method for utilizing experimental data to improve the efficiency of numerical calculations of free energy profiles from molecular dynamics simulations. The method involves umbrella sampling simulations with restraining potentials based on a known approximate estimate of the free energy profile derived solely from experimental data. The use of the experimental data results in optimal restraining potentials, guides the simulation along relevant pathways, and decreases overall computational time. In demonstration of the method, two systems are showcased. First, guided, unguided (regular) umbrella sampling simulations and exhaustive sampling simulations are compared to each other in the calculation of the free energy profile for the distance between the ends of a pentapeptide. The guided simulation use restraints based on a simulated "experimental" potential of mean force of the end-to-end distance that would be measured by fluorescence resonance energy transfer (obtained from exhaustive sampling). Statistical analysis shows a dramatic improvement in efficiency for a 5 window guided umbrella sampling over 5 and 17 window unguided umbrella sampling simulations. Moreover, the form of the potential of mean force for the guided simulations evolves, as one approaches convergence, along the same milestones as the extensive simulations, but exponentially faster. Second, the method is further validated by replicating the forced unfolding pathway of the titin I27 domain using guiding umbrella sampling potentials determined from actual single molecule pulling data. Comparison with unguided umbrella sampling reveals that the use of guided sampling encourages unfolding simulations to converge faster to a forced unfolding pathway that agrees with previous results and produces a more accurate potential of mean force.
Mills
Maria
M
Department of Chemistry, University of California, Irvine, California 92697, USA.
Andricioaei
Ioan
I
D000595:Amino Acid Sequence; D064211:Connectin; D005240:Feasibility Studies; D008958:Models, Molecular; D009124:Muscle Proteins / Q000737:chemistry / Q000378:metabolism; D009842:Oligopeptides / Q000737:chemistry; D011489:Protein Denaturation; D011494:Protein Kinases / Q000737:chemistry / Q000378:metabolism; D017434:Protein Structure, Tertiary; D013816:Thermodynamics; D013997:Time Factors
D064211:Connectin; D009124:Muscle Proteins; D009842:Oligopeptides; D011494:Protein Kinases