Polarizable force field development for lipids and their efficient applications in membrane proteins

Abstract

Polarizable force fields have been developed due to the intrinsic problem of additive force fields in modeling electrostatic interactions. Because of the capability to accurately describe the behavior of systems with significant changes in their electrostatic environments, polarizable force fields might be a decent tool to study membrane‐related systems, such as lipid bilayers, though not so much progresses have been made. In this overview article we described the developments of a variety of polarizable force fields, including the corresponding theories, benchmark examples, and more specifically we were focused on the applications on lipid membranes. WIREs Comput Mol Sci 2017, 7:e1312. doi: 10.1002/wcms.1312 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics

Interplay between Electrostatic and Hydrophobic Interactions in the pH-Dependent Adsorption of Ibuprofen onto Acid-Functionalized Multiwalled Carbon Nanotubes

“…30,32 Because of its simpler equations, MD can deal with larger systems than QM and, therefore, it provides qualitative and quantitative information, which is not accessible from experimental methods, to understand the underlying physicochemical mechanisms, interactions, and molecule functionality within the timescale that simulations are performed. 23,29,30 The quality of the information from MD simulations depends on the force field applied during calculations. 29 Although many force fields have been developed for studying nanomaterials, some have been found to show discrepancies with experimental data over a period of time.…”

“…23,29,30 The quality of the information from MD simulations depends on the force field applied during calculations. 29 Although many force fields have been developed for studying nanomaterials, some have been found to show discrepancies with experimental data over a period of time. 30 Therefore, it is of utmost importance to undertake proper parameterization of force fields to fit QM calculations 32 and thus provide true values close to experimental ones.…”

Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors

“…[1][2][3] Most modern force fields are developed by fitting functional forms to the Born-Oppenheimer energy surface of the molecule. [3][4][5][6] Afterwards, Monte Carlo and molecular dynamics are used to simulate atoms as classical particles moving on this Born-Oppenheimer surface, 6 ignoring quantum effects on the nuclear dynamics.…”

“…Biomolecular simulation methods have proven increasingly useful for understanding properties of biomolecules, such as protein binding and protein folding. , The most popular simulation methods today are molecular dynamics (MD) and Monte Carlo (MC) simulations, both of which rely on empirical force fields to model interactions between molecules. − Some modern force fields currently under development fit functional forms to the Born–Oppenheimer energy surface of the molecule, and other force fields use both data about the Born–Oppenheimer surface and experimental data. − Afterward, Monte Carlo and molecular dynamics are used to simulate atoms as classical particles moving on this Born–Oppenheimer surface, ignoring quantum effects from the nuclear dynamics.…”

Higher Accuracy Achieved in the Simulations of Protein Structure Refinement, Protein Folding, and Intrinsically Disordered Proteins Using Polarizable Force Fields

“…Despite its significant advantage of obtaining information not available via experimental techniques, MD’s predictive capabilities are still limited by the accuracy of the molecular mechanics force fields (FFs) which serve as the backbone of MD simulation . According to the difference in describing electrostatic properties, these force fields can be divided into two groups: classical additive force fields and polarizable force fields. − In the widely used classical additive force fields (CFFs), such as AMBER, CHARMM, GROMOS, and OPLS, the electrostatic term is described with Coulombic interactions between fixed partial charges. − In polarizable force fields (PFFs), such as AMOEBA and Drude, the induced dipole or Drude oscillator model is implemented to account for the electronic polarization effect during the simulation process. − …”