Many-body effects and simulations of potassium channels

TY - JOUR

T1 - Many-body effects and simulations of potassium channels

AU - Illingworth, Christopher J.

AU - Domene, Carmen

PY - 2009/6/8

Y1 - 2009/6/8

N2 - The electronic polarizability of an ion or a molecule is a measure of the relative tendency of its electron cloud to be distorted from its normal shape by an electric field. On the molecular scale, in a condensed phase, any species sits in an electric. eld due to its neighbours, and the resulting polarization is an important contribution to the total interaction energy. Electrostatic interactions are crucial for determining the majority of chemical physical properties of the system and electronic polarization is a fundamental component of these interactions. Thus, polarization effects should be taken into account if accurate descriptions are desired. In classical computer simulations, the forces required to drive the system are typically based on interatomic interaction potentials derived in part from electronic structure calculations or from experimental data. Owing to the difficulties in including polarization effects in classical force fields, most of them are based just on pairwise additive interaction potentials. At present, major efforts are underway to develop polarizable interaction potentials for biomolecular simulations. In this review, various ways of introducing explicit polarizability into biomolecular models and force fields are reviewed, and the progress that might be achieved in applying such methods to study potassium channels is described.

AB - The electronic polarizability of an ion or a molecule is a measure of the relative tendency of its electron cloud to be distorted from its normal shape by an electric field. On the molecular scale, in a condensed phase, any species sits in an electric. eld due to its neighbours, and the resulting polarization is an important contribution to the total interaction energy. Electrostatic interactions are crucial for determining the majority of chemical physical properties of the system and electronic polarization is a fundamental component of these interactions. Thus, polarization effects should be taken into account if accurate descriptions are desired. In classical computer simulations, the forces required to drive the system are typically based on interatomic interaction potentials derived in part from electronic structure calculations or from experimental data. Owing to the difficulties in including polarization effects in classical force fields, most of them are based just on pairwise additive interaction potentials. At present, major efforts are underway to develop polarizable interaction potentials for biomolecular simulations. In this review, various ways of introducing explicit polarizability into biomolecular models and force fields are reviewed, and the progress that might be achieved in applying such methods to study potassium channels is described.

KW - molecular dynamics simulations

KW - polarization effects

KW - force fields

KW - ab initio

KW - K+ channels

KW - MOLECULAR-DYNAMICS SIMULATIONS

KW - POLARIZABLE FORCE-FIELDS

KW - SMALL ORGANIC-MOLECULES

KW - QUANTUM-MECHANICAL CALCULATIONS

KW - ACCURATE INDUCTION ENERGIES

KW - CLASSICAL DRUDE OSCILLATORS

KW - FLUCTUATING CHARGE MODEL

KW - KCSA K+ CHANNEL

KW - AB-INITIO

KW - ATOMIC CHARGES

U2 - 10.1098/rspa.2009.0014

DO - 10.1098/rspa.2009.0014

M3 - Literature review

SN - 1364-5021

VL - 465

SP - 1701

EP - 1716

JO - Royal Society of London. Proceedings A. Mathematical, Physical and Engineering Sciences

JF - Royal Society of London. Proceedings A. Mathematical, Physical and Engineering Sciences

IS - 2106

ER -