ABSTRACT

Abbreviations: Alm, alamethicin; BD, Brownian dynamics; gA, gramicidin A; KcsA, K channel from Streptomyces lividans; M2δ, synthetic M2 peptide from nAChR M2 helix of δ-subunit; MC, Monte Carlo; MD, molecular dynamics; nAChR, nicotinic acetylcholine receptor; PB, Poisson-Boltzmann; PNP, Poisson-Nernst-Planck

2.1 Introduction

2.1.1 Scope of this chapter

This chapter deals with computer simulations of ion channel proteins. I review briefly the key properties of ion channels for which there is structural information, 1-58488-362-6/04/$0.00+$ 1.50

and discuss different simulation approaches. In my opinion, the general goal of simulations of ion channels could be stated as follows:

The goal of simulation studies is to link the structure of ion channels in atomic detail to ion currents, including a fundamental understanding of how ion channels are controlled by external factors such as voltage, ligand binding, ion gradients, pH, and interactions with toxins and other blockers.