Simulation of the selectivity of a calcium channel Dezso Boda a,* , David D. Busath b , Douglas Henderson c a Department of Physical Chemistry, University of Veszprem, H-8201 Veszprem, P.O. Box 158, Hungary b Department of Zoology and Center for Neuroscience, Brigham Young University, Provo UT 84062, USA c Department of Chemistry and Biochemistry, Brigham Young University, Provo UT 84602, USA Abstract Our recent simulations of the selectivity of the filter of a calcium channel are reported and discussed briefly. The model calcium filter that is used is a smooth cylinder embedded in a membrane with smooth surfaces. The four glutamate side chains of the calcium channel filter are modeled as eight half-charged oxygen ions that are confined to remain within the filter but are otherwise mobile. This model filter has a strong preference for calcium ions over sodium ions because of the ability of a calcium ion to deliver twice the charge of a sodium ion while occupying the about same volume and so satisfy local charge neutrality in the confined space of the filter more efficiently. # 2002 Elsevier Science B.V. All rights reserved. PACS: 87.10.þe; 68.05.-n; 87.15.-v; 87.16.-b Keywords: Selectivity; Channels; Monte Carlo; Electrolytes; Protein 1. Introduction This paper on biophysics departs somewhat from the tradition of this series of meetings. However, it certainly falls within the scope of this conference. What surface could be more heterogeneous than a membrane with a hole? The membrane itself is het- erogeneous; however, we will ignore this and focus on the hole or channel. A channel is a protein with a hole through which ions can pass. The calcium channel, that adsorbs calcium ions in preference to sodium ions, is of interest because its structure is reasonably well-under- stood and calcium channels deliver the signal that causes the heart to beat. In previous papers [1,2] we considered the filter to be an infinitely long cylinder. This is quite common. Goulding et al. [3], Lynden-Bell and Rasaiah [4], Tang et al. [5–7], and no doubt others, have used infinite cylinders to represent channels. In this paper we represent the filter by a more realistic finite cylinder. 2. Model Here we consider only the filter of the channel. The most important structural elements of the filter of a calcium channel are the four glutamate side chains that are attached to and protrude from the wall of the filter. Each of these glutamates ends in a carboxylate group that we represent by two half- charged oxygen ions. The glutamates are long and flexible so that the oxygen can be almost everywhere in the filter. Thus, we follow Nonner et al. [8] and replace the four glutamates by eight half-charged Applied Surface Science 196 (2002) 154–156 * Corresponding author. Fax: þ36-88-423409. E-mail addresses: boda@almos.vein.hu (D. Boda), david_busath@byu.edu (D.D. Busath), doug@huey.byu.edu (D. Henderson). 0169-4332/02/$ – see front matter # 2002 Elsevier Science B.V. All rights reserved. PII:S0169-4332(02)00051-X