Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

Water as a structural element in an ion channel

The structure of the KcsA ion channel, a potassium channel of the bacterium S. Lividans, was worked out about three years ago by Doyle, et al (Doyle and others 1998). The channel bears strong structural similarity to the inner (pore) section of voltage gated potassium channels of eukaryotes. In particular, it is a tetramer of, primarily, two transmembrane segments that appear to resemble the S5 and S6 segments of the voltage-gated channels of eukaryotes, plus the selectivity filter that links the two. However, the S. Lividans channel gates with a proton (i.e., when the pH drops sufficiently), rather than with a drop in membrane potential. Here, we consider a mechanism that is consistent with this fact, with the known structure, and with what is also known about gating from the work of Perozo and coworkers (1999)(Perozo and others 1999). The latter group showed that in gating, the lower section of the channel swung outward by a few tenths of a nm. They did not answer the question of why a proton would allow this to happen. Perozo and coworkers(Cuello and others 2001)found that a glutamate, E118, is perhaps the most important of a critical set of charged residues that affected gating. The structure of the channel includes four E118 in the gating region, as the channel is a tetramer; the 4 glu are spaced closely enough to allow the formation of a H5O2 (partial positive charge) hydrogen bonded to three of the four glu side chain carboxyl residues.

Gaussian98 was used to do density functional calculations (B3LYP/D95V level) on a system with added water and each E118 truncated to acetic acid (the positions of the carboxyl, and the penultimate C, were preserved). It was found that the O-H-O distance was short, approximately 2.4 A when the charge was -2 or -3, but approximately normal, around 2.7 A, when the system charge was -1 or 0 (Green 2001). Short H-bonds tend to be strong compared to normal H-bonds. In the gas phase, or with low dielectric constants, as found in proteins, the bonds may be more than 10 kT stronger than normal. It is proposed that in this case, the H-bonds behave as they would in such a low dielectric medium. However, there should be water molecules in the vicinity, even if they are oriented and thus not available to contribute significantly to the dielectric constant. A number of additional calculations have been carried out to ascertain the structural contribution of the H5O2. For one, the group has been expanded, and single point calculations carried out, to determine whether the response is harmonic (it is, to an excellent approximation). Then four water molecules were added to the system, optimized at low level (HF/3-21G*), followed by reoptimization of the H5O2 and then expansion for some cases. It appears that the forces holding the waters in place are strong, and at -2 charge (the most critical case) expansion occurs against a force of at least several kT/0.05 A. This supports the argument that the H5O2 is a structural element in the channel.

References and Footnotes
  1. Cuello LG, Sompornpisut A, Perozo E. 2001. Molecular characterization of the pH sensor in KcsA. Biophys. J. 80:A839.
  2. Doyle DA, Cabral JM, Pfuetzner RA, Kuo A, Gulbis JM, Cohen SL, Chait BT, MacKinnon R. 1998. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280:69-77.
  3. Green ME. 2001. The role of H+ in gating the KcsA channel: ab initio calculations on a possible gating region. Biophys. J. 80:A837.
  4. Perozo E, Marien Cortes D, Cuello L. 1999. Structural Rearrangements underlying K+-channel gating. Science 285:73-78.

Michael E. Green

Department of Chemistry, City College of CUNY, New York NY 10031
Telephone: (212) 650-6034; Fax: (212) 650-6107; Email: green@sci.ccny.cuny.edu