What can be deduced about the structure of Shaker from available data? Benoit Roux Weill Medical College of Cornell University, 1300 York Ave, New York, NY 10021, USA Abstract. Voltage-gated K + channels are transmembrane proteins that control and regulate the £ow of K + ions across cell membranes in response to changes in membrane potential and are essential for the propagation of action potentials in the nervous system. One of the most studied voltage-gated channels is Shaker. Available experimental results clearly provide speci¢c constraints on the structure of the channel, even though the direct translation of the available information into 3D structures is not trivial. The goal of this work is to develop a computational approach to construct and re¢ne 3D models of Shaker by incorporating and integrating available experimental data. Our approach is based on comparative modelization and global conformational optimization using energy restraints extracted from experimental data. 2002 Ion channels ö from atomic resolution physiology to functional genomics. Wiley, Chichester (Novartis Foundation Symposium 245) p 84^108 The activity of voltage-gated ion channels is the basic molecular mechanism underlying the electrical excitability of nerves and muscles (Hodgkin & Huxley 1952). These channels are specialized transmembrane proteins, which control and regulate the £ow of ions across cell membranes by opening and closing (‘gating’) in response to changes in membrane potential (Hille 1992). The ¢rst identi¢ed and best-studied voltage-gated channel is the Shaker K + channel from the fruit£y Drosophilia melanogaster (Tempel et al 1987); the corresponding voltage-gated K + (K v ) channels in mammals are K v 1.1^K v 1.7 (Jan & Jan 1997). Normally closed at hyperpolarized resting potentials, Shaker K + channels undergo a conformational transition from a closed to an open state at depolarization potentials (Cha et al 1999, Glauner et al 1999). Studies have shown that Shaker and all the channels in the K v family are structurally and functionally similar. They are formed by four identical or homologous domains, or subunits (MacKinnon 1991). Analysis of the amino acid sequence suggests that each subunit contains six putative transmembrane (TM) segments, S1 to S6 (Jan & Jan 1997, Tempel et al 1987). The second (S2) 84 !"# $%&##’()* +,"- ./"-01 2’)"(3/0"# 4%5)0"("65 /" +3#1/0"#&( 7’#"-01)* 8"9&,/0) +"3#:&/0"# ;5-<")03- =>?! "#$%&’ ()* +,-.’, /0 12’3#20 4#56 78, 97&-’ :! 1##,’ ;#<02-3=. ! >#?72.-@ A#%8,7.-#8 (BB(! CD4>E BF)GBFH)IG*FJ