title: Role of methyl-induced polarization in ion binding.
abstract: The chemical property of methyl groups that renders them indispensable to biomolecules is their hydrophobicity. Quantum mechanical studies undertaken here to understand the effect of point substitutions on potassium (K-) channels illustrate quantitatively how methyl-induced polarization also contributes to biomolecular function. K- channels regulate transmembrane salt concentration gradients by transporting K(+) ions selectively. One of the K(+) binding sites in the channel's selectivity filter, the S4 site, also binds Ba(2+) ions, which blocks K(+) transport. This inhibitory property of Ba(2+) ions has been vital in understanding K-channel mechanism. In most K-channels, the S4 site is composed of four threonine amino acids. The K channels that carry serine instead of threonine are significantly less susceptible to Ba(2+) block and have reduced stabilities. We find that these differences can be explained by the lower polarizability of serine compared with threonine, because serine carries one less branched methyl group than threonine. A T→S substitution in the S4 site reduces its polarizability, which, in turn, reduces ion binding by several kilocalories per mole. Although the loss in binding affinity is high for Ba(2+), the loss in K(+) binding affinity is also significant thermodynamically, which reduces channel stability. These results highlight, in general, how biomolecular function can rely on the polarization induced by methyl groups, especially those that are proximal to charged moieties, including ions, titratable amino acids, sulfates, phosphates, and nucleotides.
authors.affiliation: Theory Department, Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany.
authors.forename: Mariana
authors.initials: M
authors.lastname: Rossi
authors.forename: Alexandre
authors.initials: A
authors.lastname: Tkatchenko
authors.forename: Susan B
authors.initials: SB
authors.lastname: Rempe
authors.forename: Sameer
authors.initials: S
authors.lastname: Varma
mesh_terms: D000465:Algorithms; D019943:Amino Acid Substitution; D001464:Barium / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D015640:Ion Channel Gating / Q000235:genetics / Q000502:physiology*; D017136:Ion Transport / Q000235:genetics / Q000502:physiology; D008956:Models, Chemical; D008958:Models, Molecular; D011188:Potassium / Q000737:chemistry* / Q000378:metabolism; D015221:Potassium Channels / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017434:Protein Structure, Tertiary; D012694:Serine / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013816:Thermodynamics; D013912:Threonine / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D015221:Potassium Channels; D001464:Barium; D013912:Threonine; D012694:Serine; D011188:Potassium
keywords: density-functional theory; dispersion; ion channels; methylation; quantum chemistry