Aerobic respiration in bacteria, Archaea, and mitochondria is performed by oxygen reductase members of the heme-copper oxidoreductase superfamily. These enzymes are redox-driven proton pumps which conserve part of the free energy released from oxygen reduction to generate a proton motive force. The oxygen reductases can be divided into three main families based on evolutionary and structural analyses (A-, B- and C-families), with the B- and C-families evolving after the A-family. The A-family utilizes two proton input channels to transfer protons for pumping and chemistry, whereas the B- and C-families require only one. Generally, the B- and C-families also have higher apparent oxygen affinities than the A-family. Here we use whole cell proton pumping measurements to demonstrate differential proton pumping efficiencies between representatives of the A-, B-, and C-oxygen reductase families. The A-family has a coupling stoichiometry of 1 H + /e - , whereas the B- and C-families have coupling stoichiometries of 0.5 H + /e - . The differential proton pumping stoichiometries, along with differences in the structures of the proton-conducting channels, place critical constraints on models of the mechanism of proton pumping. Most significantly, it is proposed that the adaptation of aerobic respiration to low oxygen environments resulted in a concomitant reduction in energy conservation efficiency, with important physiological and ecological consequences.

Oxygen reductase members of the heme-copper superfamily are terminal respiratory oxidases in mitochondria and many aerobic bacteria and archaea, coupling the reduction of molecular oxygen to water to the translocation of protons across the plasma membrane. The protons required for catalysis and pumping in the oxygen reductases are derived from the cytoplasmic side of the membrane, transferred via proton-conducting channels comprised of hydrogen bond chains containing internal water molecules along with polar amino acid side chains. Recent analyses identified eight oxygen reductase families in the superfamily: the A-, B-, C-, D-, E-, F-, G-, and H-families of oxygen reductases. Two proton input channels, the K-channel and the D-channel, are well established in the A-family of oxygen reductases (exemplified by the mitochondrial cytochrome c oxidases and by the respiratory oxidases from Rhodobacter sphaeroides and Paracoccus denitrificans). Each of these channels can be identified by the pattern of conserved polar amino acid residues within the protein. The C-family (cbb3 oxidases) is the second most abundant oxygen reductase family after the A-family, making up more than 20% of the sequences of the heme-copper superfamily. In this work, sequence analyses and structural modeling have been used to identify likely proton channels in the C-family. The pattern of conserved polar residues supports the presence of only one proton input channel, which is spatially analogous to the K-channel in the A-family. There is no pattern of conserved residues that could form a D-channel analogue or an alternative proton channel. The functional importance of the residues proposed to be part of the K-channel was tested by site-directed mutagenesis using the cbb3 oxidases from R. sphaeroides and Vibrio cholerae. Several of the residues proposed to be part of the putative K-channel had significantly reduced catalytic activity upon mutation: T219V, Y227F/Y228F, N293D, and Y321F. The data strongly suggest that in the C-family only one channel functions for the delivery of both catalytic and pumped protons. In addition, it is also proposed that a pair of acidic residues, which are totally conserved among the C-family, may be part of a proton-conducting exit channel for pumped protons. The residues homologous to these acidic amino acids are highly conserved in the cNOR family of nitric oxide reductases and have previously been implicated as part of a proton-conducting channel delivering protons from the periplasmic side of the membrane to the enzyme active site in the cNOR family. It is possible that the C-family contains a homologous proton-conducting channel that delivers pumped protons in the opposite direction, from the active site to the periplasm.

Escherichia coli is known to couple aerobic respiratory catabolism to ATP synthesis by virtue of the primary generators of the proton motive force-NADH dehydrogenase I, cytochrome bo 3 , and cytochrome bd-I. An E. coli mutant deficient in NADH dehydrogenase I, bo 3 and bd-I can, nevertheless, grow aerobically on nonfermentable substrates, although its sole terminal oxidase cytochrome bd-II has been reported to be nonelectrogenic. In the current work, the ability of cytochrome bd-II to generate a proton motive force is reexamined. Absorption and fluorescence spectroscopy and oxygen pulse methods show that in the steady-state, cytochrome bd-II does generate a proton motive force with a H þ ∕e − ratio of 0.94 AE 0.18. This proton motive force is sufficient to drive ATP synthesis and transport of nutrients. Microsecond time-resolved, single-turnover electrometry shows that the molecular mechanism of generating the proton motive force is identical to that in cytochrome bd-I. The ability to induce cytochrome bd-II biosynthesis allows E. coli to remain energetically competent under a variety of environmental conditions. A erobic bacteria produce ATP via (i) oxygen-independent, substrate-level phosphorylation in glycolysis and the Krebs cycle, or (ii) oxidative phosphorylation, in which the electron flow, through the aerobic respiratory electron transport chain, generates a proton motive force ðΔp % Þ which, in turn, drives the ATP synthase. The proton motive force (Δp out-in , where it is specified that the gradient is measured "outside-minus-inside") is equivalent to the transmembrane electrochemical proton gradient and has chemical ðΔpH out-in Þ and electrical ðΔΨ out-in Þ components. At 298 K, in mV units,

Background: Cholesterol modulates inwardly rectifying potassium (Kir) channels. Results: A two-way molecular cytosolic switch controls channel modulation by cholesterol and PI(4,5)P 2 . Conclusion: Cholesterol and PI(4,5)P 2 induce a common gating pathway of Kir2.1 despite their opposite impact on channel function. Significance: These findings provide insights into structure-function relationship of ion channels and contribute to understanding of the mechanisms underlying their regulation by lipids.

The aa3-type cytochrome c oxidase from Rhodobacter sphaeroides utilizes two proton-input channels to provide all the protons for chemistry (water formation) and proton pumping. The D-channel is responsible for the uptake of all pumped protons, 4 protons per O2. Several substitutions for either N139 or N207, near the entrance of the D-channel, were previously reported to decouple the proton pump from oxidase activity. In the current work, the characteristics of additional mutations in this region of the protein (N139, N207, N121 and S142) are determined to elucidate the mechanism of decoupling. With the exception of the substitution of a large, hydrophobic residue (N139L), all the mutations of N139 resulted in an enzyme with high oxidase activity but with severely diminished proton pumping stoichiometry. Whereas N207D was previously shown to be decoupled, N207A and N207T exhibit nearly wild type behavior. The new data display a pattern. Small, non-ionizable substitutions for N139 or N121 result in decoupling the proton pump while maintaining high turnover rates. These residues are directly hydrogen bonded to two water molecules (Water6574 and water6584) that are part of the single-file chain of water molecules within the D-channel leading to E286 at the top of the channel. The data suggest that the integrity of this water chain within the D-channel is critical for rapid proton transfer. The mechanism of decoupling is most likely due to slowing the rate of proton delivery below a threshold that is required for protonation of the putative proton loading site. Protons delivered outside this time-window are delivered to the active site where they are consumed in the formation of water. The rate of proton delivery required to protonate the pump site must be significantly faster than the rate of delivery of protons to the catalytic site. For this reason, mutations can result in decoupling the proton pump without slowing the catalytic turnover by the enzyme.

Key pointsr Inwardly rectifying potassium channels (Kir) play key roles in regulating membrane excitability and K + homeostasis in multiple cell types. Our earlier studies showed that Kir2 channels, one of the major subfamilies of Kir, are suppressed by membrane cholesterol and that cholesterol stabilizes these channels in a closed 'silent' state.r This paper addresses a fundamental question of how Kir2 channels are regulated by caveolins, the major structural proteins of caveolae, and the relationship between the sensitivity of the channels to caveolin and to cholesterol.r In this study, we present direct evidence that caveolin-1 is a negative regulator of Kir2 function and that cholesterol and caveolin-1 regulate the channels by a common mechanism.r This study also challenges a general notion that cholesterol depletion alters ion channel function by disrupting caveolae, demonstrating that neither caveolin-1 nor intact caveolae are required for cholesterol sensitivity of Kir2 channels.r Furthermore, we present first insights into the structural determinants of the cross-talk between the sensitivity of Kir2 channels to caveolin and to cholesterol. Abstract A growing number of studies show that different types of ion channels localize in caveolae and are regulated by the level of membrane cholesterol. Furthermore, it has been proposed that cholesterol-induced regulation of ion channels might be attributed to partitioning into caveolae and association with caveolin-1 (Cav-1). We tested, therefore, whether Cav-1 regulates the function of inwardly rectifying potassium channels Kir2.1 that play major roles in the regulation of membrane potentials of numerous mammalian cells. Our earlier studies demonstrated that Kir2.1 channels are cholesterol sensitive. In this study, we show that Kir2.1 channels co-immunoprecipitate with Cav-1 and that co-expression of Kir2.1 channels with Cav-1 in HEK293 cells results in suppression of Kir2 current indicating that Cav-1 is a negative regulator of Kir2 function. These observations are confirmed by comparing Kir currents in bone marrow-derived macrophages isolated from Cav-1 −/− and wild-type animals. We also show, however, that Kir2 channels maintain their sensitivity to cholesterol in HEK293 cells that have very low levels of endogenous Cav-1 and in bone marrow-derived macrophages isolated from Cav-1 −/− knockout mice. Thus, these studies indicate that Cav-1 and/or intact caveolae are not required for cholesterol sensitivity of Kir channels. Moreover, a single point mutation of Kir2.1, L222I that abrogates the sensitivity of the channels to cholesterol also abolishes their sensitivity to Cav-1 suggesting that the two modulators regulate Kir2 channels via a common mechanism.

The cbb3-type cytochrome c oxidases are members of the heme-copper proton pumping respiratory oxygen reductases. The structure of the cbb3-type oxidase from Pseudomonas stutzeri reveals that, in addition to the six redox-active metal centers (two hemes b, three hemes c and CuB), the enzyme also contains at least one Ca2+. The calcium bridges two propionate carboxyls at the interface between the low-spin heme b and the active-site heme b3 and, in addition, is ligated to a serine in subunit CcoO and by a glutamate in CcoN. The glutamate that is ligated to Ca2+ is one of a pair of glutamic acid residues that has previously been suggested to be part of a proton exit pathway for pumped protons. In the current work, mutants in these glutamates are investigated in the cbb3-type oxidases from Vibrio cholerae and from Rhodobacter sphaeroides. Metal analysis shows that each of these wild type enzymes contains Ca2+. Mutations of the glutamate expected to ligate the Ca2+ in each of these enzymes (E126 in V. cholerae; E180 in R. sphaeroides) result in the loss of activity as well as loss of Ca2+. Mutations in the nearby glutamate (E129 in V. cholerae; E183 in R. sphaeroides) also resulted in loss of oxidase activity and loss of Ca2+. It is concluded that the Ca2+ is essential for assembly of the fully functional enzyme and that neither of the glutamates is likely to be part of a pathway for pumped protons within the cbb3-type oxygen reductases. A more likely role for these glutamates is the maintenance of the structural integrity of the active conformation of the enzyme.

The transition of the selectivity filter of Kþ channels between its two known important functional states, namely the conductive state and the slow