Investigating the Broad Matrix-Gate Network in the Mitochondrial ADP/ATP Carrier through Molecular Dynamics Simulations

The mitochondrial ADP/ATP carrier (AAC) exports ATP and imports ADP through alternating between cytosol-open (c-) and matrix-open (m-) states. The salt bridge networks near the matrix side (m-gate) and cytosol side (c-gate) are thought to be crucial for state transitions, yet our knowledge on these networks is still limited. In the current work, we focus on more conserved m-gate network in the c-state AAC. All-atom molecular dynamics (MD) simulations on a variety of mutants and the CATR-AAC complex have revealed that: (1) without involvement of other positive residues, the charged residues from the three Px[DE]xx[KR] motifs only are prone to form symmetrical inter-helical network; (2) R235 plays a determinant role for the asymmetry in m-gate network of AAC; (3) R235 significantly strengthens the interactions between H3 and H5; (4) R79 exhibits more significant impact on m-gate than R279; (5) CATR promotes symmetry in m-gate mainly through separating R234 from D231 and fixing R79; (6) vulnerability of the H2-H3 interface near matrix side could be functionally important. Our results provide new insights into the highly conserved yet variable m-gate network in the big mitochondrial carrier family.     

Investigations of mitochondrial adenine nucleotide translocation by means of nucleotide analogs.

ATP and ADP are transferred across the inner mitochondrial membrane by means of a carrier (translocator), an inner membrane integral lipoprotein. Translocation of the adenine nucleotides occurs in two steps: specific binding and transport. By using substrate analogs with modified adenine, phosphate, or ribose moieties it is possible to check which structural properties of the substrate are essential for binding and transport.     

Molecular mechanism of thiamine pyrophosphate import into mitochondria: a molecular simulation study

The import of thiamine pyrophosphate (TPP) through both mitochondrial membranes was studied using a total of 3-µs molecular dynamics simulations. Regarding the translocation through the mitochondrial outer membrane, our simulations support the conjecture that TPP uses the voltage-dependent anion channel, the major pore of this membrane, for its passage to the intermembrane space, as its transport presents significant analogies with that used by other metabolites previously studied, in particular with ATP. As far as passing through the mitochondrial inner membrane is concerned, our simulations show that the specific carrier of TPP has a single binding site that becomes accessible, through an alternating access mechanism. The preference of this transporter for TPP can be rationalized mainly by three residues located in the binding site that differ from those identified in the ATP/ADP carrier, the most studied member of the mitochondrial carrier family. The simulated transport mechanism of TPP highlights the essential role, at the energetic level, of the contributions coming from the formation and breakage of two networks of salt bridges, one on the side of the matrix and the other on the side of the intermembrane space, as well as the interactions, mainly of an ionic nature, formed by TPP upon its binding. The energy contribution provided by the cytosolic network establishes a lower barrier than that of the matrix network, which can be explained by the lower interaction energy of TPP on the matrix side or possibly a uniport activity.

     

A coulombic hypothesis of mitochondrial energy transduction

A coulombic (electrostatic) interpretation of mitochondrial energy transduction is proposed as an alternative to the chemiosmotic (electrochemical) view. Both the hypotheses accept the importance of proton translocation across the inner membrane as a primary consequence of electron transport; only the coulombic hypothesis gives significance to the conjoint phenomenon of negative fixed charge formation.     

Haematoporphyrin derivative (Photofrin II) photosensitization of isolated mitochondria: inhibition of ADP/ATP translocator

To gain further insight into the mechanism by which irradiation of mitochondria in the presence of haematoporphyrin derivative (Photofrin II) (PF II) causes impairment of mitochondrial oxidative phosphorylation, the rate of ADP/ATP exchange via the ADP/ATP translocator was measured fluorometrically is isolated rat liver mitochondria. In accord with noncompetitive inhibition, PF II photosensitization decreases the maximum rate of exchange Vmax (20.8 and 9.6 nmol ATP effluxed min-1 x mg protein in the control and after 2 min irradiation, respectively) without changing the ADP affinity for the carrier (Km = 5 microM in both cases). Comparison of the rate of oxygen uptake by mitochondria stimulated by either ADP or by the uncoupler carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP) confirms that the adenine nucleotide carrier is a major target of photodynamic action which causes oxidative phosphorylation impairment.     

Energy metabolism in mitochondria

Mitochondria are separate metabolic compartments within the cell. The functional boundary of the mitochondrial compartment is the inner membrane. This membrane contains the enzymatic apparatus for the electron transport and oxidative phosphorylation. The substrate breakdown cycles are localized in the mitochondrial matrix space. Specific carriers are responsible for the exchange of ADP, ATP, phosphate, and intermediates of the citric acid cycle between the matrix space and the extramitochondrial space. The particular importance of the adenine nucleotide transport to the regulation of the energy metabolism of the cell is discussed in detail.     

Polymeric liquid membrane electrodes incorporated with macrocyclic hexaamines for screening adenine nucleotides

Lipophilic macrocyclic hexaamines supported by a poly(vinyl chloride) PVC matrix were used for the construction of liquid membrane electrodes sensitive toward adenine nucleotide polyanions. The membrane potential strongly depended on the pH of the sample solution. This phenomenon occurs due to the ability of the ionophore to accept protons. Therefore, the optimum pH was determined based on potential pH profile. The potential measurements were carried out at pH 6.0 in the presence of 10(-2) M 2-[N-morpholino] ethanesulfonic acid (MES) buffer. The potential response of these electrodes toward ATP(-4) and/or HATP(-3) was close to the Nernstian slope. The selectivities against ADP(-3), AMP(-2), HPO(4)(-2), and monovalent inorganic anions were estimated using the matched potential method. Chloride ions slightly affected potential response of the electrodes toward ATP(-4)/HATP(-3). The influence of ionophore chemical structure on the selectivity and the sensitivity of these electrodes is briefly discussed.     

A turn-on two-photon fluorescent probe for ATP and ADP

An acedan derivative containing Zn(II)-DPA has been developed as a two-photon probe for nucleoside phosphates, which shows enhanced fluorescence toward ATP and ADP at physiological pH 7.4 among other competing anions including AMP; the probe is permeable to cell membranes and thus can be directly used for two-photon imaging of ATP and ADP in live cells.     

β-Biguanidinium-cyclodextrin: a supramolecular mimic of mitochondrial ADP/ATP carrier protein

We reported a novel mono-β-cyclodextrin derivative, mono-6-deoxy-6-biguanidino-β-cyclodextrin (β-biGCD), which was investigated as a mimic of ADP/ATP carrier (AAC). Its affinity toward AMP, ADP, and ATP was evaluated by means of isothermal titration calorimetry (ITC). The association constants (K_a) of β-biGCD binding to AMP, ADP, and ATP were determined to be (1.07±0.04)×10⁶, (5.86±0.02)×10⁶, and (4.33±0.06)×10⁶ L mol⁻¹, respectively, which were 100-fold higher than mono-guanidino-β-cyclodextrin (ca. 10⁴ L mol⁻¹). UV spectroscopic titrations further confirmed the above results. The interaction between β-biGCD and nucleotides was probed by docking simulation. These results reveal that the biguanidinium moiety mimics the arginine residues of mitochondrial AAC protein.     

The molecular mechanism of dicarboxylic acid transport in Escherichia coli K 12.

It is the purpose of this communication to review the properties of the dicarboxylic acid transport system in Escherichia coli K 12, in particular the role of various dicarboxylate transport proteins, and the disposition of these components in the cytoplasmic membrane. The dicarboxylate transport system is an active process and is responsible for the uptake of succinate, fumarate, and malate. Membrane vesicles prepared from the EDTA, lysozyme, and osmotic shock treatment take up the dicarboxylic acids in the presence of an electron donor. Genetic analysis of various transport mutants indicates that there is only one dicarboxylic acid transport system present in Escherichia coli K 12, and that at least 3 genes, designated cbt, dct A, and dct B, are involved in this transport system. The products corresponding to the 3 genes are: a periplasmic binding protein (PBP) specified by cbt, and 2 membrane integral proteins, SBP 1 and SBP 2, specified by dct B and dct A, respectively. Components SBP 1 and SBP 2 appear to be exposed on both the inner and outer surfaces of the membrane, and lie in close proximity to each other. The substrate recognition sites of SBP 2 and SBP 1 are exposed on the outer and inner surfaces of the membrane respectively. The data presently available suggest that dicarboxylic acids may be translocated across the membrane via a transport channel. A tentative working model on the mechanism of translocation of dicarboxylic acids across the cell envelope by the periplasmic binding protein, and the 2 membrane carrier proteins is presented.     

The binding of Mn2+ and ADP to myosin.

The metal ion requirement of myosin-ADP binding was investigated by use of Mn2+. Mn2+ binds to two sets of noninteracting sites on myosin which are characterized by affinity constants of 10(6) and 10(3), M(-1) at 0.016 M KCl concentration. The maximum number of sites is 2 for the high affinity and 20-25 for the low affinity set. Binding of Mn2+ to the high affinity sites increases the affinity of ADP binding to myosin. F-actin inhibits ADP binding (Kiely, B., and Martonosi, A., Biochim. Biophys. Acta 172: 158-170 [1969]), but even at F-actin concentrations much higher than that required to saturate the actin binding sites of myosin or its proteolytic fragments, significant ADP binding remained. The actin insensitive portion of ADP binding was inhibited by 10(-4) M inorganic pyrophosphate or ATP. The results are discussed on the basis of a model in which actin and ADP bind to myosin at distinct but interacting sites.     

The effect of component partitioning on potassium picrate transport across multicomponent supported liquid membranes

Supported liquid membrane experiments were performed with systematically varied liquid membrane compositions including dicyclohexyl-18-crown-6 ether as the carrier and various ratios of methylene chloride and a 35 carbon aliphatic oil. The partitioning of the crown ether species toward the membrane phase increased markedly with methylene chloride addition to the aliphatic oil. p]The unanticipated unsteady state transport of potassium picrate across the liquidfilled microporous membranes resulted from evaporation of methylene chloride from the aqueous reservoirs and subsequent depletion from the membrane phase. The depletion of methylene chloride from the liquid membrane caused progressively reduced partitioning of the carrier and carrier complexes to the membrane relative to the contiguous aqueous phases. The reduction in carrier concentration in the membrane phase resulted in progressively decreased concentration gradients of the carrier complex. The rate of potassium picrate transport decreased during the course of the experiments even though the upstream potassium concentration was insignificantly decreased and the downstream concentration of potassium picrate remained small compared with the upstream concentration. p]These experimental results focus attention upon the important practical problem of non-infinite partitioning of carrier and key solvent components between the membrane phase and the contiguous aqueous phases. Subtle changes in the carrier distribution coefficient markedly compromise process efficacy since the volume ratio of the aqueous and membrane phases is enormous.     

杯芳烃的超分子化学研究（IV）：对-叔丁基杯[4]芳烃对ATP的分子识别及液膜传输作用

采用气泡式准乳化液膜法,研究了对-叔丁基杯[4]芳烃对ATP分子的液膜传输 作用,讨论了源相与吸收相的组成、酸度、源相中的ATP的起始浓度及吸收相中 NH_3·H_2O浓度等因素对传输结果的影响;进而讨论了对-叔丁基杯[4]芳烃对ATP 的分子识别作用和液膜传输机理。     

Binding of AMP,ADP, and ATP Nucleotides by Polyammonium Macrocycles

The macrocyclic polyamines 4 – 6 , when protonated, bind strongly and selectively nucleotides (AMP, ADP, ATP) and pyrophosphate in aqueous solution. The stoichiometry of the complexes formed was determined by titration experiments followed by ³¹ P-NMR spectroscopy. Compounds 4 and 5 form 1:1 complexes with ATP, ADP, and pyrophosphate, whereas 6 forms complexes with ATP and ADP involving 2 nucleotides and 1 receptor molecule. The stability constants of these complexes have been determined by pH-metric measurements. At pH 7, both 5 and 6 give complexes of mainly the fully protonated species 5 . 6H ⁺ and 6 . 8H ⁺, whereas 4 yields predominantly complexes of 4 . 5H ⁺ and 4 . 4H ⁺.     

Detection of carbonyl-modified proteins in interfibrillar rat mitochondria using N'-aminooxymethylcarbonylhydrazino-D-biotin as an aldehyde/keto-reactive probe in combination with Western blot analysis and tandem mass spectrometry

There is now a large body of supporting data available that links oxidative modifications of proteins to a large number of diseases, degenerative disorders and aging. However, the detailed analysis of oxidative protein modifications remains challenging. Here, we report a new efficient method for identification of oxidatively modified proteins in complex biological samples which is based on the use of an aldehyde-reactive probe, N'-aminooxymethylcarbonylhydrazino-D-biotin (ARP), in combination with Western-type analyses and MS. The biotinylated hydroxylamine derivative forms a chemically stable oxime derivative with the aldehyde/keto group found in carbonyl-modified proteins. The biotin tag is detected by avidin affinity staining. ARP-positive proteins are subsequently subjected to in-gel trypsinization and MS/MS for protein identification. We demonstrate the usefulness of the method for the analysis of protein extracts obtained from interfibrillar heart mitochondria (IFM) from young and old rats. In this study, we identified as putative major protein targets of oxidative modifications the mitochondrial matrix protein, aconitase, the inner mitochondrial membrane protein, ADP/ATP translocase, and constituents of the electron transport chain complexes IV and V. An age-related increase of carbonyl levels was found for aconitase and ATP synthase.     

Conformation of ATP and ADP Molecules in Aqueous Solutions Determined by High-Energy X-ray Diffraction

High-energy X-ray diffraction measurements were carried out at 26 °C for aqueous 1.0, 2.0 and 2.05 mol% disodium adenosine 5′-triphosphate (ATP) and 2.0 and 2.05 mol% disodium adenosine 5′-diphosphate (ADP) solutions in order to obtain direct experimental information on the intramolecular conformations of ATP and ADP molecules in aqueous solutions. Observed interference terms were analyzed in terms of the intramolecular geometry of the ATP and ADP molecules. Dihedral angles between adenine and the ribose group (t ₁), ribose-ring and methylene group of ribose (t ₂), and the methylene group of ribose and triphosphate (or diphosphate) group (t ₃), were determined through the least-squares fitting procedure of the observed interference term.     

Mitochondrial Oxidative Phosphorylation

Mitochondria can form ATP from ADP and inorganic phosphate, the required energy being supplied by respiration. This coupled process, which in sufficiently aerated normal animal cells furnishes the bulk of the cellular ATP, is termed oxidative phosphorylation. The overall reaction is intimately associated with the mitochondrial inner membrane and proceeds via a primary high-energy intermediate. This intermediate, in a manner as yet unknown, energizes the anhydride formation between ADP and inorganic phosphate. The coupling between respiration and ATP synthesis is mediated by proteins of the mitochondrial inner membrane which are known as “coupling factors”. The mechanism of oxidative phosphorylation is at present being discussed in terms of three hypotheses which are generally referred to as “chemical”, “chemiosmotic”, and “conformational” hypotheses. None of these hypotheses has as yet been experimentally verified.     

Polymer inclusion membranes: The concept of fixed sites membrane revised

The mechanism of facilitated transport of metal ions across polymer inclusion membranes (PIMs) is revised on the basis of transport flux measurements and of new data brought by techniques sensitive to local inter-molecular interactions and molecular diffusion. Cellulose triacetate (CTA) membranes built with two types of inclusion carriers: a liquid one Aliquat 336 and a crystalline one Lasalocid A, both able to carry metal ions across PIMs and supported liquid membranes (SLMs) made of the same components, have been compared. Both PIM systems show similar effects for what concern the need of a carrier threshold concentration for the occurrence of a transport flux across PIM as revealed by flux and fluorescence correlation spectroscopy (FCS) measurements, and the dependence of the chemical nature of plasticizers on the metal ion flux. These systems also present similar Raman and far IR signatures of structural evolution of PIMs with the increase of the carrier concentration within the CTA matrix.

All the presented data are interpreted as concern PIMs, according to an evolution of chemical interactions between components of the polymeric membrane able to lead to a phase transition. This phase transition type of the carrier-plasticized polymer system is induced by the increase of carrier concentration in the polymer chains. The PIM progressively organizes itself like a liquid SLM because of the enhancement of preferential solvent interactions between the carrier and the plasticizer.

The main conclusion of this study is that the classically adopted “hopping” transport mechanism between fixed carrier sites in a PIM does not apply to such carrier chemically unbound to polymer membrane systems.     

ATP-dependent active transport simulations based on a phosphatase-channel-kinase membrane structure

Simulations of coupled interactions involving enzymatic reaction diffusion and electrostatic interactions were conducted under a fixed phosphatase-channel-kinase (PCK) topology oriented from the outside to the inside of a charged membrane structure. Depending on the phosphatase and kinase locations, we recently demonstrated that active transport of a phosphorylated substrate may occur via this PCK topology. The present analysis demonstrates that, if in addition to this topology, a phosphatase activity (P(1)) is also present on the inner side of the membrane, but outside the unstirred layer surrounding the inner membrane surface, then active transport of the corresponding unphosphorylated substrate may also occur. Therefore, this PCK membrane topology, which behaves as a specific ATP-dependent transporter, appears as a general topology permitting; first, on its own the active transport of a phosphorylated substrate; second, when associated with a phosphatase acting in the bulk of the receiver compartment, the active transport of the corresponding unphosphorylated substrate, that is, in most cases, the transport of an uncharged substrate. The general mathematical model given permits the active transport of a phosphorylated substrate to be analyzed (in the absence of P(1)), the active transport of an unphosphorylated substrate (in the presence of P(1)), whatever the charge distributions on both sides of the membrane surface and whatever the positions of the membrane-bound phosphatase and the membrane-bound kinase. This general model also takes into account the consumption of ATP occurring into the receiver compartment during the time course of these transport phenomena. A broad analysis of the role played by the main parameters taken into account in the model was conducted to precisely define the physicochemical conditions and the membrane topology needed for the highest active transports within the shortest time.     

Vanadate (Vi) and ADP induced domain motions in myosin head by DSC and EPR

Thermal stability and internal dynamics of myosin head in psoas muscle fibres of rabbit in the intermediate state AM.ADP.P_i - mimicked by AM.ADP.V_i - of the ATP hydrolysis cycle was studied by differential scanning calorimetry and spin label electron paramagnetic resonance spectroscopy. Three overlapping endotherms were detected in rigor, in strongly binding ADP and weakly binding AM.ADP.V_i state of myosin to actin. The transition at 54.0°C can be assigned to the 50 k actin-binding domain. The transition at highest temperature (67.3°C) represents the unfolding of actin and the contributions arising from the nucleotide-myosin head interaction. The transition at 58.4°C reflects the melting of the large rod part of myosin. Nucleotide binding (ADP, ATP plus orthovanadate) induced shifts of the melting temperatures and produced changes in the calorimetric enthalpies. The changes of the EPR parameters indicated local rearrangements of the internal structure in myosin heads in agreement with DSC findings. This revised version was published online in July 2006 with corrections to the Cover Date.