Structures of the intermediates in the catalytic cycle of mitochondrial cytochrome c oxidase

Cytochrome c oxidase is the terminal complex of the respiratory chains in the mitochondria of nearly all eu-karyotes. It catalyzes the reduction of molecular O-2 to water using electrons from the respiratory chain, delivered via cytochrome c on the external surface of the inner mitochondrial membrane. The protons required for water formation are taken from the matrix side of the membrane, making catalysis vectorial. This vectorial feature is further enhanced by the fact that the redox catalysis is coupled to the translocation of protons from the inside to the outside of the inner mitochondrial membrane. We are dealing with a molecular machine that converts redox free energy into a protonmotive force (pmf). Here, we review the current extensive knowledge of the structural changes in the active heme-copper site that accompany catalysis, based on a large variety of time-resolved spectroscopic experiments, X-ray and cryoEM structures, and advanced computational chemistry.Peer reviewe

Fluctuation-Induced Interactions between Rods on Membranes and Interfaces

We consider the interaction between two rods embedded in a fluctuating surface which is governed by either surface tension or rigidity. The modification of fluctuations by the rods leads to an attractive long-range interaction that falls off as $1/R^4$ with their separation. The orientational dependence of the resulting interaction is non-trivial and may lead to interesting patterns of rod-like objects on such surfaces.Comment: Revtex, 10 pages, one figur

Collective shuttling of attracting particles in asymmetric narrow channels

The rectification of a single file of attracting particles subjected to a low frequency ac drive is proposed as a working mechanism for particle shuttling in an asymmetric narrow channel. Increasing the particle attraction results in the file condensing, as signalled by the dramatic enhancement of the net particle current. Magnitude and direction of the current become extremely sensitive to the actual size of the condensate, which can then be made to shuttle between two docking stations, transporting particles in one direction, with an efficiency much larger than conventional diffusive models predict

Diffusion-controlled generation of a proton-motive force across a biomembrane

Respiration in bacteria involves a sequence of energetically-coupled electron and proton transfers creating an electrochemical gradient of protons (a proton-motive force) across the inner bacterial membrane. With a simple kinetic model we analyze a redox loop mechanism of proton-motive force generation mediated by a molecular shuttle diffusing inside the membrane. This model, which includes six electron-binding and two proton-binding sites, reflects the main features of nitrate respiration in E. coli bacteria. We describe the time evolution of the proton translocation process. We find that the electron-proton electrostatic coupling on the shuttle plays a significant role in the process of energy conversion between electron and proton components. We determine the conditions where the redox loop mechanism is able to translocate protons against the transmembrane voltage gradient above 200 mV with a thermodynamic efficiency of about 37%, in the physiologically important range of temperatures from 250 to 350 K.Comment: 26 pages, 4 figures. A similar model is used in arXiv:0806.3233 for a different biological system. Minor changes in the Acknowledgements sectio

Phase Behaviour of Amphiphilic Monolayers: Theory and Simulation

Coarse grained models of monolayers of amphiphiles (Langmuir monolayers) have been studied theoretically and by computer simulations. We discuss some of the insights obtained with this approach, and present new simulation results which show that idealised models can successfully reproduce essential aspects of the generic phase behaviour of Langmuir monolayers.Comment: To appear in J. Phys.: Cond. Matte

Ligand binding and conformational dynamics of the E. coli nicotinamide nucleotide transhydrogenase revealed by hydrogen/deuterium exchange mass spectrometry

Nicotinamide nucleotide transhydrogenases are integral membrane proteins that utilizes the proton motive force to reduce NADP+ to NADPH while converting NADH to NAD+. Atomic structures of various transhydrogenases in different ligand-bound states have become available, and it is clear that the molecular mechanism involves major conformational changes. Here we utilized hydrogen/deuterium exchange mass spectrometry (HDX-MS) to map ligand binding sites and analyzed the structural dynamics of E. coli transhydrogenase. We found different allosteric effects on the protein depending on the bound ligand (NAD+, NADH, NADP+, NADPH). The binding of either NADP+ or NADPH to domain III had pronounced effects on the transmembrane helices comprising the proton-conducting channel in domain II. We also made use of cyclic ion mobility separation mass spectrometry (cyclic IMS-MS) to maximize coverage and sensitivity in the transmembrane domain, showing for the first time that this technique can be used for HDX-MS studies. Using cyclic IMS-MS, we increased sequence coverage from 68 % to 73 % in the transmembrane segments. Taken together, our results provide important new insights into the transhydrogenase reaction cycle and demonstrate the benefit of this new technique for HDX-MS to study ligand binding and conformational dynamics in membrane proteins

Proton Wires in an Electric Field: the Impact of Grotthuss Mechanism on Charge Translocation

We present the results of the modeling of proton translocation in finite H-bonded chains in the framework of two-stage proton transport model. We explore the influence of reorientation motion of protons, as well as the effect of electric field and proton correlations on system dynamics. An increase of the reorientation energy results in the transition of proton charge from the surrounding to the inner water molecules in the chain. Proton migration along the chain in an external electric field has a step-like character, proceeding with the occurrence of electric field threshold-type effects and drastic redistribution of proton charge. Electric field applied to correlated chains induces first a formation of ordered dipole structures for lower field strength, and than, with a further field strength increase, a stabilization of states with Bjerrum D-defects. We analyze the main factors responsible for the formation/annihilation of Bjerrum defects showing the strong influence of the complex interplay between reorientation energy, electric field and temperature in the dynamics of proton wire.Comment: 28 pages, 9 figure

Fluctuation-Induced Interactions between Rods on a Membrane

We consider the interaction between two rods embedded in a fluctuating surface. The modification of fluctuations by the rods leads to an attractive long-range interaction between them. We consider fluctuations governed by either surface tension (films) or bending rigidity (membranes). In both cases the interaction falls off with the separation of the rods as $1/R^4$. The orientational part of the interaction is proportional to $\cos^2\left[ \theta_1+\theta_2 \right]$ in the former case, and to $\cos^2\left[ 2\left(\theta_1+\theta_2\right) \right]$ in the latter, where $\theta_1$ and $\theta_2$ are angles between the rods and the line joining them. These interactions are somewhat reminiscent of dipolar forces and will tend to align collections of such rods into chains.Comment: REVTEX, 14 pages, with 2 Postscript figure

Charge-Reversal Instability in Mixed Bilayer Vesicles

Bilayer vesicles form readily from mixtures of charged and neutral surfactants. When such a mixed vesicle binds an oppositely-charged object, its membrane partially demixes: the adhesion zone recruits more charged surfactants from the rest of the membrane. Given an unlimited supply of adhering objects one might expect the vesicle to remain attractive until it was completely covered. Contrary to this expectation, we show that a vesicle can instead exhibit {\it adhesion saturation,} partitioning spontaneously into an attractive zone with definite area fraction, and a repulsive zone. The latter zone rejects additional incoming objects because counterions on the interior of the vesicle migrate there, effectively reversing the membrane's charge. The effect is strongest at high surface charge densities, low ionic strength, and with thin, impermeable membranes. Adhesion saturation in such a situation has recently been observed experimentally [H. Aranda-Espinoza {\it et al.}, {\sl Science} {\bf285} 394--397 (1999)]

Structure of symmetric and asymmetric "ripple" phases in lipid bilayers

We reproduce the symmetric and asymmetric ``rippled'' $P_{\beta'}$ states of lipid membranes by Monte Carlo simulations of a coarse-grained molecular model for lipid-solvent mixtures. The structure and properties compare favorably with experiments. The asymmetric ripple state is characterized by a periodic array of fully interdigitated ``defect'' lines. The symmetric ripple state maintains a bilayer structure, but is otherwise structurally similar. The formation of both ripple states is driven by the propensity of lipid molecules with large head groups to exhibit splay.Comment: 4 pages, 4 figure