Mechanism Of Energy Transduction Research Articles

Singing whales generate high levels of particle motion: implications for acoustic communication and hearing?

Acoustic signals are fundamental to animal communication, and cetaceans are often considered bioacoustic specialists. Nearly all studies of their acoustic communication focus on sound pressure measurements, overlooking the particle motion components of their communication signals. Here we characterized the levels of acoustic particle velocity (and pressure) of song produced by humpback whales. We demonstrate that whales generate acoustic fields that include significant particle velocity components that are detectable over relatively long distances sufficient to play a role in acoustic communication. We show that these signals attenuate predictably in a manner similar to pressure and that direct particle velocity measurements can provide bearings to singing whales. Whales could potentially use such information to determine the distance of signalling animals. Additionally, the vibratory nature of particle velocity may stimulate bone conduction, a hearing modality found in other low-frequency specialized mammals, offering a parsimonious mechanism of acoustic energy transduction into the massive ossicles of whale ears. With substantial concerns regarding the effects of increasing anthropogenic ocean noise and major uncertainties surrounding mysticete hearing, these results highlight both an unexplored pathway that may be available for whale acoustic communication and the need to better understand the biological role of acoustic particle motion.

The thermodynamic efficiency of ATP synthesis in oxidative phosphorylation

As the chief energy source of eukaryotic cells, it is important to determine the thermodynamic efficiency of ATP synthesis in oxidative phosphorylation (OX PHOS). Previous estimates of the thermodynamic efficiency of this vital process have ranged from Lehninger's original back-of-the-envelope calculation of 38% to the often quoted value of 55–60% in current textbooks of biochemistry, to high values of 90% from recent information theoretic considerations, and reports of realizations of close to ideal 100% efficiencies by single molecule experiments. Hence this problem has been reinvestigated from first principles. The overall thermodynamic efficiency of ATP synthesis in the mitochondrial energy transduction OX PHOS process has been found to lie between 40 and 41% from four different approaches based on a) estimation using structural and biochemical data, b) fundamental nonequilibrium thermodynamic analysis, c) novel insights arising from Nath's torsional mechanism of energy transduction and ATP synthesis, and d) the overall balance of cellular energetics. The torsional mechanism also offers an explanation for the observation of a thermodynamic efficiency approaching 100% in some experiments. Applications of the unique, molecular machine mode of functioning of F1FO-ATP synthase involving direct inter-conversion of chemical and mechanical energies in the design and fabrication of novel, man-made mechanochemical devices have been envisaged, and some new ways to exorcise Maxwell's demon have been proposed. It is hoped that analysis of the fundamental problem of energy transduction in OX PHOS from a fresh perspective will catalyze new avenues of research in this interdisciplinary field.

A micrometre-sized heat engine operating between bacterial reservoirs

Artificial micro heat engines are prototypical models to explore and elucidate the mechanisms of energy transduction in a regime that is dominated by fluctuations [1-2]. Micro heat engines realized hitherto mimicked their macroscopic counterparts and operated between reservoirs that were effectively thermal [3-7]. For such reservoirs, temperature is a well-defined state variable and stochastic thermodynamics provides a precise framework for quantifying engine performance [8-9]. It remains unclear whether these concepts readily carry over to situations where the reservoirs are out-of-equilibrium [10], a scenario of particular importance to the functioning of synthetic [11-12] and biological [13] micro engines and motors. Here we experimentally realized a micrometer-sized active Stirling engine by periodically cycling a colloidal particle in a time-varying harmonic optical potential across bacterial baths at different activities. Unlike in equilibrium thermal reservoirs, the displacement statistics of the trapped particle becomes increasingly non-Gaussian with activity. We show that as much as $\approx$ 85\% of the total power output and $\approx$ 50\% of the overall efficiency stems from large non-Gaussian particle displacements alone. Most remarkably, at the highest activities investigated, the efficiency of our quasi-static active heat engines surpasses the equilibrium saturation limit of Stirling efficiency - the maximum efficiency of a Stirling engine with the ratio of cold and hot reservoir temperatures ${T_C\over T_H} \to 0$. Crucially, the failure of effective temperature descriptions [14-16] for active reservoirs highlights the dire need for theories that can better capture the physics of micro motors and heat engines that operate in strongly non-thermal environments.

Magnetic levitation-based electromagnetic energy harvesting: a semi-analytical non-linear model for energy transduction.

Magnetic levitation has been used to implement low-cost and maintenance-free electromagnetic energy harvesting. The ability of levitation-based harvesting systems to operate autonomously for long periods of time makes them well-suited for self-powering a broad range of technologies. In this paper, a combined theoretical and experimental study is presented of a harvester configuration that utilizes the motion of a levitated hard-magnetic element to generate electrical power. A semi-analytical, non-linear model is introduced that enables accurate and efficient analysis of energy transduction. The model predicts the transient and steady-state response of the harvester a function of its motion (amplitude and frequency) and load impedance. Very good agreement is obtained between simulation and experiment with energy errors lower than 14.15% (mean absolute percentage error of 6.02%) and cross-correlations higher than 86%. The model provides unique insight into fundamental mechanisms of energy transduction and enables the geometric optimization of harvesters prior to fabrication and the rational design of intelligent energy harvesters.

Reduction of Chemically Stable Multibonds: Nitrogenase-Like Biosynthesis of Tetrapyrroles.

The sophisticated biochemistry of nitrogenase plays a fundamental role for the biosynthesis of tetrapyrrole molecules, acting as key components of photosynthesis and methanogenesis. Three nitrogenase-like metalloenzymes have been characterized to date. Synthesis of chlorophylls and bacteriochlorophylls involves the reduction of the C17-C18 double bond of the conjugated ring system of protochlorophyllide which is catalyzed by the multi-subunit enzyme dark operative protochlorophyllide oxidoreductase (DPOR). Subsequently, biosynthesis of all bacteriochlorophylls requires the reduction of the C7-C8 double bond by a second nitrogenase-like enzyme termed chlorophyllide oxidoreductase (COR). Mechanistically, DPOR and COR make use of a reductase component which links ATP hydrolysis to conformational changes. This dynamic switch protein is triggering the transient association between the reductase and the core catalytic protein complex, thereby facilitating the transduction of electrons via two [4Fe4S] clusters. X-ray crystallographic structural investigations in combination with biochemical experiments revealed the molecular basis of the underlying energy transduction mechanism. The unique nickel-containing tetrapyrrole cofactor F430 is located in the active site of methyl-coenzyme M reductase, which is catalyzing the final step of methane formation in methanogenic archaea. The nitrogenase-like protein NflH/NflD has been proposed to catalyze one or more ring reduction steps during the biosynthesis of F430. The present working hypothesis mirrors a DPOR and COR related enzyme mechanism of NflH/NflD. Furthermore, nfl-encoded proteins were suggested as "simplified" ancestors lying basal in the phylogenetic tree between nitrogenase and DPOR/COR.

A Self‐Assembled Respiratory Chain that Catalyzes NADH Oxidation by Ubiquinone‐10 Cycling between Complex I and the Alternative Oxidase

AbstractComplex I is a crucial respiratory enzyme that conserves the energy from NADH oxidation by ubiquinone‐10 (Q10) in proton transport across a membrane. Studies of its energy transduction mechanism are hindered by the extreme hydrophobicity of Q10, and they have so far relied on native membranes with many components or on hydrophilic Q10 analogues that partition into membranes and undergo side reactions. Herein, we present a self‐assembled system without these limitations: proteoliposomes containing mammalian complex I, Q10, and a quinol oxidase (the alternative oxidase, AOX) to recycle Q10H2 to Q10. AOX is present in excess, so complex I is completely rate determining and the Q10 pool is kept oxidized under steady‐state catalysis. The system was used to measure a fully‐defined KM value for Q10. The strategy is suitable for any enzyme with a hydrophobic quinone/quinol substrate, and could be used to characterize hydrophobic inhibitors with potential applications as pharmaceuticals, pesticides, or fungicides.

A Self-Assembled Respiratory Chain that Catalyzes NADH Oxidation by Ubiquinone-10 Cycling between Complex I and the Alternative Oxidase.

Complex I is a crucial respiratory enzyme that conserves the energy from NADH oxidation by ubiquinone‐10 (Q10) in proton transport across a membrane. Studies of its energy transduction mechanism are hindered by the extreme hydrophobicity of Q10, and they have so far relied on native membranes with many components or on hydrophilic Q10 analogues that partition into membranes and undergo side reactions. Herein, we present a self‐assembled system without these limitations: proteoliposomes containing mammalian complex I, Q10, and a quinol oxidase (the alternative oxidase, AOX) to recycle Q10H2 to Q10. AOX is present in excess, so complex I is completely rate determining and the Q10 pool is kept oxidized under steady‐state catalysis. The system was used to measure a fully‐defined K M value for Q10. The strategy is suitable for any enzyme with a hydrophobic quinone/quinol substrate, and could be used to characterize hydrophobic inhibitors with potential applications as pharmaceuticals, pesticides, or fungicides.

Conformational Reorganization Coupled to the Ionization of Internal Lys Residues in Proteins.

Ionizable groups buried in the hydrophobic interior of proteins are essential for energy transduction and catalysis. Because the protein interior is usually neither as polar nor as polarizable as water, these groups tend to have anomalous pKa values, and their ionization tends to be coupled to conformational reorganization. To elucidate mechanisms of energy transduction in proteins, it is necessary to understand the structural determinants of the pKa values of these buried groups, including the range and character of the conformational reorganization that the ionization of these buried groups can elicit. The L25K and L125K variants of staphylococcal nuclease (SNase) were used to characterize the diverse types of structural reorganization that can be promoted by the ionization of buried groups. NMR relaxation dispersion and ZZ-exchange experiments were used to identify the locations and measure the time scales and extent of pH-dependent conformational exchange in these two proteins. The buried Lys-25 and Lys-125 residues titrate with pKa of 6.3 and 6.2, respectively. The L25K protein fluctuates between the native state and an ensemble of locally unfolded states on the 400 μs to 7 ms time scale. On the 100 to 500 ms time scale the native state exchanges with a subglobally unfolded state in which the β-barrel is partially reorganized. The equilibrium between the native state and this alternative state is highly pH dependent; at pH values below the pKa of Lys-25 the state with the partially reorganized β-barrel is the dominant state. In contrast, the L125K protein only exhibited pH-independent fluctuation in the microsecond to millisecond time scale in the region near Lys-125. The study illustrates how diverse and how localized the coupling between conformational reorganization and ionization of buried groups can be. The pH-sensitive exchange between the fully native and subglobally or locally unfolded states in time scales well into hundreds of milliseconds will challenge all computational methods for structure-based calculations of pKa values.

Induction of a proton gradient across a gold-supported biomimetic membrane by electroenzymatic H2 oxidation.

Energy-transduction mechanisms in living organisms, such as photosynthesis and respiration, store light and chemical energy in the form of an electrochemical gradient created across a lipid bilayer. Herein we show that the proton concentration at an electrode/phospholipid-bilayer interface can be controlled and monitored electrochemically by immobilizing a membrane-bound hydrogenase. Thus, the energy derived from the electroenzymatic oxidation of H2 can be used to generate a proton gradient across the supported biomimetic membrane.

Oxidative phosphorylation revisited.

The fundamentals of oxidative phosphorylation and photophosphorylation are revisited. New experimental data on the involvement of succinate and malate anions respectively in oxidative phosphorylation and photophosphorylation are presented. These new data offer a novel molecular mechanistic explanation for the energy coupling and ATP synthesis carried out in mitochondria and chloroplast thylakoids. The mechanism does not suffer from the flaws in Mitchell's chemiosmotic theory that have been pointed out in many studies since its first appearance 50 years ago, when it was hailed as a ground-breaking mechanistic explanation of what is perhaps the most important process in cellular energetics. The new findings fit very well with the predictions of Nath's torsional mechanism of energy transduction and ATP synthesis. It is argued that this mechanism, based on at least 15 years of experimental and theoretical work by Sunil Nath, constitutes a fundamentally different theory of the energy conversion process that eliminates all the inconsistencies in Mitchell's chemiosmotic theory pointed out by other authors. It is concluded that the energy-transducing complexes in oxidative phosphorylation and photosynthesis are proton-dicarboxylic acid anion cotransporters and not simply electrogenic proton translocators. These results necessitate revision of previous theories of biological energy transduction, coupling, and ATP synthesis. The novel molecular mechanism is extended to cover ATP synthesis in prokaryotes, in particular to alkaliphilic and haloalkaliphilic bacteria, essentially making it a complete theory addressing mechanistic, kinetic, and thermodynamic details. Finally, based on the new interpretation of oxidative phosphorylation, quantitative values for the P/O ratio, the amount of ATP generated per redox package of the reduced substrates, are calculated and compared with experimental values for fermentation on different substrates. It is our hope that the presentation of oxidative phosphorylation and photophosphorylation from a wholly new perspective will rekindle scientific discussion of a key process in bioenergetics and catalyze new avenues of research in a truly interdisciplinary field.

Role of Fumarate in the Operation of the Bacterial Flagellar Motor

Fumarate has previously been identified as a ‘switch factor’ that can alter the switching frequency and bias of the sense of rotation of the bacterial flagellar motor; however, despite numerous studies during the past fifty years, the molecular mechanism by which fumarate causes these effects could not be understood. We studied the motility of Salmonella by bright field and by monitoring rotation in a tethered cell assay. We carried out a detailed computerized analysis of the swimming and rotational behavior in real time under various conditions of external pHs (5.0 ± 8.0) and added fumarate concentrations (0 ± 12 mM). Based on our experimental results, we make the novel proposal that the bacterial flagellar motor contains access channels permeable to the fumarate monoanion, and that it catalyzes the overall electroneutral transport of fumarate and protons. We further postulate that each ionic species provides ∼50% of the total energy for rotation of the bacterial flagellar motor. These predictions are applicable to both the normal (say CW) mode of motor rotation as well as to the so-called “switched” (CCW) sense of rotation, depending on the direction of translocation of the ions. Hence previous proposals of fumarate as a ‘switch factor’, are false, or at best incomplete, because fumarate participates in the rotation of the flagellar motor in both normal and switched modes of operation. The new hypothesis extends to bacterial motility the essential and vital role played by dicarboxylic acid anions in oxidative phosphorylation and photosynthesis according to Nath's torsional mechanism of energy transduction and ATP synthesis (Nath, S., Beyond the Chemiosmotic Theory, Journal of Bioenergetics and Biomembranes 2010,42, 301-309).

Energy transfer within responsive pi-conjugated coassembled peptide-based nanostructures in aqueous environments.

Steady-state and time-resolved photophysical measurements demonstrate energy transfer within π-conjugated peptide nanostructures composed of oligo-(p-phenylenevinylene)-based donor units and quaterthiophene-based acceptor units in completely aqueous environments. These peptide-based assemblies encourage energy migration along the stacking axis, thus resulting in the quenching of donor emission peaks along with the development of new spectral features reminiscent of acceptor emission. These spectral changes were observed even at minute amounts of the acceptor (starting at 1 mol%), suggesting that exciton migration is involved in energy transport and supporting a funnel-like energy transduction mechanism. The reversibility of nanostructure formation and the associated photophysical responses under different conditions (pH, temperature) were also studied. This unique material design incorporates two different semiconducting units coassembled within peptide nanostructures and offers a new platform for the engineering of energy migration through bioelectronic materials in aqueous environments.

Perspectives on the microbial carbon pump with special reference to microbial respiration and ecosystem efficiency in large estuarine systems

Abstract. Although respiration-based oxidation of reduced carbon releases CO2 into the environment, it provides an ecosystem with the metabolic energy for essential biogeochemical processes, including the newly proposed microbial carbon pump (MCP). The efficiency of MCP in heterotrophic microorganisms is related to the mechanisms of energy transduction employed and hence is related to the form of respiration utilized. Anaerobic organisms typically have lower efficiencies of energy transduction and hence lower efficiencies of energy-dependent carbon transformation. This leads to a lower MCP efficiency on a per-cell basis. Substantial input of terrigenous nutrients and organic matter into estuarine ecosystems typically results in elevated heterotrophic respiration that rapidly consumes dissolved oxygen, potentially producing hypoxic and anoxic zones in the water column. The lowered availability of dissolved oxygen and the excessive supply of nutrients such as nitrate from river discharge lead to enhanced anaerobic respiration processes such as denitrification and dissimilatory nitrate reduction to ammonium. Thus, some nutrients may be consumed through anaerobic heterotrophs, instead of being utilized by phytoplankton for autotrophic carbon fixation. In this manner, eutrophied estuarine ecosystems become largely fueled by anaerobic respiratory pathways and their efficiency is less due to lowered ecosystem productivity when compared to healthy and balanced estuarine ecosystems. This situation may have a negative impact on the ecological function and efficiency of the MCP which depends on the supply of both organic carbon and metabolic energy. This review presents our current understanding of the MCP mechanisms from the view point of ecosystem energy transduction efficiency, which has not been discussed in previous literature.

Fast and Sustainable Energy Storage in Flavins Inspired by Biological Energy Metabolism for Li Rechargeable Batteries

Cellular metabolism comprises energy transduction machineries that operate by a series of redox-active components for storing energies from nutrients, which are transduced into high-energy intermediates for cellular works such as chemical synthesis, transport, and movement.Biological energy transduction mechanism hints at the construction of a man-made energy storage system. Since the pioneering work by Tarascon et al.[1] towards a sustainable lithium rechargeable battery received significant resonance, organic materials such as carbonyl, carboxyl, or quinone-based compounds have been demonstrated to be bio-inspired organic electrodes [2, 3]. The imitation of redox-active plastoquinone and ubiquinone cofactors [4] through the utilization of redox active C=O functionalities in organic electrodes is a significant step-forward to biomimetic energy storage. However, the biological energy transduction is based on numerous redox centers of versatile functionalities available in nature, not limited to the simple redox active C=O functionalities. Consideration of how natural energy transduction systems function at organelle or cellular levels by elucidating the basic components and their operating principles selected by evolution will enrich the biomimetic strategy for efficient and green energy storage.Herein, we propose new-type of redox active organic molecules containing C=N functionality, where most interest in organic electrodes has focused on the molecules with C=O functionalities, such as carbonyl, carboxylate, or quinone-based molecules [5]. Flavins, a key redox element in respiration and photosynthesis, facilitate either one- or two-electron-transfer redox processes accompanying proton transfer at nitrogen atoms of diazabutadiene motif during cellular metabolism. We have discovered that the protonation sites of a riboflavin molecule can capture two lithium ions reversibly exhibiting a high capacity of 174 mAh/g, which is comparable to that of LiFePO4. The combined ex situ characterizations and density-functional theory(DFT)-based calculation revealed that the redox reaction occurs via the two successive single-electron transfer steps at nitrogen atoms of diazabutadiene motif, which is analogous to the proton-coupled electron transfer of flavoenzymes in nature. We also demonstrated that the capacity and voltage can be tuned by the substitution of flavin cofactors, which opens up new principles in electrode design. This kind of bio-electrode is particularly unprecedented for lithium rechargeable batteries.In terms of the practical use of organic-based electrodes, however, they suffer from sluggish kinetics and poor capacity retention, which originate from low electronic conductivity and dissolution of electroactive chemicals into electrolytes. To address this issue, we further demonstrate a novel and facile design strategy for organic electrodes possessing high energy and power densities combined with excellent cyclic stability [6]. Non-covalent nanohybridization of electroactive aromatic molecules with single-walled carbon nanotubes (SWNTs) leads to reassembly of electroactive molecules from bulk crystalline particles into molecular layers on conductive scaffolds. The simple fabrication of this nanohybrid electrode in the form of a flexible, free-standing paper (free of binder/additive and current collector) results in ultrafast kinetics delivering 510 Wh/kg within 30 minutes (204 mAh/g ≈ 98% of theoretical capacity) and 272 Wh/kg of energy even within 46 seconds. Moreover, the stable anchorage of electroactive organic molecules on the sidewall of SWNTs enables above 99% capacity retention upon 100 cycles, which was hardly achieved for organic electrodes. Our approach can be extended to other aromatic organic electrode systems, bringing bio-inspired organic materials a step closer to practical cathodes in rechargeable batteries.[1] H. Chen, M. Armand, G. Demailly, F. Dolhem, P. Poizot, J.M. Tarascon, ChemSusChem 2008, 1, 348.[2] Z. Song, H. Zhan, Y. Zhou, Chem. Commun. 2009, 448.[3] M. Armand, S. Grugeon, H. Vezin, S. Laruelle, P. Ribière, P. Poizot, J.M. Tarascon, Nat. Mater. 2009, 8, 120.[4] P. Poizot, F. Dolhem, Energy Environ. Sci. 2011, 4, 2003.[5] M. Lee, J. Hong, D.-H. Seo, D.H. Nam, K.T. Nam, K. Kang, C.B. Park, Angew. Chem. Int. Ed. 2013, 52, 8322[6] J. Hong, M. Lee, H. Kim, H.-D. Lim, C.B. Park, K. Kang, Adv. Mater., 2013, In press

An Investigation into Membrane Bound Redox Carriers Involved in Energy Transduction Mechanism in Brevibacterium linens DSM 20158 with Unsequenced Genome

Brevibacterium linens (B. linens) DSM 20158 with an unsequenced genome can be used as a non-pathogenic model to study features it has in common with other unsequenced pathogens of the same genus on the basis of comparative proteome analysis. The most efficient way to kill a pathogen is to target its energy transduction mechanism. In the present study, we have identified the redox protein complexes involved in the electron transport chain of B. linens DSM 20158 from their clear homology with the shot-gun genome sequenced strain BL2 of B. linens by using the SDS-Polyacrylamide gel electrophoresis coupled with nano LC-MS/MS mass spectrometry. B. linens is found to have a branched electron transport chain (Respiratory chain), in which electrons can enter the respiratory chain either at NADH (Complex I) or at Complex II level or at the cytochrome level. Moreover, we are able to isolate, purify, and characterize the membrane bound Complex II (succinate dehydrogenase), Complex III (menaquinone cytochrome c reductase cytochrome c subunit, Complex IV (cytochrome c oxidase), and Complex V (ATP synthase) of B. linens strain DSM 20158.

Development of Molecular Shuttle Regulated by External Stimulation Utilizing Kinesin ATP Driven Motor

Kinesin is known as a dimeric motor protein, which carries cellular cargoes along microtubules by hydrolyzing ATP. Its structure and the molecular mechanism of energy transduction to move along microtubule are well studied. The kinesin has many possibility of application to the molecular machines. Previously, we introduced photochromic molecules into the functional key region of the kinesin as a photoswitch and tried to control the function of kinesin by ultraviolet (UV) and visible (VIS) light irradiations. The kinesin mutant S275C modified with thiol reactive azobenzene derivative exhibited photocontrolled ATPase activity correlating to photo isomerization. We have also demonstrated that kinesin fused with CaM at the C-terminal binds reversibly to M13-Qdots in a calcium dependent manner. As mentioned above, kinesin works as a nanodevice to be a component of bionanomachines. In this study, we tried to prepare the molecular shuttles regulated by external stimulation utilizing kinesin and other functional proteins. We designed the two chimeric kinesins. One is the kinesin motor domain (K355) fused with calmodulin (CaM) and the other is K355 fused with calmodulin target peptide M13. The chimeras were expressed by E. coli. and purified by Co-Chelate column. These kinesin chimeras showed normal ATPase activities. K355-CaM bound to K355-M13 in a calcium dependent manner and formed dimer. The dimer composed of the two chimeras induced exhibited motor activity to induce microtubule gliding. Moreover, we also tried to prepare the chimeric kinesins, K355-CaM-split GFP C-terminal domain and K355-split GFP N-terminal domain to be dimerized and fluorescently labelled spontaneously.

Investigating Protein-Protein Interaction Networks with Force Spectroscopy

Colicins are antimicrobial proteins produced by bacteria. Their highly active modes of killing make colicins of interest as a potential new class of antibiotics. However, the precise mechanism of cytotoxicity is not understood thus limiting their translation to biotechnological applications.It is thought that colicin intoxication occurs via a series of protein-protein interactions (PPIs) that span the periplasm (Housden et al. Science, 2013). Mechanical force may play a role in this process by an inside-out energy transduction mechanism. Periplasmic proteins that are subverted by colicins have either a known role in applying force during their normal function in-vivo or are highly homologous to proteins that do.In this work we study the colicin E9 system and the PPIs that remodel during its translocation across the outer and inner membranes of E. coli. Through a series of in-vitro single molecule force spectroscopy experiments performed using an atomic force microscope, we identify a mechanism by which dissociation of the highly avid colicin E9-immunity protein interaction (fM affinity, half-life days) can take place via the application of small forces (<20 pN) during colicin translocation (Farrance et al. PLoS Biol, 2013). Such a mechanism could account for the disparity between measured lifetimes of colicin-immunity protein interactions and the timescale on which colicins kill (days vs. minutes) for which immunity protein release is a prerequisite.Further and ongoing pulling experiments on other PPIs formed during colicin E9 translocation involving periplasmic proteins from the Tol complex also show interesting behaviour under applied forces. These results suggest that the PPI network formed during E9 translocation would be able to support and transduce significant forces and these may be crucial in understanding the mechanism by which colicins gain access to the cellular interior and ultimately kill their target.

Unraveling the Energy Transduction Mechanism of Resilin Elasticity-A Combination of Computational and Experimental Study

Resilin, known as a “super elastic rubber”, has drawn intensive research interests for its striking energy transduction and storage properties. However, due to lack of atomic structures of this protein and its constituent domains, no models with atomic details are available up to date to enable an in-depth understanding of the energy transductions and storage mechanism in resilin. In our current study, with model peptides, we explore the structures of the high-hydrophobicity sequence and the repeating unit of the Exon III domain of resilin at the atomic level. Bioinformatics method predicts interesting β-sheet and β-turn structures for the above respective sequences, which is consistent with earlier and present experimental acquisitions. Long-time molecular dynamics simulations with the explicit solvent model further confirm these structural features. The peptide secondary and tertiary structures, and peptide-water interactions are investigated in details with simulations, and the results are compared to experimental measurements from Fourier Transform Infrared Spectroscopy (FTIR) and Differential Scanning Calorimetry (DSC). The present study offers an atomistic view of resilin and elastomeric proteins in general where β-turn-related structures serve as fundamental units of the structure and elasticity.

Intramolecular Polarization Induces Electron–Hole Charge Separation in Light-Harvesting Molecular Triads

Artificial light-harvesting supramolecular structures reproduce the light-to-electrochemical energy transduction mechanisms observed in natural photosynthesis. Among them the prototypical carotenoid(C)–porphyrin(P)–fullerene(C60) type of structures have been the most studied. Several experiments performed in such structures, and others alike, have shown that the photoexcited state C– 1P–C60 decays to the metastable charge-separated state C– P•+ −C60•– within a few picoseconds, whereas the final charge-separated state, C•+– P −C60•–, is obtained within hundreds of picoseconds. This paper introduces a nonlinear polarizable extended Hückel Hamiltonian that describes the charge dynamics and charge-separation effects in such triads by means of quantum dynamics simulations performed on the photoexcited electron–hole pair. The results are interpreted on the basis of the discrete self-trapping equation and enlighten the role played by the polarizability on charge-separation phenomena.

Mitochondrial Complex I

Complex I (NADH:ubiquinone oxidoreductase) is crucial for respiration in many aerobic organisms. In mitochondria, it oxidizes NADH from the tricarboxylic acid cycle and β-oxidation, reduces ubiquinone, and transports protons across the inner membrane, contributing to the proton-motive force. It is also a major contributor to cellular production of reactive oxygen species. The redox reaction of complex I is catalyzed in the hydrophilic domain; it comprises NADH oxidation by a flavin mononucleotide, intramolecular electron transfer along a chain of iron-sulfur clusters, and ubiquinone reduction. Redox-coupled proton translocation in the membrane domain requires long-range energy transfer through the protein complex, and the molecular mechanisms that couple the redox and proton-transfer half-reactions are currently unknown. This review evaluates extant data on the mechanisms of energy transduction and superoxide production by complex I, discusses contemporary mechanistic models, and explores how mechanistic studies may contribute to understanding the roles of complex I dysfunctions in human diseases.