Energy Transduction Processes Research Articles

Impact of hexavalent chromium on mammalian cell bioenergetics: phenotypic changes, molecular basis and potential relevance to chromate-induced lung cancer

Occupational exposure to hexavalent chromium [Cr(VI)] has been firmly associated with the development of several pathologies, notably lung cancer. According to the current paradigm, the evolution of normal cells to a neoplastic state is accompanied by extensive metabolic reprogramming, namely at the level of energy-transducing processes. Thus, a complete understanding of the molecular basis of Cr(VI)-induced lung cancer must encompass the elucidation of the impact of Cr(VI) on metabolism. Research in this area is still in its infancy. Nonetheless, Cr(VI)-induced metabolic phenotypes are beginning to emerge. Specifically, it is now well documented that Cr(VI) exposure inhibits respiration and negatively affects the cellular energy status. Furthermore, preliminary results suggest that it also upregulates glucose uptake and lactic acid fermentation. From a mechanistic point of view, there is evidence that Cr(VI) exposure can interfere with energy transducing pathways at different levels, namely gene expression, intracellular protein levels and/or protein function. Loss of thiol redox control likely plays a key role in these processes. The transcriptional networks that control energy transduction can likewise be affected. Data also suggest that Cr(VI) exposure might compromise energy transducing processes through changes in the intracellular pools of their substrates. This article reviews, for the first time, the information available on Cr(VI) impact on mammalian cell bioenergetics. It aims to provide a framework for the understanding of the role played by bioenergetics in Cr(VI)-induced carcinogenesis and is also intended as a guide for future research efforts in this area.

Mitochondrial ion channels as oncological targets

Mitochondria, the key bioenergetic intracellular organelles, harbor a number of proteins with proven or hypothetical ion channel functions. Growing evidence points to the important contribution of these channels to the regulation of mitochondrial function, such as ion homeostasis imbalances profoundly affecting energy transducing processes, reactive oxygen species production and mitochondrial integrity. Given the central role of mitochondria in apoptosis, their ion channels with the potential to compromise mitochondrial function have become promising targets for the treatment of malignancies. Importantly, in vivo evidence demonstrates the involvement of the proton-transporting uncoupling protein, a mitochondrial potassium channel, the outer membrane located porin and the permeability transition pore in tumor progression/control. In this review, we focus on mitochondrial channels that have been assigned a definite role in cell death regulation and possess clear oncological relevance. Overall, based on in vivo and in vitro genetic and pharmacological evidence, mitochondrial ion channels are emerging as promising targets for cancer treatment.

Cytochrome c assembly

Cytochromes c are central proteins in energy transduction processes by virtue of their functions in electron transfer in respiration and photosynthesis. They have heme covalently attached to a characteristic CXXCH motif via protein-catalyzed post-translational modification reactions. Several systems with diverse constituent proteins have been identified in different organisms and are required to perform the heme attachment and associated functions. The necessary steps are translocation of the apocytochrome polypeptide to the site of heme attachment, transport and provision of heme to the appropriate compartment, reduction and chaperoning of the apocytochrome, and finally, formation of the thioether bonds between heme and two cysteines in the cytochrome. Here we summarize the established classical models for these processes and present recent progress in our understanding of the individual steps within the different cytochrome c biogenesis systems.

Structure of ADP-aluminium fluoride-stabilized protochlorophyllide oxidoreductase complex

Photosynthesis uses chlorophylls for the conversion of light into chemical energy, the driving force of life on Earth. During chlorophyll biosynthesis in photosynthetic bacteria, cyanobacteria, green algae and gymnosperms, dark-operative protochlorophyllide oxidoreductase (DPOR), a nitrogenase-like metalloenzyme, catalyzes the chemically challenging two-electron reduction of the fully conjugated ring system of protochlorophyllide a. The reduction of the C-17=C-18 double bond results in the characteristic ring architecture of all chlorophylls, thereby altering the absorption properties of the molecule and providing the basis for light-capturing and energy-transduction processes of photosynthesis. We report the X-ray crystallographic structure of the substrate-bound, ADP-aluminium fluoride-stabilized (ADP·AlF(3)-stabilized) transition state complex between the DPOR components L(2) and (NB)(2) from the marine cyanobacterium Prochlorococcus marinus. Our analysis permits a thorough investigation of the dynamic interplay between L(2) and (NB)(2). Upon complex formation, substantial ATP-dependent conformational rearrangements of L(2) trigger the protein-protein interactions with (NB)(2) as well as the electron transduction via redox-active [4Fe-4S] clusters. We also present the identification of artificial "small-molecule substrates" of DPOR in correlation with those of nitrogenase. The catalytic differences and similarities between DPOR and nitrogenase have broad implications for the energy transduction mechanism of related multiprotein complexes that are involved in the reduction of chemically stable double and/or triple bonds.

The V499G/Y501H Mutation Impairs Fast Motor Kinetics of Prestin and Has Significance for Defining Functional Independence of Individual Prestin Subunits

Outer hair cells (OHCs) are a mammalian innovation for mechanically amplifying sound energy to overcome the viscous damping of the cochlear partition. Although the voltage-dependent OHC membrane motor, prestin, has been demonstrated to be essential for mammalian cochlear amplification, the molecular mechanism by which prestin converts electrical energy into mechanical displacement/force remains elusive. Identifying mutations that alter the motor function of prestin provides vital information for unraveling the energy transduction mechanism of prestin. We show that the V499G/Y501H mutation does not deprive prestin of its voltage-induced motor activity, but it does significantly impair the fast motor kinetics and voltage operating range. Furthermore, mutagenesis studies suggest that Val-499 is the primary site responsible for these changes. We also show that V499G/Y501H prestin forms heteromers with wild-type prestin and that the fast motor kinetics of wild-type prestin is not affected by heteromer formation with V499G/Y501H prestin. These results suggest that prestin subunits are individually functional within a given multimer.

Mimicking the respiratory burst myeloperoxidase system of polymorphonuclear neutrophil granulocytes to aid the wound healing behaviors of articular cartilage

Purpose: Articular cartilage exhibits a limited ability to remove damaged tissue from its surfaces, a step integral for efficient mammalian wound healing that is typically enabled by polymorphonuclear neutrophil granulocytes in other tissue types. This limited ability constrains articular cartilage wound healing behaviors, contributing to lesion progression and the disease burden of osteoarthritis. The respiratory burst myeloperoxidase system of polymorphonuclear neutrophil granulocytes produces low stability protonating agents involved in exothermic tissue homeostasis and repair mechanisms through disproportionation redox reactions. Because these protonating agents facilitate the removal of damaged interstitial matrices through biopolymer disaggregation in order to assist differentiated tissue assembly activities, this study evaluates the capability of alternating current redox magnetohydrodynamic technology to mimic this respiratory burst to aid the wound healing behaviors of articular cartilage by creating a healthy lesion site devoid of damaged tissue. Methods: An alternating current redox magnetohydrodynamic device fashioned as a physiochemical scalpel was deployed in 0.9% sodium chloride solutions at 300 mOsm/L and at 20oC. Figure 1 demonstrates the device producing solution changes that are delivered to tissue surfaces as an engineered irrigant during endoscopic procedures designed to stabilize articular cartilage lesions. To determine if the engineered irrigant resembles the protic solvent generated by azurophilic granules, the resultant irrigant temperature and protonation potential were measured as a function of power input during device activation controlled for 5 second steady-state treatment conditions. Irrigant protonation potential was determined by measuring solution electrochemical potential relative to [H+] as a function of differential proton sequestration in the irrigant during device activation. Results: Alternating current redox magnetohydrodynamics in saline solutions is represented in Figure 2. As depicted in Figure 3, the protonation potential increased with direct correlation to power delivery (p < 0.02; R2 = 0.311) and commensurate with a minimal change in irrigant temperature (∼0-5o C) above the baseline 20o C, reflecting features characteristic of the protic solvent generated by the azurophilic degranulation of polymorphonuclear neutrophil granulocytes during the early phases of wound healing. Conclusions: Because resection precision that eliminates both volumetric and functional over-resection is required before surgical lesion stabilization can be an effective aid to articular cartilage wound healing behaviors, polymorphonuclear neutrophil granulocyte function is a valuable therapeutic design resource. Protonation coupled conformational dynamics is an energy transduction processes that achieves nanometer resection precision through a guest chemical denaturization process below the isoelectric point of exposed damaged interstitial tissue matrices. Because of high proton motilities in water solutions, stoichiometric protonation is a very rapid charge redistribution process that leads to biopolymer disaggregation through molecular cleavage planes accessible due to normal tissue surface barrier losses and degenerate matrix properties characteristic of damage tissue sites. Figure 4 illustrates a representative integrated cell viability stain section image that demonstrates removing the bioburden of damaged tissue without iatrogenic over-resection in a human explant model of osteoarthritis by adapting alternating current redox magnetohydrodynamic technology for tissue rescue surgical procedures.

Single Molecule Measurement of the Myosin V Energy Transduction Process

Myosin V is an ATPase molecular motor that takes 36 nm processive steps along actin filaments in a hand-over-hand fashion. Experiments using gold nano particles have revealed that this movement consists of two processes: a deterministic lever arm swing and diffusional Brownian search. Although both are thought to contribute to the ATP chemo-mechanical energy transduction, details of their contributions remain poorly understood.

Dynamic Quantum-mechanical Effects of Vibrational Excitations on Protein Conformation

Many proteins undergo significant structural changes following the hydrolysis of a bound nucleoside triphosphate (NTP) molecule. Davydov has proposed that, in the protein myosin, vibrational excitations are taken advantage of in the energy transduction process following this hydrolysis. Using an atomistic, mixed quantum-classical molecular dynamics model, we have attempted to obtain a more detailed understanding of how this process might take place. Our results indicate that vibrational excitations may be capable of inducing transitions of protein domains from less helical to more helical states. We discuss examples of protein systems for which small changes in ??-helical structure are known to lead to biologically-significant structural effects. Evidence is reviewed supporting a model in which vibrational excitations can lead to utilization of the energy released in NTP hydrolysis through important changes in protein structure following the contraction of a protein α-helix.

How many ionizable groups can sit on a protein hydrophobic core?

Full or partial burial of ionizable groups in the hydrophobic interior of proteins underlies the large modulation in group properties (modified pK value, high nucleophilicity, enhanced capability of interaction with chemical moieties of the substrate, etc.) linked to biological function. Indeed, the few internal ionizable residues found in proteins are known to play important functional roles in catalysis and, in general, in energy transduction processes. However, ionizable-group burial is expected to be seriously disruptive and, it is important to note, most functional sites contain not just one, but several ionizable residues. Hence, the adaptations involved in the development of function in proteins (through in vitro engineering or during the course of natural evolution) are not fully understood. Here, we explore experimentally how proteins respond to the accumulation of hydrophobic-to-ionizable residue substitutions. For this purpose, we have constructed a combinatorial library targeting a hydrophobic cluster in a consensus-engineered, stabilized form of a small model protein. Contrary to naïve expectation, half of the variants randomly selected from the library are soluble, folded, and active, despite including up to four mutations. Furthermore, for these variants, the dependence of stability with the number of mutations is not synergistic and catastrophic, but smooth and approximately linear. Clearly, stabilized protein scaffolds may be robust enough to withstand many disruptive hydrophobic-to-ionizable residue mutations, even when they are introduced in the same region of the structure. These results should be relevant for protein engineering and may have implications for the understanding of the early evolution of enzymes.

Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange.

A computational tool that offers accurate pKa values and atomically detailed knowledge of protonation-coupled conformational dynamics is valuable for elucidating mechanisms of energy transduction processes in biology, such as enzyme catalysis and electron transfer as well as proton and drug transport. Toward this goal we present a new technique of embedding continuous constant pH molecular dynamics within an explicit-solvent representation. In this technique we make use of the efficiency of the generalized-Born (GB) implicit-solvent model for estimating the free energy of protein solvation while propagating conformational dynamics using the more accurate explicit-solvent model. Also, we employ a pH-based replica exchange scheme to significantly enhance both protonation and conformational state sampling. Benchmark data of five proteins including HP36, NTL9, BBL, HEWL, and SNase yield an average absolute deviation of 0.53 and a root mean squared deviation of 0.74 from experimental data. This level of accuracy is obtained with 1 ns simulations per replica. Detailed analysis reveals that explicit-solvent sampling provides increased accuracy relative to the previous GB-based method by preserving the native structure, providing a more realistic description of conformational flexibility of the hydrophobic cluster, and correctly modeling solvent mediated ion-pair interactions. Thus, we anticipate that the new technique will emerge as a practical tool to capture ionization equilibria while enabling an intimate view of ionization coupled conformational dynamics that is difficult to delineate with experimental techniques alone.

Empirical Method For Calculation of Pka Values of Internal Ionizable Groups in Proteins

Internal ionizable groups are essential for energy transduction processes. They usually titrate with highly perturbed pKa values; the molecular determinants of these pKa values are poorly understood. Structure-based calculation of the pKa values of internal ionizable groups is extremely challenging and of high importance owing to the functional roles of these groups. We have used a large set of variants of staphylococcal nuclease with internal Lys, Asp and Glu of known pKa to examine the performance of a variety of standard methods (FDPB, MCCE, PROPKA, Karlsberg) for pKa calculations, and to guide the development of an empirical computational protocol useful to calculate pKa values for these challenging cases.

3M0912 ミオシンVエネルギー変換素過程の1分子計測(分子モーター4,第49回年会講演予稿集)

3M0912 ミオシンVエネルギー変換素過程の1分子計測(分子モーター4,第49回年会講演予稿集)

Ultrafast Interfacial Proton-Coupled Electron Transfer

Interfaces between metallic or semiconducting solids and protic solvent adsorbates or liquids represent one of the most important, and yet hardly explored material environments for proton coupled electron transfer (PCET) processes. PCET mediated dynamical phenomena driven by light, electron, and chemical potentials are central in energy transduction processes of vast economic and environmental importance including the photocatalytic splitting of H₂O, the photo and electrochemical reduction of CO₂, and the conversion of chemical to electrical energy in fuel cells. Experimental and theoretical investigations of the dynamical aspects of PCET at solid surfaces are particularly challenging because relatively localized charges within a solvent couple in the presence of strong interfacial potentials to delocalized states of electronic continua of semiconductor or metal electrodes. Moreover, the localized charges are never the bare protons and electrons that balance chemical equations, but rather are dressed particles with associated polarization clouds inhomogeneously distributed and comprised variously of free electrons, lattice ions, and solvent molecules. The polarization clouds screen the Coulomb potential on the medium specific time scales and impose energetic costs associated with transport through the inhomogeneous region of interfaces between the solid and molecular environments. We introduce some recent theoretical studies aimed at providing an atomisticmore » description on metal-protic solvent interface and modeling of simple processes such as the discharge of H⁺ at a metal interface. Because of the paucity of experimental research and embryonic stage of theory, our goal is to present some key theoretical concepts and early experimental efforts based primarily on a surface science approach to ultrafast electron induced dynamics. In order to introduce some key features of interfacial PCET in the strong and intermediate coupling regimes, we discuss specific examples of photoinduced dissociation of alkanes on metals and photoinduced PCET dynamics of methanol covered TiO₂ surfaces.« less

Fluorescent Chemosensor for Detection of PPi Through the Inhibition of Excimer Emission in Water

, PPi) is involved in energy transduc-tion and metabolic processes within cells. For example, the concomitant release of PPi is indispensable to intracellular enzymatic reactions such as DNA polymerization catalyzed by DNA polymerase and the synthesis of cyclic adenosine mono-phosphate (cAMP), a second messenger used for signal trans-duction in many different organisms, catalyzed by adenylyl cyclase.

Photosynthesis in silico. Understanding complexity from molecules to ecosystems

Photosynthesis in silico. Understanding complexity from molecules to ecosystems

Initial changes in the transcriptome of Euphorbia esula seeds induced to germinate with a combination of constant and diurnal alternating temperatures

We investigated transcriptome changes in Euphorbia esula (leafy spurge) seeds with a focus on the effect of constant and diurnal fluctuating temperature on dormancy and germination. Leafy spurge seeds do not germinate when incubated for 21 days at 20 degrees C constant temperatures, but nearly 30% germinate after 21 days under fluctuating temperatures 20:30 degrees C (16:8 h). Incubation at 20 degrees C for 21 days followed by 20:30 degrees C resulted in approximately 63% germination in about 10 days. A cDNA microarray representing approximately 22,000 unique sequences was used to profile transcriptome changes in the first day after transfer of seeds from constant to alternating temperature conditions. Functional classification based on MIPS and gene ontology revealed active metabolism including up-regulation of energy, protein synthesis, and signal transduction processes. Down-regulated processes included translation elongation, translation, and some biosynthetic processes. Subnetwork analysis identified genes involved in abscisic acid, sugar, and circadian clock signaling as key regulators of physiological activity in seeds soon after the transfer to alternating conditions.

Simulating Efflux Pumps: The Extrusion Mechanism of Substrates

Bacteria use multidrug efflux pumps to extrude toxic substrates through their cell membranes. The RND transporters of the AcrAB-TolC (E.Coli) and MexAB-OprM (P.Aeruginosa) systems are able to export structurally and chemically different substrates, being responsible of multidrug resistance. While the energy conversion takes place in the transmembrane domain of AcrB and MexB, the energy is transducted towards the periplasmic part and used there to initiate what is believed to be a three-cyclic peristaltic pumping. Using different computational methods like adaptive bias force (ABF) and targeted molecular dynamics (TMD), we have investigated the mechanism of substrate uptake and pumping. With ABF we have studied the passage of antibiotics from the periplasm and protein-lipid interface into the inner pore of the pump, while TMD has been used to assess the effect of conformational changes on the extrusion of drugs (located into one of the proposed binding pockets). Finally, analysis of water distribution in the transmembrane region represents an important step to identify features of the energy transduction process. Comparison between the active pumps AcrB and MexB (which show different resistance patterns despite their homology) provide insights into the microscopic details of their functioning.View Large Image | View Hi-Res Image | Download PowerPoint Slide

Crystal Structure of the Heme-IsdC Complex, the Central Conduit of the Isd Iron/Heme Uptake System in Staphylococcus aureus

Pathogens such as Staphylococcus aureus require iron to survive and have evolved specialized proteins to steal heme from their host. IsdC is the central conduit of the Isd (iron-regulated surface determinant) multicomponent heme uptake machinery; staphylococcal cell-surface proteins such as IsdA, IsdB, and IsdH are thought to funnel their molecular cargo to IsdC, which then mediates the transfer of the iron-containing nutrient to the membrane translocation system IsdDEF. The structure of the heme-IsdC complex reveals a novel heme site within an immunoglobulin-like domain and sheds light on its binding mechanism. The folding topology is reminiscent of the architecture of cytochrome f, cellobiose dehydrogenase, and ethylbenzene dehydrogenase; in these three proteins, the heme is bound in an equivalent position, but interestingly, IsdC features a distinct binding pocket with the ligand located next to the hydrophobic core of the beta-sandwich. The iron is coordinated with a tyrosine surrounded by several non-polar side chains that cluster into a tightly packed proximal side. On the other hand, the distal side is relatively exposed with a short helical peptide segment that acts as a lip clasping onto almost half of the porphyrin plane. This structural feature is argued to play a role in the mechanism of binding and release by switching to an open conformation and thus loosening the interactions holding the heme. The structure of the heme-IsdC complex provides a template for the understanding of other proteins, such as IsdA, IsdB, and IsdH, that contain the same heme-binding module as IsdC, known as the NEAT (near transporter) domain.

The power to reduce: pyridine nucleotides – small molecules with a multitude of functions

The pyridine nucleotides NAD and NADP play vital roles in metabolic conversions as signal transducers and in cellular defence systems. Both coenzymes participate as electron carriers in energy transduction and biosynthetic processes. Their oxidized forms, NAD+ and NADP+, have been identified as important elements of regulatory pathways. In particular, NAD+ serves as a substrate for ADP-ribosylation reactions and for the Sir2 family of NAD+-dependent protein deacetylases as well as a precursor of the calcium mobilizing molecule cADPr (cyclic ADP-ribose). The conversions of NADP+ into the 2'-phosphorylated form of cADPr or to its nicotinic acid derivative, NAADP, also result in the formation of potent intracellular calcium-signalling agents. Perhaps, the most critical function of NADP is in the maintenance of a pool of reducing equivalents which is essential to counteract oxidative damage and for other detoxifying reactions. It is well known that the NADPH/NADP+ ratio is usually kept high, in favour of the reduced form. Research within the past few years has revealed important insights into how the NADPH pool is generated and maintained in different subcellular compartments. Moreover, tremendous progress in the molecular characterization of NAD kinases has established these enzymes as vital factors for cell survival. In the present review, we summarize recent advances in the understanding of the biosynthesis and signalling functions of NAD(P) and highlight the new insights into the molecular mechanisms of NADPH generation and their roles in cell physiology.

Energy Transduction in Biological Systems: A Mesoscopic Non-Equilibrium Thermodynamics Perspective

We review recent efforts aimed at analyzing energy transduction processes in biological systems from the perspective of mesoscopic non-equilibrium thermodynamics. The inherent nonlinear nature of many of these systems, which undergo activated processes, has over the years impeded the use of classical non-equilibrium thermodynamics for their description, because this theory accounts only for the linear regime of these processes.