Rotary protein motors

A computational model of the inhibition of Mycobacterium tuberculosis ATPase by a new drug candidate R207910

Diarylquinolines (DARQs) are a new class of potent inhibitors of the ATPase of Mycobacterium tuberculosis. We have created a homology model of a binding site for this class of compounds located on the contact area of the a-subunit (gene atpB) and c-subunits (gene atpE) of Mycobacterium tuberculosis ATPase. The binding pocket that was identified from the analysis of the homology model is formed by 4 helices of three c-subunits and 2 helices of the a-subunit. The lead compound of the DARQ series, R207910, was docked into the pocket using a simulated annealing, multiple conformer, docking algorithm. Different stereoisomers were treated separately. The best docking pose for each stereoisomer was optimized by molecular dynamics simulation on the 5300 atoms of the binding region and ligand. The interaction energies in the computed complexes enable us to rank the different stereoisomers in order of interaction strength with the ATPase binding pockets. We propose that the activity of R207910 against Mycobacterium tuberculosis is based on interference of the compound with the escapement geometry of the proton transfer chain. Upon binding the compound mimics the conserved Arg-186 residue of the a-subunit and interacts in its place with the conserved acidic residue Glu-61 of the c-subunit. This mode of action is corroborated by the good agreement between the computed interaction energies and the observed pattern of stereo-specificity in the model of the binding region.

Statistics of entropy production in linearized stochastic systems

We consider a wide class of linear stochastic problems driven off the equilibrium by a multiplicative asymmetric force. The force breaks detailed balance, maintained otherwise, thus producing entropy. The large deviation function of the entropy production in the system is calculated explicitly. The general result is illustrated using an example of a polymer immersed in a gradient flow and subject to thermal fluctuations.

Identification of differentially regulated proteins in a patient with Leber's Congenital Amaurosis--a proteomic study

BACKGROUND

To identify the pattern of protein expression in the retina from a patient with Leber's Congenital Amaurosis (LCA) secondary to a mutation in the AIPL1 gene. The retina from one eye of a patient with LCA and 7 control eyes were studied. The tissue was subjected to high resolution two-dimensional gel electrophoresis, image analysis and mass spectrometry, in an effort to identify differentially regulated proteins.

RESULTS

In the LCA retina seven protein spots were differentially expressed. Six proteins were significantly up-regulated of which three could be identified as: alphaA-crystallin, triosephophate isomerase, and an N-terminal fragment of the beta-chain of ATP synthase. One protein spot that was down-regulated in the LCA retina was identified as a C-terminal fragment of beta-tubulin.

CONCLUSION

Retinal tissue in LCA is characterised by an up-regulation of alphaA-crystallin, triosephosphate isomerase, and ATP synthase (beta-chain fragment) and down-regulation of a fragment of beta-tubulin. These proteins/protein fragments may play a crucial role for the retinal degeneration processes in LCA and other retinal dystrophies.

Synthetic molecular motors and mechanical machines

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Biological effects of deuteronation: ATP synthase as an example

Background

In nature, deuterium/hydrogen ratio is ~1/6600, therefore one of ~3300 water (H₂O) molecules is deuterated (HOD + D₂O). In body fluids the ratio of deuterons to protons is ~1/15000 because of the lower ionization constant of heavy water. The probability of deuteronation rather than protonation of Asp 61 on the subunit c of F₀ part of ATP synthase is also ~1/15000. The contribution of deuteronation to the pKa of Asp 61 is 0.35.

Theory and Discussion

In mitochondria, the release of a deuteron into the matrix side half-channel of F₀ is likely to be slower than that of a proton. As another example, deuteronation may slow down electron transfer in the electron transport chain (ETC) by interfering with proton coupled electron transport reactions (PCET), and increase free radical production through the leakage of temporarily accumulated electrons at the downstream complexes.

Conclusion

Deuteronation, as exemplified by ATP synthase and the ETC, may interfere with the conformations and functions of many macromolecules and contribute to some pathologies like heavy water toxicity and aging.

Visions for novel biophysical elucidations of extracellular matrix networks

The extracellular matrix consists of multifunctional molecules, which are composed of a large numbers of different domains. Clearly these domains and even the entire molecules do not function independently as isolated species, but interact with each other in large networks. In many cases specific regions of the networks may be considered as molecular machines in which the different molecules are arranged in highly defined spatial structures and act in a dynamic, concerted fashion. At present most structural information is limited to single molecules, and dynamics have been measured mainly for pairs of interacting partners in solution. Work needs to be extended to large integrated systems and the functions of molecular machines need to be explored. Electron tomography, fluorescence resonance energy transfer, and other biophysical techniques are very promising.

Photo-driven molecular devices

In this critical review, we discuss switching of the light-powered bistable rotaxanes and catenanes and highlight the practical applications of some of these systems. Photoactive molecular and supramolecular machines are comprised of two parts-1) a switching element, based on noncovalent interactions within the recognition units, which is responsible for executing mechanical movement, and 2) a light-harvesting unit which utilizes light to control the competitive interactions between the recognition sites. We also survey another class of molecular devices, namely molecular rotary motors--i.e., those that behave like their macroscopic counterparts--in which photochemically and thermally induced mechanical movement relies on isomerizations of a pivotal C=C bond, leading to a rotation of the top propeller part with respect to the stationary bottom part of the helical shaped chiral molecule. (146 references.).

Myosin-V is a mechanical ratchet

Myosin-V is a linear molecular motor that hydrolyzes ATP to move processively toward the plus end of actin filaments. Motion of this motor under low forces has been studied recently in various single-molecule assays. In this paper we show that myosin-V reacts to high forces as a mechanical ratchet. High backward loads can induce rapid and processive backward steps along the actin filament. This motion is completely independent of ATP binding and hydrolysis. In contrast, forward forces cannot induce ATP-independent forward steps. We can explain this pronounced mechanical asymmetry by a model in which the strength of actin binding of a motor head is modulated by the lever arm conformation. Knowledge of the complete force-velocity dependence of molecular motors is important to understand their function in the cellular environment.

Biological application of multi-component nanowires in hybrid devices powered by F1-ATPase motors

In this paper, construction of hybrid device by integrating nanowires with F(1)-ATPase motors is described. The nickel nanowires and multi-segment nanowires, including gold and nickel, were fabricated by electrochemical deposition in nanoporous templates. The nickel nanowires functionalized by biotinylated peptide can be assembled directly onto F(1)-ATPase motors to act as the propellers. If the multi-component nanowires, including gold and nickel, were selectively functionalized by the thiol group modified ssDNA and the synthetic peptide, respectively, the biotinylated F(1)-ATPase motors can be attached to the biotinylated peptide on nickel segment of the nanowires. Then, the multi-component nanowires can also be used as the propellers, and one may observe the rotations of the multi-component nanowires driven by F(1)-ATPase motors. Therefore, introduction of multiple segments along the length of a nanowire can lead to a variety of multiple chemical functionalities, which can be selectively bound to cells and special biomolecules. This method provides an insight for the construction of other hybrid devices with its controlling arrangement of different biomolecule on designed nanometer scale structures.

Demonstration of a controllable three-dimensional Brownian motor in symmetric potentials

We demonstrate a Brownian motor, based on cold atoms in optical lattices, where isotropic random fluctuations are rectified in order to induce controlled atomic motion in arbitrary directions. In contrast to earlier demonstrations of ratchet effects, our Brownian motor operates in potentials that are spatially and temporally symmetric, but where spatiotemporal symmetry is broken by a phase shift between the potentials and asymmetric transfer rates between them. The Brownian motor is demonstrated in three dimensions and the noise-induced drift is controllable in our system.

Proton in the well and through the desolvation barrier

The concept of the membrane proton well was suggested by Peter Mitchell to account for the energetic equivalence of the chemical (DeltapH) and electrical (Deltapsi) components of the proton-motive force. The proton well was defined as a proton-conducting crevice passing down into the membrane dielectric and able to accumulate protons in response to the generation either of Deltapsi or of DeltapH. In this review, the concept of proton well is contrasted to the desolvation penalty of > 500 meV for transferring protons into the membrane core. The magnitude of the desolvation penalty argues against deep proton wells in the energy-transducing enzymes. The shallow DeltapH- and Deltapsi-sensitive proton traps, mechanistically linked to the functional groups in the membrane interior, seem more realistic. In such constructs, the draw of a trapped proton into the membrane core can happen at the expense of some exergonic reaction, e.g., release of another proton from the membrane into the aqueous phase. It is argued that the proton transfer in the ATP synthase and the cytochrome bc complex could proceed in this way.

Motor potential profile and a robust method for extracting it from time series of motor positions

Molecular motors are small, and, as a result, motor operation is dominated by high-viscous friction and large thermal fluctuations from the surrounding fluid environment. The small size has hindered, in many ways, the studies of physical mechanisms of molecular motors. For a macroscopic motor, it is possible to observe/record experimentally the internal operation details of the motor. This is not yet possible for molecular motors. The chemical reaction in a molecular motor has many occupancy states, each having a different effect on the motor motion. The overall effect of the chemical reaction on the motor motion can be characterized by the motor potential profile. The potential profile reveals how the motor force changes with position in a motor step, which may lead to insights into how the chemical reaction is coupled to force generation. In this article, we propose a mathematical formulation and a robust method for constructing motor potential profiles from time series of motor positions measured in single molecule experiments. Numerical examples based on simulated data are shown to demonstrate the method. Interestingly, it is the small size of molecular motors (negligible inertia) that makes it possible to recover the potential profile from time series of motor positions. For a macroscopic motor, the variation of driving force within a cycle is smoothed out by the large inertia.

Model of active transport of ions in biomembranes based on ATP-dependent change of height of diffusion barriers to ions

A closed model of the active transport was constructed taking into account ATP-dependent opening and closing of barriers to ions and the relationship between the membrane potential and the work of ionic pumps under the condition of electroneutrality inside the cell. The internal consistency of the model was verified by the fulfillment of Onsager's reciprocity relation. It was demonstrated that at the limit of large energy barriers the operation of the system of the active transport is equivalent to the "turning segment" model, which was proposed by the authors earlier. Values of the resting potential and the intracellular concentration of ions were obtained for different types of cells. These results were in qualitative agreement with relevant experimental data.

Nanoscopic medicine: the next frontier

The extraordinary progress that has taken place in cell science and optical nanoscale microscopy has led recently to the concept of medical nanoscopy. Here, we lay out a concept for developing live cell nanoscopy into a comprehensive diagnostic and therapeutic scheme referred to as nanoscopic medicine, which integrates live cell nanoscopy with the structural and functional studies of nanoscopic protein machines (NPMs), the systems biology of NPMs, fluorescent labeling, nanoscopic analysis, and nanoscopic intervention, in order to advance the medical frontier toward the nanoscopic fundament of the cell. It aims at the diagnosis and therapy of diseases by directly visualizing, analyzing, and modifying NPMs and their networks in living cells and tissues.

Requirements on models and models of active transport of ions in biomembranes

Requirements on models of the active transport of ions in biomembranes have been formulated. The basic requirements include an explicit dependence of the resting potential and intracellular concentrations of ions on the difference of ATP-ADP chemical potentials, a consideration of the reversibility of the ionic pump operation, a correlation between theoretical and experimental data on the resting potential and intracellular concentrations of ions for different types of cells, the pump efficiency approaching 100%, and a tendency of the resting potential to the Donnan potential if the active transport is blocked. A model satisfying the aforementioned requirements has been proposed by the authors as an example.

Bovine factor B: cloning, expression, and characterization

Bovine factor B, a polypeptide required for the coupled activity of the mitochondrial ATP synthase complex, was cloned. A novel expression system for overproducing the recombinant bovine factor B was developed, which yielded the recombinant polypeptide at a level of 12-15 mg of protein per liter of bacterial culture. Reconstitution of the recombinant polypeptide with factor B-depleted ammonia, EDTA-treated submitochondrial particles (AE-SMP) restored the formation of substrate-driven DeltapH gradient across vesicular membranes, presumably by blocking a proton leak. The proton leak in the AE-SMP could also be blocked by the F0 inhibitors oligomycin and dicyclohexylcarbodiimide, but not the F1-ATPase inhibitors efrapeptin and aurovertin B. The six factor B thiols titrated rapidly with Ellman's reagent, and two of these, presumably Cys92 and Cys94, gained protection following treatment of factor B with a vicinal dithiol-specific reagent phenylarsine oxide (PAO). Similarly, Cd2+, whose binding to factor B is believed to also involve a vicinal dithiol, and PAO, protected approximately 2 Cys residues against labeling with sulfhydryl-specific fluorescent reagent fluorescein-5'-maleimide. The circular dichroism spectra showed that binding of Cd2+ and Zn2+, but not Ca2+ to bovine factor B caused small but reproducible changes in the secondary structure elements of the polypeptide.

Beyond Switches: Ratcheting a Particle Energetically Uphill with a Compartmentalized Molecular Machine

Here we correlate chemical (covalent), physical (thermodynamic), and statistical (population distribution) descriptions of behavior with the way that two new types of simple molecular machines (the threads of rotaxanes) perform the task of transporting a Brownian substrate (the rotaxane macrocycle) between two distinguishable binding sites. The first machine-substrate ensemble is a [2]rotaxane that operates through a mechanism that intrinsically causes it to change the average position of the macrocycle irreversibly. This contrasts with the behavior of classic stimuli-responsive molecular shuttles that act as reversible molecular switches. The second system is a compartmentalized molecular machine that is able to pump its substrate energetically uphill using the energy provided by a photon by means of an olefin photoisomerization. Resetting this compartmentalized molecular machine does not undo the work it has carried out or the task performed, a significant difference to a simple molecular switch and a characteristic we recognize as "ratcheting" (see Scheme 8). The ratcheting mechanism allows the [2]rotaxane to carry out the transport function envisaged for the historical thought-machines, Smoluchowski's Trapdoor and Maxwell's Pressure Demon, albeit via an unrelated mechanism and using an input of energy. We define and exemplify the terms "ratcheting" and "escapement" in mechanical terms for the molecular level and outline the fundamental phenomenological differences that exist between what constitutes a two-state Brownian switch, a two-state Brownian memory or "flip-flop", and a (two-stroke) Brownian motor. We also suggest that considering the relationship between the parts of a molecular machine and a substrate in terms of "statistical balance" and "linkage" could be useful in the design of more complex systems and in helping to understand the role of individual amino acids and peptide fragments during the directional transport of substrates by biological pumps and motors.

Autonomous artificial nanomotor powered by sunlight

Light excitation powers the reversible shuttling movement of the ring component of a rotaxane between two stations located at a 1.3-nm distance on its dumbbell-shaped component. The photoinduced shuttling movement, which occurs in solution, is based on a "four-stroke" synchronized sequence of electronic and nuclear processes. At room temperature the deactivation time of the high-energy charge-transfer state obtained by light excitation is approximately 10 micros, and the time period required for the ring-displacement process is on the order of 100 micros. The rotaxane behaves as an autonomous linear motor and operates with a quantum efficiency up to approximately 12%. The investigated system is a unique example of an artificial linear nanomotor because it gathers together the following features: (i) it is powered by visible light (e.g., sunlight); (ii) it exhibits autonomous behavior, like motor proteins; (iii) it does not generate waste products; (iv) its operation can rely only on intramolecular processes, allowing in principle operation at the single-molecule level; (v) it can be driven at a frequency of 1 kHz; (vi) it works in mild environmental conditions (i.e., fluid solution at ambient temperature); and (vii) it is stable for at least 10(3) cycles.

Operating Molecular Elevators

Inspired by the concept of multivalency in living systems, two mechanically interlocked molecules have been conceived that incorporate not once or twice but thrice the features of a pH-switchable [2]rotaxane with two orthogonal recognition sites for dibenzo[24]crown-8 (DB24C8), and 2,3-dinaphtho[24]crown-8 (DN24C8)-one a dialkylammonium ion (CH(2)NH(2)(+)CH(2)) and the other a bipyridinium dication (BIPY(2+)). Whereas at low pH, the CH(2)NH(2)(+)CH(2) sites bind the DB24C8/DN24C8 macrocycles preferentially, at high pH, deprotonation occurs with loss of hydrogen bonding and the macrocycles will move to the BIPY(2+) sites, where they can acquire some stabilizing [pi-pi] stacking interactions. Such mechanically interlocked molecules have been assembled from a trifurcated rig-like component wherein the dumbbell-like components of three [2]rotaxanes have one of their ends fused onto alternate positions (1,3,5) around a benzenoid core. The rig is mechanically interlocked by a platform based on a tritopic receptor, wherein either three benzo[24]crown-8 or three 2,3-naphtho[24]crown-8 macrocycles are fused onto a hexaoxatriphenylene core. The synthesis of these molecular elevators involves 1:1 complexation, followed by stoppering, i.e., feet are added to the rig. (1)H NMR spectroscopy and cyclic voltammetry, aided and abetted by absorption spectroscopy, have been employed to unravel the details of the mechanism by which the rig and platform components move on the alternate addition of base and acid. For each molecular elevator, the platform operates by taking three distinct steps associated with each of the three deprotonation/reprotonation processes. Thus, molecular elevators are more reminiscent of a legged animal than they are of passengers on freight elevators.

Cycle kinetics, steady state thermodynamics and motors-a paradigm for living matter physics

An integration of the stochastic mathematical models for motor proteins with Hill's steady state thermodynamics yields a rather comprehensive theory for molecular motors as open systems in the nonequilibrium steady state. This theory, a natural extension of Gibbs' approach to isothermal molecular systems in equilibrium, is compared with other existing theories with dissipative structures and dynamics. The theory of molecular motors might be considered as an archetype for studying more complex open biological systems such as biochemical reaction networks inside living cells.

Chemical and mechanical efficiencies of molecular motors and implications for motor mechanisms

Molecular motors operate in an environment dominated by viscous friction and thermal fluctuations. The chemical reaction in a motor may produce an active force at the reaction site to directly move the motor forward. Alternatively a molecular motor may generate a unidirectional motion by rectifying thermal fluctuations using free energy barriers established in the chemical reaction. The reaction cycle has many occupancy states, each having a different effect on the motor motion. The average effect of the chemical reaction on the motor motion can be characterized by the motor potential profile. The biggest advantage of studying the motor potential profile is that it can be reconstructed from the time series of motor positions measured in single-molecule experiments. In this paper, we use the motor potential profile to express the Stokes efficiency as the product of the chemical efficiency and the mechanical efficiency. We show that both the chemical and mechanical efficiencies are bounded by 100% and, thus, are properly defined efficiencies. We discuss implications of high efficiencies for motor mechanisms: a mechanical efficiency close to 100% implies that the motor potential profile is close to a constant slope; a chemical efficiency close to 100% implies that (i) the chemical transitions are not slower than the mechanical motion and (ii) the equilibrium constant of each chemical transition is close to one.

Making ATP

We present a mesoscopic model for ATP synthesis by F(1)F(o) ATPase. The model combines the existing experimental knowledge of the F(1) enzyme into a consistent mathematical model that illuminates how the stages in synthesis are related to the protein structure. For example, the model illuminates how specific interactions between the gamma, epsilon, and alpha(3)beta(3) subunits couple the F(o) motor to events at the catalytic sites. The model also elucidates the origin of ADP inhibition of F(1) in its hydrolysis mode. The methodology we develop for constructing the structure-based model should prove useful in modeling other protein motors.

Biomolecular motors: the F1-ATPase paradigm

The realization that many essential functions of living cells are performed by nanoscale motors consisting of protein complexes has given rise to an intense effort to understand their mechanisms. Considerable progress has been made in the past two years by a combination of biophysical techniques and theoretical analysis. Single-molecule studies have played a spectacular role for a variety of motors including kinesin, myosin, and polymerases. The understanding of F(1)-ATPase, the smallest biomolecular rotary motor, has made particular progress by the interplay of experimental and theoretical studies; the latter have provided information not available from experiment.

Protein structural transitions and their functional role

Living cells are a collection of molecular machines which carry out many of the functions essential for the cell's existence, differentiation and reproduction. Most, though not all, of these machines are made up of proteins. Because of their complexity, an understanding of how they work requires a synergistic combination of experimental and theoretical studies. In this paper we outline our studies of two such protein machines. One is GroEL, the chaperone from Escherichia coli, which aids in protein folding; the other is F(1)-ATPase, a motor protein which synthesizes and hydrolyses ATP.

Models of active transport of ions in biomembranes of various types of cells

Nonequilibrium statistical models of the active transport of ions in biomembranes have been constructed. Differences of chemical potentials of the ATP-ADP reaction and the electrochemical potential of ions were taken as the thermodynamic forces responsible for the flow of ions through the membrane. The active transport of ions was viewed as a cross phenomenon arising from the chemical reaction of the ATP hydrolysis. These models provide independent calculations of the resting potential at the biomembrane and concentrations of ions in a cell on the assumption the free energy of the ATP-ADP reaction is fully (without the dissipation loss) converted to the free energy of transported ions. They take into account the presence of nonpenetrating ions in a cell. It was shown that different concentrations of nonpenetrating ions have a considerable effect on the resting potential. The proposed models were compared with experimental data obtained for different types of cells including neurons, muscular cells, bacteria, plants, and mitochondria. Calculated values of the membrane potential and ion concentrations were in good qualitative agreement with experimental data.

Rotary molecular motors

The F-, V-, and A-adenosine triphosphatases (ATPases) represent a family of evolutionarily related ion pumps found in every living cell. They either function to synthesize adenosine triphosphate (ATP) at the expense of an ion gradient or they act as primary ion pumps establishing transmembrane ion motive force at the expense of ATP hydrolysis. The A-, F-, and V-ATPases are rotary motor enzymes. Synthesis or hydrolysis of ATP taking place in the three catalytic sites of the membrane extrinsic domain is coupled to ion translocation across the single ion channel in the membrane-bound domain via rotation of a central part of the complex with respect to a static portion of the enzyme. This chapter reviews recent progress in the structure determination of several members of the family of F-, A-, and V-ATPases and our current understanding of the rotary mechanism of energy coupling.

A reversible synthetic rotary molecular motor

The circumrotation of a submolecular fragment in either direction in a synthetic molecular structure is described. The movement of a small ring around a larger one occurs through positional displacements arising from biased Brownian motion that are kinetically captured and then directionally released. The sense of rotation is governed solely by the order in which a series of orthogonal chemical transformations is performed. The minimalist nature of the [2]catenane flashing ratchet design permits certain mechanistic comparisons with the Smoluchowski-Feynman ratchet and pawl. Even when no work has to be done against an opposing force and no net energy is used to power the motion, a finite conversion of energy is intrinsically required for the molecular motor to undergo directional rotation. Nondirectional rotation has no such requirement.

Making sense of it all: bacterial chemotaxis

Bacteria must be able to respond to a changing environment, and one way to respond is to move. The transduction of sensory signals alters the concentration of small phosphorylated response regulators that bind to the rotary flagellar motor and cause switching. This simple pathway has provided a paradigm for sensory systems in general. However, the increasing number of sequenced bacterial genomes shows that although the central sensory mechanism seems to be common to all bacteria, there is added complexity in a wide range of species.

Torque generation by the Fo motor of the sodium ATPase

Based on recent structural and functional findings, we have constructed a mathematical model for the sodium-driven Fo motor of the F1Fo-ATPase from the anaerobic bacterium Propionigenium modestum. The model reveals the mechanochemical principles underlying the Fo motor's operation, and explains all of the existing experimental data on wild-type and mutant Fo motors. In particular, the model predicts a nonmonotonic dependence of the ATP hydrolysis activity on the sodium concentration, a prediction confirmed by new experiments. To explain experimental observations, the positively charged stator residue (R227) must assume different positions in the ATP synthesis and hydrolysis directions. This work also illustrates how to extract a motor mechanism from dynamical experimental observations in the absence of complete structural information.

DNA transport into Bacillus subtilis requires proton motive force to generate large molecular forces

Bacteria can acquire genetic diversity, including antibiotic resistance and virulence traits, by horizontal gene transfer. In particular, many bacteria are naturally competent for uptake of naked DNA from the environment in a process called transformation. Here, we used optical tweezers to demonstrate that the DNA transport machinery in Bacillus subtilis is a force-generating motor. Single DNA molecules were processively transported in a linear fashion without observable pausing events. Uncouplers inhibited DNA uptake immediately, suggesting that the transmembrane proton motive force is needed for DNA translocation. We found an uptake rate of 80 +/- 10 bp s(-1) that was force-independent at external forces <40 pN, indicating that a powerful molecular machine supports DNA transport.

The structural mechanism of translocation and helicase activity in T7 RNA polymerase

RNA polymerase functions like a molecular motor that can convert chemical energy into the work of strand separation and translocation along the DNA during transcription. The structures of phage T7 RNA polymerase in an elongation phase substrate complex that includes the incoming nucleoside triphosphate and a pretranslocation product complex that includes the product pyrophosphate (PPi) are described here. These structures and the previously determined posttranslocation elongation complex demonstrate that two enzyme conformations exist during a cycle of single nucleotide addition. One orientation of a five-helix subdomain is stabilized by the phosphates of either the incoming NTP or by the product PPi. A second orientation of this subdomain is stable in their absence and is associated with translocation of the heteroduplex product as well as strand separation of the downstream DNA. We propose that the dissociation of the product PPi after nucleotide addition produces the protein conformational change resulting in translocation and strand separation.

A molecular elevator

We report the incrementally staged design, synthesis, characterization, and operation of a molecular machine that behaves like a nanoscale elevator. The operation of this device, which is made of a platformlike component interlocked with a trifurcated riglike component and is only 3.5 nanometers by 2.5 nanometers in size, relies on the integration of several structural and functional molecular subunits. This molecular elevator is considerably more complex and better organized than previously reported artificial molecular machines. It exhibits a clear-cut on-off reversible behavior, and it could develop forces up to around 200 piconewtons.

Polymer motors: pushing out the front and pulling up the back

Mechanical work in cells is performed by specialized motor proteins that operate in a continuous mechanochemical cycle. Less complex, but still efficient, 'one-shot' motors evolved based on the assembly and disassembly of polymers. We review the mechanisms of pushing and pulling by actin and microtubule filaments and the organizational principles of actin networks. We show how these polymer force generators are used for the propulsion of intracellular pathogens, protrusion of lamellipodia and mitotic movements. We discuss several examples of cellular forces generated by the assembly and disassembly of polymer gels.

Repeat Sequence of Epstein-Barr Virus-encoded Nuclear Antigen 1 Protein Interrupts Proteasome Substrate Processing

The Epstein-Barr virus thwarts immune surveillance through a Gly-Ala repeat (GAr) within the viral Epstein-Barr virus-encoded nuclear antigen 1 protein. The GAr inhibits proteasome processing, an early step in antigen peptide presentation, but the mechanism of proteasome inhibition has been unclear. By embedding a GAr within ornithine decarboxylase, a natural proteasome substrate that does not require ubiquitin conjugation, we now demonstrate inhibition in a purified system, excluding involvement of ubiquitin conjugation or of proteins extraneous to substrate and proteasome. We show further that the GAr acts as a stop-transfer signal in proteasome substrate processing, resulting in vivo in partial proteolysis that halts just short of the GAr. Similarly, introducing a GAr into green fluorescent protein destabilized by the ornithine decarboxylase degradation domain also stops the progress of proteolysis, leading to the accumulation of partial degradation products. We postulate that the ATP motor of the proteasome slips when it encounters the GAr, impeding further insertion and, in this way, halting degradation.

Bacterial Na+- or H+-coupled ATP Synthases Operating at Low Electrochemical Potential

In certain strictly anaerobic bacteria, the energy for growth is derived entirely from a decarboxylation reaction. A prominent example is Propionigenium modestum, which converts the free energy of the decarboxylation of (S)-methylmalonyl-CoA to propionyl-CoA (DeltaG degrees =-20.6 kJ/mol) into an electrochemical Na(+) ion gradient across the membrane. This energy source is used as a driving force for ATP synthesis by a Na(+)-translocating F(1)F(0) ATP synthase. According to bioenergetic considerations, approximately four decarboxylation events are necessary to support the synthesis of one ATP. This unique feature of using Na(+) instead of H(+) as the coupling ion has made this ATP synthase the paradigm to study the ion pathway across the membrane and its relationship to rotational catalysis. The membrane potential (Deltapsi) is the key driving force to convert ion translocation through the F(0) motor components into torque. The resulting rotation elicits conformational changes at the catalytic sites of the peripheral F(1) domain which are instrumental for ATP synthesis. Alkaliphilic bacteria also face the challenge of synthesizing ATP at a low electrochemical potential, but for entirely different reasons. Here, the low potential is not the result of insufficient energy input from substrate degradation, but of an inverse pH gradient. This is a consequence of the high environmental pH where these bacteria grow and the necessity to keep the intracellular pH in the neutral range. In spite of this unfavorable bioenergetic condition, ATP synthesis in alkaliphilic bacteria is coupled to the proton motive force (DeltamuH(+)) and not to the much higher sodium motive force (DeltamuNa(+)). A peculiar feature of the ATP synthases of alkaliphiles is the specific inhibition of their ATP hydrolysis activity. This inhibition appears to be an essential strategy for survival at high external pH: if the enzyme were to operate as an ATPase, protons would be pumped outwards to counteract the low DeltamuH(+), thus wasting valuable ATP and compromising acidification of the cytoplasm at alkaline pH.

The motility of mollicutes

Recent experiments show that the conformation of filament proteins play a role in the motility and morphology of many different types of bacteria. Conformational changes in the protein subunits may produce forces to drive propulsion and cell division. Here we present a molecular mechanism by which these forces can drive cell motion. Coupling of a biochemical cycle, such as ATP hydrolysis, to the dynamics of elastic filaments enable elastic filaments to propagate deformations that generate propulsive forces. We demonstrate this possibility for two classes of wall-less bacteria called mollicutes: the swimming of helical-shaped Spiroplasma, and the gliding motility of Mycoplasma.