Publications

The balance between linear electron transport (LET) and cyclic electron transport (CET) plays an essential role in plant adaptation and protection against photo-induced damage. This balance is largely maintained by phosphorylation-driven alterations in the PSIILHCII assembly and thylakoid membrane stacking. During the dark-to-light transition, plants shift this balance from CET, which prevails to prevent overreduction of the electron transport chain and consequent photo-induced damage, towards LET, which enables efficient CO2 assimilation and biomass production. Using freeze-fracture cryo-scanning electron microscopy and transmission electron microscopy of Arabidopsis leaves, we reveal unique membrane regions possessing characteristics of both stacked and unstacked regions of the thylakoid network that form during this transition. A notable consequence of the morphological attributes of these regions, which we refer to as stacked thylakoid doublets, is an overall increase in the proximity and connectivity of the two photosystems (PSI and PSII) that drive LET. This, in turn, reduces diffusion distances and barriers for the mobile carriers that transfer electrons between the two PSs, thereby maximizing LET and optimizing the plants ability to utilize light energy. The mechanics described here for the shift between CET and LET during the dark-to-light transition are probably also used during chromatic adaptation mediated by state transitions.

Grass pea (Lathyrus sativus L.) is a grain legume commonly grown in Asia and Africa for food and forage. It is a highly nutritious and robust crop, capable of surviving both droughts and floods. However, it produces a neurotoxic compound, β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP), which can cause a severe neurological disorder when consumed as a primary diet component. While the catalytic activity associated with β-ODAP formation was demonstrated more than 50 years ago, the enzyme responsible for this activity has not been identified. Here, we report on the identity, activity, 3D structure, and phylogenesis of this enzyme β-ODAP synthase (BOS). We show that BOS belongs to the BAHD superfamily of acyltransferases and is structurally similar to hydroxycinnamoyl transferases. Employing molecular docking, we propose a mechanism for its catalytic activity, and using heterologous expression in tobacco leaves (N. benthamiana), we demonstrate that expression of BOS in the presence of its substrates is sufficient for β-ODAP production in vivo. The identification of BOS may pave the way towards engineering β-ODAP-free grass pea cultivars, which are safe for human and animal consumption.

Oxalic acid is a small metabolite found in many plants. It serves as protection from herbivores, a chelator of metal ions, a regulator of calcium levels, and additional tasks. However, it is also a strong di-carboxylic acid that can compromise plant viability by reducing cellular pH. Several metabolic pathways have evolved to control oxalate levels in plants by enzymatic degradation. Among them is the pathway that utilizes oxalyl-CoA synthetase (OCS, EC 6.2.1.8) and ATP to convert oxalate to oxalyl-CoA. Oxalyl-CoA can then be degraded to CO or utilized as a precursor for the synthesis of other compounds. In grass pea (Lathyrus sativus L.), a grain legume grown in Asia and Africa for human and animal consumption, the neurotoxic compound β-N-oxalyl-l-α,β-diaminopropionic acid (β-ODAP) is synthesized from oxalyl-CoA and L-α,β-diaminopropionic acid (L-DAPA). Here, we report on the identification and characterization of oxalyl CoA-synthetase from grass pea (LsOCS). The gene encoding OCS was amplified from grass pea, and then expressed and purified from cells as an untagged, monomeric protein of 56 kDa. Its catalytic efficiency with oxalate, K oxalate M = 71.5 ± 13.3 μM, V max = 8.2 ± 0.8 μmole min -1 mg -1, was similar to that of OCS homologs from Arabidopsis thaliana (AtAAE3) and Medicago truncatula (MtAAE3). The enzyme was crystalized in complex with AMP and is the first OCS whose structure was determined in the thioester-forming conformation. Finally, we propose that substituting OCS with an oxalate oxidase or decarboxylase may reduce the levels of β-ODAP in grass pea.

Information theoretic approaches are ubiquitous and effective in a wide variety of bioinformatics applications. In comparative genomics, alignment-free methods, based on short DNA words, or k-mers, are particularly powerful. We evaluated the utility of varying k-mer lengths for genome comparisons by analyzing their sequence space coverage of 5805 genomes in the KEGG GENOME database. In subsequent analyses on four k-mer lengths spanning the relevant range (11, 21, 31, 41), hierarchical clustering of 1634 genus-level representative genomes using pairwise 21- and 31-mer Jaccard similarities best recapitulated a phylogenetic/taxonomic tree of life with clear boundaries for superkingdom domains and high subtree similarity for named taxons at lower levels (family through phylum). By analyzing ~14.2M prokaryotic genome comparisons by their lowest-common-ancestor taxon levels, we detected many potential misclassification errors in a curated database, further demonstrating the need for wide-scale adoption of quantitative taxonomic classifications based on whole-genome similarity.

Upon exposure to light, plant cells quickly acquire photosynthetic competence by converting pale etioplasts into green chloroplasts. This developmental transition involves the de novo biogenesis of the thylakoid system and requires reprogramming of metabolism and gene expression. Etioplast-to-chloroplast differentiation involves massive changes in plastid ultrastructure, but how these changes are connected to specific changes in physiology, metabolism, and expression of the plastid and nuclear genomes is poorly understood. Here, we describe a new experimental system in the dicotyledonous model plant tobacco (Nicotiana tabacum) that allows us to study the leaf deetiolation process at the systems level. We have determined the accumulation kinetics of photosynthetic complexes, pigments, lipids, and soluble metabolites and recorded the dynamic changes in plastid ultrastructure and in the nuclear and plastid transcriptomes. Our data describe the greening process at high temporal resolution, resolve distinct genetic and metabolic phases during deetiolation, and reveal numerous candidate genes that may be involved in light-induced chloroplast development and thylakoid biogenesis.

The vegetative tissues of resurrection plants are able to withstand severe protoplasmic dehydration and revive quickly upon rehydration. Resurrection species defined as homoiochlorophyllous retain most or part of their chlorophyll and photosynthetic complement in the dry state, and rely on various mechanisms to protect themselves against photo-damage. In this study, we investigated the changes in chlorophyll distribution, light absorption gradients as well as the alterations in ultrastructure that take place during dehydration of the homoiochlorophyllous species Craterostigma pumilum. Chlorophyll fluorescence profiles show that light absorption is attenuated in dry leaves, likely minimizing generation of reactive oxygen species. These are accompanied by changes that take place in the supramolecular organization of the photosynthetic protein complexes, and ordered functional adjustments of the photosynthetic apparatus, further lessening the excitation and electron pressures. Albeit these, the ultrastructural studies reveal that chloroplasts in dehydrated leaf tissues exhibit features indicative of oxidative stress, which are also reminiscent of senescing chloroplasts. These include mass proliferation of plastoglobules, variable degrees of thylakoid dismantling, as well as chloroplast fragmentation and seemingly vacuolar degradation of such fragments. In addition, unique vesicular structures between the two chloroplast envelope membranes were visualized, some of which appeared to detach from chloroplasts, likely en route to degradation. Together, the data indicate that homoiochlorophyllous resurrection species handle photo-induced damage during dehydration on two levels. Minimization of photo-damage is achieved by attenuation of light absorption and other photo-protective mechanisms. When this is insufficient and significant damage does occur, elimination of damaged components takes place via processes resembling senescence. Nevertheless, these processes are reversible, enabling the plants to avoid the terminal steps of senescence and, hence, to recover.

Deg proteases are involved in protein quality control in prokaryotes. Of the three Arabidopsis (Arabidopsis thaliana) homologs, Deg1, Deg5, and Deg8, located in the thylakoid lumen, Deg1 forms a homohexamer, whereas Deg5 and Deg8 form a heterocomplex. Both Deg1 and Deg5-Deg8 were shown separately to degrade photosynthetic proteins during photoinhibition. To investigate whether Deg1 and Deg5-Deg8 are redundant, a full set of Arabidopsis Deg knockout mutants were generated and their phenotypes were compared. Under all conditions tested, deg1 mutants were affected more than the wild type and deg5 and deg8 mutants. Moreover, overexpression of Deg5-Deg8 could only partially compensate for the loss of Deg1. Comparative proteomics of deg1 mutants revealed moderate up-regulation of thylakoid proteins involved in photoprotection, assembly, repair, and housekeeping and down-regulation of those that form photosynthetic complexes. Quantification of protein levels in the wild type revealed that Deg1 was 2-fold more abundant than Deg5-Deg8. Moreover, recombinant Deg1 displayed higher in vitro proteolytic activity. Affinity enrichment assays revealed that Deg1 was precipitated with very few interacting proteins, whereas Deg5-Deg8 was associated with a number of thylakoid proteins, including D1, OECs, LHCBs, Cyt b6f, and NDH subunits, thus implying that Deg5-Deg8 is capable of binding substrates but is unable to degrade them efficiently. This work suggests that differences in protein abundance and proteolytic activity underlie the differential importance of Deg1 and Deg5-Deg8 protease complexes observed in vivo.

In dicots, the key developmental process by which immature plastids differentiate into photosynthetically competent chloroplasts commences in the shoot apical meristem (SAM), within the shoot apex. Using laser-capture microdissection and single-cell RNA sequencing methodology, we studied the changes in the transcriptome along the chloroplast developmental pathway in the shoot apex of tomato seedlings. The analysis revealed the presence of transcripts for different chloroplast functions already in the stem cell-containing region of the SAM. Thereafter, an en masse up-regulation of genes encoding for various proteins occurs, including chloroplast ribosomal proteins and proteins involved in photosynthesis, photoprotection and detoxification of reactive oxygen species. The results highlight transcriptional events that operate during chloroplast biogenesis, leading to the rapid establishment of photosynthetic competence.

In this paper we propose an energy dissipation mechanism that is completely reliant on changes in the aggregation state of the phycobilisome light-harvesting antenna components. All photosynthetic organisms regulate the efficiency of excitation energy transfer (EET) to fit light energy supply to biochemical demands. Not many do this to the extent required of desert crust cyanobacteria. Following predawn dew deposition, they harvest light energy with maximum efficiency until desiccating in the early morning hours. In the desiccated state, absorbed energy is completely quenched. Time and spectrally resolved fluorescence emission measurements of the desiccated desert crust Leptolyngbya ohadii strain identified (i) reduced EET between phycobilisome components, (ii) shorter fluorescence lifetimes, and (iii) red shift in the emission spectra, compared with the hydrated state. These changes coincide with a loss of the ordered phycobilisome structure, evident from small-angle neutron and X-ray scattering and cryo-transmission electron microscopy data. Based on these observations we propose a model where in the hydrated state the organized rod structure of the phycobilisome supports directional EET to reaction centers with minimal losses due to thermal dissipation. In the desiccated state this structure is lost, giving way to more random aggregates. The resulting EET path will exhibit increased coupling to the environment and enhanced quenching.

The cyanobacterium Synechocystis PCC 6803 possesses three Rieske isoforms: PetC1, PetC2 and PetC3. While PetC1 and PetC2 have been identified as alternative subunits of the cytochrome b(6)f complex (ben, PetC3 was localized exclusively within the plasma membrane. The spatial separation of PetC3 from the photosynthetic and respiratory protein complexes raises doubt in its involvement in bioenergetic electron transfer.Here we report a detailed structural and functional characterization of the cyanobacterial PetC3 protein family indicating that PetC3 is not a component of the b(6)f and the photosynthetic electron transport as implied by gene annotation. Instead PetC3 has a distinct function in cell envelope homeostasis. Especially proteomic analysis shows that deletion of petC3 in Synechocystis PCC 6803 primarily affects cell envelope proteins including many nutrient transport systems. Therefore, the observed downregulation in the photosynthetic electron transport mainly caused by photosystem 2 inactivation-might constitute a stress adaptation. Comprehensive in silico sequence analyses revealed that PetC3 proteins are periplasmic lipoproteins tethered to the plasma membrane with a subclass consisting of soluble periplasmic proteins, i.e. their N-terminal domain is inconsistent with their integration into the b(6)f . For the first time, the structure of PetC3 was determined by X-ray crystallography at an atomic resolution revealing significant high similarities to non-b(6)f Rieske subunits in contrast to PetC1. These results suggest that PetC3 affects processes in the periplasmic compartment that only indirectly influence photosynthetic electron transport. For this reason, we suggest to rename "Photosynthetic electron transport Chain 3" (PetC3) proteins as "periplasmic Rieske proteins" (Prp). 

Cryo-scanning electron microscopy (SEM) of freeze-fractured samples allows investigation of biological structures at near native conditions. Here, we describe a technique for studying the supramolecular organization of photosynthetic (thylakoid) membranes within leaf samples. This is achieved by high-pressure freezing of leaf tissues, freeze-fracturing, double-layer coating and finally cryo-SEM imaging. Use of the double-layer coating method allows acquiring high magnification (>100,000X) images with minimal beam damage to the frozen-hydrated samples as well as minimal charging effects. Using the described procedures we investigated the alterations in supramolecular distribution of photosystem and lightharvesting antenna protein complexes that take place during dehydration of the resurrection plant Craterostigma pumilum, in situ.

Biological desert sand crusts are the foundation of desert ecosystems, stabilizing the sands and allowing colonization by higher order organisms. The first colonizers of the desert sands are cyanobacteria. Facing the harsh conditions of the desert, these organisms must withstand frequent desiccation hydration cycles, combined with high light intensities. Here, we characterize structural and functional modifications to the photosynthetic apparatus that enable a cyanobacterium, Leptolyngbya sp., to thrive under these conditions. Using multiple in vivo spectroscopic and imaging techniques, we identified two complementary mechanisms for dissipating absorbed energy in the desiccated state. The first mechanism involves the reorganization of the phycobilisome antenna system, increasing excitonic coupling between antenna components. This provides better energy dissipation in the antenna rather than directed exciton transfer to the reaction center. The second mechanism is driven by constriction of the thylakoid lumen which limits diffusion of plastocyanin to P-700. The accumulation of P-700(+) not only prevents light-induced charge separation but also efficiently quenches excitation energy. These protection mechanisms employ existing components of the photosynthetic apparatus, forming two distinct functional modes. Small changes in the structure of the thylakoid membranes are sufficient for quenching of all absorbed energy in the desiccated state, protecting the photosynthetic apparatus from photoinhibitory damage. These changes can be easily reversed upon rehydration, returning the system to its high photosynthetic quantum efficiency.

Overreduction of the photosynthetic electron transport chain may severely damage the photosynthetic apparatus as well as other constituents of the chloroplast and the cell. Here, we exposed Arabidopsis leaves to saturating light either under normal atmospheric conditions or under CO2 and O2limiting conditions, which greatly increase excitation and electron pressures by draining terminal electron acceptors. The two treatments were found to have very different, often opposing, effects on the structure of the thylakoid membranes, including the width of the granal lumenal compartment. Modulation of the latter is proposed to be related to movements of ions across the thylakoid membrane, which alter the relative osmolarity of the lumen and stroma and affect the partitioning of the proton motive force into its electrical and osmotic components. The resulting changes in thylakoid organization and lumenal width should facilitate the repair of photodamaged photosystem II complexes in response to light stress under ambient conditions, but are expected to inhibit the repair cycle when the light stress occurs concurrently with CO2 and O2 depletion. Under the latter conditions, the changes in thylakoid structure are predicted to complement other processes that restrict the flow of electrons into the highpotential chain, thus moderating the production of deleterious reactive oxygen species at photosystem I.

The chromatophores of Rhodobacter (Rb.) sphaeroides represent a minimal bio-energetic system, which efficiently converts light energy into usable chemical energy. Despite extensive studies, several issues pertaining to the morphology and molecular architecture of this elemental energy conversion system remain controversial or unknown. To tackle these issues, we combined electron microscope tomography, immuno-electron microscopy and atomic force microscopy. We found that the intracellular Rb. sphaeroides chromatophores form a continuous reticulum rather than existing as discrete vesicles. We also found that the cytochrome bci complex localizes to fragile chromatophore regions, which most likely constitute the tubular structures that interconnect the vesicles in the reticulum. In contrast, the peripheral light-harvesting complex 2 (LH2) is preferentially hexagonally packed within the convex vesicular regions of the membrane network. Based on these observations, we propose that the bci complexes are in the inter-vesicular regions and surrounded by reaction center (RC) core complexes, which in turn are bounded by arrays of peripheral antenna complexes. This arrangement affords rapid cycling of electrons between the core and bci complexes while maintaining efficient excitation energy transfer from LH2 domains to the RCs.

Biofilms are consortia of bacteria that are held together by an extracellular matrix. Cyanobacterial biofilms, which are highly ubiquitous and inhabit diverse niches, are often associated with biological fouling and cause severe economic loss. Information on the molecular mechanisms underlying biofilm formation in cyanobacteria is scarce. We identified a mutant of the cyanobacterium Synechococcus elongatus, which unlike the wild type, developed biofilms. This biofilm-forming phenotype is caused by inactivation of homologues of type II secretion /type IV pilus assembly systems and is associated with impairment of protein secretion. The conditioned medium from a wild-type culture represses biofilm formation by the secretion-mutants. This suggested that the planktonic nature of the wild-type strain is a result of a self-suppression mechanism, which depends on the deposition of a factor to the extracellular milieu. We also identified two genes that are essential for biofilm formation. Transcript levels of these genes are elevated in the mutant compared with the wild type, and are initially decreased in mutant cells cultured in conditioned medium of wild-type cells. The particular niche conditions will determine whether the inhibitor will accumulate to effective levels and thus the described mechanism allows switching to a sessile mode of existence.

A dripping faucet is an example of an everyday system that exhibits surprisingly rich dynamics ranging from periodic to chaotic. Using a simple capacitive device, we experimentally demonstrate that the dynamics is determined by the degree of synchronization between two temporally disparate processes: the time at which a drop attains a critical mass and an oscillatory process that accompanies the formation of a drop. We present a full experimental phase-space reconstruction of the ensuing dynamics.

While tightly regulated, bacterial cell morphology may change substantially in response to environmental cues. Here we describe such changes in the cyanobacterium Synechococcus sp. strain PCC7942. Once maintained in stationary phase, these rod-shaped organisms stop dividing and elongate up to 50-fold. Increase in cell length of a thymidine-auxotroph strain upon thymidine starvation implies that inhibition of DNA replication underlies cell elongation. Elongation occurs under conditions of limiting phosphorus but sufficient nitrogen levels. Once proliferative conditions are restored, elongated cells divide asymmetrically instead of exhibiting the typical fission characterized by mid-cell constriction. The progeny are of length characteristic of exponentially growing cells and are proficient of further proliferation. We propose that the ability to elongate under conditions of cytokinesis arrest together with the rapid induction of cell division upon nutrient repletion represents a beneficial cellular mechanism operating under specific nutritional conditions.

Exposure of cyanobacterial or red algal cells to high light has been proposed to lead to excitonic decoupling of the phycobilisome antennae (PBSs) from the reaction centers. Here we show that excitonic decoupling of PBSs of Synechocystis sp. PCC 6803 is induced by strong light at wavelengths that excite either phycobilin or chlorophyll pigments. We further show that decoupling is generally followed by disassembly of the antenna complexes and/or their detachment from the thylakoid membrane. Based on a previously proposed mechanism, we suggest that local heat transients generated in the PBSs by non-radiative energy dissipation lead to alterations in thermo-labile elements, likely in certain rod and core linker polypeptides. These alterations disrupt the transfer of excitation energy within and from the PBSs and destabilize the antenna complexes and/or promote their dissociation from the reaction centers and from the thylakoid membranes. Possible implications of the aforementioned alterations to adaptation of cyanobacteria to light and other environmental stresses are discussed.

Aerobic life on Earth depends on oxygenic photosynthesis. This fundamentally important process is carried out within an elaborate membranous system, called the thylakoid network. In angiosperms, thylakoid networks are constructed almost from scratch by an intricate, light-dependent process in which lipids, proteins, and small organic molecules are assembled into morphologically and functionally differentiated, three-dimensional lamellar structures. In this review, we summarize the major events that occur during this complex, largely elusive process, concentrating on those that are directly involved in network formation and potentiation and highlighting gaps in our knowledge, which, as hinted by the title, are substantial.

Single-molecule manipulation methods provide a powerful means to study protein transitions. Here we combined single-molecule force spectroscopy and steered molecular-dynamics simulations to study the mechanical properties and unfolding behavior of the small enzyme acylphosphatase (AcP). We find that mechanical unfolding of AcP occurs at relatively low forces in an all-or-none fashion and is decelerated in the presence of a ligand, as observed in solution measurements. The prominent energy barrier for the transition is separated from the native state by a distance that is unusually long for α/β proteins. Unfolding is initiated at the C-terminal strand (β_T) that lies at one edge of the β-sheet of AcP, followed by unraveling of the strand located at the other. The central strand of the sheet and the two helices in the protein unfold last. Ligand binding counteracts unfolding by stabilizing contacts between an arginine residue (Arg-23) and the catalytic loop, as well as with β_T of AcP, which renders the force-bearing units of the protein resistant to force. This stabilizing effect may also account for the decelerated unfolding of ligand-bound AcP in the absence of force.

Atomic force microscopy (AFM), developed in the late 1980s to explore atomic details on hard material surfaces, has evolved into a method capable of imaging fine structural details of biological samples. Its particular advantage in biology is that measurements can be carried out in aqueous and physiological environments, which opens the possibility to study the dynamics of biological processes in vivo. The additional potential of the AFM to measure ultralow forces at high lateral resolution has paved the way for measuring inter- and intramolecular forces of biomolecules on the single-molecule level. Molecular recognition studies using AFM open the possibility to detect specific ligandreceptor interaction forces and to observe molecular recognition of a single ligandreceptor pair. Applications include biotinavidin, antibodyantigen, nitrilotriacetate (NTA)hexahistidine 6, and cellular proteins, either isolated or in cell membranes.The general strategy is to bind ligands to AFM tips and receptors to probe surfaces (or vice versa). In a forcedistance cycle, the tip is first approached towards the surface, whereupon a single receptorligand complex is formed due to the specific ligand receptor recognition. During subsequent tipsurface retraction a temporarily increasing force is exerted on the ligandreceptor connection, thus reducing its lifetime until the interaction bond breaks at a critical (unbinding) force. Such experiments allow for estimation of affinity, rate constants, and structural data of the binding pocket. Comparing them with values obtained from ensemble-average techniques and binding energies is of particular interest. The dependences of unbinding force on the rate of load increase exerted on the receptorligand bond reveal details of the molecular dynamics of the recognition process and energy landscapes. Similar experimental strategies have also been used for studying intramolecular force properties of polymers and unfoldingrefolding kinetics of filamentous proteins. Recognition imaging, developed by combing dynamic force microscopy with force spectroscopy, allows for localization of receptor sites on surfaces with nanometer positional accuracy.

To fulfil their function, nuclear pore complexes (NPCs) must discriminate between inert proteins and nuclear transport receptors (NTRs), admitting only the latter. This specific permeation is thought to depend on interactions between hydrophobic patches on NTRs and phenylalanine-glycine (FG) or related repeats that line the NPC. Here, we tested this premise directly by conjugating different hydrophobic amino-acid analogues to the surface of an inert protein and examining its ability to cross NPCs unassisted by NTRs. Conjugation of as few as four hydrophobic moieties was sufficient to enable passage of the protein through NPCs. Transport of the modified protein proceeded with rates comparable to those measured for the innate protein when bound to an NTR and was relatively insensitive both to the nature and density of the amino acids used to confer hydrophobicity. The latter observation suggests a non-specific, small, and pliant interaction network between cargo and FG repeats.

In eukaryotic cells the nucleus is separated from the cytoplasm by a double-membraned nuclear envelope (NE). Exchange of molecules between the two compartments is mediated by nuclear pore complexes (NPCs) that are embedded in the NE membranes. The translocation of molecules such as proteins and RNAs through the nuclear membrane is executed by transport shuttling factors (karyopherines). They thereby dock to particular binding sites located all over the NPC, the so-called phenylalanine-glycin nucleoporines (FG Nups). Molecular recognition force spectroscopy (MRFS) allows investigations of the binding at the single-molecule level. Therefore the AFM tip carries a ligand for example, a particular karyopherin whereas the nuclear membrane with its receptors is mounted on a surface. Hence, one of the first requirements to study the nucleo-cytoplasmatic transport mechanism using MRFS is the development of an optimized membrane preparation that preserves structure and function of the NPCs. In this study we present a stable non-destructive preparation method of Xenopus laevis nuclear envelopes. We use micro-structured polydimethylsiloxane (PDMS) that provides an ideal platform for immobilization and biological integrity due to its elastic, chemical and mechanical properties. It is a solid basis for studying molecular recognition, transport interactions, and translocation processes through the NPC. As a first recognition system we investigate the interaction between an important transport shuttling factor, importin β, and its binding sites on the NPC, the FG-domains.

This chapter describes how the energy landscape that underlies protein-binding reactions can be revealed using dynamic force spectroscopy. The chapter begins with a detailed description of methodologies used and requirements of the experimental system, including tip and Surface materials and their functionalization strategies. The next few sections discuss the fundamentals of measuring forces using the atomic force microscope, and the basics of performing force spectroscopy measurements from a practical point of view. Next, it presents an extensive account of methods for data analysis and current theoretical treatments. The remainder of the chapter illustrates the power of this methodology by several examples in which the location of energy barriers in a binding reaction pathway and their load-dependent dynamics are measured, the overall scale of roughness of the underlying energy surface is extracted, and alternative modes of protein activation are distinguished. Biological insight gained from these data is discussed. The intent is to provide the necessary theoretical and practical knowledge to begin force spectroscopy measurements on protein interactions.

The 'new view' of proteins sees protein reactions as parallel processes occurring along funnelled energy landscapes. These landscapes are generally not smooth, but are superimposed by hills and valleys of different heights and widths leading to roughness on the energy surface. In the present paper, we describe the origins of protein energy landscape roughness, measurements of its scale and its implications.

Nuclear pore complexes are constantly confronted by large fluxes of macromolecules and macromolecular complexes that need to get into and out of the nucleus. Such bidirectional traffic occurring in a narrow channel can easily lead to jamming. How then is passage between the nucleus and cytoplasm maintained under the varying conditions that arise during the lifetime of the cell? Here, we address this question using computer simulations in which the behaviour of the ensemble of transporting cargoes is analysed under different conditions. We suggest that traffic can exist in two distinct modes, depending on the concentration of cargoes and dissociation rates of the transport receptor-cargo complexes from the pores. In one mode, which prevails when dissociation is quick and cargo concentration is low, transport in either direction proceeds uninterrupted by transport in the other direction. The result is that the overall traffic direction fluctuates rapidly and unsystematically between import and export. Remarkably, when cargo concentrations are high and disassociation is slow, another mode takes over in which traffic proceeds in one direction for a certain extent of time, after which it flips direction for another period. The switch between this, more regulated, mode of transport and the other, quickly fluctuating state, does not require an active gating mechanism but rather occurs spontaneously through the dynamics of the transported particles themselves. The determining factor for the behaviour of traffic is found to be the exit rate from the pore channel, which is directly related to the activity of the Ran system that controls the loading and release of cargo in the appropriate cellular compartment.

Atomic force microscopy (AFM), developed in the late eighties to explore atomic details on hard material surfaces, has evolved to an imaging method capable of achieving fine structural details on biological samples. Its particular advantage in biology is that the measurements can be carried out in aqueous and physiological environment, which opens the possibility to study the dynamics of biological processes in vivo. The additional potential of the AFM to measure ultra-low forces at high lateral resolution has paved the way for measuring inter- and intra-molecular forces of bio-molecules on the single molecule level. Molecular recognition studies using AFM open the possibility to detect specific ligand-receptor interaction forces and to observe molecular recognition of a single ligand-receptor pair. Applications include biotin-avidin, antibody-antigen, NTA nitrilotriacetate-hexahistidine 6, and cellular proteins, either isolated or in cell membranes. The general strategy is to bind ligands to AFM tips and receptors to probe surfaces (or vice versa), respectively. In a force-distance cycle, the tip is first approached towards the surface whereupon a single receptor-ligand complex is formed, due to the specific ligand receptor recognition. During subsequent tip-surface retraction a temporarily increasing force is exerted to the ligand-receptor connection thus reducing its lifetime until the interaction bond breaks at a critical force (unbinding force). Such experiments allow for estimation of affinity, rate constants, and structural data of the binding pocket. Comparing them with values obtained from ensemble-average techniques and binding energies is of particular interest. The dependences of unbinding force on the rate of load increase exerted to the receptor-ligand bond reveal details of the molecular dynamics of the recognition process and energy landscapes. Similar experimental strategies were also used for studying intra-molecular force properties of polymers and unfolding-refolding kinetics of filamentous proteins. Recognition imaging, developed by combing dynamic force microscopy with force spectroscopy, allows for localization of receptor sites on surfaces with nanometer positional accuracy.

Nuclear pore complexes provide the sole gateway for the exchange of material between nucleus and cytoplasm of interphase eukaryotic cells. They support two modes of transport: passive diffusion of ions, metabolites, and intermediate-sized macromolecules and facilitated, receptor-mediated translocation of proteins, RNA, and ribonucleoprotein complexes. It is generally assumed that both modes of transport occur through a single diffusion channel located within the central pore of the nuclear pore complex. To test this hypothesis, we studied the mutual effects between transporting molecules utilizing either the same or different modes of translocation. We find that the two modes of transport do not interfere with each other, but molecules utilizing a particular mode of transport do hinder motion of others utilizing the same pathway. We therefore conclude that the two modes of transport are largely segregated.

The energy landscape of proteins is thought to have an intricate, corrugated structure. Such roughness should have important consequences on the folding and binding kinetics of proteins, as well as on their equilibrium fluctuations. So far, no direct measurement of protein energy landscape roughness has been made. Here, we combined a recent theory with single-molecule dynamic force spectroscopy experiments to extract the overall energy scale of roughness ε for a complex consisting of the small GTPase Ran and the nuclear transport receptor importin-β. The results gave ε>5k_BT, indicating a bumpy energy surface, which is consistent with the ability of importin-β to accommodate multiple conformations and to interact with different, structurally distinct ligands.

The light-harvesting and energy-transducing functions of the chloroplast are performed within an intricate lamellar system of membranes, called thylakoid membranes, which are differentiated into granum and stroma lamellar domains. Using dual-axis electron microscope tomography, we determined the three-dimensional organization of the chloroplast thylakoid membranes within cryo-immobilized, freeze-substituted lettuce (Lactuca sativa) leaves. We found that the grana are built of repeating units that consist of paired layers formed by bifurcations of stroma lamellar sheets, which fuse within the granum body. These units are rotated relative to each other around the axis of the granum cylinder. One of the layers that makes up the pair bends upwards at its edge and fuses with the layer above it, whereas the other layer bends in the opposite direction and merges with the layer below. As a result, each unit in the granum is directly connected to its neighbors as well as to the surrounding stroma lamellae. This highly connected morphology has important consequences for the formation and function of the thylakoid membranes as well as for their stacking/unstacking response to variations in light conditions.

We present an approach to study the real-time dynamics of single molecules using capacitance measurements. The method is based on a nonparallel-plate microcapacitor, which has a tapered-gap geometry. A particle moving within such a capacitor induces capacitance changes that depend on its position. Monitoring these changes allows motion to be traced at a resolution which is higher than the smallest fabricated feature of the device. The detection scheme also enables the distinction between particles of different dielectric constants and the exertion of dielectrophoretic forces on the particles. This approach provides a means for studying various aspects of single-particle dynamics at high resolution, in real time, and under conditions compatible with biological systems.

gp210 is a major constituent of the nuclear pore complex (NPC) with possible structural and regulatory roles. It interacts with components of the NPC via its C-terminal domain (CTD), which follows a transmembrane domain and a massive (∼200 kDa) N-terminal region that resides in the lumen of the perinuclear space. Here, we report the solution structure of the human gp210 CTD as determined by various spectroscopic techniques. In water, the CTD adopts an extended, largely unordered conformation, which contains a significant amount of left-handed polyproline type II (PII) helical structure. The conformation of the CTD is altered by high pH, charged detergents, and the hydrogen bond-promoting reagent trifluoroethanol (TFE), which decrease the PII fraction of the fragment. TFE also induces a conformational change in a region containing an SPXX motif whose serine becomes specifically phosphorylated during mitosis. We propose that PII elements in the CTD may play a role in its interaction with the NPC and may serve as recognition sites for regulatory proteins bearing WW or other, unknown PII-binding motifs.

A common way to analyse basal and stimulated activity of eukaryotic genetic control elements, such as promoters and enhancers, is to introduce them into cells via DNA vectors containing an easily assayable reporter gene. Activity is then studied by measurement of transiently produced mRNA or reporter protein. In such assays, it is assumed that the variable measured is proportional to the transcriptional activity of the control element under investigation. Here we question the validity of this generally accepted assumption. Specifically, recent observations indicate that control elements, in addition to modulating transgene transcription, can facilitate the nuclear uptake of their carrier plasmids. This process is mediated by transcription factors or other nuclear proteins harbouring nuclear localisation signals, which bind to the control elements in the cytoplasm and transport the DNA into the nucleus through the protein nuclear import machinery. As the number of mRNA transcripts produced for an epi-chromosomally expressed transgene is directly related to its copy number inside the nucleus, such transport activity may lead to substantial overestimation of the transcriptional potency of the control element(s) studied. (C) 2001 John Wiley & Sons, Inc.

Fifteen years after its invention, the scanning force microscope (SFM) is rooted deep in the biological sciences. Here we discuss the use of SFM in biotechnology and biomedical research. The spectrum of applications reviewed includes imaging, force spectroscopy and mapping, as well as sensor applications. It is our hope that this review will be useful for researchers considering the use of SFM in their studies but are uncertain about its scope of capabilities. For the benefit of readers unfamiliar with SFM technology, the fundamentals of SFM imaging and force measurement are also briefly introduced.

Antigen-dependent activation of T lymphocytes requires T cell receptor (TCR)-mediated recognition of specific peptides, together with the MHC molecules to which they are bound. To achieve this recognition in a reasonable time frame, the TCR must scan and discriminate rapidly between thousands of MHC molecules differing from each other only in their bound peptides. Kinetic analysis of the interaction between a TCR and its cognate peptide-MHC complex indicates that both association and dissociation depend heavily on the temperature, indicating the presence of large energy barriers in both phases. Thermodynamic analysis reveals changes in heat capacity and entropy that are characteristic of protein-ligand associations in which local folding is coupled to binding. Such an "induced-fit" mechanism is characteristic of sequence-specific DNA-binding proteins that must also recognize specific ligands in the presence of a high background of competing elements. Here, we propose that induced fit may endow the TCR with its requisite discriminatory capacity and suggest a model whereby the loosely structured antigen-binding loops of the TCR rapidly explore peptide-MHC complexes on the cell surface until some critical structural complementarity is achieved through localized folding transitions. We further suggest that conformational changes, implicit in this model, may also propagate beyond the TCR antigen-binding site and directly affect self-association of ligated TCRs or TCR-CD3 interactions required for signaling.

While still incomplete, the first data concerning the biochemistry of T cell receptor-ligand interactions in cell-free systems seem to have considerable predictive value regarding whether a T cell response is strong or weak or suppressive. This data will help considerably in elucidating the mechanisms behind T cell responsiveness. Also of great interest are the first structures of T cell receptor molecules and, particularly, TCR-ligand complexes. These appear to confirm earlier suggestions of a fixed orientation for TCR engagement with peptide/MHC and should form the basis for understanding higher oligomers, evidence for which has also just emerged. We conclude with an analysis of the highly diverse CDR3 loops found in all antigen receptor molecules and suggest that such regions form the core of both TCR and antibody specificity.

T cells initiate many immune responses through the interaction of their T-cell antigen receptors (TCR) with antigenic peptides bound to major histocompatibility complex (MHC) molecules. This interaction sends a biochemical signal into the T cell by a mechanism that is not clearly understood. We have used quasi-elastic light scattering (QELS) to show that, in the presence of MHC molecules bound to a full agonist peptide, TCR/peptide-MHC complexes oligomerize in solution to form supramolecular structures at concentrations near the dissociation constant of the binding reaction. The size of the oligomers is concentration dependent and is calculated to contain two to six ternary complexes for the concentrations tested here. This effect is specific as neither molecule forms oligomers by itself, nor were oligomers observed unless the correct peptide was bound to the MHC. These results provide direct evidence for models of T-cell signalling based on the specific assembly of multiple TCR/peptide-MHC complexes in which the degree of assembly determines the extent and qualitative nature of the transduced signal. They may also explain how T cells maintain sensitivity to antigens present in only low abundance on the antigen-presenting cell.

The structure and thermal stability of empty and peptide-filled forms of the murine class II major histocompatibility complex (MHC) molecule I-Ek were studied at neutral and mildly acidic pH. The two forms have distinct circular dichroic spectra, suggesting that a conformational change may accompany peptide binding. Thermal stability profiles indicate that binding of peptide significantly increases the thermal stability of the empty heterodimers at both neutral and mildly acidic pH. Free energies calculated from these data provide a direct measure of this stabilization and show that the empty form of I-Ek is significantly more stable than that of class I MHC proteins. Furthermore, for the two MHC class II proteins that were analyzed (I-Ek and I-Ad), thermal stability was not significantly altered by acidification. In contrast, of four class I MHC molecules studied, three have shown a significant loss in complex stability at low pH. The marked stability exhibited by their empty form, as well as their resistance to low pH, as observed in this study, correlate well with the ability of class II MHC molecules to traverse and bind peptides in acidic endosomal vesicles.

Closed-circular supercoiled DNA molecules have been shown to form a cholesteric assembly within bacteria as well as in vitro under physiological DNA and salt concentrations. Circular dichroism and X-ray scattering studies indicate that the macroscopic structural properties of the chiral mesophase are directly and uniquely dictated by the supercoiling parameters of the constituent molecules. Specifically, we find that the pitch of the DNA cholesteric phase derived from supercoiled DNA is determined by the superhelical density, which, in turn, is modulated by secondary conformational changes. A direct interrelationship among four DNA structural levels, namely, DNA sequence, secondary structural transitions, the tertiary superhelical conformation, and the quaternary, supramolecular organization is accordingly pointed out. Since secondary conformational changes are both sequence and environment dependent, alterations of cellular conditions may effectively modulate the properties of the packed DNA organization, through their effects on secondary structural transitions and hence on the superhelical parameters. On the basis of these results we suggest that liquid crystallinity represents an effectively regulated packaging mode of plectonemic, nucleosome-free DNA molecules in living systems.

Extensive effort has been directed toward a quantitative evaluation of forces which operate between biomacromolecules since the characterization of such forces is essential to a thorough understanding of fundamental biological processes. However, all studies hitherto reported were conducted in vitro, using isolated species. Here we report the first quantitative characterization of forces operating between DNA molecules within living bacteria. Evaluation of x-ray scattering studies conducted on intact bacteria indicates that, at DNA-DNA surface separations characteristic of DNA assemblies, interactions are dominated by repulsive hydration forces which originate from the structuring of water molecules. The results support the notion that the mechanisms by means of which macromolecules function, fold, and interact with each other crucially depend upon their hydration properties.

The effects exerted by short runs of adenines (A-tracts), alternating (AT)_n segments, and single-stranded DNA upon the right- to left-handed DNA transition, as well as upon the energetic and structural parameters of the B/Z junctions, were investigated by using synthetic segments in which these motifs are coupled to a potentially Z-forming core. UV, CD, and ³¹P NMR studies of the salt-induced B to Z transition occurring in the various segments indicate that the transition is composed of two phases: a slow rate-determining induction of an initial structural deformation followed by a cooperative propagation of this "nucleus" in the form of a left-handed Z-DNA. The first phase is found to be crucially affected by the nature of the sequences coupled to the potentially Z-forming core. Thus, a higher rigidity of the flanking segments, such as that characterizing adenine tracts, is associated with higher energy values required for the induction of the initial conformational deformation, as well as with more defined structural parameters of the ultimate B/Z junctions. The second phase is affected mainly by the composition and sequence of the Z-forming segment. The observations that DNA conformational changes can be finely tuned and modulated by parameters pertaining to both the segment which undergoes the transition and the flanking sequences support the notion that DNA secondary motifs, such as the Z form and A-tracts, might be involved in the regulation of cellular processes.

Recent 1H nuclear magnetic resonance (n.m.r.) hydrogen exchange experiments on five different proteins have delineated the secondary structures formed in trapped, partially folded intermediates. The early forming structural elements are identifiable through a technique described in this work to predict folding pathways. The method assumes that the sequential selection of structural fragments such as α-helices and β-strands involved in the folding process is founded upon the maximal burial of solvent accessible surface from both the formation of internal structure and substructure association. The substructural elements were defined objectively by major changes in main-chain direction. The predicted folding pathways are in complete correspondence with the n.m.r. results in that the formed structural fragments found in the folding intermediates are those predicted earliest in the pathways. The technique was also applied to proteins of known tertiary structure and with fold similar to one of the five proteins examined by 1H n.m.r. The pathways for these structures also showed general consistency with the n.m.r. observations, suggesting conservation of a secondary structural framework or molten globule about which folding nucleates and proceeds.Errata: Equation 4 and 5 on page 905 are each missing a term.

Inherently curved DNA segments, associated with short runs of adenines, have been identified in many gene regulatory regions, yet their physiological significance remains unknown. The observations reported in this study indicate that intrinsically bent nucleic acid fragments are characterized by substantially attenuated affinities toward DNA-binding proteins involved in structural functions, such as H1 histone and protamine, as well as toward various DNA-modifying enzymes including ligases and exo- and endonucleases. Two mechanisms might be responsible for the altered binding properties. According to the first mechanism, the attenuated binding affinities and the bending represent two independent consequences of the unique structural parameters exhibited by A-tracts. Indeed, analysis of the degradation products obtained upon exposure of the curved sequences to various chemical nucleases points toward the narrowing of the DNA minor groove, a conformational modulation known to characterize A-tracts and to run along the axially-bent motifs, as a potential determinant of the observed binding attenuation. Alternatively, the conformational constraints which result from the stable bending might act to modulate the strength of DNA-protein interactions. Although the factor directly responsible for the altered binding affinities revealed by the bent sequences cannot as yet be conclusively resolved, it is proposed that a reiteration of this specific factor, being either an A-tract or a bend, in phase with the DNA helical repeat acts to amplify the modulation of the binding. This suggestion is based on the findings obtained from ligated DNA fragments which are composed of hexadecamers as the repetitive unit, and in which the A-tracts and the bends are reiterated out-of-phase. The binding attenuation revealed by these DNA segments is found to be considerably lower than that exhibited by the globally curved sequences. On the basis of these observations, we suggest that sequence-dependent DNA bending associated with short, phased runs of adenine might be involved in gene regulation processes.

Circular dichroism and electron microscopy studies of various in vitro DNA packaging systems indicate that all the factors which induce and modulate the secondary conformation of DNA molecules are capable of eliciting nucleic acids condensation processes into tight, highly ordered tertiary structures as well as altering the extent of order and compactness within the resulting species. Specifically, such factors include the ionic strength, the presence of particular dehydrating agents and polyamines, as well as the pH values. It is proposed that slight alterations of these parameters induce the formation of short non-B-DNA segments that propagate as a perturbation along the B-DNA double helix. The structural fluctuations of the dsDNA molecules that result from the conformational discontinuities formed at the junction sites between the B motif and the conformationally altered segments alter the elastic response of the nucleic acids and facilitate cooperative condensation processes. Moreover, the type and frequency of the structurally modified clusters interspersed within the B conformation and determined by the environmental parameters are shown to provide a means for continuous regulation of the extent and mode of DNA packaging. The ionic strength and hydrophobic environment in the close vicinity of the DNA molecules are controlled and modulated in vivo by DNA-binding proteins such as histones and protamines; similarly, pH values and polyamine concentrations are constantly regulated in living systems. It is suggested, therefore, that the secondary structural polymorphism which characterizes the DNA molecules might display a regulatory role by acting as a functional link between cellular parameters and the extent, mode, and timing of nucleic acid packaging processes.