Steady-state kinetic behaviour of functioning-dependent structures

A fundamental problem in biochemistry is that of the nature of the coordination between and within metabolic and signalling pathways. It is conceivable that this coordination might be assured by what we term functioning-dependent structures (FDSs), namely those assemblies of proteins that associate with one another when performing tasks and that disassociate when no longer performing them. To investigate a role in coordination for FDSs, we have studied numerically the steady-state kinetics of a model system of two sequential monomeric enzymes, E(1) and E(2). Our calculations show that such FDSs can display kinetic properties that the individual enzymes cannot. These include the full range of basic input/output characteristics found in electronic circuits such as linearity, invariance, pulsing and switching. Hence, FDSs can generate kinetics that might regulate and coordinate metabolism and signalling. Finally, we suggest that the occurrence of terms representative of the assembly and disassembly of FDSs in the classical expression of the density of entropy production are characteristic of living systems.     

Direct visualization of sarcoplasmic reticulum regions discharging Ca(2+)sparks in vascular myocytes

Localized Ca(2+)-release events, Ca(2+)sparks, have been suggested to be the 'elementary building blocks' of the calcium signalling system in all types of muscles. In striated muscles these occur at regular intervals along the fibre corresponding to the sarcomeric structures which do not exist in smooth muscle. We showed previously that in visceral and vascular myocytes Ca(2+)sparks occurred much more frequently at certain sites (frequent discharge sites [FDSs]). In this paper, we have related the position of FDSs to the distribution of the sarcoplasmic reticulum in the same living myocyte. The three-dimensional distribution of the SR in freshly isolated rabbit portal vein myocytes was visualized by means of high-resolution confocal imaging after staining with DiOC(6)and/or BODIPY TR-X ryanodine. Both fluorochromes revealed a similar staining pattern indicating a helical arrangement of well-developed superficial SR which occupied about 6% of the cell volume. Computing the frequency of spontaneous Ca(2+)sparks detected by means of fluo-4 fluorescence revealed that in about 70% of myocytes there was only one major FDS located on a prominent portion of superficial SR network usually within 1-2 microm of the nuclear envelope, although a few sparks occurred at other sites scattered generally in superficial locations throughout the cell. Polarized mitochondria were readily identified by accumulation of tetramethylrhodamine ethyl ester (TMRE). These were closely associated with the SR network in extra-nuclear regions. TMRE staining, however, failed to reveal any mitochondria near the FDS-related SR element. When observed, propagating [Ca(2+)](i)waves and associated myocyte contractions were initiated at FDSs. This study provide first insight into the three-dimensional arrangement of the SR in living smooth muscle cells and relates the peculiarity of the structural organization of the myocyte to the features of Ca(2+)signalling at subcellular level.     

Particle Imaging Velocimetry Evaluation of Intracranial Stents in Sidewall Aneurysm: Hemodynamic Transition Related to the Stent Design

We investigated the flow modifications induced by a large panel of commercial-off-the-shelf (COTS) intracranial stents in an idealized sidewall intracranial aneurysm (IA). Flow velocities in IA silicone model were assessed with and without stent implantation using particle imaging velocimetry (PIV). The use of the recently developed multi-time-lag method has allowed for uniform and precise measurements of both high and low velocities at IA neck and dome, respectively. Flow modification analysis of both regular (RSs) and flow diverter stents (FDSs) was subsequently correlated with relevant geometrical stent parameters. Flow reduction was found to be highly sensitive to stent porosity variations for regular stents RSs and moderately sensitive for FDSs. Consequently, two distinct IA flow change trends, with velocity reductions up to 50% and 90%, were identified for high-porosity RS and low-porosity FDS, respectively. The intermediate porosity (88%) regular braided stent provided the limit at which the transition in flow change trend occurred with a flow reduction of 84%. This transition occurred with decreasing stent porosity, as the driving force in IA neck changed from shear stress to differential pressure. Therefore, these results suggest that stents with intermediate porosities could possibly provide similar flow change patterns to FDS, favourable to curative thrombogenesis in IAs.     

Biological processes in organised media

Embedding a simple Michaelis-Menten enzyme in a gel slice may allow the catalysis of not only scalar processes but also vectorial ones, including uphill transport of a substrate between two compartments, and may make it seem as if two enzymes or transporters are present or as if an allosterically controlled enzyme/transporter is operating. The values of kinetic parameters of an enzyme in a partially hydrophobic environment are usually different from those actually measured in a homogeneous aqueous solution. This implies that fitting kinetic data (expressed in reciprocal co-ordinates) from in vivo studies of enzymes or transporters to two straight lines or a sigmoidal curve does not prove the existence of two different membrane mechanisms or allosteric control. In the artificial transport systems described here, a functional asymmetry was sufficient to induce uphill transport, therefore, although the active transport systems characterised so far correspond to proteins asymmetrically anchored in a membrane, the past or present existence of structurally symmetrical systems of transport in vivo cannot be excluded. The fact that oscillations can be induced in studies of the maintenance of the electrical potential of frog skin by addition of lithium allowed evaluation of several parameters fundamental to the functioning of the system in vivo (e.g., relative volumes of internal compartments, characteristic times of ionic exchanges between compartments). Hence, under conditions that approach real biological complexity, increasing the complexity of the behaviour of the system may provide information that cannot be obtained by a conventional, reductionist approach.     

Enzymes in Low Water Systems

Water is fundamental for enzyme action and for formation of the three-dimensional structure of proteins. Hence, it may be assumed that studies on the interplay between water and enzymes can yield insight into enzyme function and formation. This has proven correct, because the numerous studies that have been made on the behavior of water-soluble and membrane enzymes in systems with a low water content (reverse micelles or enzymes suspended in nonpolar organic solvents) have revealed properties of enzymes that are not easily appreciated in aqueous solutions. In the low water systems, it has been possible to probe the relation between solvent and enzyme kinetics, as well as some of the factors that affect enzyme thermostability and catalysis. Furthermore, the studies show that low water environments can be used to stabilize conformers that exhibit unsuspected catalytic properties, as well as intermediates of enzyme function and formation that in aqueous media have relatively short life-times. The structure of enzymes in these unnatural conditions is actively being explored.     

Structure and function of enzymes in heme biosynthesis

Tetrapyrroles like hemes, chlorophylls, and cobalamin are complex macrocycles which play essential roles in almost all living organisms. Heme serves as prosthetic group of many proteins involved in fundamental biological processes like respiration, photosynthesis, and the metabolism and transport of oxygen. Further, enzymes such as catalases, peroxidases, or cytochromes P450 rely on heme as essential cofactors. Heme is synthesized in most organisms via a highly conserved biosynthetic route. In humans, defects in heme biosynthesis lead to severe metabolic disorders called porphyrias. The elucidation of the 3D structures for all heme biosynthetic enzymes over the last decade provided new insights into their function and elucidated the structural basis of many known diseases. In terms of structure and function several rather unique proteins were revealed such as the V‐shaped glutamyl‐tRNA reductase, the dipyrromethane cofactor containing porphobilinogen deaminase, or the “Radical SAM enzyme” coproporphyrinogen III dehydrogenase. This review summarizes the current understanding of the structure–function relationship for all heme biosynthetic enzymes and their potential interactions in the cell.     

New enzymes for peptide biosynthesis in microorganisms

Peptides, biologically occurring oligomers of amino acids linked by amide bonds, are essential for living organisms. Many peptides isolated as natural products have biological functions such as antimicrobial, antivirus and insecticidal activities. Peptides often possess structural features or modifications not found in proteins, including the presence of nonproteinogenic amino acids, macrocyclic ring formation, heterocyclization, N-methylation and decoration by sugars or acyl groups. Nature employs various strategies to increase the structural diversity of peptides. Enzymes that modify peptides to yield mature natural products are of great interest for discovering new enzyme chemistry and are important for medicinal chemistry applications. We have discovered novel peptide modifying enzymes and have identified: (i) a new class of amide bond forming-enzymes; (ii) a pathway to biosynthesize a carbonylmethylene-containing pseudodipeptide structure; and (iii) two distinct peptide epimerases. In this review, an overview of our findings on peptide modifying enzymes is presented.     

The plant vesicular transport engineering for production of useful recombinant proteins

The molecular breeding of plants that have been genetically engineered for improved disease resistance and stress tolerance has been undertaken with the goal of improving food production. More recently, it has been realized that transgenic plants can serve as bioreactors for the production of proteins or compounds with industrial or clinical uses. Several different recombinant enzymes and antibodies have been produced in this manner. To maximize the potential of industrial plants as a production system for proteins, efficient expression systems utilizing promoters that optimize transgene expression, 5′-untranslated region elements for efficient translation, and appropriate post-translational modifications and localization must be developed. This review summarizes successful examples of the production of recombinant enzymes, antibodies, and vaccines using signal peptides that direct vesicular localization in transgenic plants. We further discuss the modulation of recombinant protein localization to the endoplasmic reticulum, vacuolar system, or extracellular compartments by varying the signal peptide.     

Static filling pressure in patients during induced ventricular fibrillation

The static pressure resulting after the cessation of flow is thought to reflect the filling of the cardiovascular system. In the past, static filling pressures or mean circulatory filling pressures have only been reported in experimental animals and in human corpses, respectively. We investigated arterial and central venous pressures in supine, anesthetized humans with longer fibrillation/defibrillation sequences (FDSs) during cardioverter/defibrillator implantation. In 82 patients, the average number of FDSs was 4 +/- 2 (mean +/- SD), and their duration was 13 +/- 2 s. In a total of 323 FDSs, arterial blood pressure decreased with a time constant of 2.9 +/- 1.0 s from 77.5 +/- 34.4 to 24.2 +/- 5.3 mmHg. Central venous pressure increased with a time constant of 3.6 +/- 1.3 s from 7.5 +/- 5.2 to 11.0 +/- 5.4 mmHg (36 points, 141 FDS). The average arteriocentral venous blood pressure difference remained at 13.2 +/- 6.2 mmHg. Although it slowly decreased, the pressure difference persisted even with FDSs lasting 20 s. Lack of true equilibrium pressure could possibly be due to a waterfall mechanism. However, waterfalls were identified neither between the left ventricle and large arteries nor at the level of the diaphragm in supine patients. We therefore suggest that static filling pressures/mean circulatory pressures can only be directly assessed if the time after termination of cardiac pumping is adequate, i.e., >20 s. For humans, such times are beyond ethical options.     

Proteome-level changes in the roots of Pisum sativum in response to salinity

We initiated a proteomics-based approach to identify root proteins affected by salinity in pea (Pisum sativum cv. Cutlass). Salinity stress was imposed either on 2-wk old pea plants by watering with salt water over 6 wk or by germinating and growing pea seeds for 7 days in Petri dishes. Concentrations of NaCl above 75 mM had significant negative effects on growth and development of peas in both systems. Salinity-induced root proteome-level changes in pea were investigated by 2-D electrophoresis of proteins from control, 75 and 150 mM NaCl-treated plants and seedlings. The majority of the protein spots visualised showed reproducible abundance in root protein extracts from whole plants and seedlings. Of these proteins, 35 spots that exhibited significant changes in abundance due to NaCl treatment were selected for identification using ESI-Q-TOF MS/MS. The identities of these proteins, which include pathogenesis-related (PR) 10 proteins, antioxidant enzymes such as superoxide dismutase (SOD) as well as nucleoside diphosphate kinase (NDPK) are presented, and the roles of some of them in mediating responses of pea to salinity are discussed. This is the first report of salinity-induced changes in the root proteome of pea that suggests a potential role for PR10 proteins in salinity stress responses. Our findings also suggest the possible existence of a novel signal transduction pathway involving SOD, H₂O₂, NDPK and PR10 proteins with a potentially crucial role in abiotic stress responses.     

Functional evolution of PLP‐dependent enzymes based on active‐site structural similarities

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active‐site structural similarities has not yet been undertaken. Pyridoxal‐5′‐phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP‐dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three‐dimensional‐fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. Proteins 2014; 82:2597–2608. © 2014 Wiley Periodicals, Inc.     

Role of proteins in soil carbon and nitrogen storage: controls on persistence

Mechanisms of soil organic carbon (C) and nitrogen (N) stabilization are of great interest, due to the potential for increased CO₂ release from soil organic matter (SOM) to the atmosphere as a result of global warming, and because of the critical role of soil organic N in controlling plant productivity. Soil proteins are recognized increasingly as playing major roles in stabilization and destabilization of soil organic C and N. Two categories of proteins are proposed: detrital proteins that are released upon cell death and functional proteins that are actively released into the soil to fulfill specific functions. The latter include microbial surface-active proteins (e.g., hydrophobins, chaplins, SC15, glomalin), many of which have structures that promote their persistence in the soil, and extracellular enzymes, responsible for many decomposition and nutrient cycling transformations. Here we review information on the nature of soil proteins, particularly those of microbial origin, and on the factors that control protein persistence and turnover in the soil. We discuss first the intrinsic properties of the protein molecule that affect its stability, next possible extrinsic stabilizing influences that arise as the proteins interact with other soil constituents, and lastly controls on accessibility of proteins at coarser spatial scales involving microbial cells, clay particles, and soil aggregates. We conclude that research at the interface between soil science and microbial physiology will yield rapid advances in our understanding of soil proteins. We suggest as research priorities determining the relative abundance and turnover time (age) of microbial versus plant proteins and of functional microbial proteins, including surface-active compounds.     

Liquid-liquid phase separation as a common organizing principle of intracellular space and biomembranes providing dynamic adaptive responses

This work is devoted to the phenomenon of liquid-liquid phase separation (LLPS), which has come to be recognized as fundamental organizing principle of living cells. We distinguish separation processes with different dimensions. Well-known 3D-condensation occurs in aqueous solution and leads to membraneless organelle (MLOs) formation. 2D-films may be formed near membrane surfaces and lateral phase separation (membrane rafts) occurs within the membranes themselves. LLPS may also occur on 1D structures like DNA and the cyto- and nucleoskeleton. Phase separation provides efficient transport and sorting of proteins and metabolites, accelerates the assembly of metabolic and signaling complexes, and mediates stress responses. In this work, we propose a model in which the processes of polymerization (1D structures), phase separation in membranes (2D structures), and LLPS in the volume (3D structures) influence each other. Disordered proteins and whole condensates may provide membrane raft separation or polymerization of specific proteins. On the other hand, 1D and 2D structures with special composition or embedded IDRs can nucleate condensates. We hypothesized that environmental change may trigger a LLPS which can propagate within the cell interior moving along the cytoskeleton or as an autowave. New phase propagation quickly and using a low amount of energy adjusts cell signaling and metabolic systems to new demands. Cumulatively, the interconnected phase separation phenomena in different dimensions represent a previously unexplored system of intracellular communication and regulation which cannot be ignored when considering both physiological and pathological cell processes.     

Diversity and survival of artificial lifeforms under sedimentation and random motion

Cellular automata are often used to explore the numerous possible scenarios of what could have occurred at the origins of life and before, during the prebiotic ages, when very simple molecules started to assemble and organise into larger catalytic or informative structures, or to simulate ecosystems. Artificial self-maintained spatial structures emerge in cellular automata and are often used to represent molecules or living organisms. They converge generally towards homogeneous stationary soups of still-life creatures. It is hard for an observer to believe they are similar to living systems, in particular because nothing is moving anymore within such simulated environments after few computation steps, because they present isotropic spatial organisation, because the diversity of self-maintained morphologies is poor, and because when stationary states are reached the creatures are immortal. Natural living systems, on the contrary, are composed of a high diversity of creatures in interaction having limited lifetimes and generally present a certain anisotropy of their spatial organisation, in particular frontiers and interfaces. In the present work, we propose that the presence of directional weak fields such as gravity may counter-balance the excess of mixing and disorder caused by Brownian motion and favour the appearance of specific regions, i.e. different strata or environmental layers, in which physical–chemical conditions favour the emergence and the survival of self-maintained spatial structures including living systems. We test this hypothesis by way of numerical simulations of a very simplified ecosystem model. We use the well-known Game of Life to which we add rules simulating both sedimentation forces and thermal agitation. We show that this leads to more active (vitality and biodiversity) and robust (survival) dynamics. This effectively suggests that coupling such physical processes to reactive systems allows the separation of environments into different milieux and could constitute a simple mechanism to form ecosystem frontiers or elementary interfaces that would protect and favour the development of fragile auto-poietic systems.     

Axonal transport of calmodulin: a physiologic approach to identification of long-term associations between proteins

Calmodulin is a soluble, heat-stable protein which has been shown to modulate both membrane-bound and soluble enzymes, but relatively little has been known about the in vivo associations of calmodulin. A 17,000-dalton heat-stable protein was found to move in axonal transport in the guinea pig visual system with the proteins of slow component b (SCb; 2 mm/d) along with actin and the bulk of the soluble proteins of the axon. Co-electrophoresis of purified calmodulin and radioactively labeled SCb proteins in two dimensional polyacrylamide gel electrophoresis (PAGE) demonstrated the identity of the heat-stable SCb protein and calmodulin on the basis of pI, molecular weight, and anomalous migration in the presence of Ca2+-chelating agents. No proteins co-migrating with calmodulin in two-dimensional PAGE could be detected among the proteins of slow component a (SCa; 0.3 mm/d, microtubules and neurofilaments) or fast component (FC; 250 mm/d, membrane-associated proteins). We conclude that calmodulin is transported solely as part of the SCb complex of proteins, the axoplasmic matrix. Calmodulin moves in axonal transport independent of the movements of microtubules (SCa) and membranes (FC), which suggests that the interactions of calmodulin with these structures may represent a transient interaction between groups of proteins moving in axonal transport at different rates. Axonal transport has been shown to be an effective tool for the demonstration of long-term in vivo protein associations.     

The lifestyle of prokaryotic organisms influences the repertoire of promiscuous enzymes

The metabolism of microbial organisms and its diversity are partly the result of an adaptation process to the characteristics of the environments that they inhabit. In this work, we analyze the influence of lifestyle on the content of promiscuous enzymes in 761 nonredundant bacterial and archaeal genomes. Promiscuous enzymes were defined as those proteins whose catalytic activities are defined by two or more different Enzyme Commission (E.C.) numbers. The genomes analyzed were categorized into four lifestyles for their exhaustive comparisons: free‐living, extremophiles, pathogens, and intracellular. From these analyses we found that free‐living organisms have larger genomes and an enrichment of promiscuous enzymes. In contrast, intracellular organisms showed smaller genomes and the lesser proportion of promiscuous enzymes. On the basis of our data, we show that the proportion of promiscuous enzymes in an organism is mainly influenced by the lifestyle, where fluctuating environments promote its emergence. Finally, we evidenced that duplication processes occur preferentially in metabolism of free‐living and extremophiles species. Proteins 2015; 83:1625–1631. © 2015 Wiley Periodicals, Inc.     

Golgi/granule processing of peptide hormone and neuropeptide precursors: a minireview

Proteolytic processing of precursor proteins is a phylogenetically ancient and widely used mechanism for producing biologically active peptides. Proteolytic cleavage of proproteins begins only after transport to the Golgi apparatus has been completed and in most systems may continue for many hours within newly formed secretory vesicles as these are stored in the cytosol or transported along axons to more peripheral sites of release. Paired basic residues are required for efficient proteolysis in most precursors, suggesting that a small number of specialized tryptic proteases exist that have great site selectivity but can process many sites within the same precursor or in different precursors within the same cell, or in different cells or tissues. Cleavage-site choice may be strongly influenced by other factors, such as secondary and tertiary structure, but definitive structural information on precursor proteins is lacking. Modifications such as glycosylation, phosphorylation, and sulfation also are Golgi associated but are not known to influence proteolytic processing patterns. Golgi/granule processing also rarely occurs at sites other than pairs of basic amino acids, including single basic residues ( trypsinlike ), Leu-Ala, Leu-Ser, or Tyr-Ala bonds ( chymotrysinlike ) as well as other specialized nontryptic cleavages, suggesting that mixtures of proteases coexist in the Golgi/granule system. Cathepsin B-like thiol proteases, or their precursors, have been implicated as the major processing endopeptidases in several systems. Carboxypeptidase B-like enzymes also have been identified in secretion granules in several tissues and appear to be metalloenzymes similar in mechanism to the pancreatic carboxypeptidases, but with a lower pH optimum. The role of the Golgi apparatus in sorting newly formed secreted products from lysosomal hydrolases may have permitted the development in evolution of an intimate relationship between certain of the lysosomal degradative enzymes, such as cathepsin B or its precursors, and the Golgi/granule processing systems. The sequestration of the proteolytic products of precursors within secretion granules leads to the coordinate discharge of highly complex mixtures of peptides having related or overlapping biological activities. The cosecretion of nonfunctional peptide " leftovers ," such as the proinsulin C-peptide, can serve as useful markers of secretion or cellular localization, as well as of evolutionary relation ships. Errors in cleavage due to point mutations in precursors have been identified in several systems, leading to the accumulation of incorrectly processed materials in the circulation. These and/or defects (ABSTRACT TRUNCATED AT 400 WORDS)     

Ecological barcoding of corallivory by second internal transcribed spacer sequences: hosts of coralliophiline gastropods detected by the cnidarian DNA in their stomach

The second internal transcribed spacer (ITS2) of the nuclear ribosomal RNA cluster (rDNA) is significantly smaller in the Cnidaria (120–260 bp) than in the rest of the Metazoa. ITS2 is one of the fastest evolving DNA regions among those commonly used in molecular systematics and has been proposed as a possible barcoding gene for Cnidaria to replace the currently problematic mitochondrial sequences used. We have reviewed the intraspecific and interspecific variation of ITS2 rRNA sequences in the Anthozoa. We have observed that the lower limits of the interspecific DNA divergence ranges very often overlap with intraspecific ranges, and identical sequences from individuals of different species are not rare. This finding can result in problems similar to those encountered with the mitochondrial COI, and we conclude that ITS2 does not prove significantly better than COI for standard taxonomic DNA barcoding in Anthozoa. However, ITS2 appears to be a promising gene in the ecological DNA barcoding of corallivory, where taxonomic accuracy at genus or even family level may represent a significant improvement of current knowledge. We have successfully amplified and sequenced ITS2 from template DNA extracted from foot muscle and from stomach contents of corallivorous gastropods, and from their anthozoan hosts. The small size of cnidarian ITS2 makes it a very easy and efficient tool for ecological barcoding of associations. Ecological barcoding of corallivory is an indispensable approach to the study of the associations in deep water, where direct observation is severely limited by logistics and costs.     

Electron transfer in quinoproteins

Soluble quinoprotein dehydrogenases oxidize a wide range of sugar, alcohol, amine, and aldehyde substrates. The physiological electron acceptors for these enzymes are not pyridine nucleotides but are other soluble redox proteins. This makes these enzymes and their electron acceptors excellent systems with which to study mechanisms of long-range interprotein electron transfer reactions. The tryptophan tryptophylquinone (TTQ)-dependent methylamine dehydrogenase (MADH) transfers electrons to a blue copper protein, amicyanin. It has been possible to alter the rate of electron transfer by using different redox forms of MADH, varying reaction conditions, and performing site-directed mutagenesis on these proteins. From kinetic and thermodynamic analyses of the reaction rates, it was possible to determine whether a change in rate is due a change in Delta G(0), electronic coupling, reorganization energy or kinetic mechanism. Examples of each of these cases are discussed in the context of the known crystal structures of the electron transfer protein complexes. The pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase transfers electrons to a c-type cytochrome. Kinetic and thermodynamic analyses of this reaction indicated that this electron transfer reaction was conformationally coupled. Quinohemoproteins possess a quinone cofactor as well as one or more c-type hemes within the same protein. The structures of a PQQ-dependent quinohemoprotein alcohol dehydrogenase and a TTQ-dependent quinohemoprotein amine dehydrogenase are described with respect to their roles in intramolecular and intermolecular protein electron transfer reactions.     

Structure and Function of Plant-Type Ferredoxins

The plant-type ferredoxins (Fds) are the [2Fe-2S] proteins that function primarily in photosynthesis; they transfer electrons from photoreduced Photosystem I to ferredoxin NADP(+) reductase in which NADPH is produced for CO(2) assimilation. In addition, Fds partition electrons to various ferredoxin-dependent enzymes not only for assimilations of inorganic nitrogen and sulfur and N(2) fixation but also for regulation of CO(2) assimilation cycle. Although Fds are small iron-sulfur proteins with molecular weight of 11 KDa, they are expected to interact with surprisingly many enzymes. Several Fd isoforms were found in non-photosynthetic cells as well as Fds in photosynthetic cells, leading to the recognition that they have differentiated physiological roles. In a quarter of century, X-ray crystallography and NMR spectroscopy provided wealth of structural data, which shed light on the structure-function relationship of the plant-type Fds and gave structural basis for the biochemical and spectroscopic properties so far accumulated. Thus the structural studies of Fds have come to a new era in which different roles of Fds and interactions with various enzymes are clarified on the basis of the tertiary and quaternary structures, although they are premature at present. This article reviews briefly the structures of the plant-type Fds together with their functions, properties, and interactions with Fd related enzymes. Lastly the folding motif of Fd, that has grown to be a large family by including many functionally unrelated proteins, is noted.