Helicase mechanisms and the coupling of helicases within macromolecular machines. Part I: Structures and properties of isolated helicases

Helicases are proteins that harness the chemical free energy of ATP hydrolysis to catalyze the unwinding of double-stranded nucleic acids. These enzymes have been much studied in isolation, and here we review what is known about the mechanisms of the unwinding process. We begin by considering the thermally driven 'breathing' of double-stranded nucleic acids by themselves, in order to ask whether helicases might take advantage of some of these breathing modes. We next provide a brief summary of helicase mechanisms that have been elucidated by biochemical, thermodynamic, and kinetic studies, and then review in detail recent structural studies of helicases in isolation, in order to correlate structural findings with biophysical and biochemical results. We conclude that there are certainly common mechanistic themes for helicase function, but that different helicases have devised solutions to the nucleic acid unwinding problem that differ in structural detail. In Part II of this review (to be published in the next issue of this journal) we consider how these mechanisms are further modified to reflect the functional coupling of these proteins into macromolecular machines, and discuss the role of helicases in several central biological processes to illustrate how this coupling actually works in the various processes of gene expression.     

Interactive macromolecular sites II. Role in prebiotic macromolecular selection and early cellular evolution

A general theory of the evolution of interactive surfaces or sites on cell macromolecules is presented based on the assumption that all macromolecules present in cells are covered with reactive groups to which counter sites can theoretically be made. Initially such potentially reactive sites are considered to exist in pairs. Once one member of a pair is incorporated into a cell, its opposite number is forbidden except where it may be employed to advantage for structure formation. As more and more potentially interactive sites appeared in cells during evolution, a limit was approached where one member of each pair was present. Such a limit has been termed a perfect set, and would both define a “self” and recognize foreignness. The role of perfect sets in the development of the immune system, in differentiation, and in so-called random fixation of amino acid sequences is reviewed.     

Autoimmunity: basic mechanisms and implications in endocrine diseases. Part II

Regulation of the immune response to self-antigens is a complex process that involves maintaining self-tolerance while preserving the capacity to exert an effective immune response. The primary mechanism that leads to self-tolerance is central tolerance. However, potential pathogenic autoreactive lymphocytes are normally present in the periphery of all individuals. This suggests the existence of mechanisms of peripheral tolerance that prevent the initiation of autoimmune diseases by limiting the activation of autoreactive lymphocytes. If these mechanisms of peripheral tolerance are impaired, the autoreactive lymphocytes may be activated and autoimmune diseases can develop. Several processes are involved in the maintenance of peripheral tolerance: the active suppression mediated by regulatory T cell populations, the different maturation state of antigen-presenting cells presenting the autoantigen to autoreactive lymphocytes, inducing tolerance instead of cell activation, the characteristics of B cell populations. A deeper comprehension of these mechanisms may lead to important therapeutic applications, such as the development of cellular vaccines for organ-specific autoimmune diseases. In addition, autoimmunity does not always have pathological consequences, but may exert a protective function, as suggested by several observations on the beneficial role of autoreactive T cells in central nervous system injury.     

Immunology of pregnancy: cellular mechanisms allowing fetal survival within the maternal uterus

Pregnancy success remains a fascinating phenomenon to immunologists as it defies the immunological rules of rejection. Although it was previously thought that the maternal immune system does not see the fetus, it is now well documented that fetal cells reach the maternal body and encounter host immune cells. Natural tolerance mechanisms following this interaction remain to be fully elucidated. This article reviews the current literature on mechanisms of adaptive immunity, with emphasis on regulatory T cells and heme oxygenase 1 (HO-1). We propose a scenario in which regulatory T cells create a tolerant microenvironment at the fetal-maternal interface characterised by the presence of tolerance-associated molecules such as HO-1, which has been shown to be of vital importance for fetal survival.     

Chain processes and their biophysical applications: Part II. The effect of recovery

The biological effects of radiations are studied on the basis of a general probabilistic model of successive transformations (Markoff chains). The process of recovery is taken into account as a series of reverse transitions. The theory gives methods for calculating the probability of subjecting a microorganism to an observable change within an assigned time during a process of irradiation of a homogeneous aggregate of microorganisms. Two methods of calculation are given: one requires the solution of a secular equation, the other one consists of expansions in power series of the intensities of recovery.     

Tree invasions into treeless areas: mechanisms and ecosystem processes

Non-native tree invasions occur not only in woodland or forest vegetation, but also into areas with little or no native tree presence. Limiting factors for tree establishment and survival include seasonal or annual drought, low nutrient availability, cold temperature extremes, fire, and other abiotic conditions to which trees are poorly adapted as well as biotic conditions such as herbivory and lack of soil mutualist inoculum. Tree invasions of grasslands and semi-arid riparian areas in particular are now widespread and frequently result in the rapid conversion of these habitats to woodlands or forests. In some cases, these invasions are the result of a change in extrinsic conditions such as climate, fire, and/or grazing that remove what have been previous barriers to tree establishment. However, in other cases, tree species with particular life-history and dispersal traits fill open niches or outcompete native species. Significant examples of tree invasion into treeless areas can be seen with invasions of Pinus species into temperate grasslands and fynbos shrublands, Melaleuca quinquenervia and Triadica sebifera into grassy wetlands, Prosopis and Tamarix species into semi-arid riparian zones, and Acacia and Morella invasions into nutrient-poor shrublands and barrens. The establishment of trees into treeless areas may have strong impacts on ecosystem processes, influencing biogeochemical cycling, carbon sequestration and cycling, and ecohydrology, as well possible edaphic legacies that persist even if trees are removed.     

Pyrazole-based arylalkyne cathepsin S inhibitors. Part II: Optimization of cellular potency

Basic lipophilic substituents dramatically improved the cellular potency of a previously disclosed series of pyrazole-based arylalkyne cathepsin S inhibitors. The incorporation of substituted benzylamines in the para position of the arylalkyne maintained enzymatic activity (hCatS IC₅₀ = 80–420 nM) and imparted cellular potency (IC₅₀ = 0.8–4.0 μM). Further refinement of the morpholine portion of the pharmacophore enabled the identification of bicyclic piperidines with enhanced affinity for CatS (IC₅₀ = 10–30 nM) and sub-micromolar cellular potency (JY Ii IC₅₀ = 200–720 nM).     

Nanorotors and self-assembling macromolecular machines: the torque ring of the bacterial flagellar motor

The bacterial flagellar motor (BFM) is a self-assembling rotary nanomachine. It converts a flux of cations into the mechanical rotation of long filaments that propel bacteria through viscous media. The BFM contains a torque-generating ring that is complete with molecular machinery known as the switch complex that allows it to reverse directions. With four billion years of optimization, the BFM probably offers the pinnacle of sophisticated nanorotor design. Moreover as one of the best-characterized large biomolecular complexes, it offers the potential for convergence between nanotechnology and biology, which requires an atomic level understanding of BFM structure and function. This review focuses on current molecular models of the reversible BFM and the strategies used to derive them.     

Mitochondria from human term placenta. II. Characterization of respiratory pathways and coupling mechanisms

Pathways of electron transport utilized for respiration in human term placental mitochondrial preparations were differentiated and characterized through the use of classical respiratory chain inhibitors and multiple sources of reducing equivalents. Mechanisms of associated energy conservation and utilization were examined in these preparations with uncouplers and inhibitors of phosphorylation.

Inhibition by rotenone, antimycin A and cyanide established the classical electron transport chain as the major pathway of respiration with glutamate and succinate as substrates. Approximately 20% of glutamate-supported respiration was insensitive to inhibitors and may proceed by the cytochrome P-450 linked pathway of electron transport. Approximately 50% of ascorbate-N,N,N′,N′-tetramethyl-p-phenylenediamine supported respiration was insensitive to 10⁻³ M cyanide and must utilize an undefined by-pass of cytochrome oxidase. A rotenone- and antimycin-insensitive, exterior pathway for NADH oxidation was demonstrated which could be artificially linked by exogenous cytochrome c to the cytochrome oxidase region of the classical electron transport system. Glycerol 3-phosphate also supported oxidative phosphorylation yielding ADP/O ratios of 2.

Respiration of placental mitochondria was stimulated by 2,4- dinitrophenol and gramicidin. With succinate, dinitrophenol-stimulated respiration exceeded that obtain-red in the presence of ADP. Oligomycin and atractyloside prevented the stimulation of respiration by ADP. Thus, respiration appeared coupled through normal mechanisms to ATP formation and ion transport. A preferential coupling of respiration to the energy-utilizing processes of steroid hormone biosynthesis may exist.     

Excitation-contraction coupling and extracellular calcium transients in rabbit atrium: reconstruction of basic cellular mechanisms

Interactions of electrogenic sodium-calcium exchange, calcium channel and sarcoplasmic reticulum in the mammalian heart have been explored by simulation of extracellular calcium transients measured with tetramethylmurexide in rabbit atrium. The approach has been to use the simplest possible formulations of these mechanisms, which together with a minimum number of additional mechanisms allow reconstruction of action potentials, intracellular calcium transients and extracellular calcium transients. A 3:1 sodium-calcium exchange stoichiometry is assumed. Calcium-channel inactivation is assumed to take place by a voltage-dependent mechanism, which is accelerated by a rise in intracellular calcium; intracellular calcium release becomes a major physiological regulator of calcium influx via calcium channels. A calcium release mechanism is assumed, which is both calcium- and voltage-sensitive, and which undergoes prolonged inactivation. 200 microM cytosolic calcium buffer is assumed. For most simulations only instantaneous potassium conductances are simulated so as to study the other mechanisms independently of time- and calcium-dependent outward current. Thus, the model reconstructs extracellular calcium transients and typical action-potential configuration changes during steady-state and non-steady-state stimulation from the mechanisms directly involved in trans-sarcolemmal calcium movements. The model predicts relatively small trans-sarcolemmal calcium movements during regular stimulation (ca. 2 mumol kg-1 fresh mass per excitation); calcium current is fully activated within 2 ms of excitation, inactivation is substantially complete within 30 ms, and sodium-calcium exchange significantly resists repolarization from approximately -30 mV. Net calcium movements many times larger are possible during non-steady-state stimulation. Long action potentials at premature excitations or after inhibition of calcium release can be supported almost exclusively by calcium current (net calcium influx 5-30 mumol kg-1 fresh mass); action potentials during potentiated post-stimulatory contractions can be supported almost exclusively by sodium-calcium exchange (net calcium efflux 4-20 mumol kg-1 fresh mass). Large calcium movements between the extracellular space and the sarcoplasmic reticulum can take place through the cytosol with virtually no contractile activation. The simulations provide integrated explanations of electrical activity, contractile function and trans-sarcolemmal calcium movements, which were outside the explanatory range of previous models.     

Staining kinetics in single cells. Part II. Diffusion processes inside the cell

Applying hydrodynamic conditions, which certify a negligible influence of convective diffusion, the time-dependent uptake of thionin in lymphocytes, monkey kidney cells, and their separated nuclei was measured spectroscopically. Using fixed cell material the dye transport inside the cell is not hindered due to plasma membrane and cytoplasm. The staining rate depends on the dye concentration, the pretreatment of the cell, and on the electrolyte concentration of the dye solution. The mechanism of dye migration inside the cell is in accordance with a porous matrix model. The diffusion process takes place inside the pores and channels filled with liquid and is modified by adsorption of dye molecules on the walls of the pores. A dynamic reversible equilibrium exists between migrating dye molecules and the binding sites on the pore walls described by the Freundlich adsorption isotherm. The proposed model explains the observed order of reaction of the staining kinetics.     

Mitochondria from human term placenta. II. Characterization of respiratory pathways and coupling mechanisms.

Pathways of electron transport utilized for respiration in human term placental mitochondrial preparations were differentiated and characterized through the use of classical respiratory chain inhibitors and multiple sources of reducing equivalents. Mechanisms of associated energy conservation and utilization were examined in the preparations with uncouplers and inhibitors of phosphorylation. Inhibition by rotenone, antimycin A and cyanide established the classical electron transport chain as the major pathway of respiration with glutamate and succinate as substrates. Approximately 20% of glutamate-supported respiration was insensitive to inhibitors and may proceed by the cytochrome P-450 linked pathway of electron transport. Approximately 50% of ascorbate-N,N,N',N'-tetramethyl-p-phenylenediamine supported respiration was insensitive to 10-3 M cycanide and must utilize an undefined by-pass of cytochrome oxidase. A rotenone- and antimycin-insensitive, exterior pathway for NADH oxidation was demonstrated which could be artificially linked by exogenous cytochrome c to the cytochrome oxidase region of the classical electron transport system. Glycerol 3-phosphate also supported oxidative phosphorylation yielding ADP/O ratios of 2. Respiration of placental mitochondria was stimulated by 2,4-dinitrophenol and gramicidin. With succinate, dinitrophenol-stimulated respiration exceeded that obtained in the presence of ADP. Oligomycin and atractyloside prevented the stimulation of respiration by ADP. Thus, respiration appeared coupled through normal mechanisms to ATP formation and ion transport. A preferential coupling of respiration to the energy-utilizing processes of steroid hormone biosynthesis may exist.     

Transduction of c-myb into avian myeloblastosis virus: locating points of recombination within the cellular gene.

The oncogene (v-myb) of avian myeloblastosis virus apparently arose by transduction of nucleotide sequences from a cellular gene (c-myb). In c-myb the nucleotide sequences that formed v-myb exist at seven distinct regions separated by nontransduced stretches of sequence that are flanked by eucaryotic splice signals. By contrast, the sequences at the outside boundaries of the transduced region of c-myb do not resemble splice sites. We mapped the nucleotide sequences that are homologous to the ends of v-myb with respect to the exons and introns of c-myb. The results indicate that the leftward recombination between c-myb and the transducing retrovirus occurred within an intron of the cellular gene, whereas the rightward recombination took place in an exon of c-myb. Transduction of c-myb sequences may therefore have involved a DNA rearrangement.