Identification and characterization of a +1 frameshift observed during the expression of Epstein-Barr virus IL-10 in Escherichia coli

Epstein-Barr virus IL-10 (ebvIL-10) mimics the biological functions of cellular IL-10 including a number of immunoinhibitory activities on diverse immune cells. Characterization of ebvIL-10 and several mutants, expressed in Escherichia coli, by gel filtration chromatography and mass spectrometry revealed a +1 frameshift upon ebvIL-10 expression. The frameshift is caused by the rare AGG codon at ebvIL-10 Arg159, which is followed by the most inefficient stop signal, UGAC. The frameshift was corrected by substituting the rare AGG codon with an abundant arginine codon, CGU, or by enhancing the level of tRNA that decodes the AGG codon. As a result, ebvIL-10 expression levels increased by approximately 3-fold and the purity of the protein improved from 85-95% to 98-99%. The correction of the frameshift has been essential for continuing structural and biophysical studies of ebvIL-10.

Analysis of intergenic spacer region length polymorphisms to investigate the halophilic archaeal diversity of stromatolites and microbial mats

Hamelin Pool in Western Australia is one of the two major sites in the world with active marine stromatolite formation. Surrounded by living smooth and pustular mats, these ancient laminated structures are associated with cyanobacterial communities. Recent studies have identified a wide diversity of bacteria and archaea in this habitat. By understanding and evaluating the microbial diversity of this environment we can obtain insights into the formation of early life on Earth, as stromatolites have been dated in the geological record as far back as 3.5 billion years. Automated ribosomal intergenic spacer analysis (ARISA) patterns were shown to be a useful method to genetically discriminate halophilic archaea within this environment. Patterns of known halophilic archaea are consistent, by replicate analysis, and the halophilic strains isolated from stromatolites have novel intergenic spacer profiles. ARISA-PCR, performed directly on extracted DNA from different sample sites, provided significant insights into the extent of previous unknown diversity of halophilic archaea within this environment. Cloning and sequence analysis of the spacer regions obtained from stromatolites confirmed the novel and broad diversity of halophilic archaea in this environment.

Conformational changes mediate interleukin-10 receptor 2 (IL-10R2) binding to IL-10 and assembly of the signaling complex

Interleukin-10 receptor 2 (IL-10R2) is a critical component of the IL-10.IL-10R1.IL-10R2 complex which regulates IL-10-mediated immunomodulatory responses. The ternary IL-10 signaling complex is assembled in a sequential order with the IL-10.IL-10R1 interaction occurring first followed by engagement of the IL-10R2 chain. In this study we map the IL-10R2 binding site on IL-10 using surface plasmon resonance and cell-based assays. Critical IL-10R2 binding residues are located in helix A adjacent to the previously identified IL-10R1 recognition surface. Interestingly, IL-10R2 binding residues located in the N-terminal end of helix A exhibit large structural differences between unbound cIL-10 and cIL-10.IL-10R1 crystal structures. This suggests IL-10R1-induced conformational changes regulate IL-10R2 binding and assembly of the ternary IL-10.IL-10R1.IL-10R2 complex. The basic mechanistic features of the assembly process are likely shared by six additional class-2 cytokines (viral IL-10s, IL-22, IL-26, IL-28A, IL28B, and IL-29) to promote IL-10R2 binding to six additional receptor complexes. These studies highlight the importance of structure in regulating low affinity protein-protein interactions and IL-10 signal transduction.

The unique C termini of orthopoxvirus gamma interferon binding proteins are essential for ligand binding

The orthopoxviruses ectromelia virus (ECTV) and vaccinia virus (VACV) express secreted gamma interferon binding proteins (IFN-gammaBPs) with homology to the ligand binding domains of the host's IFN-gamma receptor (IFN-gammaR1). Homology between these proteins is limited to the extracellular portions of the IFN-gammaR1 and the first approximately 200 amino acids of the IFN-gammaBPs. The remaining 60 amino acids at the C termini of the IFN-gammaBPs contain a single cysteine residue shown to be important in covalent dimerization of the secreted proteins. The function of the remaining C-terminal domain (CTD) has remained elusive, yet this region is conserved within all orthopoxvirus IFN-gammaBPs. Using a series of C-terminal deletion constructs, we have determined that the CTD is essential for IFN-gamma binding despite having no predicted homology to the IFN-gammaR1. Truncation of the ECTV IFN-gammaBP by more than two amino acid residues results in a complete loss of binding activity for both murine IFN-gamma and human IFN-gamma (hIFN-gamma), as measured by surface plasmon resonance (SPR) and bioassay. Equivalent truncation of the VACV IFN-gammaBP resulted in comparable loss of hIFN-gamma binding activity by SPR. Full-length IFN-gammaBPs were observed to form higher-ordered structures larger than the previously reported dimers. Mutants that were unable to bind IFN-gamma with high affinity in SPR experiments failed to assemble into these higher-ordered structures and migrated as dimers. We conclude that the unique CTD of orthopoxvirus IFN-gammaBPs is important for the assembly of covalent homodimers as well as the assembly of higher-ordered structures essential for IFN-gamma binding.

Characterization of monocyte-derived dendritic cells maturated with IFN-alpha

Dendritic cells (DC) are promising candidates for cancer immunotherapy. These cells can be generated from peripheral blood monocytes cultured with granulocyte macrophage-colony stimulating factor (GM-CSF) and interleukin-4 (IL-4). In order to obtain full functional capacity, maturation is required, but the most potent reagents such as LPS or polyriboinosinic polyribocytidylic acid (Poly I:C) are not approved for clinical use. We tested the ability of type I interferon (IFN) to induce such maturation. We found that 24-h IFN-alpha co-culture of day 7 monocyte-derived DC generated with GM-CSF and IL-4 induces increased numbers of DC positive for CD54 and CD40 together with the co-stimulatory molecule CD80 but not the activation marker CD83. Also, IFN-alpha maturation leads to an increase in IP-10 and MCP-1 chemokine secretion, but only a minor increase in IL-12p40 secretion. In line with this, maturation with IFN-alpha has only a small effect on induction of autologous T-cell stimulatory capacity of the DC. However, an increase in DC allogeneic T-cell stimulatory capacity was observed. These data suggest that IFN-alpha has a potential as a maturation agent used in DC-based cancer vaccine trials, but not as a single reagent.

Unique aspects of mda-7/IL-24 antitumor bystander activity: establishing a role for secretion of MDA-7/IL-24 protein by normal cells

Melanoma differentiation associated gene-7 (mda-7) was cloned using subtraction hybridization from terminally differentiated human melanoma cells. Based on structural and functional properties, mda-7 is now recognized as interleukin-24 (IL-24), a new member of the expanding IL-10 gene family. Unique properties of mda-7/IL-24 include its ability to selectively induce growth suppression, apoptosis and radiosensitization in diverse human cancer cells, without causing similar effects in normal cells. The utility of mda-7/IL-24, administered by means of a replication-incompetent adenovirus, as a gene therapy for cancer has recently received validation in patients, highlighting an important phenomenon initially observed in pancreatic tumor cells, namely a 'potent bystander apoptosis-inducing effect' in adjacent tumor cells not initially receiving this gene product. We presently investigated the contribution of mda-7/IL-24 secreted by normal cells in mediating this 'bystander effect', and document that normal cells induced to produce mda-7/IL-24 following infection with recombinant adenoviruses expressing this cytokine secrete mda-7/IL-24, which modifies the anchorage-independent growth, invasiveness, survival and sensitivity to radiation of cancer cells that contain functional IL-20/IL-22 receptors, but not in cancer cells that lack a complete set of receptors. Moreover, the combination of secreted mda-7/IL-24 and radiation engenders a 'bystander antitumor effect' not only in inherently mda-7/IL-24 or radiation-sensitive cancer cells, but also in tumor cells overexpressing the antiapoptotic proteins bcl-2 or bcl-x(L) and displaying resistance to either treatment alone. The present studies provide definitive evidence that secreted mda-7/IL-24 from normal cells can induce direct antitumor and radiation-enhancing effects that are dependent on the presence of canonical receptors for this cytokine on tumor cells. Moreover, we now describe a novel means of enhancing mda-7/IL-24's therapeutic potential by targeting normal cells to produce and release this cancer-specific apoptosis-inducing cytokine, a strategy that could be employed as an innovative way of using this unique gene product for treating metastatic disease.

Structure of insect-cell-derived IL-22

The crystal structure of interleukin-22 expressed in Drosophila melanogaster S2 cells (IL-22(Dm)) has been determined at 2.6 A resolution. IL-22(Dm) crystals contain six molecules in the asymmetric unit. Comparison of IL-22(Dm) and IL-22(Ec) (interleukin-22 produced in Escherichia coli) structures reveals that N-linked glycosylation causes only minor structural changes to the cytokine. However, 1-4 A main-chain differences are observed between the six IL-22(Dm) monomers at regions corresponding to the IL-22R1 and IL-10R2 binding sites. The structure of the carbohydrate and the conformational variation of IL22(Dm) provide new insights into IL-22 receptor recognition.

Same structure, different function crystal structure of the Epstein-Barr virus IL-10 bound to the soluble IL-10R1 chain

Human IL-10 (hIL-10) is a cytokine that modulates diverse immune responses. The Epstein-Barr virus (EBV) genome contains an IL-10 homolog (vIL-10) that shares high sequence and structural similarity with hIL-10. Although vIL-10 suppresses inflammatory responses like hIL-10, it cannot activate many other immunostimulatory functions performed by the cellular cytokine. These functional differences have been correlated with the approximately 1000-fold lower affinity of vIL-10, compared to hIL-10, for the IL-10R1 receptor chain. To define the structural basis for these observations, crystal structures of vIL-10 and a vIL-10 point mutant were determined bound to the soluble IL-10R1 receptor fragment (sIL-10R1) at 2.8 and 2.7 A resolution, respectively. The structures reveal that subtle changes in the conformation and dynamics of the vIL-10 AB and CD loops and an orientation change of vIL-10 on sIL-10R1 are the main factors responsible for vIL-10's reduced affinity for sIL-10R1 and its distinct biological profile.

Interferons, interferon-like cytokines, and their receptors

Recombinant interferon-alpha (IFN-alpha) was approved by regulatory agencies in many countries in 1986. As the first biotherapeutic approved, IFN-alpha paved the way for the development of many other cytokines and growth factors. Nevertheless, understanding the functions of the multitude of human IFNs and IFN-like cytokines has just touched the surface. This review summarizes the history of the purification of human IFNs and the key aspects of our current state of knowledge of human IFN genes, proteins, and receptors. All the known IFNs and IFN-like cytokines are described [IFN-alpha, IFN-beta, IFN-epsilon, IFN-kappa, IFN-omega, IFN-delta, IFN-tau, IFN-gamma, limitin, interleukin-28A (IL-28A), IL-28B, and IL-29] as well as their receptors and signal transduction pathways. The biological activities and clinical applications of the proteins are discussed. An extensive section on the evolution of these molecules provides some new insights into the development of these proteins as major elements of innate immunity. The overall structure of the IFNs is put into perspective in relation to their receptors and functions.

Phenotypic and functional characterization of clinical grade dendritic cells generated from patients with advanced breast cancer for therapeutic vaccination

Dendritic cells (DC) are promising candidates for cancer immunotherapy. However, it is not known whether in vitro-generated monocyte-derived DC from cancer patients are altered compared with DC from healthy donors. In a clinical phase I/II study, monocyte-derived DC were generated in vitro utilizing granulocyte macrophage colony-stimulating factor and rh-interleukin-4 (IL-4) and used for cancer immunotherapy. In this study, we tested the effect of various maturation cocktails and performed a comparative evaluation of the DC phenotype and functional characteristics. Polyriboinosinic polyribocytidylic acid (Poly I:C) + tumour necrosis factor-alpha (TNF-alpha) induced significant IL-12 p70 secretion, which was increased after addition of a decoy IL-10 receptor. The lymph node homing chemokine receptor CCR-7 expression was induced by TNF-alpha + IL-1beta + IL-6 + prostaglandin E2 but was not induced by Poly I:C + TNF-alpha. In general, DC from patients had an intermediate maturity phenotype with a significantly higher expression of CD40 and CD54 compared with healthy donors. In vitro analyses showed an unimpaired capacity of the patient-derived DC for antigen-specific (cytomegalovirus, tetanus and keyhole limpet haemocyanin) T-cell stimulation, whereas the allostimulatory capacity of patient-derived DC was significantly decreased. These data suggest that patient-derived DC are more differentiated but are less sensitive to maturation-inducing agents than DC obtained from healthy individuals.

The IL-10R2 binding hot spot on IL-22 is located on the N-terminal helix and is dependent on N-linked glycosylation

IL-22 is a class 2 alpha-helical cytokine involved in the generation of inflammatory responses. These activities require IL-22 to engage the cell surface receptors IL-22R1 and the low-affinity signaling molecule IL-10R2. IL-10R2 also interacts with five other class 2 cytokines: IL-10, IL-26, and the interferon-like cytokines IL-28A, IL-28B, and IL-29. Here, we define the IL-10R2 binding site on IL-22 using surface plasmon resonance (SPR) and site-directed mutagenesis. Surprisingly, the binding hot spot on IL-22 includes asparagine 54 (N54), which is post-translationally modified by N-linked glycosylation. Further characterization of the glycosylation reveals that only a single fucosylated N-acetyl glucosamine on N54 is required for maximal IL-10R2 binding. Biological responses of IL-22 mutants measured in cell-based luciferase assays correlate with the in vitro SPR studies. Together, these data suggest that IL-22 activity may be modulated via changes in the glycosylation state of the ligand during inflammation.

Interleukin-10 and related cytokines and receptors

The Class 2 alpha-helical cytokines consist of interleukin-10 (IL-10), IL-19, IL-20, IL-22, IL-24 (Mda-7), and IL-26, interferons (IFN-alpha, -beta, -epsilon, -kappa, -omega, -delta, -tau, and -gamma) and interferon-like molecules (limitin, IL-28A, IL-28B, and IL-29). The interaction of these cytokines with their specific receptor molecules initiates a broad and varied array of signals that induce cellular antiviral states, modulate inflammatory responses, inhibit or stimulate cell growth, produce or inhibit apoptosis, and affect many immune mechanisms. The information derived from crystal structures and molecular evolution has led to progress in the analysis of the molecular mechanisms initiating their biological activities. These cytokines have significant roles in a variety of pathophysiological processes as well as in regulation of the immune system. Further investigation of these critical intercellular signaling molecules will provide important information to enable these proteins to be used more extensively in therapy for a variety of diseases.

Interleukin-10 and related cytokines and receptors

The Class 2 alpha-helical cytokines consist of interleukin-10 (IL-10), IL-19, IL-20, IL-22, IL-24 (Mda-7), and IL-26, interferons (IFN-alpha, -beta, -epsilon, -kappa, -omega, -delta, -tau, and -gamma) and interferon-like molecules (limitin, IL-28A, IL-28B, and IL-29). The interaction of these cytokines with their specific receptor molecules initiates a broad and varied array of signals that induce cellular antiviral states, modulate inflammatory responses, inhibit or stimulate cell growth, produce or inhibit apoptosis, and affect many immune mechanisms. The information derived from crystal structures and molecular evolution has led to progress in the analysis of the molecular mechanisms initiating their biological activities. These cytokines have significant roles in a variety of pathophysiological processes as well as in regulation of the immune system. Further investigation of these critical intercellular signaling molecules will provide important information to enable these proteins to be used more extensively in therapy for a variety of diseases.

Crystallization and X-ray diffraction analysis of insect-cell-derived IL-22

Interleukin-22 is a potent mediator of cellular inflammatory responses. Crystals of interleukin-22 expressed in Drosophila melanogaster S2 cells (IL-22Dm) have been grown from polyethylene glycol solutions. To obtain crystals suitable for X-ray diffraction analysis required the separation of different IL-22Dm glycosylation variants and the inclusion of the detergent cetyltrimethylammonium bromide (CTAB) in the crystallization experiments. The crystals belong to space group P2(1), with unit-cell parameters a = 64.88, b = 62.23, c = 139.524 A, beta = 91.35 degrees, and diffract X-rays to 2.6 A resolution. The crystallographic asymmetric unit contains six IL-22Dm molecules, corresponding to a solvent content of approximately 49%.

An early stage of Mason-Pfizer monkey virus budding is regulated by the hydrophobicity of the Gag matrix domain core

Intracellular capsid transport and release of Mason-Pfizer monkey virus are dependent on myristylation of the Gag matrix domain (MA). A myristylated MA mutant, in which Thr41 and Thr78 are replaced with isoleucines, assembles capsids that are transported to the plasma membrane but are blocked in an early budding step. Since the nuclear magnetic resonance structure of MA showed that these Thr residues point into the hydrophobic core of the protein, it was hypothesized that the T41I/T78I mutant was defective in release of myristic acid from the more hydrophobic core. In order to further investigate whether an increase in the hydrophobicity of the MA core modulates capsid-membrane interactions and viral budding, three tyrosine residues (11, 28, and 67), oriented toward the MA core, were replaced individually or in a pair-wise combination with the more hydrophobic phenylalanine residue(s). As a control, Tyr82, oriented toward the outer surface of MA, was also replaced with phenylalanine. These Tyr-to-Phe substitutions did not alter capsid assembly compared to wild type in a capsid assembly assay. Pulse-chase, immunofluorescence, and electron microscopy studies demonstrated that single substitutions of Tyr11, Tyr28, and Tyr67 recapitulated the T41I/T78I mutant phenotype of decreased budding kinetics and accumulation of capsids at the plasma membrane. MA double mutants with a combination of these Tyr substitutions exhibited a phenotype that was even more defective in budding. In contrast, MA mutants with Tyr82 replaced by Phe resulted in a transport-defective phenotype. These results strongly support the hypothesis that myristic acid is sequestered inside MA prior to capsid-membrane interactions.

Induction of regulatory dendritic cells by dexamethasone and 1α,25-Dihydroxyvitamin D3

Dendritic cells (DC) modulated to induce T cell hyporesponsiveness have promising potential in immunotherapy of autoimmune disorders and for the prevention of allograft rejection. While studying the effect of immunosuppressive agents on the maturation of DC we found that 1alpha,25-Dihydroxyvitamin D(3) the active form of Vitamin D(3) (D(3)) in combination with dexamethasone (Dex) has a synergistic effect on LPS-induced maturation of DC. Monocyte-derived DCs cultured with D(3) and Dex during LPS-induced maturation have a low stimulatory effect on allogeneic T cells comparable with that of immature DCs. But in contrast to immature DCs, D3/Dex exposed DCs secrete IL-10 and show upregulated transcription of mRNA encoding the Ig-like inhibitory receptor ILT4. D3/Dex exposed DCs also inhibit alloreactivity and slightly enhance the degree of apoptosis in mature DCs. Thus, D(3)/Dex is an effective immunosuppressive drug combination for the induction of DCs capable of inducing T cell hyporesponsiveness.

Structure of interleukin-10/interleukin-10R1 complex: a paradigm for class 2 cytokine activation

The class II alpha-helical cytokine family consists of eleven members including the interferons, interleukin-10 (IL-10) and several newly discovered IL-10 homologs. The molecules display a vast array of biologic activities including the ability to induce an antiviral state, modulate inflammatory responses, and inhibit cell growth. Biologic activity is dependent on cytokine-dependent aggregation of two different cell-surface receptors. The detailed protein-protein interactions that initiate these biologic responses are amenable to study using X-ray crystallographic methods. In this article, I summarize my laboratory's contributions to understanding these recognition processes using IL-10 as the prototypic class II cytokine.

Comparison of interleukin-22 and interleukin-10 soluble receptor complexes

Interleukin-22 (IL-22) is a cellular homolog of IL-10 that stimulates the production of acute-phase reactants. IL-22 and IL-10 require different ligand-specific receptor chains (IL-22R and IL-10R1) but share a second receptor chain (IL-10R2) to initiate cellular responses. The quaternary structures and the ability of IL-22 and IL-10 to engage soluble (s) IL-10R1, IL-22R, IL-10R2 receptor chains were analyzed using size exclusion chromatography and surface plasmon resonance techniques. In contrast to IL-10, which is a homodimer, IL-22 is a monomer in solution that forms a 1:1 interaction with sIL-22R. Kinetic binding data reveal sIL-22R and sIL-10R1 exhibit specific nanomolar binding constants for IL-22 (k(on)/k(off) = 14.9 nM) and a monomeric isomer of IL-10 (IL-10M1) (k(on)/k(off) = 0.7 nM), respectively. In contrast, IL-10R2 exhibits essentially no affinity for IL-22 (K(eq) approximately 1 mM) or IL-10M1 (K(eq) approximately 2 mM) alone but displays a substantial increase in affinity for the IL-10/sIL-10R1 (K(eq) approximately 350 microM) and IL-22/sIL-22R (K(eq) approximately 45 microM) complexes. Three-dimensional models of IL-22 and IL-10 receptor complexes suggest two receptor residues (Gly-44 and Arg-96) are largely responsible for the marked differences in ligand affinity observed for sIL-10R1 and sIL-22R vs. sIL-10R2.

Crystal structures of alpha-helical cytokine-receptor complexes: we've only scratched the surface

Crystal structure analysis of alpha-helical cytokine-receptor complexes has provided numerous insights into the molecular recognition events that initiate essential cellular responses. Three-dimensional structure information gleaned from crystallographic studies has been used to understand the signal transduction process and is now guiding the design of clinically useful cytokine agonists and antagonists. The structures of twelve cytokines bound to their soluble receptor fragments have been determined to date. Stunning improvements in molecular biology as well as in crystallographic methods and equipment have greatly reduced the time required for structure determination, allowing one to focus on validating structure-based hypotheses. Examples that demonstrate the impact of this approach are described here as well as a general overview of cytokine-receptor structural biology. Despite success in defining extracellular cytokine-receptor molecular recognition events, elucidation of the intracellular receptor and associated kinase domains remains a formidable challenge.

Type I interferon structures: Possible scaffolds for the interferon-alpha receptor complex

The structures of several type I interferons (IFNs) are known. We review the structural information known for IFN alphas and compare them to other interferons and cytokines. We also review the structural information known or proposed for IFN–cell receptor complexes. However, the structure of the IFN – cell receptor – IFN receptor2 (IFNAR2) and IFN receptor1 (IFNAR1) complex has not yet been determined. This paper describes a structural model of human IFN-IFNAR2/IFNAR1 complex using human IFN-α2bdimer as the ligand. Both the structures of recombinant human IFN-α2band IFN-β were determined by X-ray crystallography as zinc-mediated dimers. Our proposed model was generated using human IFN-α2bdimer docked with IFNAR2/IFNAR1. We compare our model with the receptor complex models proposed for IFN-β and IFN-γ to contrast similarities and differences. The mutual binding sites of human IFN-α2band IFNAR2/IFNAR1 complex are consistent with available mutagenesis studies.Key words: three dimensional structure, antiviral activity, receptor, interferon.

Crystal structure of human cytomegalovirus IL-10 bound to soluble human IL-10R1

Human IL-10 (hIL-10) modulates critical immune and inflammatory responses by way of interactions with its high- (IL-10R1) and low-affinity (IL-10R2) cell surface receptors. Human cytomegalovirus exploits the IL-10 signaling pathway by expressing a functional viral IL-10 homolog (cmvIL-10), which shares only 27% sequence identity with hIL-10 yet signals through IL-10R1 and IL-10R2. To define the molecular basis of this virus-host interaction, we determined the 2.7-A crystal structure of cmvIL-10 bound to the extracellular fragment of IL-10R1 (sIL-10R1). The structure reveals cmvIL-10 forms a disulfide-linked homodimer that binds two sIL-10R1 molecules. Although cmvIL-10 and hIL-10 share similar intertwined topologies and sIL-10R1 binding sites, their respective interdomain angles differ by approximately 40 degrees. This difference results in a striking re-organization of the IL-10R1s in the putative cell surface complex. Solution binding studies show cmvIL-10 and hIL-10 share essentially identical affinities for sIL-10R1 whereas the Epstein-Barr virus IL-10 homolog (ebvIL-10), whose structure is highly similar to hIL-10, exhibits a approximately 20-fold reduction in sIL-10R1 affinity. Our results suggest cmvIL-10 and ebvIL-10 have evolved different molecular mechanisms to engage the IL-10 receptors that ultimately enhance the respective ability of their virus to escape immune detection.

Noncompetitive antibody neutralization of IL-10 revealed by protein engineering and x-ray crystallography

IL-10 is a dimeric cytokine that must engage its high-affinity cell surface receptor, IL-10R1, to induce multiple cellular activities. Here we report the 1.9 A crystal structure of an engineered IL-10 monomer (IL-10M1) in complex with a neutralizing Fab fragment (9D7Fab). 9D7Fab and IL-10R1 bind distinct nonoverlapping surfaces on IL-10M1. Antagonism of the IL-10M1/IL-10R1 interaction is the result of 9D7Fab-induced conformational changes in the CD loop of IL-10M1 that indirectly alter the structure of the IL-10R1 binding site. A single mutation (Ile87Ala) in the same CD loop region of the Epstein-Barr virus IL-10 (ebvIL-10) also reduces IL-10R1 binding affinity, suggesting that ebvIL-10 and 9D7Fab use similar allosteric mechanisms to modulate IL-10R1 affinity and biological activity.

Purification, crystallization and preliminary X-ray diffraction of a complex between IL-10 and soluble IL-10R1

A complex between interleukin-10 and the extracellular domain of its high-affinity receptor (sIL-10R1) has been crystallized from polyethylene glycol solutions. Crystals suitable for diffraction analysis required the modification of the NXS/T glycosylation sites on sIL-10R1 by site-directed mutagenesis and inclusion of the detergent cyclohexyl-methyl-beta-D-maltopyranoside in the crystallization experiments. The crystals belong to space group P3(2)12 or its enantimorph P3(1)12, with unit-cell parameters a = b = 46.23, c = 307.78 A, alpha = beta = 90, gamma = 120 degrees, and diffract X-rays to approximately 2.9 A. The IL-10 dimer is positioned on a crystallographic twofold, resulting in one IL-10 chain and one sIL-10R1 chain in the asymmetric unit, which corresponds to a solvent content of approximately 44%.

Millimeter-scale variations of stable isotope abundances in carbonates from banded iron-formations in the Hamersley Group of Western Australia

Several diamond drill cores from formations within the Hamersley Group of Western Australia have been studied for evidence of short-range variations in the isotopic compositions of the carbonates. For a set of 32 adjacent microbands analyzed in a specimen from the Marra Mamba Iron Formation, carbon isotope compositions of individual microbands ranged from -2.8 to -19.8 per mil compared to PDB and oxygen isotope compositions ranged from 10.2 to 20.8 per mil compared to SMOW. A pattern of alternating abundances was present, with the average isotopic contrasts between adjacent microbands being 3.0 per mil for carbon and 3.1 per mil for oxygen. Similar results were obtained for a suite of 34 microbands (in four groups) from the Bruno's Band unit of the Mount Sylvia Formation. Difficulties were experienced in preparing samples of single microbands from the Dales Gorge Member of the Brockman Iron Formation, but overall isotopic compositions were in good agreement with values reported by previous authors. Chemical analyses showed that isotopically light carbon and oxygen were correlated with increased concentrations of iron. The preservation of these millimeter-scale variations in isotopic abundances is interpreted as inconsistent with a metamorphic origin for the isotopically light carbon in the BIF carbonates. A biological origin is favored for the correlated variations in 13C and Fe, and it is suggested that the 13C-depleted carbonates may derive either from fermentative metabolism or from anaerobic respiration. A model is presented in which these processes occur near the sediment-water interface and are coupled with an initial oxidative precipitation of the iron.

Astrobiology: exploring the origins, evolution, and distribution of life in the Universe

The search for the origins of life and its presence beyond Earth is strengthened by new technology and by evidence that life tolerates extreme conditions and that planets are widespread. Astrobiologists learn how planets develop and maintain habitable conditions. They combine biological and information sciences to decipher the origins of life. They examine how biota, particularly microorganisms, evolve, at scales from the molecular to the biosphere level, including interactions with long-term planetary changes. Astrobiologists learn how to recognize the morphological, chemical, and spectroscopic signatures of life in order to explore both extraterrestrial samples and electromagnetic spectra reflected from extrasolar planets.

Morphological and ecological complexity in early eukaryotic ecosystems

Molecular phylogeny and biogeochemistry indicate that eukaryotes differentiated early in Earth history. Sequence comparisons of small-subunit ribosomal RNA genes suggest a deep evolutionary divergence of Eukarya and Archaea; C27-C29 steranes (derived from sterols synthesized by eukaryotes) and strong depletion of 13C (a biogeochemical signature of methanogenic Archaea) in 2,700 Myr old kerogens independently place a minimum age on this split. Steranes, large spheroidal microfossils, and rare macrofossils of possible eukaryotic origin occur in Palaeoproterozoic rocks. Until now, however, evidence for morphological and taxonomic diversification within the domain has generally been restricted to very late Mesoproterozoic and Neoproterozoic successions. Here we show that the cytoskeletal and ecological prerequisites for eukaryotic diversification were already established in eukaryotic microorganisms fossilized nearly 1,500 Myr ago in shales of the early Mesoproterozoic Roper Group in northern Australia.

Crystal structure of the IL-10/IL-10R1 complex reveals a shared receptor binding site

Interleukin 10 (IL-10) is a dimeric cytokine that plays a central role in suppressing inflammatory responses. These activities are dependent on the interaction of IL-10 with its high-affinity receptor (IL-10R1). This intermediate complex must subsequently recruit the low-affinity IL-10R2 chain before cell signaling can occur. Here we report the 2.9 A crystal structure of IL-10 bound to a soluble form of IL-10R1 (sIL-10R1). The complex consists of two IL-10s and four sIL-10R1 molecules. Several residues in the IL-10/sIL-10R1 interface are conserved in all IL-10 homologs and their receptors. The data suggests that formation of the active IL-10 signaling complex occurs by a novel molecular recognition paradigm where IL-10R1 and IL-10R2 both recognize the same binding site on IL-10.

The COOH-terminal nuclear localization sequence of interferon gamma regulates STAT1 alpha nuclear translocation at an intracellular site

We have recently shown that the nuclear localization of IFN gamma is mediated by a polybasic nuclear localization sequence (NLS) in its C terminus. This NLS is required for the full expression of biological activity of IFN gamma, both extracellularly and intracellularly. We now show that this NLS plays an integral intracellular role in the nuclear translocation of the transcription factor STAT1 alpha activated by IFN gamma. Treatment of IFN gamma with antibodies to the C-terminal region (95–133) containing the NLS blocked the induction of STAT1 alpha nuclear translocation. The antibodies had no effect on nuclear translocation of STAT1 alpha in IFN gamma treated cells. A deletion mutant of human IFN gamma, IFN gamma (1–123), which is devoid of the C-terminal NLS region was found to be biologically inactive, but was still able to bind to the IFN gamma receptor complex on cells with a K(d) similar to that of the wild-type protein. Deletion of the NLS specifically abolished the ability of IFN gamma(1–123) to initiate the nuclear translocation of STAT1 alpha, which is required for the biological activities of IFN gamma following binding to the IFN gamma receptor complex. Thus, the NLS region appears to contribute minimally to extracellular high-affinity receptor-ligand binding, yet exerts a strong functional role in STAT1 alpha nuclear localization. A high-affinity site for the interaction of the C-terminal NLS domain of IFN gamma with a K(d) approx. 3 × 10(−8) M(−1) has been described by previous studies on the intracellular cytoplasmic domain of the IFN gamma receptor alpha-chain. To examine the role of the NLS at the intracellular level, we microinjected neutralizing antibodies raised against the C-terminal NLS domain of IFN gamma into the cytoplasm of cells before treatment of cells with IFN gamma. These intracellular antibodies specifically blocked the nuclear translocation of STAT1 alpha following the subsequent treatment of these cells extracellularly with IFN gamma. These data show that the NLS domain of IFN gamma interacts at an intracellular site to regulate STAT1 alpha nuclear import. A C-terminal peptide of murine IFN gamma, IFN gamma(95–133), that contains the NLS motif, induced nuclear translocation of STAT1 alpha when taken up intracellularly by a murine macrophage cell line. Deletion of the NLS motif specifically abrogated the ability of this intracellular peptide to cause STAT1 alpha nuclear translocation. In cells activated with IFN gamma, IFN gamma was found to as part of a complex that contained STAT1 alpha and the importin-alpha analog Npi-1, which mediates STAT1 alpha nuclear import. The tyrosine phosphorylation of STAT1 alpha, the formation of the complex IFN gamma/Npi-1/STAT1 alpha complex and the subsequent nuclear translocation of STAT1 alpha were all found to be dependent on the presence of the IFN gamma NLS. Thus, the NLS of IFN gamma functions intracellularly to directly regulate the activation and ultimate nuclear translocation STAT1 alpha.

Design, characterization, and structure of a biologically active single-chain mutant of human IFN-gamma

A mutant form of human interferon-gamma (IFN-gamma SC1) that binds one IFN-gamma receptor alpha chain (IFN-gamma R alpha) has been designed and characterized. IFN-gamma SC1 was derived by linking the two peptide chains of the IFN-gamma dimer by a seven-residue linker and changing His111 in the first chain to an aspartic acid residue. Isothermal titration calorimetry shows that IFN-gamma SC1 forms a 1:1 complex with its high-affinity receptor (IFN-gamma R alpha) with an affinity of 27(+/- 9) nM. The crystal structure of IFN-gamma SC1 has been determined at 2.9 A resolution from crystals grown in 1.4 M citrate solutions at pH 7.6. Comparison of the wild-type receptor-binding domain and the Asp111-containing domain of IFN-gamma SC1 show that they are structurally equivalent but have very different electrostatic surface potentials. As a result, surface charge rather than structural changes is likely responsible for the inability of the His111-->Asp domain of to bind IFN-gamma R alpha. The AB loops of IFN-gamma SC1 adopt conformations similar to the ordered loops of IFN-gamma observed in the crystal structure of the IFN-gamma/IFN-gamma R alpha complex. Thus, IFN-gamma R alpha binding does not result in a large conformational change in the AB loop as previously suggested. The structure also reveals the final six C-terminal amino acid residues of IFN-gamma SC1 (residues 253-258) that have not been observed in any other reported IFN-gamma structures. Despite binding to only one IFN-gamma R alpha, IFN-gamma SC1 is biologically active in cell proliferation, MHC class I induction, and anti-viral assays. This suggests that one domain of IFN-gamma is sufficient to recruit IFN-gamma R alpha and IFN-gamma R beta into a complex competent for eliciting biological activity. The current data are consistent with the main role of the IFN-gamma dimer being to decrease the dissociation constant of IFN-gamma for its cellular receptors.

Design and analysis of an engineered human interleukin-10 monomer

A monomeric form of human interleukin 10 (IL-10M1) has been engineered for detailed structure-function studies on IL-10 and its receptor complexes. Wild type IL-10 (wtIL-10) is a domain swapped dimer whose structural integrity depends on the intertwining of two peptide chains. wtIL-10 was converted to a monomeric isomer by inserting 6 amino acids into the loop connecting the swapped secondary structural elements. Characterization of IL-10M1 by mass spectroscopy, size exclusion chromatography, cross-linking, and circular dichroism shows that IL-10M1 is a stable alpha-helical monomer at physiological pH whose three-dimensional structure closely resembles one domain of wtIL-10. As previously reported, incubation of wtIL-10 with a soluble form of the IL-10Ralpha (sIL-10Ralpha) generates a complex that consists of 2 wtIL-10 molecules and 4 sIL-10Ralphas. In contrast, IL-10M1 forms a 1:1 complex with the sIL-10Ralpha. Characterization of the interaction using isothermal titration calorimetry confirmed the 1:1 stoichiometry and yielded a dissociation constant of 30 nm with an apparent binding enthalpy of -12.2 kcal/mol. Despite forming a 1:1 complex, IL-10M1 is biologically active in cellular proliferation assays. These results indicate that the 1:1 interaction between IL-10M1 and IL-10Ralpha is sufficient for recruiting the signal transducing receptor chain (IL-10Rbeta) into the signaling complex and eliciting IL-10 cellular responses.

Terminal Proterozoic mid-shelf benthic microbial mats in the Centralian Superbasin and their environmental significance

A combined sedimentological and biogeochemical study has been conducted on several Terminal Proterozoic mid-shelf microbial mat facies from the Centralian Super-basin. Isotopic and organic geochemical analysis of the bitumen and kerogen indicated that two sources of organic matter from 'planktonic' and 'benthic microbial-mat' populations contributed to the sediment. The 'planktonic' source provided a suite of n-alkanes with <C20 predominance and the odd n-alkanes >C20, whereas, the 'benthic' source contributed an overlay of n-alkanes >C20 with a strong even preference, together with mid-chain methyl alkanes. Kerogen and biomarkers derived from the microbial mat were found to be depleted in 13C relative to planktonic material. Pyrite in the microbial mats was also found to be depleted in 34S compared to surrounding facies. The combination of these observations suggested that the mats may have been at least partly composed of sulfide oxidising bacteria. These organisms have specific environmental tolerances that set limits on palaeo-environment. Their requirement for oxygen indicates that the water column above the mid-shelf could not have been anoxic. Accordingly, from the results and age determinations reported here, it would appear that mid-shelf environments of the Centralian Superbasin of Australia were seeing significant levels of oxygen through the Ediacarian.

Crystal structure of ovine interferon-tau at 2.1 A resolution

Ovine interferon-tau (ovIFN-tau) is a pregnancy recognition hormone required for normal embryonic development in sheep. In addition to its novel role in reproductive physiology, ovIFN-tau displays antiviral and antiproliferative activities similar to the IFN-alpha subtypes. To probe the structural basis for its unique activity profile, the crystal structure of ovIFN-tau has been determined at 2.1 A resolution. The fold of ovIFN-tau is similar to the previously determined crystal structures of human IFN-alpha2b and human and murine IFN-beta, which each contain five alpha-helices. Comparison of ovIFN-tau with huIFN-alpha2b, huIFN-beta, and muIFN-beta reveals unexpected structural differences that occur in regions of considerable sequence identity. Specifically, main-chain differences up to 11 A occur for residues in helix A, the AB loop, helix B, and the BC loop. Furthermore, these regions are known to be important for receptor binding and biological activity. Of particular interest, a buried ion pair is observed in ovIFN-tau between Glu71 and Arg145 which displaces a conserved tryptophan residue (Trp77) from the helical bundle core. This ion pair represents a major change in the core of ovIFN-tau compared to huIFN-alpha2b. Based on amino acid sequence comparisons, these ovIFN-tau structural features may be conserved in several human IFN-alpha subtypes and IFN-omega. The structure identifies potential problems in interpreting site-directed mutagenesis data on the human IFN-alpha family that consists of 12 proteins.

Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase

Two new crystal forms of Escherichia coli thymidine phosphorylase (EC 2.4.2.4) have been found; a monoclinic form (space group P21) and an orthorhombic form (space group I222). These structures have been solved and compared to the previously determined tetragonal form (space group P43212). This comparison provides evidence of domain movement of the alpha (residues 1 to 65, 163 to 193) and alpha/beta (residues 80 to 154, 197 to 440) domains, which is thought to be critical for enzymatic activity by closing the active site cleft. Three hinge regions apparently allow the alpha and alpha/beta-domains to move relative to each other. The monoclinic model is the most open of the three models while the tetragonal model is the most closed. Phosphate binding induces formation of a hydrogen bond between His119 and Gly208, which helps to order the 115 to 120 loop that is disordered prior to phosphate binding. The formation of this hydrogen bond also appears to play a key role in the domain movement. The alpha-domain moves as a rigid body, while the alpha/beta-domain has some non-rigid body movement that is associated with the formation of the His119-Gly208 hydrogen bond. The 8 A distance between the two substrates reported for the tetragonal form indicates that it is probably not in an active conformation. However, the structural data for these two new crystal forms suggest that closing the interdomain cleft around the substrates may generate a functional active site. Molecular modeling and dynamics simulation techniques have been used to generate a hypothetical closed conformation of the enzyme. Analysis of this model suggests several residues of possible catalytic importance. The model explains observed kinetic results and satisfies requirements for efficient enzyme catalysis, most notably through the exclusion of water from the enzyme's active site.

Biological properties of recombinant alpha-interferons: 40th anniversary of the discovery of interferons

IFNs were first described as potent antiviral agents 40 years ago, and recombinant IFN-alpha2a and IFN-alpha2b were approved for the treatment of hairy cell leukemia just 11 years ago. Today, alpha-IFNs are approved worldwide for the treatment of a variety of malignancies and virologic diseases. Although the exact mechanism of action of IFN-alpha in the treatment of such diseases is not fully understood, many advances have been made in the characterization of the physicochemical and diverse biological properties of this highly pleiotropic cytokine. Here we review recent developments in our understanding of the antiviral and immunoregulatory properties of IFN-alpha, the nature of the multisubunit IFN-alpha receptor, and the molecular mechanisms of signal transduction. Where available, we have included comparative data on recombinant alpha-IFNs derived from both naturally occurring and nonnaturally occurring synthetic genes. We also review clinical data and data on the side effects and antigenicity of different sources of recombinant alpha-IFNs in humans. These latter topics are of clinical interest, because they may potentially affect the efficacy of these various products. Hopefully, what is already known about IFN will prompt further exploration into the mechanism(s) of action of IFN-alpha and thus deliver new applications for this prototypic cytokine, whose full therapeutic potential is yet to be realized.

Review of recent developments in the molecular characterization of recombinant alfa interferons on the 40th anniversary of the discovery of interferon

Recombinant alfa interferons (IFN-alpha s) are approved worldwide for the treatment of a variety of cancers and diseases of virologic origin. A series of recent advances in the molecular characterization of recombinant IFN-alpha s have allowed the determination of the three-dimensional IFN-alpha 2b structure by high-resolution x-ray crystallography. We review here recent developments in our understanding of the molecular and physicochemical properties of recombinant IFN-alpha, including our current state of knowledge of the IFN-alpha gene family and the multiple species of human leukocyte IFN. Based on the reported three-dimensional structure of IFN-alpha 2b, we propose a molecular model for the IFN-alpha 2b receptor complex and predict models for the naturally occurring subtypes IFN-alpha 1 and IFN-alpha 8, as well as the synthetic, non-naturally occurring consensus IFN. Such models provide molecular insights into the mechanism of action of IFN-alpha.

Three-dimensional models of interferon-alpha subtypes IFN-con1, IFN-alpha8, andIFN-alpha1 derived from the crystal structure of IFN-alpha2b

The crystal structure of human interferon (Hu-IFN)-alpha2b has been determined at 2.9 A resolution. This experimentally derived model provides an accurate structural scaffold on which amino acid changes between the different human IFN-alpha subtypes may be compared. Accurate structural data are essential to identify structurally important residues buried in the hydrophobic core of the molecule from solvent accessible residues that may participate in receptor binding. Furthermore, the location and chemical composition of each amino acid substitution may be used to predict potential conformation changes that may occur in the different subtypes. The possible structural and surface effects of these amino acid changes on receptor binding and biologic activity are analyzed in the context of a proposed IFN-alpha receptor complex model. This model can be improved and corrected as additional biochemical and experimental structural data are obtained. These modeling techniques have been used to assess the structural and functional consequences of amino acid changes between Hu-IFN-alpha2b and consensus IFN (IFN-con1), Hu-IFN-alpha8, and Hu-IFN-alpha1, which each have distinct receptor-binding and biologic properties. Amino acids in IFN-alpha1 and IFN-alpha8 were identified that may explain the lower specific activities of these subtypes versus the activity of IFN-alpha2b. In contrast, a molecular explanation for the reported differences between IFN-alpha2b in receptor binding affinity of either IFN-alpha8 or IFN-con1 was not readily apparent. Notably, 15 of the 19 amino acid differences in IFN-con1 compared with IFN-alpha2b are located on the exterior surface, where they may enhance the antigenicity of this synthetic, nonnaturally occurring IFN. These modeling studies should assist in the design of further experiments to clarify these observations.

Zinc mediated dimer of human interferon-alpha 2b revealed by X-ray crystallography

BACKGROUND

The human alpha-interferon (huIFN-alpha) family displays broad spectrum antiviral, antiproliferative and immunomodulatory activities on a variety of cell types. The diverse biological activities of the IFN-alpha's are conveyed to cells through specific interactions with cell-surface receptors. Despite considerable effort, no crystal structure of a member of this family has yet been reported, because the quality of the protein crystals have been unsuitable for crystallographic studies. Until now, structural models of the IFN-alpha's have been based on the structure of murine IFN-beta (muIFN-beta). These models are likely to be inaccurate, as the amino acid sequence of muIFN-beta differs significantly from the IFN-alpha's at proposed receptor-binding sites. Structural information on a huIFN-alpha subtype would provide an improved basis for modeling the structures of the entire IFN-alpha family.

RESULTS

The crystal structure of recombinant human interferon-alpha 2b (huIFN-alpha 2b) has been determined at 2.9 A resolution. HuIFN-alpha 2b exists in the crystal as a noncovalent dimer, which associates in a novel manner. Unlike other structurally characterized cytokines, extensive interactions in the dimer interface are mediated by a zinc ion (Zn2+). The overall fold of huIFN-alpha 2b is most similar to the structure of muIFN-beta. Unique to huIFN-alpha 2b is a 3(10) helix in the AB loop which is held to the core of the molecule by a disulfide bond.

CONCLUSIONS

The structure of huIFN-alpha 2b provides an accurate model for analysis of the > 15 related type 1 interferon molecules. HuIFN-alpha 2b displays considerable structural similarity with muIFN-beta, interleukin-10 and interferon-gamma, which also bind related class 2 cytokine receptors. From these structural comparisons and numerous studies on the effects of mutations on biological activity, we have identified protein surfaces that appear to be important in receptor activation. This study also reveals the potential biological importance of the huIFN-alpha 2b dimer.

Purification and crystallization of a complex between human interferon gamma receptor (extracellular domain) and human interferon gamma

X-ray diffraction quality crystals have been obtained from a complex between interferon gamma and the extracellular domain of its high-affinity cell surface receptor. The crystals were obtained from interferon gamma/interferon gamma receptor complexes purified by size exclusion chromatography. Diffraction quality crystals required analyzing these complex samples by isoelectric focusing gels to select purified complex fractions devoid of unbound interferon gamma. These studies used interferon gamma receptor engineered with an eight amino acid N-terminal deletion to eliminate heterogeneity generated due to proteolytic cleavage. In addition, the receptor was expressed in an E. coli secretion cell line which eliminated the need to refold the protein. Hexagonal crystals were grown from 1.6 M ammonium phosphate solutions and belong to a spacegroup of P6(5)22 with unit cell dimensions a = 145.9 A and c = 180.3 A. These crystals diffract to at least 2.9 A resolution when exposed to synchrotron radiation. SDS PAGE analysis of the crystals demonstrated that both interferon gamma and the receptor were present. Analysis of the x-ray diffraction data revealed that the crystals contain complexes with a stoichiometry of 2:1 receptor: ligand within the crystallographic asymmetric unit and consist of approximately 55% solvent.

Ancient hydrothermal ecosystems on earth: a new palaeobiological frontier

Thermal springs are common in the oceans and on land. Early in the history of the Earth they would have been even more abundant, because of a higher heat flow. A thermophilic lifestyle has been proposed for the common ancestor of extant life, and hydrothermal ecosystems can be expected to have existed on Earth since life arose. Though there has been a great deal of recent research on this topic by biologists, palaeobiologists have done little to explore ancient high temperature environments. Exploration geologists and miners have long known the importance of hydrothermal systems, as they are sources for much of our gold, silver, copper, lead and zinc. Such systems are particularly abundant in Archaean and Proterozoic successions. Despite the rarity of systematic searches of these by palaeobiologists, already 12 fossiliferous Phanerozoic deposits are known. Five are 'black smoker' type submarine deposits that formed in the deep ocean and preserve a vent fauna like that in the modern oceans; the oldest is Devonian. Three are from shallow marine deposits of Carboniferous age. As well as 'worm tubes', several of these contain morphological or isotopic evidence of microbial life. The oldest well established fossiliferous submarine thermal spring deposit is Cambro-Ordovician; microorganisms of at least three or four types are preserved in this. One example each of Carboniferous and Jurassic sub-lacustrine fossiliferous thermal springs are known. There are two convincing examples of fossiliferous subaerial hydrothermal deposits. Both are Devonian. Several known Proterozoic and Archaean deposits are likely to preserve a substantial palaeobiological record, and all the indications are that there must be numerous deposits suitable for study. Already it is demonstrable that in ancient thermal spring deposits there is a record of microbial communities preserved as stromatolites, microfossils, isotope distribution patterns and hydrocarbon biomarkers.

Lithofacies and biofacies of mid-Paleozoic thermal spring deposits in the Drummond Basin, Queensland, Australia

The Devonian to Carboniferous sinters of the Drummond Basin, Australia, are among the oldest well established examples of fossil subaerial hot springs. Numerous subaerial and subaqueous spring deposits are known from the geological record as a result of the occurrence of economic mineral deposits in many of them. Some are reported to contain fossils, but very few have been studied by paleobiologists; they represent an untapped source of paleobiological information on the history of hydrothermal ecosystems. Such systems are of special interest, given the molecular biological evidence that thermophilic bacteria lie near the root of the tree of extant life. The Drummond Basin sinters are very closely comparable with modern examples in Yellowstone National Park and elsewhere. Thirteen microfacies are recognisable in the field, ranging from high temperature apparently abiotic geyserite through various forms of stromatolitic sinter probably of cyanobacterial origin to ambient temperature marsh deposits. Microfossils in the stromatolites are interpreted as cyanobacterial sheaths. Herbaceous lycopsids occur in the lower temperature deposits.

The limits of palaeontological knowledge: finding the gold among the dross

Palaeontological interpretation rests on two interwoven sets of comparisons with the modern world. Palaeobiological interpretation relies on the placement of fossils within a phylogenetic and functional framework based primarily on the comparative biology of living organisms. Analogy to currently observable chemical, physical and taphonomic processes enables palaeoenvironmental inferences to be drawn from geological data. In older rocks, comparisons with the modern Earth can become tenuous, limiting palaeontological interpretation. The problem reaches its apogee in Archaean successions, yet pursuit of multiple lines of evidence establishes that complex microbial communities, fuelled by autotrophy and, likely, photoautotrophy, existed 3500 million years ago. Although Archaean palaeontology has to date focused on silicified coastal sediments, improved understanding of Earth's earliest biosphere may depend on the development of alternative environmental and taphonomic analogies. Spring precipitates and hydrothermal metal deposits are promising candidates. Terrestrial organisms may be of limited value in interpreting such fossils as may be found on Mars, although some points of comparison could prove general. Given limited opportunities for exploration, proper choice of environmental analogy is critical. Spring precipitates constitute excellent deposits for addressing questions of biology on another planet.

Crystal structure of interleukin 10 reveals an interferon gamma-like fold

The crystal structure of recombinant human interleukin 10 (rhIL-10) has been determined by X-ray crystallography at 2.0 A resolution. Interleukin 10 is a dimer composed of identical polypeptide chains related by a 2-fold axis. The molecule is predominantly alpha-helical. The main-chain fold resembles that of interferon gamma (IFN-gamma) in which the structural integrity of each domain is dependent on the intertwining of helices from each peptide chain. Comparison of rhIL-10 and IFN-gamma reveals differences in helix lengths and orientations of the 2-fold related domains. Interleukin 10 and IFN-gamma contain several conserved residues in their internal cores which suggest a possible "fingerprint" for detection of other members of this fold.

Crystal structure of a complex between interferon-gamma and its soluble high-affinity receptor

The crystal structure of interferon-gamma bound to the extracellular fragment of its high-affinity cell-surface receptor reveals the first view of a class-2 cytokine receptor-ligand complex. In the complex, one interferon-gamma homodimer binds two receptor molecules. Unlike the class-1 growth hormone receptor complex, the two interferon-gamma receptors do not interact with one another and are separated by 27 A. Upon receptor binding, the flexible AB loop of interferon-gamma undergoes a conformational change that includes the formation of a 3(10) helix.

Crystallization and preliminary X-ray investigation of recombinant human interleukin 10

Crystals of recombinant human interleukin 10 have been grown from solutions of ammonium sulfate. The crystals are tetragonal, space group P4(1)2(1)2 or P4(3)2(1)2; the unit cell axes are a = 36.5 A and c = 221.9 A. There is the equivalent of one polypeptide chain in the asymmetric unit. The crystals are stable to X-rays and diffract to at least 2.5 A resolution.

Drug binding by calmodulin: crystal structure of a calmodulin-trifluoperazine complex

The crystal structure of calmodulin (CaM) bound to trifluoperazine (TFP) has been determined and refined to a resolution of 2.45 A. Only one TFP is bound to CaM, but that is sufficient to cause distortion of the central alpha-helix and juxtaposition of the N- and C-terminal domains similar to that seen in CaM-polypeptide complexes. The drug makes extensive contacts with residues in the C-terminal domain of CaM but only a few contacts with one residue in the N-terminal domain. The structure suggests that substrate binding to the C-terminal domain is sufficient to cause the conformational changes in calmodulin that lead to activation of its targets.