Pyroptosis: mechanisms and diseases

Currently, pyroptosis has received more and more attention because of its association with innate immunity and disease. The research scope of pyroptosis has expanded with the discovery of the gasdermin family. A great deal of evidence shows that pyroptosis can affect the development of tumors. The relationship between pyroptosis and tumors is diverse in different tissues and genetic backgrounds. In this review, we provide basic knowledge of pyroptosis, explain the relationship between pyroptosis and tumors, and focus on the significance of pyroptosis in tumor treatment. In addition, we further summarize the possibility of pyroptosis as a potential tumor treatment strategy and describe the side effects of radiotherapy and chemotherapy caused by pyroptosis. In brief, pyroptosis is a double-edged sword for tumors. The rational use of this dual effect will help us further explore the formation and development of tumors, and provide ideas for patients to develop new drugs based on pyroptosis.

Above-bandgap voltages from ferroelectric photovoltaic devices

In conventional solid-state photovoltaics, electron-hole pairs are created by light absorption in a semiconductor and separated by the electric field spaning a micrometre-thick depletion region. The maximum voltage these devices can produce is equal to the semiconductor electronic bandgap. Here, we report the discovery of a fundamentally different mechanism for photovoltaic charge separation, which operates over a distance of 1-2 nm and produces voltages that are significantly higher than the bandgap. The separation happens at previously unobserved nanoscale steps of the electrostatic potential that naturally occur at ferroelectric domain walls in the complex oxide BiFeO(3). Electric-field control over domain structure allows the photovoltaic effect to be reversed in polarity or turned off. This new degree of control, and the high voltages produced, may find application in optoelectronic devices.

Conduction at domain walls in oxide multiferroics

Domain walls may play an important role in future electronic devices, given their small size as well as the fact that their location can be controlled. Here, we report the observation of room-temperature electronic conductivity at ferroelectric domain walls in the insulating multiferroic BiFeO(3). The origin and nature of the observed conductivity are probed using a combination of conductive atomic force microscopy, high-resolution transmission electron microscopy and first-principles density functional computations. Our analyses indicate that the conductivity correlates with structurally driven changes in both the electrostatic potential and the local electronic structure, which shows a decrease in the bandgap at the domain wall. Additionally, we demonstrate the potential for device applications of such conducting nanoscale features.

Protective role of CD40 in Leishmania major infection at two distinct phases of cell-mediated immunity

CD40-deficient mice are susceptible to Leishmania major infection while their wild-type littermates can resolve the infection. Upon stimulation with L. major antigens, draining lymph node T cells of the mutant mice and the susceptible mice, BALB/c, secrete comparable amounts of IL-4. The mutant mice produce less IFN gamma than wild-type mice. The expression of IL-12 p40 mRNA was significantly lower in L. major antigen-stimulated cells of mutant mice than those of wild-type or BALB/c mice. In normal mice, engagement of CD40 activates macrophages to a leishmanicidal state in vitro in the presence of IFN gamma. The results suggest that the CD40-CD40 ligand interaction plays an important role in two critical steps of cell-mediated immunity to L. major infection: the generation of a Th1 response and activation of macrophages to a leishmanicidal state.

First-line icotinib versus cisplatin/pemetrexed plus pemetrexed maintenance therapy for patients with advanced EGFR mutation-positive lung adenocarcinoma (CONVINCE): a phase 3, open-label, randomized study

BACKGROUND

Icotinib has been previously shown to be non-inferior to gefitinib in non-selected advanced non-small-cell lung cancer patients when given as second- or further-line treatment. In this open-label, randomized, phase 3 CONVINCE trial, we assessed the efficacy and safety of first-line icotinib versus cisplatin/pemetrexed plus pemetrexed maintenance in lung adenocarcinoma patients with epidermal growth factor receptor (EGFR) mutation.

PATIENTS AND METHODS

Eligible participants were adults with stage IIIB/IV lung adenocarcinoma and exon 19/21 EGFR mutations. Participants were randomly allocated (1 : 1) to receive oral icotinib or 3-week cycle of cisplatin plus pemetrexed for up to four cycles; non-progressive patients after four cycles were maintained with pemetrexed until disease progression or intolerable toxicity. The primary end point was progression-free survival (PFS) assessed by independent response evaluation committee. Other end points included overall survival (OS) and safety.

RESULTS

Between January 2013 and August 2014, 296 patients were randomized, and 285 patients were treated (148 to icotinib, 137 to chemotherapy). Independent response evaluation committee-assessed PFS was significantly longer in the icotinib group (11.2 versus 7.9 months; hazard ratio, 0.61, 95% confidence interval 0.43-0.87; P = 0.006). No significant difference for OS was observed between treatments in the overall population or in EGFR-mutated subgroups (exon 19 Del/21 L858R). The most common grade 3 or 4 adverse events (AEs) in the icotinib group were rash (14.8%) and diarrhea (7.4%), compared with nausea (45.9%), vomiting (29.2%), and neutropenia (10.9%) in the chemotherapy group. AEs (79.1% versus 94.2%; P < 0.001) and treatment-related AEs (54.1% versus 90.5%; P < 0.001) were significantly fewer in the icotinib group than in the chemotherapy group.

CONCLUSIONS

First-line icotinib significantly improves PFS of advanced lung adenocarcinoma patients with EGFR mutation with a tolerable and manageable safety profile. Icotinib should be considered as a first-line treatment for this patient population.

Phylogenetic distinction of iNOS and IDO function in mesenchymal stem cell-mediated immunosuppression in mammalian species

Mammalian mesenchymal stem cells (MSCs) have been shown to be strongly immunosuppressive in both animal disease models and human clinical trials. We have reported that the key molecule mediating immunosuppression by MSCs is species dependent: indoleamine 2,3-dioxygenase (IDO) in human and inducible nitric oxide synthase (iNOS) in mouse. In the present study, we isolated MSCs from several mammalian species, each of a different genus, and investigated the involvement of IDO and iNOS during MSC-mediated immunosuppression. The characterization of MSCs from different species was by adherence to tissue culture plastic, morphology, specific marker expression, and differentiation potential. On the basis of the inducibility of IDO and iNOS by inflammatory cytokines in MSCs, the tested mammalian species fall into two distinct groups: IDO utilizers and iNOS utilizers. MSCs from monkey, pig, and human employ IDO to suppress immune responses, whereas MSCs from mouse, rat, rabbit, and hamster utilize iNOS. Interestingly, based on the limited number of species tested, the iNOS-utilizing species all belong to the phylogenetic clade, Glires. Although the evolutionary significance of this divergence is not known, we believe that this study provides critical guidance for choosing appropriate animal models for preclinical studies of MSCs.

miR-23b-3p regulates the chemoresistance of gastric cancer cells by targeting ATG12 and HMGB2

Chemotherapy is an important treatment modality for gastric cancer (GC); however, it usually fails because of drug resistance, especially multidrug resistance (MDR). Previously, we found a novel subset of MDR-associated microRNAs (miRNAs) through high-throughput functional screening. In this report, we investigated the exact roles and mechanisms of miR-23b-3p in the MDR of GC. Using gain or loss-of-function in in vitro and in vivo experiments, we found that overexpression of miR-23b-3p reversed cancer cell resistance to multiple chemotherapeutics in vitro and sensitize tumors to chemotherapy in vivo. Reporter gene assay and western blot analysis showed that ATG12 and HMGB2 were the direct targets of miR-23b-3p. Meanwhile, ATG12 and HMGB2 were positively associated with the occurrence of autophagy. Reducing the expression of these target genes by siRNA or inhibition of autophagy both sensitized GC cells to chemotherapy. These findings suggest that a miR-23b-3p/ATG12/HMGB2/autophagy-regulatory loop has a critical role in MDR in GC. In addition, miR-23b-3p could be used as a prognostic factor for overall survival in GC. In conclusion, our data demonstrated that miR-23b-3p inhibited autophagy mediated by ATG12 and HMGB2 and sensitized GC cells to chemotherapy, and suggested the potential application of miR-23b-3p in drug resistance prediction and treatment.

Negative feedback regulation of IgE synthesis by murine CD23

Immunoglobulin E is found in nanogram amounts in normal human and mouse serum. It is increased during parasitic infestations and mediates allergy. CD23, the low-affinity receptor for IgE (Fc epsilon RII), has been proposed as an important regulator of IgE synthesis. The type-II transmembrane lectin CD23 is expressed in the mouse on B cells and follicular dendritic cells. In humans there are two forms of CD23 which differ in their intracellular amino-terminal 6/7 amino acids; expression of the A-form corresponds to that of murine CD23, whereas the B-form is also found on T and other haematopoietic cells. CD23 has been implicated in cellular adhesion, antigen presentation, as a growth and differentiation factor for human B, T and plasma cells, and as a signal transduction molecule (reviewed in refs 3, 8). Here we disrupt the gene coding for murine CD23 (ref. 9) to clarify the role of CD23 in vivo and find that B- and T-cell development is normal in these CD23-deficient mice. Immune responses to the helminth Nippostrongylus brasiliensis are unaffected. In contrast, immunization with thymus-dependent antigens leads to increased and sustained specific IgE antibody titres compared with controls. Formation of germinal centres is normal. These results suggest that murine CD23 acts as a negative feedback component of IgE regulation.

Reversible electric control of exchange bias in a multiferroic field-effect device

Electric-field control of magnetization has many potential applications in magnetic memory storage, sensors and spintronics. One approach to obtain this control is through multiferroic materials. Instead of using direct coupling between ferroelectric and ferromagnetic order parameters in a single-phase multiferroic material, which only shows a weak magnetoelectric effect, a unique method using indirect coupling through an intermediate antiferromagnetic order parameter can be used. In this article, we demonstrate electrical control of exchange bias using a field-effect device employing multiferroic (ferroelectric/antiferromagnetic) BiFeO(3) as the dielectric and ferromagnetic La(0.7)Sr(0.3)MnO(3) as the conducting channel; we can reversibly switch between two distinct exchange-bias states by switching the ferroelectric polarization of BiFeO(3). This is an important step towards controlling magnetization with electric fields, which may enable a new class of electrically controllable spintronic devices and provide a new basis for producing electrically controllable spin-polarized currents.

Significant prognosticators after primary radiotherapy in 903 nondisseminated nasopharyngeal carcinoma evaluated by computer tomography

PURPOSE

To evaluate the significant prognosticators in nasopharyngeal carcinoma (NPC).

METHODS AND MATERIALS

From 1984 to 1989, 903 treatment-naive nondisseminated (MO) NPC were given primary radical radiotherapy to 60-62.5 Gy in 6 weeks. All patients had computed tomographic (CT) and endoscopic evaluation of the primary tumor. Potentially significant parameters (the patient's age and sex, the anatomical structures infiltrated by the primary lesion, the cervical nodal characteristics, the tumor histological subtypes, and various treatment variables were analyzed by both monovariate and multivariate methods for each of the five clinical endpoints: actuarial survival, disease-free survival, free from distant metastasis, free from local failure, and free from regional failure.

RESULTS

The significant prognosticators predicting for an increased risk of distant metastases and poorer survival included male sex, skull base and cranial nerve(s) involvement, advanced Ho's N level, and presence of fixed or partially fixed nodes or nodes contralateral to the side of the bulk of the nasopharyngeal primary. Advanced patient age led to significantly worse survival and poorer local tumor control. Local and regional failures were both increased by tumor infiltrating the skull base and/or the cranial nerves. In addition, regional failure was increased significantly by advancing Ho's N level. Parapharyngeal tumor involvement was the strongest independent prognosticator that determined distant metastasis and survival rates in the absence of the overriding prognosticators of skull base infiltration, cranial nerve(s) palsy, and cervical nodal metastasis.

CONCLUSIONS

The significant prognosticators are delineated after the advent of CT and these should form the foundation of the modern stage classification for NPC.

Trends in cancer mortality in China: an update

BACKGROUND

Cancer deaths of China with the world population nearly a quarter will have a severe impact on global cancer trend and burden. The study aims to provide a comprehensive overview of long-term trends in cancer mortality in China.

MATERIALS AND METHODS

We used joinpoint analysis to detect changes in trends and generalized additive models to study birth cohort effect of risk factors between 1987 and 2009.

RESULTS

Mortality of all cancers declined steadily in urban areas, but not in rural areas. Decreasing mortality from cancers of the stomach, esophagus, nasopharynx, and cervix uteri was observed, while lung and female breast cancer mortality increased. Mortality from leukemia remained relatively stable, and cancer of liver, colorectal, and bladder had different trends between the rural and urban areas. Generational risks peaked in the cohorts born around 1925-1930 and tended to decline in successive cohorts for most cancers except for leukemia, whose relative risks were rising in the very recent cohorts.

CONCLUSION

The observed trends primarily reflect dramatic changes in socioeconomic development and lifestyle in China over the past two decades, and mortality from cancers of lung and female breast still represents a major public health priority for the government.

A comparative study of patient controlled epidural analgesia (PCEA) and continuous infusion epidural analgesia (CIEA) during labour

In a randomised, single-blinded, placebo-controlled study, 27 parturients in labour receiving epidural 0.125 per cent bupivacaine, were assessed to evaluate the efficacy of patient-controlled epidural analgesia (PCEA) compared with continuous infusion epidural analgesia (CIEA). Group A (n = 14) received a background infusion of 4 ml.hr-1 0.125 per cent bupivacaine, with further 4 ml aliquots, self-administered, as required (up to 16 ml.hr-1). Group B (n = 11) received a continuous infusion of 12 ml.hr-1 through the same PCA apparatus, but with the demand-button deactivated. Both groups were similar in respect to age, height, weight, duration and outcome of labour, birthweight and neonatal Apgar scores. Patients in Group A (PCEA) received significantly less local anaesthetic than those in Group B (11.2 vs 15.2 mg.hr-1). Pain relief was similar in both groups. Patients expressed overall satisfaction with PCEA, appreciating control over their own pain relief and less reliance on medical staff. PCEA is a safe, effective means of providing optimal analgesia during labour, with minimal local anaesthetic requirement.

Nanospace engineering of KOH activated carbon

This paper demonstrates that nanospace engineering of KOH activated carbon is possible by controlling the degree of carbon consumption and metallic potassium intercalation into the carbon lattice during the activation process. High specific surface areas, porosities, sub-nanometer (<1 nm) and supra-nanometer (1-5 nm) pore volumes are quantitatively controlled by a combination of KOH concentration and activation temperature. The process typically leads to a bimodal pore size distribution, with a large, approximately constant number of sub-nanometer pores and a variable number of supra-nanometer pores. We show how to control the number of supra-nanometer pores in a manner not achieved previously by chemical activation. The chemical mechanism underlying this control is studied by following the evolution of elemental composition, specific surface area, porosity, and pore size distribution during KOH activation and preceding H(3)PO(4) activation. The oxygen, nitrogen, and hydrogen contents decrease during successive activation steps, creating a nanoporous carbon network with a porosity and surface area controllable for various applications, including gas storage. The formation of tunable sub-nanometer and supra-nanometer pores is validated by sub-critical nitrogen adsorption. Surface functional groups of KOH activated carbon are studied by microscopic infrared spectroscopy.

Role of hepcidin in murine brain iron metabolism

Brain iron homeostasis is maintained by a balance of both iron uptake and release, and accumulating evidence has revealed that brain iron concentrations increase with aging. Hepcidin, an iron regulatory hormone produced by hepatocytes in response to inflammatory stimuli, iron, and hypoxia, has been shown to be the long-sought hormone responsible for the regulation of body iron balance and recycling in mammals. In this study, we report that hepcidin is widely expressed in the murine brain. In cerebral cortex, hippocampus and striatum, hepcidin mRNA levels increased with aging. Injection of hepcidin into the lateral cerebral ventricle resulted in decreased Fpn1 protein levels in cerebral cortex, hippocampus, and striatum. Additionally, treatment of primary cultured neurons with hepcidin caused decreased neuronal iron release and Fpn1 protein levels. Together, our data provide further evidence that hepcidin may be involved in the regulation of brain iron metabolism.

Anti-cancer activities of tea epigallocatechin-3-gallate in breast cancer patients under radiotherapy

The purpose of this study was to test the hypothesis that administration of epigallocatechin-3-gallate (EGCG), a polyphenol present in abundance in widely consumed tea, inhibits cell proliferation, invasion, and angiogenesis in breast cancer patients. EGCG in 400 mg capsules was orally administered three times daily to breast cancer patients undergoing treatment with radiotherapy. Parameters related to cell proliferation, invasion, and angiogenesis were analyzed while blood samples were collected at different time points to determine efficacy of the EGCG treatment. Compared to patients who received radiotherapy alone, those given radiotherapy plus EGCG for an extended time period (two to eight weeks) showed significantly lower serum levels of vascular endothelial growth factor (VEGF), hepatocyte growth factor (HGF), and reduced activation of metalloproteinase-9 and metalloproteinase-2 (MMP9/MMP2). Addition of sera obtained from patients treated with combination of radiotherapy and EGCG feeding for 2-8 weeks to in vitro cultures of highly-metastatic human MDA-MB-231 breast cancer cells resulted in the following significant changes: (1) suppression of cell proliferation and invasion; (2) arrest of cell cycles at the G0/G1 phase; (3) reduction of activation of MMP9/MMP2, expressions of Bcl-2/Bax, c-Met receptor, NF-κB, and the phosphorylation of Akt. MDA-MB-231 cells exposed to 5-10 µM EGCG also showed significant augmentation of the apoptosis inducing effects of γ-radiation, concomitant with reduced NF-κB protein level and AKT phosphorylation. These results provide hitherto unreported evidence that EGCG potentiated efficacy of radiotherapy in breast cancer patients, and raise the possibility that this tea polyphenol has potential to be a therapeutic adjuvant against human metastatic breast cancer.

Electric modulation of conduction in multiferroic Ca-doped BiFeO3 films

Many interesting materials phenomena such as the emergence of high-Tc superconductivity in the cuprates and colossal magnetoresistance in the manganites arise out of a doping-driven competition between energetically similar ground states. Doped multiferroics present a tantalizing evolution of this generic concept of phase competition. Here, we present the observation of an electronic conductor-insulator transition by control of band-filling in the model antiferromagnetic ferroelectric BiFeO3 through Ca doping. Application of electric field enables us to control and manipulate this electronic transition to the extent that a p-n junction can be created, erased and inverted in this material. A 'dome-like' feature in the doping dependence of the ferroelectric transition is observed around a Ca concentration of approximately 1/8, where a new pseudo-tetragonal phase appears and the electric modulation of conduction is optimized. Possible mechanisms for the observed effects are discussed on the basis of the interplay of ionic and electronic conduction. This observation opens the door to merging magnetoelectrics and magnetoelectronics at room temperature by combining electronic conduction with electric and magnetic degrees of freedom already present in the multiferroic BiFeO3.

Interface control of bulk ferroelectric polarization

The control of material interfaces at the atomic level has led to novel interfacial properties and functionalities. In particular, the study of polar discontinuities at interfaces between complex oxides lies at the frontier of modern condensed matter research. Here we employ a combination of experimental measurements and theoretical calculations to demonstrate the control of a bulk property, namely ferroelectric polarization, of a heteroepitaxial bilayer by precise atomic-scale interface engineering. More specifically, the control is achieved by exploiting the interfacial valence mismatch to influence the electrostatic potential step across the interface, which manifests itself as the biased-voltage in ferroelectric hysteresis loops and determines the ferroelectric state. A broad study of diverse systems comprising different ferroelectrics and conducting perovskite underlayers extends the generality of this phenomenon.

A flexible light-directed DNA chip synthesis gated by deprotection using solution photogenerated acids

Oligonucleotide microarrays or oDNA chips are effective decoding and analytical tools for genomic sequences and are useful for a broad range of applications. Therefore, it is desirable to have synthesis methods of DNA chips that are highly flexible in sequence design and provide high quality and general adoptability. We report herein, DNA microarray synthesis based on a flexible biochip method. Our method simply uses photogenerated acid (PGA) in solution to trigger deprotection of the 5'-OH group in conventional nucleotide phosphoramidite monomers (i.e. PGA-gated deprotection), with the rest of the reactions in the synthesis cycle the same as those used for routine synthesis of oligonucleotides. The complete DNA chip synthesis process is accomplished on a regular DNA synthesizer that is coupled with a UV-VIS projection display unit for performing digital photolithography. Using this method, oDNA chips containing probes of newly discovered genes can be quickly and easily synthesized at high yields in a conventional laboratory setting. Furthermore, the PGA-gated chemistry should be applicable to microarray syntheses of a variety of combinatorial molecules, such as peptides and organic molecules.

Microscopic origin of the giant ferroelectric polarization in tetragonal-like BiFeO(3)

We report direct experimental evidence for a room-temperature, ∼130  μC/cm(2) ferroelectric polarization from the tetragonal-like BiFeO(3) phase. The physical origin of this remarkable enhancement of ferroelectric polarization has been investigated by a combination of x-ray absorption spectroscopy, scanning transmission electron microscopy, and first principles calculations. A large strain-induced Fe-ion displacement relative to the oxygen octahedra, combined with the contribution of Bi 6s lone pair electrons, is the mechanism driving the large ferroelectric polarization in this tetragonal-like phase.

Eukaryotic elongation factor-2 kinase regulates the cross-talk between autophagy and pyroptosis in doxorubicin-treated human melanoma cells in vitro

Eukaryotic elongation factor-2 kinase (eEF-2K), a negative regulator of protein synthesis, has been shown to play an important role in modulating autophagy and apoptosis in tumor cells under various stresses. In this study, we investigated the regulatory role of eEF-2K in pyroptosis (a new form of programmed necrosis) in doxorubicin-treated human melanoma cells. We found that doxorubicin (0.5-5 μmol/L) induced pyroptosis in melanoma cell lines SK-MEL-5, SK-MEL-28, and A-375 with high expression of DFNA5, but not in human breast cancer cell line MCF-7 with little expression of DFNA5. On the other hand, doxorubicin treatment activated autophagy in the melanoma cells; inhibition of autophagy by transfecting the cells with siRNA targeting Beclin1 or by pretreatment with chloroquine (20 μmol/L) significantly augmented pyroptosis, thus sensitizing the melanoma cells to doxorubicin. We further demonstrated that doxorubicin treatment activated eEF-2K in the melanoma cells, and silencing of eEF-2K blunted autophagic responses, but promoted doxorubicin-induced pyroptotic cell death. Taken together, the above results demonstrate that eEF-2K dictates the cross-talk between pyroptosis and autophagy in doxorubicin-treated human melanoma cells; suppression of eEF-2K results in inhibiting autophagy and augmenting pyroptosis, thus modulating the sensitivity of melanoma cells to doxorubicin, suggesting that targeting eEF-2K may reinforce the antitumor efficacy of doxorubicin, offering a new insight into tumor chemotherapy.

Objective voice analysis for dysphonic patients: a multiparametric protocol including acoustic and aerodynamic measurements

The purpose was to determine the clinical value of a multiparametric objective voice evaluation protocol including acoustic and aerodynamic parameters measured mainly on a sustained /a/. This was done by comparison with perceptual analysis of continuous speech by a jury composed of 6 experienced listeners. Voice samples (continuous speech) from 63 male patients with dysphonia and 21 control subjects with normal voices were recorded and assesed by a jury of listeners. The jury was instructed to classify voice samples according to the G (overall dysphonia) component of the GRBAS score on a 4-point scale ranging from 0 for normal to 3 for severe dysphonia. Objective parameters were recorded on an EVA workstation. As usual with this type of system, parameters were measured mainly on a sustained /a/. Measured parameters included fundamental frequency (F0), intensity, jitter, shimmer, signal-to-noise ratio, Lyapunov coefficient (LC), oral airflow (OAF), maximum phonatory time (MPT), and vocal range (range). Estimated subglottic pressure (ESGP) was determined on a series of /pa/. Discriminant analysis was performed to detect correlation between jury classification and combinations of parameters. Results showed that a nonlinear combination of only six parameters (range, LC, ESGP, MPT, signal-to-noise ratio, and F0) allowed 86% concordance with jury classification. Discussion deals with the relative importance of the different objective parameters for discriminant analysis. Special emphasis is placed on two measurements rarely made in routine clinical workup, i.e., estimated subglottic pressure and Lyapunov coefficient.

Interface ferromagnetism and orbital reconstruction in BiFeO3-La(0.7)Sr(0.3)MnO3 heterostructures

We report the formation of a novel ferromagnetic state in the antiferromagnet BiFeO3 at the interface with ferromagnet La(0.7)Sr(0.3)MnO3. Using x-ray magnetic circular dichroism at Mn and Fe L(2,3) edges, we discovered that the development of this ferromagnetic spin structure is strongly associated with the onset of a significant exchange bias. Our results demonstrate that the magnetic state is directly related to an electronic orbital reconstruction at the interface, which is supported by the linearly polarized x-ray absorption measurement at the oxygen K edge.

Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions

We report the crystal structure of an NH2-terminal 388-residue fragment of T4 DNA polymerase (protein N388) refined at 2.2 A resolution. This fragment contains both the 3'-5' exonuclease active site and part of the autologous mRNA binding site (J. D. Karam, personal communication). The structure of a complex between the apoprotein N388 and a substrate, p(dT)3, has been refined at 2.5 A resolution to a crystallographic R-factor of 18.7%. Two divalent metal ion cofactors, Zn(II) and Mn(II), have been located in crystals of protein N388 which had been soaked in solutions containing Zn(II), Mn(II), or both. The structure of the 3'-5' exonuclease domain of protein N388 closely resembles the corresponding region in the Klenow fragment despite minimal sequence identity. The side chains of four carboxylate residues that serve as ligands for the two metal ions required for catalysis are located in geometrically equivalent positions in both proteins with a rms deviation of 0.87 A. There are two main differences between the 3'-5' exonuclease active site regions of the two proteins: (I) the OH of Tyr-497 in the Klenow fragment interacts with the scissile phosphate in the active site whereas the OH of the equivalent tyrosine (Tyr-320) in protein N388 points away from the active center; (II) different residues form of the binding pocket for the 3'-terminal bases of the substrate. In the protein N388 complex the 3'-terminal base of p(dT)3 is rotated approximately 60 degrees relative to the position that the corresponding base occupies in the p(dT)3 complex with the Klenow fragment. Finally, a separate domain (residues 1-96) of protein N388 may be involved in mRNA binding that results in translational regulation of T4 DNA polymerase (Pavlov & Karam, 1994).