The structure of the MICU1-MICU2 complex unveils the regulation of the mitochondrial calcium uniporter.

The MICU1-MICU2 heterodimer regulates the mitochondrial calcium uniporter (MCU) and mitochondrial calcium uptake. Herein, we present two crystal structures of the MICU1-MICU2 heterodimer, in which Ca2+ -free and Ca2+ -bound EF-hands are observed in both proteins, revealing both electrostatic and hydrophobic interfaces. Furthermore, we show that MICU1 interacts with EMRE, another regulator of MCU, through a Ca2+ -dependent alkaline groove. Ca2+ binding strengthens the MICU1-EMRE interaction, which in turn facilitates Ca2+ uptake. Conversely, the MICU1-MCU interaction is favored in the absence of Ca2+ , thus inhibiting the channel activity. This Ca2+ -dependent switch illuminates how calcium signals are transmitted from regulatory subunits to the calcium channel and the transition between gatekeeping and activation channel functions. Furthermore, competition with an EMRE peptide alters the uniporter threshold in resting conditions and elevates Ca2+ accumulation in stimulated mitochondria, confirming the gatekeeper role of the MICU1-MICU2 heterodimer. Taken together, these structural and functional data provide new insights into the regulation of mitochondrial calcium uptake.

The Study of a Novel Paeoniflorin-Converting Enzyme from Cunninghamella blakesleeana.

Paeoniflorin is a glycoside compound found in Paeonia lactiflora Pall that is used in traditional herbal medicine and shows various protective effects on the cardio-cerebral vascular system. It has been reported that the pharmacological effects of paeoniflorin might be generated by its metabolites. However, the bioavailability of paeoniflorin by oral administration is low, which greatly limits its clinical application. In this paper, a paeoniflorin-converting enzyme gene (G6046, GenBank accession numbers: OP856858) from Cunninghamella blakesleeana (AS 3.970) was identified by comparative analysis between MS analysis and transcriptomics. The expression, purification, enzyme activity, and structure of the conversion products produced by this paeoniflorin-converting enzyme were studied. The optimal conditions for the enzymatic activity were found to be pH 9, 45 °C, resulting in a specific enzyme activity of 14.56 U/mg. The products were separated and purified by high-performance counter-current chromatography (HPCCC). Two main components were isolated and identified, 2-amino-2-p-hydroxymethyl-methyl alcohol-benzoate (tirs-benzoate) and 1-benzoyloxy-2,3-propanediol (1-benzoyloxypropane-2,3-diol), via UPLC-Q-TOF-MS and NMR. Additionally, paeoniflorin demonstrated the ability to metabolize into benzoic acid via G6046 enzyme, which might exert antidepressant effects through the blood-brain barrier into the brain.

YdfD, a Lysis Protein of the Qin Prophage, Is a Specific Inhibitor of the IspG-Catalyzed Step in the MEP Pathway of Escherichia coli.

Bacterial cryptic prophage (defective prophage) genes are known to drastically influence host physiology, such as causing cell growth arrest or lysis, upon expression. Many phages encode lytic proteins to destroy the cell envelope. As natural antibiotics, only a few lysis target proteins were identified. ydfD is a lytic gene from the Qin cryptic prophage that encodes a 63-amino-acid protein, the ectopic expression of which in Escherichia coli can cause nearly complete cell lysis rapidly. The bacterial 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway is responsible for synthesizing the isoprenoids uniquely required for sustaining bacterial growth. In this study, we provide evidence that YdfD can interact with IspG, a key enzyme involved in the MEP pathway, both in vivo and in vitro. We show that intact YdfD is required for the interaction with IspG to perform its lysis function and that the mRNA levels of ydfD increase significantly under certain stress conditions. Crucially, the cell lysis induced by YdfD can be abolished by the overexpression of ispG or the complementation of the IspG enzyme catalysis product methylerythritol 2,4-cyclodiphosphate. We propose that YdfD from the Qin cryptic prophage inhibits IspG to block the MEP pathway, leading to a compromised cell membrane and cell wall biosynthesis and eventual cell lysis.

The crystal structure of MICU2 provides insight into Ca2+ binding and MICU1-MICU2 heterodimer formation.

The mitochondrial calcium uniporter (MCU) complex mediates the uptake of Ca2+ into mitochondria. Its activity is regulated by a heterodimer of MICU1 and MICU2, two EF-hand-containing proteins that act as the main gatekeeper of the uniporter. Herein we report the crystal structure of human MICU2 at 1.96 Å resolution. Our structure reveals a dimeric architecture of MICU2, in which each monomer adopts the canonical two-lobe structure with a pair of EF-hands in each lobe. Both Ca2+ -bound and Ca2+ -free EF-hands are observed in our structure. Moreover, we characterize the interaction sites within the MICU2 homodimer, as well as the MICU1-MICU2 heterodimer in both Ca2+ -free and Ca2+ -bound conditions. Glu242 in MICU1 and Arg352 in MICU2 are crucial for apo heterodimer formation, while Phe383 in MICU1 and Glu196 in MICU2 significantly contribute to the interaction in the Ca2+ -bound state. Based on our structural and biochemical analyses, we propose a model for MICU1-MICU2 heterodimer formation and its conformational transition from apo to a more compact Ca2+ -bound state, which expands our understanding of this co-regulatory mechanism critical for MCU's mitochondrial calcium uptake function.

Conformational Plasticity of the Active Site Entrance in E. coli Aspartate Transcarbamoylase and Its Implication in Feedback Regulation.

Aspartate transcarbamoylase (ATCase) has been studied for decades and Escherichia coli ATCase is referred as a "textbook example" for both feedback regulation and cooperativity. However, several critical questions about the catalytic and regulatory mechanisms of E. coli ATCase remain unanswered, especially about its remote feedback regulation. Herein, we determined a structure of E. coli ATCase in which a key residue located (Arg167) at the entrance of the active site adopted an uncommon open conformation, representing the first wild-type apo-form E. coli ATCase holoenzyme that features this state. Based on the structure and our results of enzymatic characterization, as well as molecular dynamic simulations, we provide new insights into the feedback regulation of E. coli ATCase. We speculate that the binding of pyrimidines or purines would affect the hydrogen bond network at the interface of the catalytic and regulatory subunit, which would further influence the stability of the open conformation of Arg167 and the enzymatic activity of ATCase. Our results not only revealed the importance of the previously unappreciated open conformation of Arg167 in the active site, but also helped to provide rationalization for the mechanism of the remote feedback regulation of ATCase.

Separation and purification of lanosterol, dihydrolanosterol, and cholesterol from lanolin by high-performance counter-current chromatography dual-mode elution method.

Lanosterol is a potential drug for cataracts treatment, which can reverse the aggregation of intracrystalline proteins. The low concentration in lanolin calls for high-performance separation methods. In this study, a counter-current chromatography dual-mode elution method was developed for the first time to separate and purify lanosterol from hexane extract of lanolin after saponification, in which the column was first eluted with the lower phase as mobile phase in head-to-tail mode, followed by the upper phase in the tail-to-head mode. High purity of lanosterol, dihydrolanosterol, and cholesterol can be obtained simultaneously. A solvent system composed of n-heptane/acetonitrile/ethyl acetate (5:5:1, v/v/v) was selected and optimized via partition coefficient determination. Compounds such as 111 mg lanosterol, 84 mg dihydrolanosterol, and 183 mg cholesterol with high purity of 99.77, 95.71, and 91.43%, respectively, analyzed by high-performance liquid chromatography were obtained within 80 min from 700 mg crude extract from 1.78 g lanolin. The method was also used to improve the purity of commercial lanosterol product from 66.97 to above 99%. Counter-current chromatography could serve as a potential and powerful technique for commercial production of highly pure lanosterol.

Identification of a new nucleotide binding site by structural alignment and site directed mutagenesis.

Nucleotide binding proteins are involved in many important cellular processes and form one of the largest protein families. Traditionally, the identification of nucleotide binding motif, such as the ATP binding P-loop, has relied on the comparison of protein sequences, consideration of the function of each of the proteins and the identification of signature motifs within the sequence. Sometimes, it is difficult to identify nucleotide binding proteins based on sequence alignment because of increased evolutionary distances. In such cases, structural alignments can provide a better guide for comparing specific features of sequences because the overall structures of these motifs are conserved despite low sequence identity. In the present study, on the basis of bioinformatics and structural comparison of three representative protein structures of Ham1 superfamily, YjjX, YggV, and YhdE, previously identified as nucleotide binding proteins, we have identified a novel nucleotide binding motif (T/SXXXXK/R). The importance of this signature motif in binding of nucleotides was validated using site directed mutagenesis. Mutations of conserved residues of the loop either decreased or completely abolished the nucleotide binding activity of the protein. We used the conserved motif identified in the study to search for other proteins having a similar motif. Two proteins, GTP cyclohydrolase II and dephospho-CoA pyrophosphorylase showed presence of the loop, suggesting that this nucleotide binding motif is not unique in the Ham1 superfamily, but represents a novel NTP recognition motif.

Structure of the bifunctional isocitrate dehydrogenase kinase/phosphatase.

The Escherichia coli isocitrate dehydrogenase kinase/phosphatase (AceK) is a unique bifunctional enzyme that phosphorylates or dephosphorylates isocitrate dehydrogenase (ICDH) in response to environmental changes, resulting in the inactivation or, respectively, activation of ICDH. ICDH inactivation short-circuits the Krebs cycle by enabling the glyoxlate bypass. It was the discovery of AceK and ICDH that established the existence of protein phosphorylation regulation in prokaryotes. As a 65-kDa protein, AceK is significantly larger than typical eukaryotic protein kinases. Apart from the ATP-binding motif, AceK does not share sequence homology with any eukaryotic protein kinase or phosphatase. Most intriguingly, AceK possesses the two opposing activities of protein kinase and phosphatase within one protein, and specifically recognizes only intact ICDH. Additionally, AceK has strong ATPase activity. It has been shown that AceK kinase, phosphatase and ATPase activities reside at the same site, although the molecular basis of such multifunctionality and its regulation remains completely unknown. Here we report the structures of AceK and its complex with ICDH. The AceK structure reveals a eukaryotic protein-kinase-like domain containing ATP and a regulatory domain with a novel fold. As an AceK phosphatase activator and kinase inhibitor, AMP is found to bind in an allosteric site between the two AceK domains. An AMP-mediated conformational change exposes and shields ATP, acting as a switch between AceK kinase and phosphatase activities, and ICDH-binding induces further conformational change for AceK activation. The substrate recognition loop of AceK binds to the ICDH dimer, allowing higher-order substrate recognition and interaction, and inducing critical conformational change at the phosphorylation site of ICDH.

Expression and purification of human WWP2 HECT domain in Escherichia coli.

WWP2 (WW domain-containing protein 2) is an E3 ubiquitin ligase belonging to the NEDD4-like protein family involved in various cell regulations, such as carcinogenesis, transcription control and cellular transport. Compared with homologues, WWP2 is difficult to express and no practical protocols have been developed for WWP2 preparation in large scale. Recently, domain structures of homologues of WWP2 have been determined by crystallography and NMR, but none for WWP2 has been attained. In this work, through a combination of extensive screening of ∼100 constructs, expression strategies and host systems, we have found a soluble HECT domain truncation (WHP2) of WWP2 which is amendable for preparation scale expression in Escherichia coli. We have also established a relatively simple purification process to achieve highly pure WHP2 protein by employing immobilized metal-affinity chromatography followed by salting out, ion exchange chromatography and finally, size exclusion chromatography. We are able to obtain about 60mg/L of the soluble WHP2. The identity and structure of the expressed WHP2 have been analyzed by mass spectrometry and circular dichroism. The native ability of WHP2 to bind different partners has been revealed by pull-down assay.

Phosphoryl transfer reaction catalyzed by membrane diacylglycerol kinase: a theoretical mechanism study.

Diacylglycerol kinase is an integral membrane protein which catalyzes phosphoryl transfer from ATP to diacylglycerol. As the smallest kinase known, it shares no sequence homology with conventional kinases and possesses a distinct trimer structure. Thus far, its catalytic mechanism remains elusive. Using molecular dynamics and quantum mechanics calculations, we investigated the co-factor and the substrate binding and phosphoryl transfer mechanism. Based on the analysis of density functional theory calculations, we reveal that the phosphorylation reaction of diacylglycerol kinase features the same phosphoryl transfer mechanism as other kinases, despite its unique structural properties. Our results further show that the active site is relatively open and able to accommodate ligands in multiple orientations, suggesting that the optimization of binding orientations and conformational changes would occur prior to actual phosphoryl transfer.

[Early evaluations of BISAP plus C-reactive protein in predicting the severity of acute pancreatitis].

OBJECTIVE: To explore the early evaluations of Bedside Index for Severity in Acute Pancreatitis (BISAP) plus C-reactive protein (CRP) in predicting the severity and prognosis of acute pancreatitis (AP). METHODS: A total of 114 cases of AP at our hospital over the last 2 years were retrospectively analyzed. The levels of amylase, serum glucose, serum calcium, CRP and D-dimer in 24 hours were measured. According to the evaluation standard, the scores of BISAP, acute physiology and chronic health evaluation (APACHE II), Ranson and computed tomography severity index (CTSI) were obtained. Mild acute pancreatitis (MAP), moderately severe acute pancreatitis (MSAP), severe acute pancreatitis (SAP), death toll and their proportion were compared in different BISAP scores. Correlation analyses were conducted for BISAP scores and laboratory indices, CRP and different scoring systems. We compared the evaluative value of BISAP plus CRP and other scoring systems in SAP. RESULTS: With rising BISAP scores, both severity and mortality increased in acute pancreatitis (χ(2) = 78.616, P < 0.01). BISAP scores were positively correlated with CRP, D-dimer and serum glucose (r = 0.451, 0.329, 0.241, P < 0.01) and negatively correlated with serum calcium ((r = -0.315, P < 0.01). CRP was positively correlated with APACHE-II, Ranson's, BISAP and CTSI scores (r = 0.407, 0.392, 0.451, 0.427, P < 0.001). When CRP was included into the BISAP scores, the area under the curve (AUC) of predicting SAP was 0.873 and the AUC of predicting death 0.909 so that BISAP score plus CRP had a good predictive value for the severity of AP and death. CONCLUSION: In clinical practice, the simple BISAP scoring system may predict the severity of AP. And BISAP score plus CRP has a better predictive value for AP.

Structures of an Eph receptor tyrosine kinase and its potential activation mechanism.

Eph receptor tyrosine kinases (RTKs) and their ephrin ligands play a crucial role in both physiological and pathophysiological processes, including tumourigenesis. A previous study of Eph RTKs established a regulatory role for the juxtamembrane segment (JMS) in kinase activation through the phosphorylation of two tyrosines within the JMS. Here, structures of EphA2 representing various activation states are presented. By determining the unphosphorylated inactive and phosphorylated active structures as well as an alternative conformation, conformational changes during kinase activation have been revealed. It is shown that phosphorylation of a tyrosine residue (Tyr772) in the activation loop without direct involvement of the JMS is sufficient to activate the EphA2 kinase. This mechanistic finding is in contrast to the mechanism of other Eph RTKs, such as EphB2, in which phosphorylation of the two JMS tyrosines initiates the dissociation of the JMS and triggers activation-loop phosphorylation for kinase activation. Furthermore, experiments demonstrate that the EphA2 substrate PTEN, a phosphatase that has been implicated in tumour suppression, acts to regulate the phosphorylation states of EphA2, exemplifying a unique reciprocal enzyme-substrate system. Based on these studies, it is therefore suggested that EphA2 may possess an alternate activation mechanism distinct from other Eph RTKs.

Synthesis, structure, and magnetic properties of Dy2Co2L10(bipy)2 and Ln2Ni2L10(bipy)2, Ln = La, Gd, Tb, Dy, and Ho: slow magnetic relaxation in Dy2Co2L10(bipy)2 and Dy2Ni2L10(bipy)2.

The 3,5-dichlorobenzoate anion, L(-), serves as a bridging ligand and 2,2'-bipyridine, bipy, as a terminal bidentate ligand to yield, through hydrothermal syntheses, the tetranuclear clusters Dy2Co2L10(bipy)2, 1, and Ln2Ni2L10(bipy)2, where Ln is the trivalent La, 2, Gd, 3, Tb, 4, Dy, 5, or Ho, 6, ion. Single-crystal X-ray diffraction reveals that the six complexes are all isomorphous with the monoclinic P21/c space group and with lattice parameters that decrease with the lanthanide contraction. The two cobalt(II) or nickel(II) and two Ln(III) cations are linked by the 10 L(-) anions to generate Dy2Co2 or Ln2Ni2 3d-4f cationic heteronuclear clusters with a slightly bent Co···Dy···Dy···Co or Ni···Ln···Ln···Ni arrangement. Direct current magnetic susceptibility studies reveal that the complexes are essentially paramagnetic, with room-temperature χ(M)T values close to the expected values for two cobalt(II) or nickel(II) and two Ln(III) cations. The temperature dependence of χ(M)T for 1 and 5 is well reproduced by ab initio calculations with the inclusion of weak magnetic exchange between the cobalt(II) or nickel(II) and a dysprosium(III) and between two dysprosium(III) ions. The calculated magnetic exchange parameters are J(Dy-Co) = 0.2 cm(-1) and J(Dy-Dy) = 0.02 cm(-1) for 1 and J(Dy-Ni) = -0.2 cm(-1) and J(Dy-Dy) = 0.03 cm(-1) for 5. Alternating current magnetic susceptibility studies reveal that 1 and 5 exhibit slow magnetic relaxation with effective energy barriers, Ueff, for the reversal of the magnetization for 1 of 82(2) cm(-1) in a 0 Oe dc bias field and 79.4(5) cm(-1) in a 1000 Oe dc bias field and, for 5, 73(1) cm(-1) in a 0 dc bias field; the calculated energies of 66.1(1) and 61.0(1) cm(-1) for the first excited spin-orbit state of dysprosium(III) in 1 and 5 agree rather well with these effective energy barriers. The entire Arrhenius plots of the logarithm of τ, the relaxation rate of the magnetization in 1 and 5, have been fit with contributions from quantum tunneling, direct Raman scattering, and Orbach thermal processes. The observation of a low-temperature magnetization reversal mechanism in 5 but not in 1 may be understood through the calculated exchange energy spectrum in their ground state.

Structure of Escherichia coli tyrosine kinase Etk reveals a novel activation mechanism.

While protein tyrosine (Tyr) kinases (PTKs) have been extensively characterized in eukaryotes, far less is known about their emerging counterparts in prokaryotes. The inner-membrane Wzc/Etk protein belongs to the bacterial PTK family, which has an important function in regulating the polymerization and transport of virulence-determining capsular polysaccharide (CPS). The kinase uses a unique two-step activation process involving intra-phosphorylation of a Tyr residue, although the molecular mechanism remains unknown. Herein, we report the first crystal structure of a bacterial PTK, the C-terminal kinase domain of Escherichia coli Tyr kinase (Etk) at 2.5-A resolution. The fold of the Etk kinase domain differs markedly from that of eukaryotic PTKs. Based on the observed structure and supporting mass spectrometric evidence of Etk, a unique activation mechanism is proposed that involves the phosphorylated Tyr residue, Y574, at the active site and its specific interaction with a previously unidentified key Arg residue, R614, to unblock the active site. Both in vitro kinase activity and in vivo antibiotics resistance studies using structure-guided mutants further support the novel activation mechanism.

Two acentric mononuclear molecular complexes with unusual magnetic and ferroelectric properties.

Two acentric, i.e., noncentrosymmetric, mononuclear complexes, Co(5-ATZ)(4)Cl(2), 1, and Cu(5-ATZ)(4)Cl(2), 2, where 5-ATZ is the monodentate 5-amino-1-H-tetrazole ligand, have been prepared and characterized. Both complexes crystallize in the tetragonal system with the P4nc space group, a member of the polar noncentrosymmetric 4mm class, and thus both 1 and 2 can exhibit ferroelectric and nonlinear optical properties. Magnetic studies indicate that 1 is a paramagnetic high-spin cobalt(II) complex with a rather extensive spin-orbit coupling, modeled as a zero-field splitting parameter, D, of ±91(3) cm(-1) and with very weak long-range antiferromagnetic exchange interactions. Direct current (dc) and ac magnetic studies indicate that 2 is a paramagnetic copper(II) complex that exhibits weak ferromagnetic exchange interactions below 15 K. Both 1 and 2 exhibit ferroelectric hysteresis loops at room temperature with remanent polarizations of 0.015 µC/cm(2) and coercive electric fields of 5.5 and 5.7 kV/cm, respectively.

A Novel Porous PDMS-AgNWs-PDMS (PAP)-Sponge-Based Capacitive Pressure Sensor.

The development of capacitive pressure sensors with low cost, high sensitivity and facile fabrication techniques is desirable for flexible electronics and wearable devices. In this project, a highly sensitive and flexible capacitive pressure sensor was fabricated by sandwiching a porous PAP sponge dielectric layer between two copper electrodes. The porous PAP sponge dielectric layer was fabricated by introducing highly conductive silver nanowires (AgNWs) into the PDMS sponge with 100% sucrose as a template and with a layer of polydimethylsiloxane (PDMS) film coating the surface. The sensitivity of the PAP sponge capacitive pressure sensor was optimized by increasing the load amount of AgNWs. Experimental results demonstrated that when the load amount of AgNWs increased to 150 mg in the PAP sponge, the sensitivity of the sensor was the highest in the low-pressure range of 0-1 kPa, reaching 0.62 kPa-1. At this point, the tensile strength and elongation of sponge were 1.425 MPa and 156.38%, respectively. In addition, the specific surface area of PAP sponge reached 2.0 cm2/g in the range of 0-10 nm pore size, and showed excellent waterproof performance with high elasticity, low hysteresis, light weight, and low density. Furthermore, as an application demonstration, ~110 LED lights were shown to light up when pressed onto the optimized sensor. Hence, this novel porous PAP-sponge-based capacitive pressure sensor has a wide range of potential applications in the field of wearable electronics.

YihE is a novel binding partner of Rho and regulates Rho-dependent transcription termination in the Cpx stress response.

The conjugative pilus expression (Cpx) stress response system can sense cell envelope stressors, such as misfolded proteins, and upregulate proteases to modify or degrade damaged proteins. YihE is a protein kinase implicated in the Cpx system, and Rho is a transcription termination factor in prokaryotes, but no functional connection between YihE and Rho has been reported. Here, we found that YihE can interact with Rho to form a binary complex with a stoichiometric ratio of 6:1 (Rho:YihE). A low resolution of Rho crystal structure in the presence of YihE was determined. YihE overexpression helped lessen the aberrant effects caused by Rho overexpression, including long cell morphology and other Rho-mediated phenotypes. Overall, YihE is a Rho binding partner that acts as a Rho antagonist in the Cpx stress. YihE binding to Rho would compete RNA from binding to Rho, thereby helping bacteria cope with stress through the regulation of Rho-dependent transcription termination.

PLK1-mediated phosphorylation of PPIL2 regulates HR via CtIP.

Homologous recombination (HR) is an error-free DNA double-strand break (DSB) repair pathway, which safeguards genome integrity and cell viability. Human C-terminal binding protein (CtBP)-interacting protein (CtIP) is a central regulator of the pathway which initiates the DNA end resection in HR. Ubiquitination modification of CtIP is known in some cases to control DNA resection and promote HR. However, it remains unclear how cells restrain CtIP activity in unstressed cells. We show that the ubiquitin E3 ligase PPIL2 is recruited to DNA damage sites through interactions with an HR-related protein ZNF830, implying PPIL2's involvement in DNA repair. We found that PPIL2 interacts with and ubiquitinates CtIP at the K426 site, representing a hereunto unknown ubiquitination site. Ubiquitination of CtIP by PPIL2 suppresses HR and DNA resection. This inhibition of PPIL2 is also modulated by phosphorylation at multiple sites by PLK1, which reduces PPIL2 ubiquitination of CtIP. Our findings reveal new regulatory complexity in CtIP ubiquitination in DSB repair. We propose that the PPIL2-dependent CtIP ubiquitination prevents CtIP from interacting with DNA, thereby inhibiting HR.