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1.
Nature ; 606(7916): 1027-1031, 2022 06.
Article in English | MEDLINE | ID: mdl-35580630

ABSTRACT

Around 250 million people are infected with hepatitis B virus (HBV) worldwide1, and 15 million may also carry the satellite virus hepatitis D virus (HDV), which confers even greater risk of severe liver disease2. The HBV receptor has been identified as sodium taurocholate co-transporting polypeptide (NTCP), which interacts directly with the first 48 amino acid residues of the N-myristoylated N-terminal preS1 domain of the viral large protein3. Despite the pressing need for therapeutic agents to counter HBV, the structure of NTCP remains unsolved. This 349-residue protein is closely related to human apical sodium-dependent bile acid transporter (ASBT), another member of the solute carrier family SLC10. Crystal structures have been reported of similar bile acid transporters from bacteria4,5, and these models are believed to resemble closely both NTCP and ASBT. Here we have used cryo-electron microscopy to solve the structure of NTCP bound to an antibody, clearly showing that the transporter has no equivalent of the first transmembrane helix found in other SLC10 proteins, and that the N terminus is exposed on the extracellular face. Comparison of our structure with those of related proteins indicates a common mechanism of bile acid transport, but the NTCP structure displays an additional pocket formed by residues that are known to interact with preS1, presenting new opportunities for structure-based drug design.


Subject(s)
Bile Acids and Salts , Cryoelectron Microscopy , Hepatitis B virus , Organic Anion Transporters, Sodium-Dependent , Receptors, Virus , Symporters , Antibodies , Bile Acids and Salts/metabolism , Hepatitis B virus/metabolism , Hepatocytes/metabolism , Humans , Organic Anion Transporters, Sodium-Dependent/chemistry , Organic Anion Transporters, Sodium-Dependent/metabolism , Organic Anion Transporters, Sodium-Dependent/ultrastructure , Receptors, Virus/chemistry , Receptors, Virus/metabolism , Receptors, Virus/ultrastructure , Symporters/chemistry , Symporters/metabolism , Symporters/ultrastructure
2.
PLoS Biol ; 20(8): e3001714, 2022 08.
Article in English | MEDLINE | ID: mdl-35913979

ABSTRACT

Galanin is a neuropeptide expressed in the central and peripheral nervous systems, where it regulates various processes including neuroendocrine release, cognition, and nerve regeneration. Three G-protein coupled receptors (GPCRs) for galanin have been discovered, which is the focus of efforts to treat diseases including Alzheimer's disease, anxiety, and addiction. To understand the basis of the ligand preferences of the receptors and to assist structure-based drug design, we used cryo-electron microscopy (cryo-EM) to solve the molecular structure of GALR2 bound to galanin and a cognate heterotrimeric G-protein, providing a molecular view of the neuropeptide binding site. Mutant proteins were assayed to help reveal the basis of ligand specificity, and structural comparison between the activated GALR2 and inactive hß2AR was used to relate galanin binding to the movements of transmembrane (TM) helices and the G-protein interface.


Subject(s)
Galanin/chemistry , Heterotrimeric GTP-Binding Proteins , Receptor, Galanin, Type 2/chemistry , Cryoelectron Microscopy , Galanin/metabolism , Heterotrimeric GTP-Binding Proteins/metabolism , Humans , Ligands , Receptor, Galanin, Type 2/metabolism
3.
Cell ; 136(1): 85-96, 2009 Jan 09.
Article in English | MEDLINE | ID: mdl-19135891

ABSTRACT

Condensins are key mediators of chromosome condensation across organisms. Like other condensins, the bacterial MukBEF condensin complex consists of an SMC family protein dimer containing two ATPase head domains, MukB, and two interacting subunits, MukE and MukF. We report complete structural views of the intersubunit interactions of this condensin along with ensuing studies that reveal a role for the ATPase activity of MukB. MukE and MukF together form an elongated dimeric frame, and MukF's C-terminal winged-helix domains (C-WHDs) bind MukB heads to constitute closed ring-like structures. Surprisingly, one of the two bound C-WHDs is forced to detach upon ATP-mediated engagement of MukB heads. This detachment reaction depends on the linker segment preceding the C-WHD, and mutations on the linker restrict cell growth. Thus ATP-dependent transient disruption of the MukB-MukF interaction, which creates openings in condensin ring structures, is likely to be a critical feature of the functional mechanism of condensins.


Subject(s)
Adenosine Triphosphatases/chemistry , Bacteria/chemistry , Bacterial Proteins/chemistry , DNA-Binding Proteins/chemistry , Multiprotein Complexes/chemistry , Adenosine Triphosphatases/metabolism , Adenosine Triphosphate , Bacteria/metabolism , Bacterial Proteins/metabolism , Binding Sites , DNA/metabolism , DNA-Binding Proteins/metabolism , Models, Molecular , Multiprotein Complexes/metabolism , Protein Structure, Tertiary
4.
Proc Natl Acad Sci U S A ; 118(13)2021 03 30.
Article in English | MEDLINE | ID: mdl-33753488

ABSTRACT

Chloride ion-pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl- into cells. How the ClR initiates the transport is elusive. Here, we show the dynamics of ion transport observed with time-resolved serial femtosecond (fs) crystallography using the Linac Coherent Light Source. X-ray pulses captured structural changes in ClR upon flash illumination with a 550 nm fs-pumping laser. High-resolution structures for five time points (dark to 100 ps after flashing) reveal complex and coordinated dynamics comprising retinal isomerization, water molecule rearrangement, and conformational changes of various residues. Combining data from time-resolved spectroscopy experiments and molecular dynamics simulations, this study reveals that the chloride ion close to the Schiff base undergoes a dissociation-diffusion process upon light-triggered retinal isomerization.


Subject(s)
Chloride Channels/metabolism , Chlorides/metabolism , Rhodopsins, Microbial/metabolism , Cations, Monovalent/metabolism , Chloride Channels/isolation & purification , Chloride Channels/radiation effects , Chloride Channels/ultrastructure , Crystallography/methods , Electromagnetic Radiation , Lasers , Molecular Dynamics Simulation , Nocardioides , Protein Conformation, alpha-Helical/radiation effects , Protein Structure, Tertiary/radiation effects , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Recombinant Proteins/radiation effects , Recombinant Proteins/ultrastructure , Retinaldehyde/metabolism , Retinaldehyde/radiation effects , Rhodopsins, Microbial/isolation & purification , Rhodopsins, Microbial/radiation effects , Rhodopsins, Microbial/ultrastructure , Water/metabolism
5.
Proc Natl Acad Sci U S A ; 117(9): 4741-4748, 2020 03 03.
Article in English | MEDLINE | ID: mdl-32071219

ABSTRACT

Hemoglobin is one of the best-characterized proteins with respect to structure and function, but the internal ligand diffusion pathways remain obscure and controversial. Here we captured the CO migration processes in the tense (T), relaxed (R), and second relaxed (R2) quaternary structures of human hemoglobin by crystallography using a high-repetition pulsed laser technique at cryogenic temperatures. We found that in each quaternary structure, the photodissociated CO molecules migrate along distinct pathways in the α and ß subunits by hopping between the internal cavities with correlated side chain motions of large nonpolar residues, such as α14Trp(A12), α105Leu(G12), ß15Trp(A12), and ß71Phe(E15). We also observe electron density evidence for the distal histidine [α58/ß63His(E7)] swing-out motion regardless of the quaternary structure, although less evident in α subunits than in ß subunits, suggesting that some CO molecules have escaped directly through the E7 gate. Remarkably, in T-state Fe(II)-Ni(II) hybrid hemoglobins in which either the α or ß subunits contain Ni(II) heme that cannot bind CO, the photodissociated CO molecules not only dock at the cavities in the original Fe(II) subunit, but also escape from the protein matrix and enter the cavities in the adjacent Ni(II) subunit even at 95 K, demonstrating the high gas permeability and porosity of the hemoglobin molecule. Our results provide a comprehensive picture of ligand movements in hemoglobin and highlight the relevance of cavities, nonpolar residues, and distal histidines in facilitating the ligand migration.


Subject(s)
Hemoglobins/chemistry , Hemoglobins/metabolism , Carbon Monoxide/metabolism , Crystallography, X-Ray , Diffusion , Heme/chemistry , Histidine/chemistry , Humans , Ligands , Models, Molecular , Protein Conformation , Protein Subunits/chemistry , Protein Subunits/metabolism , Recombinant Fusion Proteins
6.
Genes Dev ; 29(15): 1649-60, 2015 Aug 01.
Article in English | MEDLINE | ID: mdl-26215567

ABSTRACT

The pre-mRNA splicing reaction of eukaryotic cells has to be carried out extremely accurately, as failure to recognize the splice sites correctly causes serious disease. The small subunit of the U2AF heterodimer is essential for the determination of 3' splice sites in pre-mRNA splicing, and several single-residue mutations of the U2AF small subunit cause severe disorders such as myelodysplastic syndromes. However, the mechanism of RNA recognition is poorly understood. Here we solved the crystal structure of the U2AF small subunit (U2AF23) from fission yeast, consisting of an RNA recognition motif (RRM) domain flanked by two conserved CCCH-type zinc fingers (ZFs). The two ZFs are positioned side by side on the ß sheet of the RRM domain. Further mutational analysis revealed that the ZFs bind cooperatively to the target RNA sequence, but the RRM domain acts simply as a scaffold to organize the ZFs and does not itself contact the RNA directly. This completely novel and unexpected mode of RNA-binding mechanism by the U2AF small subunit sheds light on splicing errors caused by mutations of this highly conserved protein.


Subject(s)
Models, Molecular , Nuclear Proteins/chemistry , RNA Splice Sites , Ribonucleoproteins/chemistry , Schizosaccharomyces/physiology , Zinc Fingers/physiology , Amino Acid Motifs , Binding Sites , DNA Mutational Analysis , Protein Binding , Protein Structure, Quaternary , Protein Structure, Tertiary , Schizosaccharomyces/chemistry , Splicing Factor U2AF
7.
Biophys J ; 121(14): 2767-2780, 2022 07 19.
Article in English | MEDLINE | ID: mdl-35689380

ABSTRACT

Hemoglobins M (Hbs M) are human hemoglobin variants in which either the α or ß subunit contains a ferric heme in the α2ß2 tetramer. Though the ferric subunit cannot bind O2, it regulates O2 affinity of its counterpart ferrous subunit. We have investigated resonance Raman spectra of two Hbs, M Iwate (α87His → tyrosine [Tyr]) and M Boston (α58His → Tyr), having tyrosine as a heme axial ligand at proximal and distal positions, respectively, that exhibit unassigned resonance Raman bands arising from ferric (not ferrous) hemes at 899 and 876 cm-1. Our quantum chemical calculations using density functional theory on Fe-porphyrin models with p-cresol and/or 4-methylimidazole showed that the unassigned bands correspond to the breathing-like modes of Fe3+-bound Tyr and are sensitive to the Fe-O-C(Tyr) angle. Based on the frequencies of the Raman bands, the Fe-O-C(Tyr) angles of Hbs M Iwate and M Boston were predicted to be 153.5° and 129.2°, respectively. Consistent with this prediction, x-ray crystallographic analysis showed that the Fe-O-C(Tyr) angles of Hbs M Iwate and M Boston in the T quaternary structure were 153.6° and 134.6°, respectively. It also showed a similar Fe-O bond length (1.96 and 1.97 Å) and different tilting angles.


Subject(s)
Hemoglobin M , Crystallography , Density Functional Theory , Heme/chemistry , Hemoglobin M/chemistry , Hemoglobin M/metabolism , Humans , Spectrum Analysis, Raman , Tyrosine/chemistry , Vibration
8.
Biochem Biophys Res Commun ; 635: 277-282, 2022 12 20.
Article in English | MEDLINE | ID: mdl-36308907

ABSTRACT

X-ray fluorescence holography (XFH) is a relatively new technique capable of providing unique three-dimensional structural information around specific atoms that act as a light source in crystalline samples. So far, XFH has typically been applied to inorganic materials such as dopants in metals and semiconductors. Here, we investigate the possibility of using XFH to visualize the metal active site in sperm whale myoglobin (Mb), a monomeric oxygen storage heme protein. We demonstrate that the atomic images reconstructed from the hologram data of crystals of carbonmonoxy myoglobin (MbCO) are moderately consistent with the crystal structure, which is also determined in this study by X-ray crystallography in the near-atomic resolution, as well as simulation results. These results open up a new avenue for the application of XFH to local atomic and electronic structure imaging of metal-sites in biomolecules.


Subject(s)
Holography , Myoglobin , Myoglobin/chemistry , X-Rays , Holography/methods , Crystallography, X-Ray , Heme/chemistry , Metals , Protein Conformation
9.
J Virol ; 95(24): e0093821, 2021 11 23.
Article in English | MEDLINE | ID: mdl-34613794

ABSTRACT

Sodium taurocholate cotransporting polypeptide (NTCP) is a receptor that is essential for hepatitis B virus (HBV) entry into the host cell. A number of HBV entry inhibitors targeting NTCP have been reported to date; these inhibitors have facilitated a mechanistic analysis of the viral entry process. However, the mechanism of HBV internalization into host cells after interaction of virus with NTCP remains largely unknown. Recently, we reported that troglitazone, a thiazolidinedione derivative, specifically inhibits both HBV internalization and NTCP oligomerization, resulting in inhibition of HBV infection. Here, using troglitazone as a chemical probe to investigate entry process, the contribution of NTCP oligomerization to HBV internalization was evaluated. Using surface plasmon resonance and transporter kinetics, we found that troglitazone directly interacts with NTCP and noncompetitively interferes with NTCP-mediated bile acid uptake, suggesting that troglitazone allosterically binds to NTCP, rather than to the bile acid-binding pocket. Additionally, alanine scanning mutagenesis showed that a mutation at phenylalanine 274 of NTCP (F274A) caused a loss of HBV susceptibility and disrupted both the oligomerization of NTCP and HBV internalization without affecting viral attachment to the cell surface. An inhibitor of the interaction between NTCP and epidermal growth factor receptor (EGFR), another host cofactor essential for HBV internalization, impeded NTCP oligomerization. Meanwhile, coimmunoprecipitation analysis revealed that neither troglitazone nor the F274A mutation in NTCP affects the NTCP-EGFR interaction. These findings suggest that NTCP oligomerization is initiated downstream of the NTCP-EGFR interaction and then triggers HBV internalization. This study provides significant insight into the HBV entry mechanisms. IMPORTANCE Hepatitis B virus (HBV) infection is mediated by a specific interaction with sodium taurocholate cotransporting polypeptide (NTCP), a viral entry receptor. Although the virus-receptor interactions are believed to trigger viral internalization into host cells, the exact molecular mechanisms of HBV internalization are not understood. In this study, we revealed the mode of action whereby troglitazone, a specific inhibitor of HBV internalization, impedes NTCP oligomerization and identified NTCP phenylalanine 274 as a residue essential for this oligomerization. We further analyzed the association between NTCP oligomerization and HBV internalization, a process that is mediated by epidermal growth factor receptor (EGFR), another essential host cofactor for HBV internalization. Our study provides critical information on the mechanism of HBV entry and suggests that oligomerization of the viral receptor serves as an attractive target for drug discovery.


Subject(s)
Hepatitis B virus/physiology , Organic Anion Transporters, Sodium-Dependent/metabolism , Protein Multimerization , Receptors, Virus/metabolism , Symporters/metabolism , Virus Internalization/drug effects , Biological Transport , ErbB Receptors/genetics , ErbB Receptors/metabolism , Hep G2 Cells , Hepatocytes/drug effects , Hepatocytes/metabolism , Hepatocytes/virology , Humans , Organic Anion Transporters, Sodium-Dependent/genetics , Symporters/genetics , Troglitazone/pharmacology , Virus Attachment/drug effects
10.
Proc Natl Acad Sci U S A ; 116(17): 8487-8492, 2019 04 23.
Article in English | MEDLINE | ID: mdl-30952782

ABSTRACT

Sodium taurocholate cotransporting polypeptide (NTCP) is a host cell receptor required for hepatitis B virus (HBV) entry. However, the susceptibility of NTCP-expressing cells to HBV is diverse depending on the culture condition. Stimulation with epidermal growth factor (EGF) was found to potentiate cell susceptibility to HBV infection. Here, we show that EGF receptor (EGFR) plays a critical role in HBV virion internalization. In EGFR-knockdown cells, HBV or its preS1-specific fluorescence peptide attached to the cell surface, but its internalization was attenuated. PreS1 internalization and HBV infection could be rescued by complementation with functional EGFR. Interestingly, the HBV/preS1-NTCP complex at the cell surface was internalized concomitant with the endocytotic relocalization of EGFR. Molecular interaction between NTCP and EGFR was documented by immunoprecipitation assay. Upon dissociation from functional EGFR, NTCP no longer functioned to support viral infection, as demonstrated by either (i) the introduction of NTCP point mutation that disrupted its interaction with EGFR, (ii) the detrimental effect of decoy peptide interrupting the NTCP-EGFR interaction, or (iii) the pharmacological inactivation of EGFR. Together, these data support the crucial role of EGFR in mediating HBV-NTCP internalization into susceptible cells. EGFR thus provides a yet unidentified missing link from the cell-surface HBV-NTCP attachment to the viral invasion beyond the host cell membrane.


Subject(s)
Hepatitis B virus , Organic Anion Transporters, Sodium-Dependent , Symporters , Virus Internalization , ErbB Receptors/genetics , ErbB Receptors/metabolism , Hep G2 Cells , Hepatitis B virus/pathogenicity , Hepatitis B virus/physiology , Host-Pathogen Interactions/genetics , Host-Pathogen Interactions/physiology , Humans , Organic Anion Transporters, Sodium-Dependent/genetics , Organic Anion Transporters, Sodium-Dependent/metabolism , Symporters/genetics , Symporters/metabolism
11.
Molecules ; 27(7)2022 Apr 02.
Article in English | MEDLINE | ID: mdl-35408716

ABSTRACT

Phospholipase is an enzyme that hydrolyzes various phospholipid substrates at specific ester bonds and plays important roles such as membrane remodeling, as digestive enzymes, and the regulation of cellular mechanism. Phospholipase proteins are divided into following the four major groups according to the ester bonds they cleave off: phospholipase A1 (PLA1), phospholipase A2 (PLA2), phospholipase C (PLC), and phospholipase D (PLD). Among the four phospholipase groups, PLA1 has been less studied than the other phospholipases. Here, we report the first molecular structures of plant PLA1s: AtDSEL and CaPLA1 derived from Arabidopsis thaliana and Capsicum annuum, respectively. AtDSEL and CaPLA1 are novel PLA1s in that they form homodimers since PLAs are generally in the form of a monomer. The dimerization domain at the C-terminal of the AtDSEL and CaPLA1 makes hydrophobic interactions between each monomer, respectively. The C-terminal domain is also present in PLA1s of other plants, but not in PLAs of mammals and fungi. An activity assay of AtDSEL toward various lipid substrates demonstrates that AtDSEL is specialized for the cleavage of sn-1 acyl chains. This report reveals a new domain that exists only in plant PLA1s and suggests that the domain is essential for homodimerization.


Subject(s)
Arabidopsis , Phospholipases A1 , Plant Proteins , Arabidopsis/enzymology , Capsicum/enzymology , Dimerization , Esters , Phospholipases A1/chemistry , Plant Proteins/chemistry
12.
J Biol Chem ; 295(3): 800-807, 2020 01 17.
Article in English | MEDLINE | ID: mdl-31836663

ABSTRACT

Sodium taurocholate cotransporting polypeptide (NTCP) is expressed at the surface of human hepatocytes and functions as an entry receptor of hepatitis B virus (HBV). Recently, we have reported that epidermal growth factor receptor (EGFR) is involved in NTCP-mediated viral internalization during the cell entry process. Here, we analyzed which function of EGFR is essential for mediating HBV internalization. In contrast to the reported crucial function of EGFR-downstream signaling for the entry of hepatitis C virus (HCV), blockade of EGFR-downstream signaling proteins, including mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase (PI3K), and signal transducer and activator of transcription (STAT), had no or only minor effects on HBV infection. Instead, deficiency of EGFR endocytosis resulting from either a deleterious mutation in EGFR or genetic knockdown of endocytosis adaptor molecules abrogated internalization of HBV via NTCP and prevented viral infection. EGFR activation triggered a time-dependent relocalization of HBV preS1 to the early and late endosomes and to lysosomes in concert with EGFR transport. Suppression of EGFR ubiquitination by site-directed mutagenesis or by knocking down two EGFR-sorting molecules, signal-transducing adaptor molecule (STAM) and lysosomal protein transmembrane 4ß (LAPTM4B), suggested that EGFR transport to the late endosome is critical for efficient HBV infection. Cumulatively, these results support the idea that the EGFR endocytosis/sorting machinery drives the translocation of NTCP-bound HBV from the cell surface to the endosomal network, which eventually enables productive viral infection.


Subject(s)
Endocytosis/genetics , Endosomes/genetics , ErbB Receptors/genetics , Hepatitis B/genetics , Adaptor Proteins, Signal Transducing/chemistry , Adaptor Proteins, Signal Transducing/genetics , Endosomal Sorting Complexes Required for Transport/chemistry , Endosomal Sorting Complexes Required for Transport/genetics , Endosomes/chemistry , ErbB Receptors/chemistry , Hep G2 Cells , Hepacivirus/chemistry , Hepacivirus/genetics , Hepacivirus/pathogenicity , Hepatitis B/metabolism , Hepatitis B/virology , Hepatitis B virus/chemistry , Hepatitis B virus/genetics , Hepatitis B virus/pathogenicity , Hepatocytes/metabolism , Hepatocytes/virology , Humans , MAP Kinase Kinase 1/genetics , Membrane Proteins/chemistry , Membrane Proteins/genetics , Oncogene Proteins/chemistry , Oncogene Proteins/genetics , Organic Anion Transporters, Sodium-Dependent , Phosphatidylinositol 3-Kinases/genetics , Phosphoproteins/chemistry , Phosphoproteins/genetics , STAT Transcription Factors/genetics , Symporters , Viral Envelope Proteins/chemistry , Viral Envelope Proteins/genetics , Virus Internalization
13.
Biochem Biophys Res Commun ; 575: 90-95, 2021 10 20.
Article in English | MEDLINE | ID: mdl-34461441

ABSTRACT

tRNATyr of Nanoarchaeum equitans has a remarkable feature with an extra guanosine residue at the 5'-terminus. However, the N. equitans tRNATyr mutant without extra guanosine at the 5'-end was tyrosylated by tyrosyl-tRNA synthase (TyrRS). We solved the crystal structure of N. equitans TyrRS at 2.80 Å resolution. By comparing the present solved structure with the complex structures TyrRS with tRNATyr of Thermus thermophilus and Methanocaldococcus jannaschii, an arginine substitution mutant of N. equitans TyrRS at Ile200 (I200R), which is the putative closest candidate to the 5'-phosphate of C1 of N. equitans tRNATyr, was prepared. The I200R mutant tyrosylated not only wild-type tRNATyr but also the tRNA without the G-1 residue. Further tyrosylation analysis revealed that the second base of the anticodon (U35), discriminator base (A73), and C1:G72 base pair are strong recognition sites.


Subject(s)
Archaeal Proteins/chemistry , Crystallography, X-Ray/methods , Guanosine/chemistry , Nanoarchaeota/enzymology , RNA, Transfer, Tyr/chemistry , Tyrosine-tRNA Ligase/chemistry , Aminoacylation , Archaeal Proteins/genetics , Archaeal Proteins/metabolism , Models, Molecular , Protein Structural Elements , RNA, Transfer, Tyr/genetics , RNA, Transfer, Tyr/metabolism , Tyrosine-tRNA Ligase/genetics , Tyrosine-tRNA Ligase/metabolism
14.
Adv Exp Med Biol ; 1293: 129-139, 2021.
Article in English | MEDLINE | ID: mdl-33398810

ABSTRACT

Photoactivated adenylyl cyclase (PAC) was first discovered to be a sensor for photoavoidance in the flagellate Euglena gracilis. PAC is a flavoprotein that catalyzes the production of cAMP upon illumination with blue light, which enables us to optogenetically manipulate intracellular cAMP levels in various biological systems. Recent progress in genome sequencing has revealed several related proteins in bacteria and ameboflagellates. Among them, the PACs from sulfur bacterium Beggiatoa sp. and cyanobacterium Oscillatoria acuminata have been well characterized, including their crystalline structure. Although there have not been many reported optogenetic applications of PACs so far, they have the potential to be used in various fields within bioscience.


Subject(s)
Adenylyl Cyclases/metabolism , Adenylyl Cyclases/radiation effects , Light , Adenylyl Cyclases/genetics , Flavoproteins/genetics , Flavoproteins/metabolism , Optogenetics , Oscillatoria/genetics , Oscillatoria/metabolism
15.
J Biol Chem ; 294(3): 794-804, 2019 01 18.
Article in English | MEDLINE | ID: mdl-30455349

ABSTRACT

Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate because of a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 Å, and compared this structure with a cryogenic ClR structure obtained with synchrotron X-ray crystallography. The XFEL-derived ClR structure revealed that the all-trans retinal (ATR) region and positions of two coordinated chloride ions slightly differed from those of the synchrotron-derived structure. Moreover, the XFEL structure enabled identification of one additional water molecule forming a hydrogen bond network with a chloride ion. Analysis of the channel cavity and a difference distance matrix plot (DDMP) clearly revealed additional structural differences. B-factor information obtained from the non-cryogenic structure supported a motility change on the residual main and side chains as well as of chloride and water molecules because of temperature effects. Our results indicate that non-cryogenic structures and time-resolved XFEL experiments could contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.


Subject(s)
Actinomycetales/chemistry , Chloride Channels/chemistry , Rhodopsins, Microbial/chemistry , Crystallography, X-Ray , Protein Domains
16.
Proc Natl Acad Sci U S A ; 114(32): 8562-8567, 2017 08 08.
Article in English | MEDLINE | ID: mdl-28739908

ABSTRACT

The photoactivated adenylate cyclase (PAC) from the photosynthetic cyanobacterium Oscillatoria acuminata (OaPAC) detects light through a flavin chromophore within the N-terminal BLUF domain. BLUF domains have been found in a number of different light-activated proteins, but with different relative orientations. The two BLUF domains of OaPAC are found in close contact with each other, forming a coiled coil at their interface. Crystallization does not impede the activity switching of the enzyme, but flash cooling the crystals to cryogenic temperatures prevents the signature spectral changes that occur on photoactivation/deactivation. High-resolution crystallographic analysis of OaPAC in the fully activated state has been achieved by cryocooling the crystals immediately after light exposure. Comparison of the isomorphous light- and dark-state structures shows that the active site undergoes minimal changes, yet enzyme activity may increase up to 50-fold, depending on conditions. The OaPAC models will assist the development of simple, direct means to raise the cyclic AMP levels of living cells by light, and other tools for optogenetics.


Subject(s)
Adenylyl Cyclases/metabolism , Adenylyl Cyclases/physiology , Adenylyl Cyclases/genetics , Allosteric Site , Bacterial Proteins/metabolism , Catalytic Domain , Cell Line , Crystallography, X-Ray , Cyanobacteria/metabolism , Cyclic AMP/metabolism , Flavins/metabolism , Humans , Light , Optogenetics/methods , Oscillatoria/metabolism , Protein Domains , Protein Structure, Tertiary
17.
Biochem Biophys Res Commun ; 511(2): 228-233, 2019 04 02.
Article in English | MEDLINE | ID: mdl-30771900

ABSTRACT

This study reports the X-ray crystallographic structure of the glycyl-tRNA synthetase (GlyRS) of Nanoarchaeum equitans - a hyperthermophilic archaeal species. This is the first archaeal GlyRS crystal structure elucidated. The GlyRS comprises an N-terminal catalytic domain and a C-terminal anticodon-binding domain with a long ß-sheet inserted between these domains. An unmodified transcript of the wild-type N. equitans tRNAGly was successfully glycylated using GlyRS. Substitution of the discriminator base A73 of tRNAGly with any other nucleotide caused a significant decrease in glycylation activity. Mutational analysis of the second base-pair C2G71 of the acceptor stem of tRNAGly elucidated the importance of the base-pair, especially G71, as an identity element for recognition by GlyRS. Glycylation assays using tRNAGly G71 substitution mutants and a GlyRS mutant where Arg223 is mutated to alanine strengthen the possibility that the carbonyl oxygen at position 6 of G71 would hydrogen-bond with the guanidine nitrogen of Arg223 in N. equitans GlyRS.


Subject(s)
Archaeal Proteins/chemistry , Glycine-tRNA Ligase/chemistry , Nanoarchaeota/enzymology , Amino Acid Sequence , Archaeal Proteins/metabolism , Crystallography, X-Ray , Glycine-tRNA Ligase/metabolism , Models, Molecular , Nanoarchaeota/chemistry , Nanoarchaeota/metabolism , Protein Conformation , RNA, Transfer/chemistry , RNA, Transfer/metabolism , Sequence Alignment
18.
Arterioscler Thromb Vasc Biol ; 38(4): 744-756, 2018 04.
Article in English | MEDLINE | ID: mdl-29437575

ABSTRACT

OBJECTIVE: Inflammation provoked by the imbalance of fatty acid composition, such as excess saturated fatty acids (SFAs), is implicated in the development of metabolic diseases. Recent investigations suggest the possible role of the NLRP3 (nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain containing 3) inflammasome, which regulates IL-1ß (interleukin 1ß) release and leads to inflammation, in this process. Therefore, we investigated the underlying mechanism by which SFAs trigger NLRP3 inflammasome activation. APPROACH AND RESULTS: The treatment with SFAs, such as palmitic acid and stearic acid, promoted IL-1ß release in murine primary macrophages while treatment with oleic acid inhibited SFA-induced IL-1ß release in a dose-dependent manner. Analyses using polarized light microscopy revealed that intracellular crystallization was provoked in SFA-treated macrophages. As well as IL-1ß release, the intracellular crystallization and lysosomal dysfunction were inhibited in the presence of oleic acid. These results suggest that SFAs activate NLRP3 inflammasome through intracellular crystallization. Indeed, SFA-derived crystals activated NLRP3 inflammasome and subsequent IL-1ß release via lysosomal dysfunction. Excess SFAs also induced crystallization and IL-1ß release in vivo. Furthermore, SFA-derived crystals provoked acute inflammation, which was impaired in IL-1ß-deficient mice. CONCLUSIONS: These findings demonstrate that excess SFAs cause intracellular crystallization and subsequent lysosomal dysfunction, leading to the activation of the NLRP3 inflammasome, and provide novel insights into the pathogenesis of metabolic diseases.


Subject(s)
Fatty Acids/toxicity , Inflammasomes/agonists , Inflammation/chemically induced , Macrophage Activation/drug effects , Macrophages, Peritoneal/drug effects , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , Acetyltransferases/genetics , Acetyltransferases/metabolism , Animals , Cells, Cultured , Crystallization , Fatty Acid Elongases , Fatty Acids/metabolism , Inflammasomes/metabolism , Inflammation/genetics , Inflammation/metabolism , Inflammation/prevention & control , Interleukin-1beta/genetics , Interleukin-1beta/metabolism , Lysosomes/drug effects , Lysosomes/metabolism , Lysosomes/pathology , Macrophages, Peritoneal/metabolism , Macrophages, Peritoneal/pathology , Mice, Inbred C57BL , Mice, Knockout , NLR Family, Pyrin Domain-Containing 3 Protein/deficiency , NLR Family, Pyrin Domain-Containing 3 Protein/genetics , Signal Transduction/drug effects
19.
Proc Natl Acad Sci U S A ; 113(24): 6659-64, 2016 06 14.
Article in English | MEDLINE | ID: mdl-27247413

ABSTRACT

Cyclic-AMP is one of the most important second messengers, regulating many crucial cellular events in both prokaryotes and eukaryotes, and precise spatial and temporal control of cAMP levels by light shows great promise as a simple means of manipulating and studying numerous cell pathways and processes. The photoactivated adenylate cyclase (PAC) from the photosynthetic cyanobacterium Oscillatoria acuminata (OaPAC) is a small homodimer eminently suitable for this task, requiring only a simple flavin chromophore within a blue light using flavin (BLUF) domain. These domains, one of the most studied types of biological photoreceptor, respond to blue light and either regulate the activity of an attached enzyme domain or change its affinity for a repressor protein. BLUF domains were discovered through studies of photo-induced movements of Euglena gracilis, a unicellular flagellate, and gene expression in the purple bacterium Rhodobacter sphaeroides, but the precise details of light activation remain unknown. Here, we describe crystal structures and the light regulation mechanism of the previously undescribed OaPAC, showing a central coiled coil transmits changes from the light-sensing domains to the active sites with minimal structural rearrangement. Site-directed mutants show residues essential for signal transduction over 45 Å across the protein. The use of the protein in living human cells is demonstrated with cAMP-dependent luciferase, showing a rapid and stable response to light over many hours and activation cycles. The structures determined in this study will assist future efforts to create artificial light-regulated control modules as part of a general optogenetic toolkit.


Subject(s)
Adenylyl Cyclases/chemistry , Bacterial Proteins/chemistry , Cyclic AMP/chemistry , Oscillatoria/enzymology , Adenylyl Cyclases/genetics , Adenylyl Cyclases/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Cyclic AMP/genetics , Cyclic AMP/metabolism , Enzyme Activation/genetics , Enzyme Activation/radiation effects , HEK293 Cells , Humans , Light , Oscillatoria/genetics , Protein Domains , Second Messenger Systems/genetics , Second Messenger Systems/radiation effects , Structure-Activity Relationship
20.
J Biol Chem ; 292(44): 18258-18269, 2017 11 03.
Article in English | MEDLINE | ID: mdl-28931607

ABSTRACT

Although X-ray crystallography is the most commonly used technique for studying the molecular structure of proteins, it is not generally able to monitor the dynamic changes or global domain motions that often underlie allostery. These motions often prevent crystal growth or reduce crystal order. We have recently discovered a crystal form of human hemoglobin that contains three protein molecules allowed to express a full range of quaternary structures, whereas maintaining strong X-ray diffraction. Here we use this crystal form to investigate the effects of two allosteric effectors, phosphate and bezafibrate, by tracking the structures and functions of the three hemoglobin molecules following the addition of each effector. The X-ray analysis shows that the addition of either phosphate or bezafibrate not only induces conformational changes in a direction from a relaxed-state to a tense-state, but also within relaxed-state populations. The microspectrophotometric O2 equilibrium measurements on the crystals demonstrate that the binding of each effector energetically stabilizes the lowest affinity conformer more strongly than the intermediate affinity one, thereby reducing the O2 affinity of tense-state populations, and that the addition of bezafibrate causes an ∼5-fold decrease in the O2 affinity of relaxed-state populations. These results show that the allosteric pathway of hemoglobin involves shifts of populations rather than a unidirectional conversion of one quaternary structure to another, and that minor conformers of hemoglobin may have a disproportionate effect on the overall O2 affinity.


Subject(s)
Models, Molecular , Oxygen/metabolism , alpha-Globins/metabolism , beta-Globins/metabolism , Algorithms , Allosteric Regulation , Bezafibrate/chemistry , Bezafibrate/metabolism , Crystallography, X-Ray , Humans , Indicators and Reagents/chemistry , Indicators and Reagents/metabolism , Kinetics , Ligands , Oxidation-Reduction , Oxygen/chemistry , Phosphates/chemistry , Phosphates/metabolism , Protein Conformation , Protein Interaction Mapping , Protein Multimerization , Protein Refolding , Protein Stability , Protein Structure, Quaternary , alpha-Globins/chemistry , beta-Globins/chemistry
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