scholarly journals Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX

IUCrJ ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Dongqing Pan ◽  
Ryo Oyama ◽  
Tomomi Sato ◽  
Takanori Nakane ◽  
Ryo Mizunuma ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Abc Transporters ◽  
Hydroxypropyl Methylcellulose ◽  
Multi Drug Resistance ◽  
Cubic Phase ◽  
Cyanidioschyzon Merolae ◽  
Sufficient Information ◽  
Type I ◽  
Type Ii ◽  
Exit Region

CmABCB1 is a Cyanidioschyzon merolae homolog of human ABCB1, a well known ATP-binding cassette (ABC) transporter responsible for multi-drug resistance in various cancers. Three-dimensional structures of ABCB1 homologs have revealed the snapshots of inward- and outward-facing states of the transporters in action. However, sufficient information to establish the sequential movements of the open–close cycles of the alternating-access model is still lacking. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has proven its worth in determining novel structures and recording sequential conformational changes of proteins at room temperature, especially for medically important membrane proteins, but it has never been applied to ABC transporters. In this study, 7.7 monoacylglycerol with cholesterol as the host lipid was used and obtained well diffracting microcrystals of the 130 kDa CmABCB1 dimer. Successful SFX experiments were performed by adjusting the viscosity of the crystal suspension of the sponge phase with hydroxypropyl methylcellulose and using the high-viscosity sample injector for data collection at the SACLA beamline. An outward-facing structure of CmABCB1 at a maximum resolution of 2.22 Å is reported, determined by SFX experiments with crystals formed in the lipidic cubic phase (LCP-SFX), which has never been applied to ABC transporters. In the type I crystal, CmABCB1 dimers interact with adjacent molecules via not only the nucleotide-binding domains but also the transmembrane domains (TMDs); such an interaction was not observed in the previous type II crystal. Although most parts of the structure are similar to those in the previous type II structure, the substrate-exit region of the TMD adopts a different configuration in the type I structure. This difference between the two types of structures reflects the flexibility of the substrate-exit region of CmABCB1, which might be essential for the smooth release of various substrates from the transporter.

scholarly journals EPR Spectroscopy of MolB2C2-A Reveals Mechanism of Transport for a Bacterial Type II Molybdate Importer

2013 ◽  
Vol 288 (29) ◽  
pp. 21228-21235 ◽  
Author(s):  
Austin J. Rice ◽  
Frances J. D. Alvarez ◽  
Kathryn M. Schultz ◽  
Candice S. Klug ◽  
Amy L. Davidson ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Abc Transporters ◽  
Epr Spectroscopy ◽  
Vitamin B ◽  
Type I ◽  
Type Ii ◽  
Bacterial Type ◽  
Uptake Of Nutrients ◽  
Structure And Activity ◽  
Alternating Access

In bacteria, ATP-binding cassette (ABC) transporters are vital for the uptake of nutrients and cofactors. Based on differences in structure and activity, ABC importers are divided into two types. Type I transporters have been well studied and employ a tightly regulated alternating access mechanism. Less is known about Type II importers, but much of what we do know has been observed in studies of the vitamin B12 importer BtuC2D2. MolB2C2 (formally known as HI1470/71) is also a Type II importer, but its substrate, molybdate, is ∼10-fold smaller than vitamin B12. To understand mechanistic differences among Type II importers, we focused our studies on MolBC, for which alternative conformations may be required to transport its relatively small substrate. To investigate the mechanism of MolBC, we employed disulfide cross-linking and EPR spectroscopy. From these studies, we found that nucleotide binding is coupled to a conformational shift at the periplasmic gate. Unlike the larger conformational changes in BtuCD-F, this shift in MolBC-A is akin to unlocking a swinging door: allowing just enough space for molybdate to slip into the cell. The lower cytoplasmic gate, identified in BtuCD-F as “gate I,” remains open throughout the MolBC-A mechanism, and cytoplasmic gate II closes in the presence of nucleotide. Combining our results, we propose a peristaltic mechanism for MolBC-A, which gives new insight in the transport of small substrates by a Type II importer.

scholarly journals New Aspects of Neotropical Polycystic (Echinococcus vogeli) and Unicystic (Echinococcus oligarthrus) Echinococcosis

2008 ◽  
Vol 21 (2) ◽  
pp. 380-401 ◽  
Author(s):  
Antonio D'Alessandro ◽  
Robert L. Rausch
Keyword(s):  
South America ◽  
Abdominal Cavity ◽  
Geographic Origin ◽  
Morphological Characteristics ◽  
Total Mortality ◽  
Medical Problem ◽  
Sufficient Information ◽  
Type I ◽  
Type Ii ◽  
Characteristic Type

SUMMARY Of the four species of the genus Echinococcus (Cestoda) distinguished by biological and morphological characteristics, two species, E. vogeli and E. oligarthrus, occur widely in the Neotropics. Approximately 200 cases of polycystic echinococcosis (PE) have been recorded from 12 countries in South America. Following early proliferation of E. vogeli in the human host, typically in the liver, the metacestode usually spreads in the peritoneal and pleural cavities, and numerous organs may be invaded. The clinical characteristics of PE in 81 patients with sufficient information are reviewed. Type I disease consists of polycysts in the liver and abdominal cavity (37% of the patients had this characteristic); type II is similar to type I but also includes hepatic insufficiency (26%); type III consists of cysts in liver and chest (14%); type IV consists of cysts only in the mesenteries (16%); and type V consists of cysts calcified in liver and lung (4%). The percentage of patients with polycysts in the liver was 81%, and the percentage of patients with polycysts in the chest was 14%. PE is most ready diagnosed by geographic origin of the patient and by means of ultrasound or computerized tomography scanning showing cysts and calcifications. The highest mortality was for patients with type II disease, due to hepatic failure and its complications. There were five patients who died due to surgical accidents, whereas 35 cases had uncomplicated surgery. Twenty-three patients died of PE, making the total mortality 29% (23 of 78 cases). None of the 13 patients treated only with albendazole, the most efficacious treatment, was completely cured. PE represents a severe medical problem in South America. A reevaluation of the characteristics of the metacestode of E. oligarthrus indicated that it is unicystic. Only three human cases are known (two with infection in the orbit and one with infection in the heart). The metacestode of E. oligarthrus, in contrast with that of E. vogeli, consists of a spherical, fluid-filled vesicle that enlarges concentrically and is not known to undergo exogenous proliferation.

scholarly journals ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bárbara Abreu ◽  
Carlos Cruz ◽  
A. Sofia F. Oliveira ◽  
Cláudio M. Soares
Keyword(s):  
Conformational Changes ◽  
Abc Transporters ◽  
Atp Hydrolysis ◽  
Binding Pocket ◽  
Potential Of Mean Force ◽  
Type I ◽  
Concomitant Increase ◽  
Transport Cycle ◽  
Dynamics Simulations ◽  
Key Residues

AbstractATP binding cassette (ABC) transporters employ ATP hydrolysis to harness substrate translocation across membranes. The Escherichia coli MalFGK2E maltose importer is an example of a type I ABC importer and a model system for this class of ABC transporters. The MalFGK2E importer is responsible for the intake of malto-oligossacharides in E.coli. Despite being extensively studied, little is known about the effect of ATP hydrolysis and nucleotide exit on substrate transport. In this work, we studied this phenomenon using extensive molecular dynamics simulations (MD) along with potential of mean force calculations of maltose transport across the pore, in the pre-hydrolysis, post-hydrolysis and nucleotide-free states. We concluded that ATP hydrolysis and nucleotide exit trigger conformational changes that result in the decrease of energetic barriers to maltose translocation towards the cytoplasm, with a concomitant increase of the energy barrier in the periplasmic side of the pore, contributing for the irreversibility of the process. We also identified key residues that aid in positioning and orientation of maltose, as well as a novel binding pocket for maltose in MalG. Additionally, ATP hydrolysis leads to conformations similar to the nucleotide-free state. This study shows the contribution of ATP hydrolysis and nucleotide exit in the transport cycle, shedding light on ABC type I importer mechanisms.

scholarly journals Crystal structure of the ferredoxin reductase component of carbazole 1,9a-dioxygenase from Janthinobacterium sp. J3

2021 ◽  
Vol 77 (7) ◽  
Author(s):  
Yuji Ashikawa ◽  
Zui Fujimoto ◽  
Kengo Inoue ◽  
Hisakazu Yamane ◽  
Hideaki Nojiri
Keyword(s):  
Crystal Structure ◽  
Electron Transfer ◽  
Conformational Changes ◽  
Docking Simulation ◽  
Type I ◽  
Type Ii ◽  
Class Iii ◽  
Docking Simulations ◽  
Ferredoxin Reductase ◽  
C Terminus

Carbazole 1,9a-dioxygenase (CARDO), which consists of an oxygenase component and the electron-transport components ferredoxin (CARDO-F) and ferredoxin reductase (CARDO-R), is a Rieske nonheme iron oxygenase (RO). ROs are classified into five subclasses (IA, IB, IIA, IIB and III) based on their number of constituents and the nature of their redox centres. In this study, two types of crystal structure (type I and type II) were resolved of the class III CARDO-R from Janthinobacterium sp. J3 (CARDO-RJ3). Superimposition of the type I and type II structures revealed the absence of flavin adenine dinucleotide (FAD) in the type II structure along with significant conformational changes to the FAD-binding domain and the C-terminus, including movements to fill the space in which FAD had been located. Docking simulation of NADH into the FAD-bound form of CARDO-RJ3 suggested that shifts of the residues at the C-terminus caused the nicotinamide moiety to approach the N5 atom of FAD, which might facilitate electron transfer between the redox centres. Differences in domain arrangement were found compared with RO reductases from the ferredoxin–NADP reductase family, suggesting that these differences correspond to differences in the structures of their redox partners ferredoxin and terminal oxygenase. The results of docking simulations with the redox partner class III CARDO-F from Pseudomonas resinovorans CA10 suggested that complex formation suitable for efficient electron transfer is stabilized by electrostatic attraction and complementary shapes of the interacting regions.

scholarly journals Phonon Characterization, Structural and Optical Properties of Type-II CdSe/CdTe core/shell and Type-II/type-I CdSe/CdTe/ZnS core/shell/shell Quantum Dots

2020 ◽  
Vol 36 (3) ◽  
Author(s):  
Nguyen Xuan Ca ◽  
Nguyen Thi Hien
Keyword(s):  
Quantum Dots ◽  
Optical Properties ◽  
Excitation Power ◽  
Cubic Phase ◽  
Core Shell ◽  
Type I ◽  
Type Ii ◽  
X Ray Diffraction ◽  
Cdte Core ◽  
Observation Results

The CdSe, type-II CdSe/CdTe core/shell and type-II/type-I CdSe/CdTe/ZnS core/shell/shell  quantum dots (QDs) were successfully synthesized in a noncoordinating solvent. The phonon characterizations, optical properties and structures of the synthesized QDs were characterized by Raman scattering (RS) spectra, photoluminescence (PL) spectroscopy, PL-decay lifetime, absorption spectroscopy (Abs), and X-ray diffraction (XRD). The growth of QDs was monitored by using RS, which demonstrated the formation of correct of the core/shell and core/shell/shell structures. Observation results from XRD reveal that all QDs crystallize in the cubic phase with zinc-blende structure. The typical characteristics of spatially indirect recombination for type-II QDs were observed through Abs and PL spectroscopy. The ZnS shell significantly enhanced the PL quantum yeild (QY), the optical durability, the chemical stability and separating CdSe/CdTe QDs from the surroundings. The effect of excitation power on the PL properties of the CdSe core,  CdSe/CdTe and CdSe/CdTe/ZnS QDs has been investigated.

Heat-Etching with a Bullivant Type II Simple Freeze-Cleave Device

1970 ◽  
Vol 28 ◽  
pp. 106-107 ◽  
Author(s):  
Ronald S. Weinstein ◽  
N. Scott McNutt
Keyword(s):  
New Zealand ◽  
General Hospital ◽  
Massachusetts General Hospital ◽  
Type I ◽  
Type Ii ◽  
Collaborative Effort ◽  
Temperature And Pressure ◽  
The University

The Type I simple cold block device was described by Bullivant and Ames in 1966 and represented the product of the first successful effort to simplify the equipment required to do sophisticated freeze-cleave techniques. Bullivant, Weinstein and Someda described the Type II device which is a modification of the Type I device and was developed as a collaborative effort at the Massachusetts General Hospital and the University of Auckland, New Zealand. The modifications reduced specimen contamination and provided controlled specimen warming for heat-etching of fracture faces. We have now tested the Mass. General Hospital version of the Type II device (called the “Type II-MGH device”) on a wide variety of biological specimens and have established temperature and pressure curves for routine heat-etching with the device.

Labelling of non-A, non-B hepatitis infected chimpanzee hepatocytes with nuclease-gold conjugates

1984 ◽  
Vol 42 ◽  
pp. 250-251
Author(s):  
G. D. Gagne ◽  
M. F. Miller ◽  
D. A. Peterson
Keyword(s):  
Endoplasmic Reticulum ◽  
Experimental Infection ◽  
Uranyl Acetate ◽  
Type I ◽  
Cellular Injury ◽  
Type Ii ◽  
Tubular Structures ◽  
Type Iii ◽  
Type Iv ◽  
Infected Chimpanzee

Experimental infection of chimpanzees with non-A, non-B hepatitis (NANB) or with delta agent hepatitis results in the appearance of characteristic cytoplasmic alterations in the hepatocytes. These alterations include spongelike inclusions (Type I), attached convoluted membranes (Type II), tubular structures (Type III), and microtubular aggregates (Type IV) (Fig. 1). Type I, II and III structures are, by association, believed to be derived from endoplasmic reticulum and may be morphogenetically related. Type IV structures are generally observed free in the cytoplasm but sometimes in the vicinity of type III structures. It is not known whether these structures are somehow involved in the replication and/or assembly of the putative NANB virus or whether they are simply nonspecific responses to cellular injury. When treated with uranyl acetate, type I, II and III structures stain intensely as if they might contain nucleic acids. If these structures do correspond to intermediates in the replication of a virus, one might expect them to contain DNA or RNA and the present study was undertaken to explore this possibility.

Comparative surface and ultrastructural views of methylotrophic bacteria by TEM, STEM, SE, and freeze-etch electron microscopy.

1987 ◽  
Vol 45 ◽  
pp. 792-793
Author(s):  
T.A. Fassel ◽  
M.J. Schaller ◽  
M.E. Lidstrom ◽  
C.C. Remsen
Keyword(s):  
Cytoplasmic Membrane ◽  
Structural Features ◽  
Methylotrophic Bacteria ◽  
Type I ◽  
Type Ii ◽  
Membrane Complex ◽  
Oxidation Of Methane ◽  
Methane Oxidizing Bacteria ◽  
Wall Structures ◽  
Methylomonas Albus

Methylotrophic bacteria play an Important role in the environment in the oxidation of methane and methanol. Extensive intracytoplasmic membranes (ICM) have been associated with the oxidation processes in methylotrophs and chemolithotrophic bacteria. Classification on the basis of ICM arrangement distinguishes 2 types of methylotrophs. Bundles or vesicular stacks of ICM located away from the cytoplasmic membrane and extending into the cytoplasm are present in Type I methylotrophs. In Type II methylotrophs, the ICM form pairs of peripheral membranes located parallel to the cytoplasmic membrane. Complex cell wall structures of tightly packed cup-shaped subunits have been described in strains of marine and freshwater phototrophic sulfur bacteria and several strains of methane oxidizing bacteria. We examined the ultrastructure of the methylotrophs with particular view of the ICM and surface structural features, between representatives of the Type I Methylomonas albus (BG8), and Type II Methylosinus trichosporium (OB-36).

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