A urea channel from Bacillus cereus reveals a novel hexameric structure

2012 ◽  
Vol 445 (2) ◽  
pp. 157-166 ◽  
Author(s):  
Gerard H. M. Huysmans ◽  
Nathan Chan ◽  
Jocelyn M. Baldwin ◽  
Vincent L. G. Postis ◽  
Svetomir B. Tzokov ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Structure And Function ◽  
Size Exclusion ◽  
Fluorescent Labelling ◽  
Transmembrane Helices ◽  
Cryo Electron Microscopy ◽  
C Terminus ◽  
Exclusion Chromatography ◽  
Urea Channel ◽  
And Function

Urea is exploited as a nitrogen source by bacteria, and its breakdown products, ammonia and bicarbonate, are employed to counteract stomach acidity in pathogens such as Helicobacter pylori. Uptake in the latter is mediated by UreI, a UAC (urea amide channel) family member. In the present paper, we describe the structure and function of UACBc, a homologue from Bacillus cereus. The purified channel was found to be permeable not only to urea, but also to other small amides. CD and IR spectroscopy revealed a structure comprising mainly α-helices, oriented approximately perpendicular to the membrane. Consistent with this finding, site-directed fluorescent labelling indicated the presence of seven TM (transmembrane) helices, with a cytoplasmic C-terminus. In detergent, UACBc exists largely as a hexamer, as demonstrated by both cross-linking and size-exclusion chromatography. A 9 Å (1 Å=0.1 nm) resolution projection map obtained by cryo-electron microscopy of two-dimensional crystals shows that the six protomers are arranged in a planar hexameric ring. Each exhibits six density features attributable to TM helices, surrounding a putative central channel, while an additional helix is peripherally located. Bioinformatic analyses allowed individual TM regions to be tentatively assigned to the density features, with the resultant model enabling identification of residues likely to contribute to channel function.

Structure and Function Relationship of Murine Insulin-like Peptide 5 (INSL5): Free C-Terminus Is Essential for RXFP4 Receptor Binding and Activation

Biochemistry ◽  
2011 ◽  
Vol 50 (39) ◽  
pp. 8352-8361 ◽  
Author(s):  
Alessia Belgi ◽  
Mohammed A. Hossain ◽  
Fazel Shabanpoor ◽  
Linda Chan ◽  
Suode Zhang ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Structure And Function ◽  
C Terminus ◽  
Function Relationship ◽  
Structure And Function Relationship ◽  
And Function ◽  
Relationship Of

Role of the C-Terminus of the High-Conductance Calcium-Activated Potassium Channel in Channel Structure and Function

Biochemistry ◽  
2005 ◽  
Vol 44 (30) ◽  
pp. 10135-10144 ◽  
Author(s):  
William A. Schmalhofer ◽  
Manuel Sanchez ◽  
Ge Dai ◽  
Ashvin Dewan ◽  
Lorena Secades ◽  
...  
Keyword(s):  
Potassium Channel ◽  
Structure And Function ◽  
Channel Structure ◽  
C Terminus ◽  
And Function ◽  
Calcium Activated Potassium Channel ◽  
High Conductance

scholarly journals Molecular cloning and biochemical characterization of rabbit factor XI

2002 ◽  
Vol 367 (1) ◽  
pp. 49-56 ◽  
Author(s):  
Dipali SINHA ◽  
Mariola MARCINKIEWICZ ◽  
David GAILANI ◽  
Peter N. WALSH
Keyword(s):  
Human Factor ◽  
Biochemical Characterization ◽  
Protein A ◽  
Size Exclusion ◽  
Factor Xi ◽  
Sds Page ◽  
Exclusion Chromatography ◽  
Intracellular Process ◽  
And Function

Human factor XI, a plasma glycoprotein required for normal haemostasis, is a homodimer (160kDa) formed by a single interchain disulphide bond linking the Cys-321 of each Apple 4 domain. Bovine, porcine and murine factor XI are also disulphide-linked homodimers. Rabbit factor XI, however, is an 80kDa polypeptide on non-reducing SDS/PAGE, suggesting that rabbit factor XI exists and functions physiologically either as a monomer, as does prekallikrein, a structural homologue to factor XI, or as a non-covalent homodimer. We have investigated the structure and function of rabbit factor XI to gain insight into the relation between homodimeric structure and factor XI function. Characterization of the cDNA sequence of rabbit factor XI and its amino acid translation revealed that in the rabbit protein a His residue replaces the Cys-321 that forms the interchain disulphide linkage in human factor XI, explaining why rabbit factor XI is a monomer in non-reducing SDS/PAGE. On size-exclusion chromatography, however, purified plasma rabbit factor XI, like the human protein and unlike prekallikrein, eluted as a dimer, demonstrating that rabbit factor XI circulates as a non-covalent dimer. In functional assays rabbit factor XI and human factor XI behaved similarly. Both monomeric and dimeric factor XI were detected in extracts of cells expressing rabbit factor XI. We conclude that the failure of rabbit factor XI to form a covalent homodimer due to the replacement of Cys-321 with His does not impair its functional activity because it exists in plasma as a non-covalent homodimer and homodimerization is an intracellular process.

scholarly journals Mode of induction of platelet-derived extracellular vesicles is a critical determinant of their phenotype and function

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
P. M. Ferreira ◽  
E. Bozbas ◽  
S. D. Tannetta ◽  
N. Alroqaiba ◽  
R. Zhou ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Size Exclusion ◽  
Biological Functions ◽  
Critical Determinant ◽  
Agonist Stimulation ◽  
Exclusion Chromatography ◽  
Average Size ◽  
And Function ◽  
Free Plasma ◽  
Insight Into

Abstract Platelet-derived extracellular vesicles (PDEVs) are the most abundant amongst all types of EVs in the circulation. However, the mechanisms leading to PDEVs release, their role in coagulation and phenotypic composition are poorly understood. PDEVs from washed platelets were generated using different stimuli and were characterised using nanoparticle tracking analysis. Procoagulant properties were evaluated by fluorescence flow cytometry and calibrated automated thrombography. EVs from plasma were isolated and concentrated using a novel protocol involving a combination of size exclusion chromatography and differential centrifugation, which produces pure and concentrated EVs. Agonist stimulation enhanced PDEV release, but did not alter the average size of EVs compared to those produced by unstimulated platelets. Agonist stimulation led to lower negatively-charged phospholipid externalization in PDEVs, which was reflected in the lower procoagulant activity compared to those generated without agonist stimulation. Circulating EVs did not have externalized negatively-charged phospholipids. None of the 4 types of EVs presented tissue factor. The mechanism by which PDEV formation is induced is a critical determinant of its phenotype and function. Importantly, we have developed methods to obtain clean, concentrated and functional EVs derived from platelet-free plasma and washed platelets, which can be used to provide novel insight into their biological functions.

Abstract 15070: Micu1 Regulates Mitochondrial Cristae Structure and Function Independent of the Mitochondrial Calcium Uniporter Channel

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Dhanendra Tomar ◽  
Manfred Thomas ◽  
Joanne Garbincius ◽  
Devin Kolmetzky ◽  
Oniel Salik ◽  
...  
Keyword(s):  
Mitochondrial Membrane ◽  
Coiled Coil ◽  
Structure And Function ◽  
Membrane Dynamics ◽  
Size Exclusion ◽  
Null Mouse ◽  
Intermembrane Space ◽  
Inner Mitochondrial Membrane ◽  
Cytochrome C Release ◽  
And Function

Background: MICU1 is an EF-hand domain containing Ca 2+ -sensor regulating the mitochondrial Ca 2+ uniporter channel and mitochondrial Ca 2+ uptake. MICU1-null mouse and fly models display perinatal lethality with disorganized mitochondrial architecture. Interestingly, these phenotypes are distinct from other mtCU loss-of-function models ( MCU, MICU2, EMRE, MCUR1 ) and thus are likely not explained solely by changes in matrix Ca 2+ content. Using size-exclusion proteomics and co-immunofluorescence, we found that MICU1 localizes to mitochondrial complexes lacking MCU. These observations suggest that MICU1 may have additional cellular functions independent of the MCU. Methods: Biotin-based proximity labeling and proteomics, protein biochemistry, live-cell Ca 2+ imaging, electron microscopy, confocal and super-resolution imaging were utilized to identify and validate MICU1 novel functions. Results: The expression of a MICU1-BioID2 fusion protein in MCU +/+ and MCU -/- cells allowed the identification of the total vs. MCU-independent MICU1 interactome. LC-MS analysis of purified biotinylated proteins identified the mitochondrial contact site and cristae organizing system (MICOS) components Mitofilin (MIC60) and Coiled-coil-helix-coiled-coil helix domain containing 2 (CHCHD2) as MCU independent novel MICU1 interactors. We demonstrate that MICU1 is essential for proper organization of the MICOS complex and that MICU1 ablation results in altered cristae organization, mitochondrial ultrastructure, mitochondrial membrane dynamics, membrane potential, and cell death signaling. We hypothesize that MICU1 is a MICOS Ca 2+ - sensor since perturbing MICU1 is sufficient to modulate cytochrome c release independent of Ca 2+ uptake across the inner mitochondrial membrane. Conclusions: Here, we provide the first experimental evidence of an intermembrane space Ca 2+ - sensor regulating mitochondrial membrane dynamics, independent of changes in matrix Ca 2+ content. This study provides a novel paradigm to understand Ca 2+ -dependent regulation of mitochondrial structure and function and may help explain the mitochondrial remodeling reported to occur in numerous disease states.

scholarly journals The ribosome and its role in protein folding: looking through a magnifying glass

2017 ◽  
Vol 73 (6) ◽  
pp. 509-521 ◽  
Author(s):  
Abid Javed ◽  
John Christodoulou ◽  
Lisa D. Cabrita ◽  
Elena V. Orlova
Keyword(s):  
Protein Folding ◽  
Structural Biology ◽  
Polypeptide Chain ◽  
Structure And Function ◽  
Cellular Activity ◽  
Cryo Electron Microscopy ◽  
Nascent Chain ◽  
Exit Tunnel ◽  
Dynamics Simulations ◽  
And Function

Protein folding, a process that underpins cellular activity, begins co-translationally on the ribosome. During translation, a newly synthesized polypeptide chain enters the ribosomal exit tunnel and actively interacts with the ribosome elements – the r-proteins and rRNA that line the tunnel – prior to emerging into the cellular milieu. While understanding of the structure and function of the ribosome has advanced significantly, little is known about the process of folding of the emerging nascent chain (NC). Advances in cryo-electron microscopy are enabling visualization of NCs within the exit tunnel, allowing early glimpses of the interplay between the NC and the ribosome. Once it has emerged from the exit tunnel into the cytosol, the NC (still attached to its parent ribosome) can acquire a range of conformations, which can be characterized by NMR spectroscopy. Using experimental restraints within molecular-dynamics simulations, the ensemble of NC structures can be described. In order to delineate the process of co-translational protein folding, a hybrid structural biology approach is foreseeable, potentially offering a complete atomic description of protein folding as it occurs on the ribosome.

scholarly journals PsEst3, a new psychrophilic esterase from the Arctic bacterium Paenibacillus sp. R4: crystallization and X-ray crystallographic analysis

2018 ◽  
Vol 74 (6) ◽  
pp. 367-372
Author(s):  
Hyun Kim ◽  
Ae Kyung Park ◽  
Jun Hyuck Lee ◽  
Seung Chul Shin ◽  
Hyun Park ◽  
...  
Keyword(s):  
Expression System ◽  
Crystallographic Analysis ◽  
Size Exclusion ◽  
The Arctic ◽  
Diffusion Method ◽  
X Ray ◽  
Cell Parameters ◽  
Paenibacillus Sp ◽  
Exclusion Chromatography ◽  
And Function

Esterases are very useful biocatalysts in industry: they hydrolyze esters and split them into a carboxylic acid and an alcohol. The psychrophilic esterase PsEst3 was obtained from Paenibacillus sp. R4, which was isolated from the active layer of the permafrost in Council, Alaska. PsEst3 was successfully overexpressed using a psychrophilic chaperonin co-expression system and was purified by nickel-affinity and size-exclusion chromatography. Recombinant PsEst3 was crystallized at 290 K using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.1 Å resolution. The crystal was determined to belong to space group P4132 or P4332, with unit-cell parameters a = b = c = 145.33 Å. Further crystallographic analysis needs to be conducted to investigate the structure and function of this esterase.

scholarly journals Very Small Apolipoprotein A-I-containing Particles from Human Plasma: Isolation and Quantification by High-Performance Size-Exclusion Chromatography

2000 ◽  
Vol 46 (2) ◽  
pp. 207-223 ◽  
Author(s):  
M Nazeem Nanjee ◽  
Eliot A Brinton
Keyword(s):  
Human Plasma ◽  
Size Exclusion Chromatography ◽  
High Performance ◽  
Hdl Cholesterol ◽  
Preparative Method ◽  
Size Exclusion ◽  
Crossed Immunoelectrophoresis ◽  
Exclusion Chromatography ◽  
In Series ◽  
And Function

Abstract Background: Very small apolipoprotein (apo) A-I-containing lipoprotein (Sm LpA-I) particles with pre-β electrophoretic mobility may play key roles as “nascent” and/or “senescent” HDL; however, methods for their isolation are difficult and often semiquantitative. Methods: We developed a preparative method for separating Sm LpA-I particles from human plasma by high-performance size-exclusion chromatography (HP-SEC), using two gel permeation columns (Superdex 200 and Superdex 75) in series and measuring apo A-I content in column fractions in 30 subjects with HDL-cholesterol (HDL-C) concentrations of 0.4–3.83 mmol/L. Results: Three major sizes of apo A-I-containing particles were detected: an ∼15-nm diameter (∼700 kDa) species; a 7.5–12 nm (100–450 kDa) species; and a 5.8–6.3 nm species (40–60 kDa, Sm LpA-I particles), containing 0.2–3%, 80–96%, and 2–15% of plasma total apo A-I, respectively. Two subjects with severe HDL deficiency had increased relative apo A-I content in Sm LpA-I: 25% and 37%, respectively. The percentage of apo A-I in Sm LpA-I correlated positively with fasting plasma triglyceride concentrations (r = 0.581; P <0.0005) and inversely with total apo A-I (r = −0.551; P <0.0013) and HDL-C concentrations (r = −0.532; P <0.0017), although the latter two relationships were largely attributable to extremely hypoalphalipoproteinemic subjects. The percentage of apo A-I in Sm LpA-I correlated with that in pre-β-migrating species by crossed immunoelectrophoresis (r = 0.98; P <0.0001; n = 24) and with that in the d >1.21 kg/L fraction by ultracentrifugation (r = 0.86; P <0.001; n = 20). Sm LpA-I particles, on average, appear to contain two apo A-I and four phospholipid molecules but little or no apo A-II, triglyceride, or cholesterol. Conclusions: We present a new HP-SEC method for size separation of native HDL particles from plasma, including Sm Lp A-I, which may play important roles in the metabolism of HDL and in its contribution(s) to protection against atherosclerosis. This method provides a basis for further studies of the structure and function of Sm Lp A-I.

scholarly journals An Epithelial Ca2+-Sensor Protein is an Alternative to Calmodulin to Compose Functional KCNQ1 Channels

2015 ◽  
Vol 36 (5) ◽  
pp. 1847-1861 ◽  
Author(s):  
Atsushi Inanobe ◽  
Chizuru Tsuzuki ◽  
Yoshihisa Kurachi
Keyword(s):  
Fluorescent Protein ◽  
Size Exclusion ◽  
Cellular Functions ◽  
Kcnq Channels ◽  
C Terminus ◽  
Sensor Protein ◽  
Voltage Dependent ◽  
Exclusion Chromatography ◽  
Green Fluorescent ◽  
Sensor Proteins

Background/Aims: KCNQ channels transport K+ ions and participate in various cellular functions. The channels directly assemble with auxiliary proteins such as a ubiquitous Ca2+-sensor protein, calmodulin (CaM), to configure the physiological properties in a tissue-specific manner. Although many CaM-like Ca2+-sensor proteins have been identified in eukaryotes, how KCNQ channels selectively interact with CaM and how the homologues modulate the functionality of the channels remain unclear. Methods: We developed protocols to evaluate the interaction between the green fluorescent protein-tagged C-terminus of KCNQ1 (KCNQ1cL) and Ca2+-sensors by detecting its fluorescence in size exclusion chromatography and electrophoresed gels. The effects of Ca2+-sensor proteins on KCNQ1 activity was measured by two electrode voltage clamp technique of Xenopus oocytes. Results: When co-expressed CaM and KCNQ1cL, they assemble in a 4:4 stoichiometry, forming a hetero-octamer. Among nine CaM homologues tested, Calml3 was found to form a hetero-octamer with KCNQ1cL and to associate with the full-length KCNQ1 in a competitive manner with CaM. When co-expressed in oocytes, Calml3 rendered KCNQ1 channels resistant to the voltage-dependent depletion of phosphatidylinositol 4,5-bisphosphate by voltage-sensitive phosphatase. Conclusion: Since Calml3 is closely related to CaM and is prominently expressed in epithelial cells, Calml3 may be a constituent of epithelial KCNQ1 channels and underscores the molecular diversity of endogenous KCNQ1 channels.

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