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1.
Nature ; 621(7977): 206-214, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37648856

ABSTRACT

Transient receptor potential (TRP) channels are a large, eukaryotic ion channel superfamily that control diverse physiological functions, and therefore are attractive drug targets1-5. More than 210 structures from more than 20 different TRP channels have been determined, and all are tetramers4. Despite this wealth of structures, many aspects concerning TRPV channels remain poorly understood, including the pore-dilation phenomenon, whereby prolonged activation leads to increased conductance, permeability to large ions and loss of rectification6,7. Here, we used high-speed atomic force microscopy (HS-AFM) to analyse membrane-embedded TRPV3 at the single-molecule level and discovered a pentameric state. HS-AFM dynamic imaging revealed transience and reversibility of the pentamer in dynamic equilibrium with the canonical tetramer through membrane diffusive protomer exchange. The pentamer population increased upon diphenylboronic anhydride (DPBA) addition, an agonist that has been shown to induce TRPV3 pore dilation. On the basis of these findings, we designed a protein production and data analysis pipeline that resulted in a cryogenic-electron microscopy structure of the TRPV3 pentamer, showing an enlarged pore compared to the tetramer. The slow kinetics to enter and exit the pentameric state, the increased pentamer formation upon DPBA addition and the enlarged pore indicate that the pentamer represents the structural correlate of pore dilation. We thus show membrane diffusive protomer exchange as an additional mechanism for structural changes and conformational variability. Overall, we provide structural evidence for a non-canonical pentameric TRP-channel assembly, laying the foundation for new directions in TRP channel research.


Subject(s)
Protein Multimerization , TRPV Cation Channels , Anhydrides/chemistry , Anhydrides/pharmacology , Data Analysis , Diffusion , Protein Subunits/chemistry , Protein Subunits/drug effects , Protein Subunits/metabolism , TRPV Cation Channels/chemistry , TRPV Cation Channels/drug effects , TRPV Cation Channels/metabolism , TRPV Cation Channels/ultrastructure , Microscopy, Atomic Force , Molecular Targeted Therapy , Cryoelectron Microscopy , Protein Structure, Quaternary/drug effects , Protein Multimerization/drug effects
2.
Arch Biochem Biophys ; 708: 108940, 2021 09 15.
Article in English | MEDLINE | ID: mdl-34058149

ABSTRACT

Nanomaterials, such as graphene oxide (GO), are increasingly being investigated for their suitability in biomedical applications. Tubulin is the key molecule for the formation of microtubules crucial for cellular function and proliferation, and as such an appealing target for developing anticancer drug. Here we employ biophysical techniques to study the effect of GO on tubulin structure and how the changes affect the tubulin/microtubule assembly. GO disrupts the structural integrity of the protein, with consequent retardation of tubulin polymerization. Investigating the anticancer potential of GO, we found that it is more toxic to human colon cancer cells (HCT116), as compared to human embryonic kidney epithelial cells (HEK293). Immunocytochemistry indicated the disruption of microtubule assembly in HCT116 cells. GO arrested cells in the S phase with increased accumulation in Sub-G1 population of cell cycle, inducing apoptosis by generating reactive oxygen species (ROS) in a dose- and time-dependent manner. GO inhibited microtubule formation by intervening into the polymerization of tubulin heterodimers both in vitro and ex vivo, resulting in growth arrest at the S phase and ROS induced apoptosis of HCT116 colorectal carcinoma cells. There was no significant harm to the HEK293 kidney epithelial cells used as control. Our report of pristine GO causing ROS-induced apoptosis of cancer cells and inhibition of tubulin-microtubule assembly can be of interest in cancer therapeutics and nanomedicine.


Subject(s)
Colorectal Neoplasms/pathology , Graphite/toxicity , Microtubules/drug effects , Cell Cycle/drug effects , Dose-Response Relationship, Drug , HCT116 Cells , Humans , Microtubules/metabolism , Organosilicon Compounds , Protein Multimerization/drug effects , Protein Structure, Quaternary/drug effects , Quaternary Ammonium Compounds , Tubulin/chemistry
3.
Proteins ; 89(9): 1216-1225, 2021 09.
Article in English | MEDLINE | ID: mdl-33983654

ABSTRACT

The main protease Mpro , 3CLpro is an important target from coronaviruses. In spite of having 96% sequence identity among Mpros from SARS-CoV-1 and SARS-CoV-2; the inhibitors used to block the activity of SARS-CoV-1 Mpro so far, were found to have differential inhibitory effect on Mpro of SARS-CoV-2. The possible reason could be due to the difference of few amino acids among the peptidases. Since, overall 3-D crystallographic structure of Mpro from SARS-CoV-1 and SARS-CoV-2 is quite similar and mapping a subtle structural variation is seemingly impossible. Hence, we have attempted to study a structural comparison of SARS-CoV-1 and SARS-CoV-2 Mpro in apo and inhibitor bound states using protein structure network (PSN) based approach at contacts level. The comparative PSNs analysis of apo Mpros from SARS-CoV-1 and SARS-CoV-2 uncovers small but significant local changes occurring near the active site region and distributed throughout the structure. Additionally, we have shown how inhibitor binding perturbs the PSG and the communication pathways in Mpros . Moreover, we have also investigated the network connectivity on the quaternary structure of Mpro and identified critical residue pairs for complex formation using three centrality measurement parameters along with the modularity analysis. Taken together, these results on the comparative PSN provide an insight into conformational changes that may be used as an additional guidance towards specific drug development.


Subject(s)
Coronavirus 3C Proteases/chemistry , SARS-CoV-2/enzymology , Severe acute respiratory syndrome-related coronavirus/enzymology , Apoenzymes/antagonists & inhibitors , Apoenzymes/chemistry , Apoenzymes/metabolism , Binding Sites , Coronavirus 3C Proteases/antagonists & inhibitors , Coronavirus 3C Proteases/metabolism , Holoenzymes/chemistry , Holoenzymes/metabolism , Models, Molecular , Protease Inhibitors/pharmacology , Protein Multimerization/drug effects , Protein Structure, Quaternary/drug effects
4.
Biochemistry ; 60(15): 1165-1177, 2021 04 20.
Article in English | MEDLINE | ID: mdl-33792309

ABSTRACT

Differential scanning calorimetry and differential scanning fluorimetry were used to measure the thermal stability of human retinoid X receptor-α ligand binding domain (RXRα LBD) homodimer in the absence or presence of rexinoid and coactivator peptide, GRIP-1. The apo-RXRα LBD homodimer displayed a single thermal unfolding transition with a Tm of 58.7 °C and an unfolding enthalpy (ΔH) of 673 kJ/mol (12.5 J/g), much lower than average value (35 J/g) of small globular proteins. Using a heat capacity change (ΔCp) of 15 kJ/(mol K) determined by measurements at different pH values, the free energy of unfolding (ΔG) of the native state was 33 kJ/mol at 37 °C. Rexinoid binding to the apo-homodimer increased Tm by 5 to 9 °C and increased the ΔG of the native homodimer by 12 to 20 kJ/mol at 37 °C, consistent with the nanomolar dissociation constant (Kd) of the rexinoids. GRIP-1 binding to holo-homodimers containing rexinoid resulted in additional increases in ΔG of 14 kJ/mol, a value that was the same for all three rexinoids. Binding of rexinoid and GRIP-1 resulted in a combined 50% increase in unfolding enthalpy, consistent with reduced structural fluidity and more compact folding observed in other published structural studies. The complexes of UAB110 and UAB111 are each more stable than the UAB30 complex by 8 kJ/mol due to enhanced hydrophobic interactions in the binding pocket because of their larger end groups. This increase in thermodynamic stability positively correlates with their improved RXR activation potency. Thermodynamic measurements are thus valuable in predicting agonist potency.


Subject(s)
Peptides/pharmacology , Protein Multimerization/drug effects , Retinoid X Receptor alpha/chemistry , Hydrogen-Ion Concentration , Kinetics , Protein Stability/drug effects , Protein Structure, Quaternary/drug effects , Thermodynamics
5.
Biochemistry ; 59(48): 4591-4600, 2020 12 08.
Article in English | MEDLINE | ID: mdl-33231438

ABSTRACT

The selective targeting of protein-protein interactions remains a significant determinant for the proper modulation and regulation of cell apoptosis. Prototypic galectins such as human galectin-7 (GAL-7) are characterized by their ability to form homodimers that control the molecular fate of a cell by mediating subtle yet critical glycan-dependent interactions between pro- and anti-apoptotic molecular partners. Altering the structural architecture of GAL-7 can therefore result in resistance to apoptosis in various human cancer cells, further illustrating its importance in cell survival. In this study, we used a combination of biophysical and cellular assays to illustrate that binding of a water-soluble meso-tetraarylporphyrin molecule to GAL-7 induces protein oligomerization and modulation of GAL-7-induced apoptosis in human Jurkat T cells. Our results suggest that the integrity of the GAL-7 homodimer architecture is essential for its molecular function, in addition to providing an interesting porphyrin binding modulator for controlling apoptosis in mammalian cells.


Subject(s)
Galectins/chemistry , Galectins/metabolism , Mesoporphyrins/chemistry , Mesoporphyrins/metabolism , Apoptosis/drug effects , Binding Sites/drug effects , Galectins/pharmacology , Humans , In Vitro Techniques , Jurkat Cells , Molecular Docking Simulation , Nuclear Magnetic Resonance, Biomolecular , Protein Binding , Protein Interaction Domains and Motifs/drug effects , Protein Multimerization/drug effects , Protein Structure, Quaternary/drug effects , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Recombinant Proteins/pharmacology , Scattering, Small Angle , Solubility , X-Ray Diffraction
6.
Biomolecules ; 10(9)2020 09 02.
Article in English | MEDLINE | ID: mdl-32887365

ABSTRACT

Acid-sensing ion channel (ASIC) subunits 1a and 3 are highly expressed in central and peripheral sensory neurons, respectively. Endogenous biomolecule zinc plays a critical role in physiological and pathophysiological conditions. Here, we found that currents recorded from heterologously expressed ASIC1a/3 channels using the whole-cell patch-clamp technique were regulated by zinc with dual effects. Co-application of zinc dose-dependently potentiated both peak amplitude and the sustained component of heteromeric ASIC1a/3 currents; pretreatment with zinc between 3 to 100 µM exerted the same potentiation as co-application. However, pretreatment with zinc induced a significant inhibition of heteromeric ASIC1a/3 channels when zinc concentrations were over 250 µM. The potentiation of heteromeric ASIC1a/3 channels by zinc was pH dependent, as zinc shifted the pH dependence of ASIC1a/3 currents from a pH50 of 6.54 to 6.77; whereas the inhibition of ASIC1a/3 currents by zinc was also pH dependent. Furthermore, we systematically mutated histidine residues in the extracellular domain of ASIC1a or ASIC3 and found that histidine residues 72 and 73 in both ASIC1a and ASIC3, and histidine residue 83 in the ASIC3 were responsible for bidirectional effects on heteromeric ASIC1a/3 channels by zinc. These findings suggest that histidine residues in the extracellular domain of heteromeric ASIC1a/3 channels are critical for zinc-mediated effects.


Subject(s)
Acid Sensing Ion Channels/chemistry , Acid Sensing Ion Channels/physiology , Acid Sensing Ion Channels/genetics , Animals , CHO Cells , Cations/metabolism , Cations/pharmacology , Cricetulus , Electric Conductivity , Histidine/chemistry , Histidine/genetics , Hydrogen-Ion Concentration , Mutagenesis, Site-Directed , Patch-Clamp Techniques , Protein Structure, Quaternary/drug effects , Protein Subunits/chemistry , Protein Subunits/genetics , Protein Subunits/physiology , Sequence Alignment , Zinc/metabolism , Zinc/pharmacology
7.
Int J Mol Sci ; 21(16)2020 Aug 05.
Article in English | MEDLINE | ID: mdl-32764343

ABSTRACT

The antigen-antibody complex (AAC) has novel functions for immunomodulation, encouraging the application of diverse quaternary protein structures for vaccination. In this study, GA733 antigen and anti-GA733 antibody proteins were both co-expressed to obtain the AAC protein structures in a F1 plant obtained by crossing the plants expressing each protein. In F1 plant, the antigen and antibody assembled to form a large quaternary circular ACC structure (~30 nm). The large quaternary protein structures induced immune response to produce anticancer immunoglobulins G (IgGs) that are specific to the corresponding antigens in mouse. The serum containing the anticancer IgGs inhibited the human colorectal cancer cell growth in the xenograft nude mouse. Taken together, antigens and antibodies can be assembled to form AAC protein structures in plants. Plant crossing represents an alternative strategy for the formation of AAC vaccines that efficiently increases anticancer antibody production.


Subject(s)
Antibodies, Anti-Idiotypic/pharmacology , Antigen-Antibody Complex/immunology , Epithelial Cell Adhesion Molecule/immunology , Neoplasms/drug therapy , Plantibodies/pharmacology , Animals , Antibodies, Anti-Idiotypic/immunology , Antigen-Antibody Complex/pharmacology , Cancer Vaccines/immunology , Cell Adhesion Molecules/immunology , Humans , Immunity/drug effects , Immunity/immunology , Immunoglobulin G/immunology , Immunomodulation/drug effects , Immunomodulation/immunology , Mice , Neoplasms/immunology , Plantibodies/immunology , Protein Structure, Quaternary/drug effects , Xenograft Model Antitumor Assays
8.
Bioorg Chem ; 96: 103608, 2020 03.
Article in English | MEDLINE | ID: mdl-32058103

ABSTRACT

Protein kinase CK2, a heterotetrameric holoenzyme composed of two catalytic chains (CK2α) attached to a homodimer of regulatory subunits (CK2ß), is a target for drug development for cancer therapy. Here, we describe the tetraiodobenzimidazole derivative ARC-3140, a bisubstrate inhibitor addressing the ATP site and the substrate-binding site of CK2 with extraordinary affinity (Ki = 84 pM). In a crystal structure of ARC-3140 in complex with CK2α, three copies of the inhibitor are visible, one of them at the CK2ß interface of CK2α. Subsequent interaction studies based on microscale thermophoresis and fluorescence anisotropy changes revealed a significant impact of ARC-3140 and of its tetrabromo equivalent ARC-1502 on the CK2α/CK2ß interaction. A structural inspection revealed that ARC-3140, unlike CK2ß antagonists described so far, interferes with both sub-interfaces of the bipartite CK2α/CK2ß interaction. Thus, ARC-3140 is a lead for the further development of highly effective compounds perturbating the quaternary structure of the CK2α2ß2 holoenzyme.


Subject(s)
Benzimidazoles/chemistry , Benzimidazoles/pharmacology , Casein Kinase II/antagonists & inhibitors , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/pharmacology , Casein Kinase II/chemistry , Casein Kinase II/metabolism , Catalytic Domain/drug effects , Crystallography, X-Ray , Halogenation , Humans , Molecular Docking Simulation , Protein Multimerization/drug effects , Protein Structure, Quaternary/drug effects , Protein Subunits/antagonists & inhibitors , Protein Subunits/chemistry , Protein Subunits/metabolism
9.
Spectrochim Acta A Mol Biomol Spectrosc ; 230: 118036, 2020 Apr 05.
Article in English | MEDLINE | ID: mdl-31931358

ABSTRACT

In this work, the effects of I2 on the activities and conformational structures of digestive enzymes, trypsin and pepsin were studied. The results indicated that the enzyme activities were decreased to some extent in the presence of I2, especially trypsin. Upon gradual addition of I2, the intrinsic fluorescence quenching of trypsin and pepsin were observed by mainly static collision and hydrophobic forces. I2 is more likely to cause the fluorescence quenching of trypsin than that of pepsin. Compared with pepsin, trypsin has a greater ability to bind with I2. The synchronous fluorescence spectral results indicated that I2 induced the quaternary structure changes of trypsin/pepsin and changed the hydrophobicity of Tyr and Trp residues. In addition, molecular docking was used to obtain the binding mode and the various amino acid residues of trypsin and pepsin with I2. These investigations may constitute a solid work to further explain the process of migration and transformation of I2 in digestive system.


Subject(s)
Iodine/pharmacology , Pepsin A/metabolism , Protease Inhibitors/pharmacology , Trypsin Inhibitors/pharmacology , Trypsin/metabolism , Animals , Molecular Docking Simulation , Pepsin A/antagonists & inhibitors , Pepsin A/chemistry , Protein Binding , Protein Structure, Quaternary/drug effects , Swine , Trypsin/chemistry
10.
Nat Commun ; 10(1): 5795, 2019 12 19.
Article in English | MEDLINE | ID: mdl-31857588

ABSTRACT

Tumour necrosis factor (TNF) is a cytokine belonging to a family of trimeric proteins; it has been shown to be a key mediator in autoimmune diseases such as rheumatoid arthritis and Crohn's disease. While TNF is the target of several successful biologic drugs, attempts to design small molecule therapies directed to this cytokine have not led to approved products. Here we report the discovery of potent small molecule inhibitors of TNF that stabilise an asymmetrical form of the soluble TNF trimer, compromising signalling and inhibiting the functions of TNF in vitro and in vivo. This discovery paves the way for a class of small molecule drugs capable of modulating TNF function by stabilising a naturally sampled, receptor-incompetent conformation of TNF. Furthermore, this approach may prove to be a more general mechanism for inhibiting protein-protein interactions.


Subject(s)
Anti-Inflammatory Agents/pharmacology , Arthritis, Experimental/drug therapy , Protein Multimerization/drug effects , Signal Transduction/drug effects , Tumor Necrosis Factor-alpha/antagonists & inhibitors , Animals , Anti-Inflammatory Agents/therapeutic use , Arthritis, Experimental/immunology , Cell Line , Crystallography, X-Ray , Drug Discovery , Male , Mice , Molecular Dynamics Simulation , Neutrophil Infiltration/drug effects , Neutrophils/drug effects , Neutrophils/immunology , Protein Stability/drug effects , Protein Structure, Quaternary/drug effects , Receptors, Tumor Necrosis Factor, Type I/immunology , Receptors, Tumor Necrosis Factor, Type I/metabolism , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Recombinant Proteins/ultrastructure , Signal Transduction/immunology , Structure-Activity Relationship , Treatment Outcome , Tumor Necrosis Factor-alpha/immunology , Tumor Necrosis Factor-alpha/isolation & purification , Tumor Necrosis Factor-alpha/metabolism , Tumor Necrosis Factor-alpha/ultrastructure
11.
Biochem Biophys Res Commun ; 515(2): 366-371, 2019 07 23.
Article in English | MEDLINE | ID: mdl-31155294

ABSTRACT

Flaviviruses are emerging arthropod-borne viruses posing a great threat to human beings worldwide. The E dimer configuration of the flavivirus was prominent during viral assembly, maturation and entry. Neutralization antibodies targeting E dimer played the important role in controlling the flavivirus infection. Previously, the ideal drug target of small molecular inhibitors of JEV was viral proteases and polymerases. The crystal structure of JEV E protein showed a conserved pocket in it is important at membrane fusion step. Recently, a set of anti-virus drugs has been found by virtual screening. Here, we show that the fusion-loop pocket of JEV E protein was a conservative region and an ideal drug target. ChemDiv-3 from virtual screening as the lead compound was found to show a relatively modest inhibition effect for JEV in vitro and in vivo test and could interfere with the formation of JEV sE dimer. ChemDiv-3 interacts with the amino acid residues ASN 313, PRO 314, ALA 315, and VAL 323 in E protein via hydrogen bonds for occupation of the fusion-loop pocket. The key binding sites LYS 312, ALA 513 and THR 317 forming the fusion-loop pocket are the same and other auxiliary sites are similar among the flavivirus. Taken together, the fusion-loop pocket of the flavivirus could be one promising target for drug discovery.


Subject(s)
Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Encephalitis Virus, Japanese/chemistry , Encephalitis Virus, Japanese/drug effects , Viral Envelope Proteins/chemistry , Viral Envelope Proteins/drug effects , Amino Acid Sequence , Animals , Binding Sites/genetics , Databases, Pharmaceutical , Disease Models, Animal , Drug Design , Drug Evaluation, Preclinical , Encephalitis Virus, Japanese/genetics , Encephalitis, Japanese/drug therapy , Female , Humans , Mice , Mice, Inbred BALB C , Molecular Docking Simulation , Protein Multimerization/drug effects , Protein Structure, Quaternary/drug effects , Structure-Activity Relationship , User-Computer Interface , Viral Envelope Proteins/genetics
12.
Nat Commun ; 10(1): 2635, 2019 06 14.
Article in English | MEDLINE | ID: mdl-31201302

ABSTRACT

Multidrug efflux pumps actively expel a wide range of toxic substrates from the cell and play a major role in intrinsic and acquired drug resistance. In Gram-negative bacteria, these pumps form tripartite assemblies that span the cell envelope. However, the in situ structure and assembly mechanism of multidrug efflux pumps remain unknown. Here we report the in situ structure of the Escherichia coli AcrAB-TolC multidrug efflux pump obtained by electron cryo-tomography and subtomogram averaging. The fully assembled efflux pump is observed in a closed state under conditions of antibiotic challenge and in an open state in the presence of AcrB inhibitor. We also observe intermediate AcrAB complexes without TolC and discover that AcrA contacts the peptidoglycan layer of the periplasm. Our data point to a sequential assembly process in living bacteria, beginning with formation of the AcrAB subcomplex and suggest domains to target with efflux pump inhibitors.


Subject(s)
Bacterial Outer Membrane Proteins/metabolism , Carrier Proteins/physiology , Escherichia coli Proteins/metabolism , Escherichia coli Proteins/physiology , Escherichia coli/physiology , Lipoproteins/metabolism , Membrane Transport Proteins/metabolism , Multidrug Resistance-Associated Proteins/metabolism , Anti-Bacterial Agents/pharmacology , Carrier Proteins/drug effects , Carrier Proteins/ultrastructure , Cryoelectron Microscopy/methods , Drug Resistance, Multiple, Bacterial/drug effects , Electron Microscope Tomography/methods , Escherichia coli/drug effects , Escherichia coli/ultrastructure , Escherichia coli Proteins/antagonists & inhibitors , Escherichia coli Proteins/drug effects , Escherichia coli Proteins/ultrastructure , Intravital Microscopy/methods , Multidrug Resistance-Associated Proteins/antagonists & inhibitors , Peptidoglycan/metabolism , Periplasm/metabolism , Protein Binding/drug effects , Protein Structure, Quaternary/drug effects
13.
JCI Insight ; 4(8)2019 04 18.
Article in English | MEDLINE | ID: mdl-30996141

ABSTRACT

Cystic fibrosis (CF) is characterized by increased mucus viscosity and delayed mucociliary clearance that contributes to progressive decline of lung function. Mucus in the respiratory and GI tract is excessively adhesive in the presence of airway dehydration and excess extracellular Ca2+ upon mucin release, promoting hyperviscous, densely packed mucins characteristic of CF. Therapies that target mucins directly through ionic interactions remain unexploited. Here we show that poly (acetyl, arginyl) glucosamine (PAAG), a polycationic biopolymer suitable for human use, interacts directly with mucins in a Ca2+-sensitive manner to reduce CF mucus viscoelasticity and improve its transport. Notably, PAAG induced a linear structure of purified MUC5B and altered its sedimentation profile and viscosity, indicative of proper mucin expansion. In vivo, PAAG nebulization improved mucociliary transport in CF rats with delayed mucus clearance, and cleared mucus plugging in CF ferrets. This study demonstrates the potential use of a synthetic glycopolymer PAAG as a molecular agent that could benefit patients with a broad array of mucus diseases.


Subject(s)
Cystic Fibrosis/drug therapy , Glucosamine/analogs & derivatives , Mucin-5B/metabolism , Mucociliary Clearance/drug effects , Mucus/drug effects , Polymers/pharmacology , Animals , Cystic Fibrosis/genetics , Cystic Fibrosis/pathology , Cystic Fibrosis Transmembrane Conductance Regulator/genetics , Disease Models, Animal , Ferrets , Glucosamine/pharmacology , Glucosamine/therapeutic use , Humans , Mice , Mice, Inbred CFTR , Mucin-5B/chemistry , Mucus/metabolism , Polymers/therapeutic use , Protein Structure, Quaternary/drug effects , Rats , Respiratory Mucosa/drug effects , Respiratory Mucosa/pathology , Viscosity/drug effects
14.
Int J Biol Macromol ; 130: 10-18, 2019 Jun 01.
Article in English | MEDLINE | ID: mdl-30794903

ABSTRACT

The human Receptor for Advanced Glycation End Products (hRAGE) is a pattern recognition receptor implicated in inflammation and adhesion. It is involved in both innate and adaptive immunity. Its aberrant signaling is tied to the pathogenesis of diabetic complications, neurodegenerative disorders, and chronic inflammatory responses. Previous structural studies have focused on its extracellular domains with their canonical constant and variable Ig folds, and to a much lesser extent, the intrinsically disorder cytoplasmic domain. No experimental data are reported on the transmembrane domain, which is integral to signaling. We have constructed, expressed and purified the transmembrane domain attached to the cytoplasmic domain of hRAGE in E. coli. Multiple self-associated forms of these domains were observed in vitro. This pattern of mixed oligomers resembled previously reported in vivo forms of the complete receptor. The self-association of these two domains was further characterized using: SDS-PAGE, intrinsic tryptophan fluorescence and heteronuclear NMR spectroscopy. NMR conditions were assessed across time and temperature within micelles. Our data show that the transmembrane and cytoplasmic domains of hRAGE undergo dynamic oligomerizations that can occur in the absence of its extracellular domains or ligand binding. And, such associations are only partially disrupted even with prolonged incubation in strong detergents.


Subject(s)
Cell Membrane/metabolism , Cytoplasm/metabolism , Micelles , Protein Multimerization/drug effects , Receptor for Advanced Glycation End Products/chemistry , Sodium Dodecyl Sulfate/pharmacology , Amino Acid Sequence , Cell Line , Humans , Protein Domains/drug effects , Protein Structure, Quaternary/drug effects , Sodium Dodecyl Sulfate/chemistry
15.
Biophys J ; 116(5): 847-859, 2019 03 05.
Article in English | MEDLINE | ID: mdl-30777305

ABSTRACT

The oligomeric organization of the voltage-dependent anion-selective channel (VDAC) and its interactions with hexokinase play integral roles in mitochondrially mediated apoptotic signaling. Various small to large assemblies of VDAC are observed in mitochondrial outer membranes, but they do not predominate in detergent-solubilized VDAC samples. In this study, a cholesterol analog, cholesteryl-hemisuccinate (CHS), was shown to induce the formation of detergent-soluble VDAC multimers. The various oligomeric states of VDAC induced by the addition of CHS were deciphered through an integrated biophysics approach using microscale thermophoresis, analytical ultracentrifugation, and size-exclusion chromatography small angle x-ray scattering. Furthermore, CHS stabilizes the interaction between VDAC and hexokinase (Kd of 27 ± 6 µM), confirming the biological relevance of oligomers generated. Thus, sterols such as cholesterol in higher eukaryotes or ergosterol in fungi may regulate the VDAC oligomeric state and may provide a potential target for the modulation of apoptotic signaling by effecting VDAC-VDAC and VDAC-hexokinase interactions. In addition, the integrated biophysical approach described provides a powerful platform for the study of membrane protein complexes in solution.


Subject(s)
Cholesterol Esters/pharmacology , Protein Multimerization/drug effects , Voltage-Dependent Anion Channels/chemistry , Fungal Proteins/chemistry , Fungal Proteins/metabolism , Hexokinase/metabolism , Neurospora crassa , Protein Structure, Quaternary/drug effects , Protein Structure, Secondary/drug effects , Voltage-Dependent Anion Channels/metabolism
16.
J Biosci Bioeng ; 127(4): 515-519, 2019 Apr.
Article in English | MEDLINE | ID: mdl-30340956

ABSTRACT

Protein is a promising material for fabricating the biocompatible films used in the biomedical fields and food industry. Previously, we successfully prepared a water-insoluble albumin film possessing native albumin properties such as resistance to cell adhesion and drug-binding ability. Here, I quantitatively investigated the conformation of albumin in a film state using circular dichroism (CD) spectroscopy. The albumin film was prepared by crosslinking albumin with ethylene glycol diglycidyl ether (EGDE). CD measurements of albumin films revealed that approximately 70% of the α-helical structure was retained after film formation. Albumin molecules in the films acquired high stability. The conformation of albumin was completely retained even after heating at 100 °C for 1 h. For comparison, crosslinked albumin film was also prepared using glutaraldehyde (GA). Unlike EGDE-crosslinking, GA-crosslinking induced significant conformational changes in albumin; 46% of the α-helical structure was destroyed in GA-crosslinked albumin films. Cell adhesion studies showed that EGDE-crosslinked albumin film maintained the cell-nonadhesive property inherent in native albumin. This property was lost in GA-crosslinked albumin film, and cells adhesion occurred at a level comparable to that of cell culture dishes. These results indicate that EGDE-crosslinking is a useful method for preparing albumin films in which the native albumin structure and property are retained. The approach described here provides valuable information for creating protein films possessing high functionality.


Subject(s)
Membranes, Artificial , Serum Albumin/chemistry , Cell Adhesion/drug effects , Circular Dichroism , Coated Materials, Biocompatible/chemistry , Cross-Linking Reagents/pharmacology , Epoxy Resins/pharmacology , Glutaral/pharmacology , Materials Testing , Protein Multimerization/drug effects , Protein Structure, Quaternary/drug effects , Serum Albumin/drug effects , Serum Albumin/metabolism , Spectrum Analysis/methods , Tissue Scaffolds/chemistry , Water/chemistry
17.
PLoS One ; 13(12): e0209150, 2018.
Article in English | MEDLINE | ID: mdl-30557391

ABSTRACT

Human mini-brains (MB) are cerebral organoids that recapitulate in part the complexity of the human brain in a unique three-dimensional in vitro model, yielding discrete brain regions reminiscent of the cerebral cortex. Specific proteins linked to neurodegenerative disorders are physiologically expressed in MBs, such as APP-derived amyloids (Aß), whose physiological and pathological roles and interactions with other proteins are not well established in humans. Here, we demonstrate that neuroectodermal organoids can be used to study the Aß accumulation implicated in Alzheimer's disease (AD). To enhance the process of protein secretion and accumulation, we adopted a chemical strategy of induction to modulate post-translational pathways of APP using an Amyloid-ß Forty-Two Inducer named Aftin-5. Secreted, soluble Aß fragment concentrations were analyzed in MB-conditioned media. An increase in the Aß42 fragment secretion was observed as was an increased Aß42/Aß40 ratio after drug treatment, which is consistent with the pathological-like phenotypes described in vivo in transgenic animal models and in vitro in induced pluripotent stem cell-derived neural cultures obtained from AD patients. Notably in this context we observe time-dependent Aß accumulation, which differs from protein accumulation occurring after treatment. We show that mini-brains obtained from a non-AD control cell line are responsive to chemical compound induction, producing a shift of physiological Aß concentrations, suggesting that this model can be used to identify environmental agents that may initiate the cascade of events ultimately leading to sporadic AD. Increases in both Aß oligomers and their target, the cellular prion protein (PrPC), support the possibility of using MBs to further understand the pathophysiological role that underlies their interaction in a human model. Finally, the potential application of MBs for modeling age-associated phenotypes and the study of neurological disorders is confirmed.


Subject(s)
Alzheimer Disease/pathology , Amyloid beta-Peptides/biosynthesis , Brain/pathology , Organoids/drug effects , Organoids/metabolism , Peptide Fragments/biosynthesis , Phenotype , Small Molecule Libraries/pharmacology , Amyloid beta-Peptides/chemistry , Amyloid beta-Peptides/metabolism , Gene Expression Regulation/drug effects , Humans , Peptide Fragments/chemistry , Peptide Fragments/metabolism , PrPC Proteins/metabolism , Protein Multimerization , Protein Structure, Quaternary/drug effects
18.
Mol Microbiol ; 110(4): 550-561, 2018 11.
Article in English | MEDLINE | ID: mdl-30168204

ABSTRACT

LysR-type transcriptional regulators (LTTRs) generally bind to target promoters in two conformations, depending on the availability of inducing ligands. OccR is an LTTR that regulates the octopine catabolism operon of Agrobacterium tumefaciens. OccR binds to a site located between the divergent occQ and occR promoters. Octopine triggers a conformational change that activates the occQ promoter, and does not affect autorepression. This change shortens the length of bound DNA and relaxes a high-angle DNA bend. Here, we describe the crystal structure of the ligand-binding domain (LBD) of OccR apoprotein and holoprotein. Pairs of LBDs form dimers with extensive hydrogen bonding, while pairs of dimers interact via a single helix, creating a tetramer interface. Octopine causes a 70° rotation of each dimer with respect to the opposite dimer, precisely at the tetramer interface. We modeled the DNA binding domain (DBD), linker helix and bound DNA onto the apoprotein and holoprotein. The two DBDs of the modeled apoprotein lie far apart and the bound DNA between them has a high-angle DNA bend. In contrast, the two DBDs of the holoprotein lie closer to each other, with a low DNA bend angle. This inter-dimer pivot fully explains earlier studies of this LTTR.


Subject(s)
Agrobacterium tumefaciens/genetics , Arginine/analogs & derivatives , Bacterial Proteins/metabolism , DNA-Binding Proteins/metabolism , Protein Structure, Quaternary/drug effects , Transcription Factors/metabolism , Transcriptional Activation/genetics , Arginine/pharmacology , Bacterial Proteins/genetics , Binding Sites/physiology , Carrier Proteins/genetics , Carrier Proteins/metabolism , Crystallography, X-Ray , DNA, Bacterial/genetics , DNA-Binding Proteins/genetics , Membrane Proteins/genetics , Membrane Proteins/metabolism , Promoter Regions, Genetic/drug effects , Promoter Regions, Genetic/genetics , Protein Binding/physiology , Transcription Factors/genetics
19.
Nature ; 558(7710): 470-474, 2018 06.
Article in English | MEDLINE | ID: mdl-29899443

ABSTRACT

Acetyl-CoA carboxylase catalyses the ATP-dependent carboxylation of acetyl-CoA, a rate-limiting step in fatty acid biosynthesis1,2. Eukaryotic acetyl-CoA carboxylases are large, homodimeric multienzymes. Human acetyl-CoA carboxylase occurs in two isoforms: the metabolic, cytosolic ACC1, and ACC2, which is anchored to the outer mitochondrial membrane and controls fatty acid ß-oxidation1,3. ACC1 is regulated by a complex interplay of phosphorylation, binding of allosteric regulators and protein-protein interactions, which is further linked to filament formation1,4-8. These filaments were discovered in vitro and in vivo 50 years ago7,9,10, but the structural basis of ACC1 polymerization and regulation remains unknown. Here, we identify distinct activated and inhibited ACC1 filament forms. We obtained cryo-electron microscopy structures of an activated filament that is allosterically induced by citrate (ACC-citrate), and an inactivated filament form that results from binding of the BRCT domains of the breast cancer type 1 susceptibility protein (BRCA1). While non-polymeric ACC1 is highly dynamic, filament formation locks ACC1 into different catalytically competent or incompetent conformational states. This unique mechanism of enzyme regulation via large-scale conformational changes observed in ACC1 has potential uses in engineering of switchable biosynthetic systems. Dissecting the regulation of acetyl-CoA carboxylase opens new paths towards counteracting upregulation of fatty acid biosynthesis in disease.


Subject(s)
Acetyl-CoA Carboxylase/chemistry , Acetyl-CoA Carboxylase/ultrastructure , Cryoelectron Microscopy , Acetyl-CoA Carboxylase/metabolism , Animals , BRCA1 Protein/chemistry , BRCA1 Protein/pharmacology , Biopolymers/chemistry , Biopolymers/metabolism , Cell Line , Citric Acid/pharmacology , Humans , Models, Molecular , Polymerization/drug effects , Protein Domains/drug effects , Protein Structure, Quaternary/drug effects , Spodoptera , Structure-Activity Relationship
20.
Nature ; 557(7704): 261-265, 2018 05.
Article in English | MEDLINE | ID: mdl-29720657

ABSTRACT

Fast chemical communication in the nervous system is mediated by neurotransmitter-gated ion channels. The prototypical member of this class of cell surface receptors is the cation-selective nicotinic acetylcholine receptor. As with most ligand-gated ion channels, nicotinic receptors assemble as oligomers of subunits, usually as hetero-oligomers and often with variable stoichiometries 1 . This intrinsic heterogeneity in protein composition provides fine tunability in channel properties, which is essential to brain function, but frustrates structural and biophysical characterization. The α4ß2 subtype of the nicotinic acetylcholine receptor is the most abundant isoform in the human brain and is the principal target in nicotine addiction. This pentameric ligand-gated ion channel assembles in two stoichiometries of α- and ß-subunits (2α:3ß and 3α:2ß). Both assemblies are functional and have distinct biophysical properties, and an imbalance in the ratio of assemblies is linked to both nicotine addiction2,3 and congenital epilepsy4,5. Here we leverage cryo-electron microscopy to obtain structures of both receptor assemblies from a single sample. Antibody fragments specific to ß2 were used to 'break' symmetry during particle alignment and to obtain high-resolution reconstructions of receptors of both stoichiometries in complex with nicotine. The results reveal principles of subunit assembly and the structural basis of the distinctive biophysical and pharmacological properties of the two different stoichiometries of this receptor.


Subject(s)
Cryoelectron Microscopy , Protein Subunits/chemistry , Protein Subunits/metabolism , Receptors, Nicotinic/metabolism , Receptors, Nicotinic/ultrastructure , Animals , Binding Sites , Electric Conductivity , Female , Humans , Immunoglobulin Fab Fragments/immunology , Immunoglobulin Fab Fragments/pharmacology , Ion Channel Gating , Mice , Mice, Inbred BALB C , Models, Molecular , Nicotine/chemistry , Nicotine/metabolism , Nicotine/pharmacology , Protein Isoforms/chemistry , Protein Isoforms/immunology , Protein Isoforms/metabolism , Protein Isoforms/ultrastructure , Protein Structure, Quaternary/drug effects , Protein Subunits/agonists , Protein Subunits/immunology , Receptors, Nicotinic/chemistry , Receptors, Nicotinic/immunology
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