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1.
J Mol Graph Model ; 118: 108365, 2023 01.
Article in English | MEDLINE | ID: mdl-36335829

ABSTRACT

The structural features that contribute to the efficacy of biased agonists targeting G protein-coupled receptors (GPCRs) towards G proteins or ß-arrestin (ß-arr) signaling pathways is nebulous, although such knowledge is critical in designing biased ligands. The dynamics of the agonist-GPCR complex is one of the critical factors in determining agonist bias. Angiotensin II type I receptor (AT1R) is an ideal model system to study the molecular basis of bias since it has multiple ß-arr2 and Gq protein biased agonists as well as experimentally solved three dimensional structures. Using Molecular Dynamics (MD) simulations for the Angiotensin II type I receptor (AT1R) bound to ten different agonists, we infer that the agonist bound receptor samples conformations with different relative weights, from both the inactive and active state ensembles of the receptor. This concept is perhaps extensible to other class A GPCRs. Such a weighted mixed ensemble recapitulates the inter-residue distance distributions measured for different agonists bound AT1R using DEER experiments. The ratio of the calculated relative strength of the allosteric communication to ß-arr2 vs Gq coupling sites scale similarly to the experimentally measured bias factors. Analysis of the inter-residue distance distributions of the activation microswitches involved in class A GPCR activation suggests that ß-arr2 biased agonists turn on different combination of microswitches with different relative strengths of activation. We put forth a model that activation microswitches behave like rheostats that tune the relative efficacy of the biased agonists toward the two signaling pathways. Finally, based on our data we propose that the agonist specific residue contacts in the binding site elicit a combinatorial response in the microswitches that in turn differentially modulate the receptor conformation ensembles resulting in differences in coupling to Gq and ß-arrestin.


Subject(s)
Angiotensin II , Receptor, Angiotensin, Type 1 , Receptor, Angiotensin, Type 1/agonists , Receptor, Angiotensin, Type 1/metabolism , Angiotensin II/chemistry , Angiotensin II/metabolism , Angiotensin II/pharmacology , Electron Spin Resonance Spectroscopy , beta-Arrestins/metabolism , Ligands , Protein Conformation
2.
Nat Commun ; 13(1): 7428, 2022 12 02.
Article in English | MEDLINE | ID: mdl-36460632

ABSTRACT

Recent studies have shown that G protein coupled receptors (GPCRs) show selective and promiscuous coupling to different Gα protein subfamilies and yet the mechanisms of the range of coupling preferences remain unclear. Here, we use Molecular Dynamics (MD) simulations on ten GPCR:G protein complexes and show that the location (spatial) and duration (temporal) of intermolecular contacts at the GPCR:Gα protein interface play a critical role in how GPCRs selectively interact with G proteins. We identify that some GPCR:G protein interface contacts are common across Gα subfamilies and others specific to Gα subfamilies. Using large scale data analysis techniques on the MD simulation snapshots we derive a spatio-temporal code for contacts that confer G protein selective coupling and validated these contacts using G protein activation BRET assays. Our results demonstrate that promiscuous GPCRs show persistent sampling of the common contacts more than G protein specific contacts. These findings suggest that GPCRs maintain contact with G proteins through a common central interface, while the selectivity comes from G protein specific contacts at the periphery of the interface.


Subject(s)
Biological Assay , Molecular Dynamics Simulation , Research Design
3.
Polymers (Basel) ; 14(1)2021 Dec 23.
Article in English | MEDLINE | ID: mdl-35012059

ABSTRACT

Changes in intraoral pH can cause changes in the chemical decomposition and surface properties of treated resin-based pits and fissure sealants (sealant). The purpose of this study is to evaluate the release of bisphenol A (BPA) from sealants under three different pH conditions over time. The test specimen was applied with 6 sealants 5 mg each on a glass plate (10 × 10 mm) and photopolymerized. The samples were immersed for 10 min, 1 h, and 24 h in solutions of pH 3.0, 6.5, and 10.0 at 37 °C. BPA release was measured using a gas chromatography-mass spectrometer. A statistical analysis was performed by two-way ANOVA and one-way ANOVA to verify the effect of pH conditions and time on BPA release. The BPA concentration in the pH 3.0 group was higher at all points than with pH 6.5 and pH 10.0 (p < 0.05), and gradually increased over time (p < 0.05). As a result, it was confirmed that low pH negatively influences BPA release. Therefore, frequent exposure to low pH due to the consumption of various beverages after sealant treatment can negatively affect the sealant's chemical stability in the oral cavity.

4.
Biochemistry ; 59(42): 4059-4071, 2020 10 27.
Article in English | MEDLINE | ID: mdl-33054162

ABSTRACT

Although multiple components of the cell membrane modulate the stability and activation of G protein-coupled receptors (GPCRs), insights into the dynamics of GPCR structures come from biophysical studies conducted in detergents. This is because of the challenges of studying activation in a multicomponent lipid bilayer. To understand the role of cellular membrane lipids and cations in GPCR activation, we performed multiscale molecular dynamics simulations (56 µs) on three different conformational states of adenosine receptor A2AR, in both the cell membrane-like lipid bilayer and in detergent micelles. Molecular dynamics (MD) simulations show that the phosphatidylinositol bisphosphate (PIP2) interacts with the basic residues in the intracellular regions of A2AR, thereby reducing the flexibility of the receptor in the inactive state and limiting the transition to the active-intermediate state. In the G protein-coupled fully active state, PIP2 stabilizes the GPCR:G protein complex. Such stiffening effects are absent in non-ionic detergent micelles, and therefore, more transitions have been observed in detergents. The inter-residue distances that change significantly upon GPCR activation are known as activation microswitches. The activation microswitches show different levels of activation in the cell membrane, in the pure POPC bilayer, and in detergents. Thus, the temporal heat map of different activation microswitches calculated from the MD simulations suggests a rheostat model of GPCR activation microswitches rather than the binary switch model. These simulation results connect the chemistry of cell membrane lipids to receptor activity, which is useful for the design of detergents mimicking the cell membrane.


Subject(s)
Cell Membrane/metabolism , Receptor, Adenosine A2A/metabolism , Humans , Lipid Bilayers/chemistry , Lipid Bilayers/metabolism , Molecular Dynamics Simulation , Phosphatidylinositol 4,5-Diphosphate/chemistry , Phosphatidylinositol 4,5-Diphosphate/metabolism , Receptor, Adenosine A2A/chemistry
5.
Biochemistry ; 59(23): 2125-2134, 2020 06 16.
Article in English | MEDLINE | ID: mdl-32437610

ABSTRACT

The structural and functional properties of G protein-coupled receptors (GPCRs) are often studied in a detergent micellar environment, but many GPCRs tend to denature or aggregate in short alkyl chain detergents. In our previous work [Lee, S., et al. (2016) J. Am. Chem. Soc. 138, 15425-15433], we showed that GPCRs in alkyl glucosides were highly dynamic, resulting in the penetration of detergent molecules between transmembrane α-helices, which is the initial step in receptor denaturation. Although this was not observed for GPCRs in dodecyl maltoside (DDM, also known as lauryl maltoside), even this detergent is not mild enough to preserve the integrity of many GPCRs during purification. Lauryl maltose neopentylglycol (LMNG) detergents have been found to have significant advantages for purifying GPCRs in a native state as they impart more stability to the receptor than DDM. To gain insights into how they stabilize GPCRs, we used atomistic molecular dynamics simulations of wild type adenosine A2A receptor (WT-A2AR), thermostabilized A2AR (tA2AR), and wild type ß2-adrenoceptor (ß2AR) in a variety of detergents (LMNG, DMNG, OGNG, and DDM). Analysis of molecular dynamics simulations of tA2AR in LMNG, DMNG, and OGNG showed that this series of detergents exhibited behavior very similar to that of an analogous series of detergents DDM, DM, and OG in our previous study. However, there was a striking difference upon comparison of the behavior of LMNG to that of DDM. LMNG showed considerably less motion than DDM, which resulted in the enhanced density of the aliphatic chains around the hydrophobic regions of the receptor and considerably more hydrogen bond formation between the head groups. This contributed to enhanced interaction energies between both detergent molecules and between the receptor and detergent, explaining the enhanced stability of GPCRs purified in this detergent. Branched detergents occlude between transmembrane helices and reduce their flexibility. Our results provide a rational foundation to develop detergent variants for stabilizing membrane proteins.


Subject(s)
Detergents/pharmacology , Micelles , Receptors, G-Protein-Coupled/chemistry , Detergents/chemistry , HEK293 Cells , Humans , Molecular Dynamics Simulation , Molecular Structure , Protein Stability/drug effects
6.
Structure ; 27(4): 703-712.e3, 2019 04 02.
Article in English | MEDLINE | ID: mdl-30713025

ABSTRACT

Agonist binding in the extracellular region of the G protein-coupled adenosine A2A receptor increases its affinity to the G proteins in the intracellular region, and vice versa. The structural basis for this effect is not evident from the crystal structures of A2AR in various conformational states since it stems from the receptor dynamics. Using atomistic molecular dynamics simulations on four different conformational states of the adenosine A2A receptor, we observed that the agonists show decreased ligand mobility, lower entropy of the extracellular loops in the active-intermediate state compared with the inactive state. In contrast, the entropy of the intracellular region increases to prime the receptor for coupling the G protein. Coupling of the G protein to A2AR shrinks the agonist binding site, making tighter receptor agonist contacts with an increase in the strength of allosteric communication compared with the active-intermediate state. These insights provide a strong basis for structure-based ligand design studies.


Subject(s)
Adenosine A2 Receptor Agonists/chemistry , Adenosine-5'-(N-ethylcarboxamide)/chemistry , Adenosine/chemistry , GTP-Binding Proteins/chemistry , Receptor, Adenosine A2A/chemistry , Adenosine/metabolism , Adenosine A2 Receptor Agonists/metabolism , Adenosine-5'-(N-ethylcarboxamide)/metabolism , Allosteric Regulation , Allosteric Site , Catalytic Domain , GTP-Binding Proteins/genetics , GTP-Binding Proteins/metabolism , Humans , Ligands , Models, Molecular , Molecular Dynamics Simulation , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protein Stability , Receptor, Adenosine A2A/genetics , Receptor, Adenosine A2A/metabolism , Thermodynamics
7.
Korean J Intern Med ; 34(5): 1068-1077, 2019 Sep.
Article in English | MEDLINE | ID: mdl-28882024

ABSTRACT

BACKGROUND/AIMS: The importance of α-cell dysfunction in the pathogenesis of type 2 diabetes has re-emerged recently. However, data on whether relative glucagon excess is present in clinical settings are scarce. We aimed to investigate associations between glucagon-to-insulin ratio and various metabolic parameters. METHODS: A total of 451 patients with type 2 diabetes naïve to insulin treatment were recruited. Using glucagon-to-insulin ratio, we divided subjects into quartiles according to both fasting and postprandial glucagon-to-insulin ratios. RESULTS: The mean age of the subjects was 58 years, with a mean body mass index of 25 kg/m2 . The patients in the highest quartile of glucagon-to-insulin ratio had higher glycated hemoglobin (HbA1c) levels. HbA1c levels were positively correlated with both fasting and postprandial glucagon-to-insulin ratios. Subjects in the highest quartile of postprandial glucagon-to-insulin ratio were more likely to exhibit uncontrolled hyperglycemia, even after adjusting for confounding factors (odds ratio, 2.730; 95% confidence interval, 1.236 to 6.028; p for trend < 0.01). CONCLUSION: Hyperglucagonemia relative to insulin could contribute to uncontrolled hyperglycemia in type 2 diabetes patients.


Subject(s)
Diabetes Mellitus, Type 2/blood , Glucagon/blood , Glycated Hemoglobin/metabolism , Insulin/blood , Adult , Aged , Biomarkers/blood , Body Mass Index , Cross-Sectional Studies , Diabetes Mellitus, Type 2/diagnosis , Fasting/blood , Female , Humans , Insulin Resistance , Male , Middle Aged , Postprandial Period
8.
Nat Chem Biol ; 14(12): 1150-1158, 2018 12.
Article in English | MEDLINE | ID: mdl-30420692

ABSTRACT

Human muscarinic receptor M2 is one of the five subtypes of muscarinic receptors belonging to the family of G-protein-coupled receptors. Muscarinic receptors are targets for multiple neurodegenerative diseases. The challenge has been designing subtype-selective ligands against one of the five muscarinic receptors. We report high-resolution structures of a thermostabilized mutant M2 receptor bound to a subtype-selective antagonist AF-DX 384 and a nonselective antagonist NMS. The thermostabilizing mutation S110R in M2 was predicted using a theoretical strategy previously developed in our group. Comparison of the crystal structures and pharmacological properties of the M2 receptor shows that the Arg in the S110R mutant mimics the stabilizing role of the sodium cation, which is known to allosterically stabilize inactive state(s) of class A GPCRs. Molecular dynamics simulations reveal that tightening of the ligand-residue contacts in M2 receptors compared to M3 receptors leads to subtype selectivity of AF-DX 384.


Subject(s)
Muscarinic Antagonists/metabolism , Pirenzepine/analogs & derivatives , Receptor, Muscarinic M2/chemistry , Receptor, Muscarinic M2/metabolism , Binding Sites , Crystallography, X-Ray , Enzyme Stability , Humans , Molecular Dynamics Simulation , Muscarinic Antagonists/chemistry , Mutation , N-Methylscopolamine/chemistry , N-Methylscopolamine/metabolism , Pirenzepine/chemistry , Pirenzepine/metabolism , Receptor, Muscarinic M2/antagonists & inhibitors
9.
Biochemistry ; 57(45): 6387-6390, 2018 11 13.
Article in English | MEDLINE | ID: mdl-30339352

ABSTRACT

Protein kinases achieve substrate selective phosphorylation through their conformational flexibility and dynamic interaction with the substrate. Designing substrate selective or kinase selective small molecule inhibitors remains a challenge because of a lack of understanding of the dynamic mechanism by which substrates are selected by the kinase. Using a combination of all-atom molecular dynamics simulations and FRET sensors, we have delineated an allosteric mechanism that results in interaction among the DFG motif, G-loop, and activation loop and structurally links the nucleotide and substrate binding interfaces in protein kinase Cα and three other Ser/Thr kinases. ATP-competitive staurosporine analogues engage this allosteric switch region located just outside the ATP binding site to displace substrate binding to varying degrees. These inhibitors function as bitopic ligands by occupying the ATP binding site and interacting with the allosteric switch region. The conserved mechanism identified in this study can be exploited to select and design bitopic inhibitors for kinases.


Subject(s)
Adenosine Triphosphate/metabolism , Protein Kinase C-alpha/antagonists & inhibitors , Protein Kinase C-alpha/metabolism , Protein Kinase Inhibitors/pharmacology , Allosteric Regulation , Allosteric Site , Binding Sites , Humans , Ligands , Molecular Dynamics Simulation , Phosphorylation , Serine/chemistry , Serine/metabolism , Threonine/chemistry , Threonine/metabolism
10.
J Chem Theory Comput ; 14(12): 6574-6585, 2018 Dec 11.
Article in English | MEDLINE | ID: mdl-30359017

ABSTRACT

Introduction of specific point mutations has been an effective strategy in enhancing the thermostability of G-protein-coupled receptors (GPCRs). Our previous work showed that a specific residue position on transmembrane helix 6 (TM6) in class A GPCRs consistently yields thermostable mutants. The crystal structure of human chemokine receptor CCR5 also showed increased thermostability upon mutation of two positions, A233D6.33 and K303E7.59. With the goal of testing the transferability of these two thermostabilizing mutations in other chemokine receptors, we tested the mutations A237D6.33 and R307E7.59 in human CCR3 for thermostability and aggregation properties in detergent solution. Interestingly, the double mutant exhibited a 6-10-fold decrease in the aggregation propensity of the wild-type protein. This is in stark contrast to the two single mutants whose aggregation properties resemble the wild type (WT). Moreover, unlike in CCR5, the two single mutants separately showed no increase in thermostability compared to the wild-type CCR3, while the double-mutant A237D6.33/R307E7.59 confers an increase of 2.6 °C in the melting temperature compared to the WT. Extensive all-atom molecular dynamics (MD) simulations in detergent micelles show that a salt bridge network between transmembrane helices TM3, TM6, and TM7 that is absent in the two single mutants confers stability in the double mutant. The free energy surface of the double mutant shows conformational homogeneity compared to the single mutants. An annular n-dodecyl maltoside detergent layer packs tighter to the hydrophobic surface of the double-mutant CCR3 compared to the single mutants providing additional stability. The purification of other C-C chemokine receptors lacking such stabilizing residues may benefit from the incorporation of these two point mutations.


Subject(s)
Cell Membrane/metabolism , Protein Engineering , Receptors, CCR3/chemistry , Receptors, CCR3/metabolism , Temperature , Humans , Hydrogen Bonding , Mutation , Protein Conformation, alpha-Helical , Protein Stability , Receptors, CCR3/genetics
11.
Cell Death Dis ; 9(3): 401, 2018 03 14.
Article in English | MEDLINE | ID: mdl-29540697

ABSTRACT

Rheumatoid arthritis (RA) is a systemic inflammatory disease that mainly affects the synovial joints. Although involvement of the fibroblast growth factor (FGF) signaling pathway has been suggested as an important modulator in RA development, no clear evidence has been provided. In this study, we found that synovial fluid basic FGF (bFGF) concentration was significantly higher in RA than in osteoarthritis (OA) patients. bFGF stimulates proliferation and migration of human fibroblast-like synoviocytes (FLSs) by activation of the bFGF-FGF receptor 3 (FGFR3)-ribosomal S6 kinase 2 (RSK2) signaling axis. Moreover, a molecular docking study revealed that kaempferol inhibited FGFR3 activity by binding to the active pocket of the FGFR3 kinase domain. Kaempferol forms hydrogen bonds with the FGFR3 backbone oxygen of Glu555 and Ala558 and the side chain of Lys508. Notably, the inhibition of bFGF-FGFR3-RSK2 signaling by kaempferol suppresses the proliferation and migration of RA FLSs and the release of activated T-cell-mediated inflammatory cytokines, such as IL-17, IL-21, and TNF-α. We further found that activated phospho-FGFR3 and -RSK2 were more highly observed in RA than in OA synovium. The hyperplastic lining and sublining lymphoid aggregate layers of RA synovium showed p-RSK2-expressing CD68+ macrophages with high frequency, while pRSK2-expressing CD4+ T-cells was observed at a lower frequency. Notably, kaempferol administration in collagen-induced arthritis mice relieved the frequency and severity of arthritis. Kaempferol reduced osteoclast differentiation in vitro and in vivo relative to the controls and was associated with the inhibition of osteoclast markers, such as tartrate-resistant acid phosphatase, integrin ß3, and MMP9. Conclusively, our data suggest that bFGF-induced FGFR3-RSK2 signaling may play a critical role during the initiation and progression of RA in terms of FLS proliferation and enhanced osteoclastogenesis, and that kaempferol may be effective as a new treatment for RA.


Subject(s)
Arthritis, Rheumatoid/prevention & control , Kaempferols/administration & dosage , Receptor, Fibroblast Growth Factor, Type 3/metabolism , Ribosomal Protein S6 Kinases, 90-kDa/metabolism , Animals , Arthritis, Rheumatoid/genetics , Arthritis, Rheumatoid/metabolism , Arthritis, Rheumatoid/physiopathology , Cell Movement/drug effects , Cell Proliferation/drug effects , Fibroblast Growth Factor 2/metabolism , Humans , Interleukin-17/genetics , Interleukin-17/metabolism , Interleukins/genetics , Interleukins/metabolism , Kaempferols/chemistry , Male , Mice , Mice, Inbred DBA , Molecular Docking Simulation , Receptor, Fibroblast Growth Factor, Type 3/antagonists & inhibitors , Receptor, Fibroblast Growth Factor, Type 3/chemistry , Receptor, Fibroblast Growth Factor, Type 3/genetics , Ribosomal Protein S6 Kinases, 90-kDa/genetics , Signal Transduction/drug effects , Synoviocytes/cytology , Synoviocytes/metabolism
12.
Mol Pharmacol ; 93(4): 288-296, 2018 04.
Article in English | MEDLINE | ID: mdl-29367258

ABSTRACT

G-protein-coupled receptors (GPCRs) mediate multiple signaling pathways in the cell, depending on the agonist that activates the receptor and multiple cellular factors. Agonists that show higher potency to specific signaling pathways over others are known as "biased agonists" and have been shown to have better therapeutic index. Although biased agonists are desirable, their design poses several challenges to date. The number of assays to identify biased agonists seems expensive and tedious. Therefore, computational methods that can reliably calculate the possible bias of various ligands ahead of experiments and provide guidance, will be both cost and time effective. In this work, using the mechanism of allosteric communication from the extracellular region to the intracellular transducer protein coupling region in GPCRs, we have developed a computational method to calculate ligand bias ahead of experiments. We have validated the method for several ß-arrestin-biased agonists in ß2-adrenergic receptor (ß2AR), serotonin receptors 5-HT1B and 5-HT2B and for G-protein-biased agonists in the κ-opioid receptor. Using this computational method, we also performed a blind prediction followed by experimental testing and showed that the agonist carmoterol is ß-arrestin-biased in ß2AR. Additionally, we have identified amino acid residues in the biased agonist binding site in both ß2AR and κ-opioid receptors that are involved in potentiating the ligand bias. We call these residues functional hotspots, and they can be used to derive pharmacophores to design biased agonists in GPCRs.


Subject(s)
Drug Design , Molecular Dynamics Simulation/trends , Receptors, G-Protein-Coupled/chemistry , Receptors, G-Protein-Coupled/metabolism , Adrenergic beta-2 Receptor Agonists/metabolism , Adrenergic beta-2 Receptor Agonists/pharmacology , Allosteric Regulation/drug effects , Allosteric Regulation/physiology , Binding Sites/drug effects , Binding Sites/physiology , Humans , Ligands , Protein Structure, Secondary , Protein Structure, Tertiary , Receptors, Adrenergic, beta-2/chemistry , Receptors, Adrenergic, beta-2/metabolism , Receptors, G-Protein-Coupled/agonists , Receptors, Opioid, kappa/agonists , Receptors, Opioid, kappa/chemistry , Receptors, Opioid, kappa/metabolism
13.
Materials (Basel) ; 10(3)2017 Mar 14.
Article in English | MEDLINE | ID: mdl-28772647

ABSTRACT

Dental light-cured resins can undergo different degrees of polymerization when applied in vivo. When polymerization is incomplete, toxic monomers may be released into the oral cavity. The present study assessed the cytotoxicity of different materials, using sample preparation methods that mirror clinical conditions. Composite and bonding resins were used and divided into four groups according to sample preparation method: uncured; directly cured samples, which were cured after being placed on solidified agar; post-cured samples were polymerized before being placed on agar; and "removed unreacted layer" samples had their oxygen-inhibition layer removed after polymerization. Cytotoxicity was evaluated using an agar diffusion test, MTT assay, and confocal microscopy. Uncured samples were the most cytotoxic, while removed unreacted layer samples were the least cytotoxic (p < 0.05). In the MTT assay, cell viability increased significantly in every group as the concentration of the extracts decreased (p < 0.05). Extracts from post-cured and removed unreacted layer samples of bonding resin were less toxic than post-cured and removed unreacted layer samples of composite resin. Removal of the oxygen-inhibition layer resulted in the lowest cytotoxicity. Clinicians should remove unreacted monomers on the resin surface immediately after restoring teeth with light-curing resin to improve the restoration biocompatibility.

14.
J Biol Chem ; 292(39): 16300-16309, 2017 09 29.
Article in English | MEDLINE | ID: mdl-28821615

ABSTRACT

Protein kinase Cα (PKCα) belongs to the family of AGC kinases that phosphorylate multiple peptide substrates. Although the consensus sequence motif has been identified and used to explain substrate specificity for PKCα, it does not inform the structural basis of substrate-binding and kinase activity for diverse substrates phosphorylated by this kinase. The transient, dynamic, and unstructured nature of this protein-protein interaction has limited structural mapping of kinase-substrate interfaces. Here, using multiscale MD simulation-based predictions and FRET sensor-based experiments, we investigated the conformational dynamics of the kinase-substrate interface. We found that the binding strength of the kinase-substrate interaction is primarily determined by long-range columbic interactions between basic (Arg/Lys) residues located N-terminally to the phosphorylated Ser/Thr residues in the substrate and by an acidic patch in the kinase catalytic domain. Kinase activity stemmed from conformational flexibility in the region C-terminal to the phosphorylated Ser/Thr residues. Flexibility of the substrate-kinase interaction enabled an Arg/Lys two to three amino acids C-terminal to the phosphorylated Ser/Thr to prime a catalytically active conformation, facilitating phosphoryl transfer to the substrate. The structural mechanisms determining substrate binding and catalytic activity formed the basis of diverse binding affinities and kinase activities of PKCα for 14 substrates with varying degrees of sequence conservation. Our findings provide insight into the dynamic properties of the kinase-substrate interaction that govern substrate binding and turnover. Moreover, this study establishes a modeling and experimental method to elucidate the structural dynamics underlying substrate selectivity among eukaryotic kinases.


Subject(s)
Models, Molecular , Protein Kinase C-alpha/metabolism , Amino Acid Substitution , Animals , Biocatalysis , Catalytic Domain , Computational Biology , Fluorescence Resonance Energy Transfer , Humans , Kinetics , Molecular Dynamics Simulation , Mutagenesis, Site-Directed , Mutation , Phosphorylation , Protein Conformation , Protein Engineering/methods , Protein Interaction Domains and Motifs , Protein Kinase C-alpha/chemistry , Protein Kinase C-alpha/genetics , Protein Processing, Post-Translational , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Sf9 Cells , Spodoptera , Structural Homology, Protein
15.
Sci Rep ; 6: 38564, 2016 12 07.
Article in English | MEDLINE | ID: mdl-27924846

ABSTRACT

Many G protein-coupled receptors show constitutive activity, resulting in the production of a second messenger in the absence of an agonist; and naturally occurring constitutively active mutations in receptors have been implicated in diseases. To gain insight into mechanistic aspects of constitutive activity, we report here the 3.3 Å crystal structure of a constitutively active, agonist-bound neurotensin receptor (NTSR1) and molecular dynamics simulations of agonist-occupied and ligand-free receptor. Comparison with the structure of a NTSR1 variant that has little constitutive activity reveals uncoupling of the ligand-binding domain from conserved connector residues, that effect conformational changes during GPCR activation. Furthermore, molecular dynamics simulations show strong contacts between connector residue side chains and increased flexibility at the intracellular receptor face as features that coincide with robust signalling in cells. The loss of correlation between the binding pocket and conserved connector residues, combined with altered receptor dynamics, possibly explains the reduced neurotensin efficacy in the constitutively active NTSR1 and a facilitated initial engagement with G protein in the absence of agonist.


Subject(s)
Molecular Dynamics Simulation , Protein Conformation , Receptors, Neurotensin/chemistry , Binding Sites , Catalytic Domain , Cell Line , GTP-Binding Proteins/chemistry , GTP-Binding Proteins/metabolism , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Ligands , Protein Binding , Receptors, Neurotensin/genetics , Receptors, Neurotensin/metabolism , Structure-Activity Relationship
16.
J Chem Theory Comput ; 12(11): 5575-5584, 2016 Nov 08.
Article in English | MEDLINE | ID: mdl-27709935

ABSTRACT

G-protein-coupled receptors (GPCRs) are transmembrane receptors involved in diverse biological functions. Despite the diversity in their amino acid sequences, class A GPCRs exhibit a conserved structural topology and possibly a common mechanism of receptor activation. To understand how this high sequence diversity translates to a conserved functional mechanism, we have compared the dynamic behavior of eight class A GPCRs comprised of six biogenic amine receptors, adenosine A2A, and the peptide receptor protease-activated receptor 1. Starting from the crystal structures of the inactive state of these receptors bound to inverse agonists or antagonists, we have performed multiple all-atom MD simulations adding up to several microseconds of simulation. We elucidated the similarities and differences in the dynamic behavior and the conformational ensembles sampled by these eight class A GPCRs. Among the six biogenic amine receptors studied here, ß2-adrenergic receptor shows the highest level of fluctuation in the sixth and seventh transmembrane helices, possibly explaining its high basal activity. In contrast, the muscarinic acetylcholine receptors show the lowest fluctuations as well as tight packing and low hydration of the transmembrane domain. All eight GPCRs show several conserved allosteric communication pipelines from the residues in the agonist binding site with the G-protein interface. Positions of the residues along these pipelines that serve as major hubs of allosteric communication are conserved in their respective structures. These findings have important implications in understanding the dynamics and allosteric mechanism of communication in class A GPCRs and hence are useful for designing conformation-specific drugs.


Subject(s)
Molecular Dynamics Simulation , Receptors, G-Protein-Coupled/chemistry , Allosteric Regulation , Binding Sites , Protein Domains , Protein Stability , Receptors, Adrenergic, beta-2/chemistry , Receptors, Adrenergic, beta-2/metabolism , Receptors, G-Protein-Coupled/metabolism , Receptors, Muscarinic/chemistry , Receptors, Muscarinic/metabolism , Water/chemistry
17.
J Am Chem Soc ; 138(47): 15425-15433, 2016 11 30.
Article in English | MEDLINE | ID: mdl-27792324

ABSTRACT

Stability of detergent-solubilized G-protein-coupled receptors (GPCRs) is crucial for their purification in a biologically relevant state, and it is well-known that short chain detergents such as octylglucoside are more denaturing than long chain detergents such as dodecylmaltoside. However, the molecular basis for this phenomenon is poorly understood. To gain insights into the mechanism of detergent destabilization of GPCRs, we used atomistic molecular dynamics simulations of thermostabilized adenosine receptor (A2AR) mutants embedded in either a lipid bilayer or detergent micelles of alkylmaltosides and alkylglucosides. A2AR mutants in dodecylmaltoside or phospholipid showed low flexibility and good interhelical packing. In contrast, A2AR mutants in either octylglucoside or nonylglucoside showed decreased α-helicity in transmembrane regions, decreased α-helical packing, and the interpenetration of detergent molecules between transmembrane α-helices. This was not observed in octylglucoside containing phospholipid. Cholesteryl hemisuccinate in dodecylmaltoside increased the energetic stability of the receptor by wedging into crevices on the hydrophobic surface of A2AR, increasing packing interactions within the receptor and stiffening the detergent micelle. The data suggest a three-stage process for the initial events in the destabilization of GPCRs by octylglucoside: (i) highly mobile detergent molecules form small micelles around the receptor; (ii) loss of α-helicity and decreased interhelical packing interactions in transmembrane regions are promoted by increased receptor thermal motion; (iii) transient separation of transmembrane helices allowed penetration of detergent molecules into the core of the receptor. The relative hydration of the headgroup and alkyl chain correlates with detergent harshness and suggests new avenues to develop milder versions of octylglucoside for receptor crystallization.


Subject(s)
Detergents/chemistry , Molecular Dynamics Simulation , Receptor, Adenosine A2A/chemistry , Mutation , Protein Stability , Receptor, Adenosine A2A/genetics
18.
Biomacromolecules ; 16(8): 2265-75, 2015 Aug 10.
Article in English | MEDLINE | ID: mdl-26176305

ABSTRACT

This study reports a synthetic polymer functionalized with catechol groups as dental adhesives. We hypothesize that a catechol-functionalized polymer functions as a dental adhesive for wet dentin surfaces, potentially eliminating the complications associated with saliva contamination. We prepared a random copolymer containing catechol and methoxyethyl groups in the side chains. The mechanical and adhesive properties of the polymer to dentin surface in the presence of water and salivary components were determined. It was found that the new polymer combined with an Fe(3+) additive improved bond strength of a commercial dental adhesive to artificial saliva contaminated dentin surface as compared to a control sample without the polymer. Histological analysis of the bonding structures showed no leakage pattern, probably due to the formation of Fe-catechol complexes, which reinforce the bonding structures. Cytotoxicity test showed that the polymers did not inhibit human gingival fibroblast cells proliferation. Results from this study suggest a potential to reduce failure of dental restorations due to saliva contamination using catechol-functionalized polymers as dental adhesives.


Subject(s)
Catechols/chemistry , Dental Cements/chemistry , Methacrylates/chemistry , Polymers/chemistry , Catechols/chemical synthesis , Composite Resins/chemical synthesis , Composite Resins/chemistry , Dental Bonding , Dental Cements/chemical synthesis , Dentin/chemistry , Humans , Materials Testing , Polymers/chemical synthesis , Surface Properties , Tensile Strength
19.
Opt Express ; 23(14): 18316-22, 2015 Jul 13.
Article in English | MEDLINE | ID: mdl-26191888

ABSTRACT

An in-line interferometer based on the intermodal coupling of a multicore fiber (MCF) is proposed and experimentally demonstrated. The in-line interferometer is fabricated by adiabatically tapering the MCF. The intermodal coupling of the in-line interferometer is strongly affected by the waist diameter of the MCF, which changes the evanescent field and the pitch size. The effect of the waist diameters of the MCF on the intermodal coupling in the in-line interferometer is theoretically and experimentally investigated. The transmission oscillations of the multiple core modes resulting from the intermodal coupling and interference substantially become stronger as the waist diameter decreases. The extinction ratio and the oscillation periodicity of the transmissions oscillations are changed by the waist diameter.

20.
Microsc Res Tech ; 78(8): 697-706, 2015 Aug.
Article in English | MEDLINE | ID: mdl-26085304

ABSTRACT

We describe the use of a rabbit maxillary sinus model, characterized by thin osseous tissue and low bone density, for the evaluation of surface-treated implants by histologically and histomorphometrically comparing the osseointegration patterns depending on the surface treatment methods. Twenty rabbits were randomly assigned to two groups of 10 animals, one receiving 5 × 3 mm customized implants (machined, MA or sandblasted and acid etched, SLA) placed in sinus and the other receiving implants placed in a tibia. Histological observation of the implant placed in sinus shows relatively more active new bone formation, characterized by trabecular bone pattern underneath the cortical bone in sinus as compared with that in tibia. Histomorphometric analysis in the rabbits receiving implants in a tibia, the NBIC (%) associated with the SLA surface implant was greater than that associated with the MA implant at 2 weeks (55.63 ± 8.65% vs. 47.87 ± 10.01%; P > 0.05) and at 4 weeks (61.76 ± 9.49% vs. 42.69 ± 10.97%; P < 0.05). Among rabbits receiving implants in a sinus, the NBIC (%) associated with the SLA surface implant was significantly greater than that associated with the MA surface implant both at 2 weeks (37.25 ± 7.27% vs. 20.98 ± 6.42%; P < 0.05) and at 4 weeks (48.82 ± 6.77% vs. 31.51 ± 9.14%; P < 0.05). As a result, we suggest that the maxillary sinus model is an appropriate animal model for assessing surface-treated implants and may be utilized for the evaluation of surface-treated implants in poor bone quality environment. Microsc. Res. Tech. 78:697-706, 2015.


Subject(s)
Dental Implants , Guided Tissue Regeneration/instrumentation , Guided Tissue Regeneration/methods , Maxillary Sinus/surgery , Models, Biological , Animals , Male , Rabbits , Surface Properties
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