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1.
Biochemistry ; 59(42): 4059-4071, 2020 10 27.
Artigo em Inglês | MEDLINE | ID: mdl-33054162

RESUMO

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.


Assuntos
Membrana Celular/metabolismo , Receptor A2A de Adenosina/metabolismo , Humanos , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Simulação de Dinâmica Molecular , Fosfatidilinositol 4,5-Difosfato/química , Fosfatidilinositol 4,5-Difosfato/metabolismo , Receptor A2A de Adenosina/química
2.
Biochemistry ; 59(23): 2125-2134, 2020 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-32437610

RESUMO

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.


Assuntos
Detergentes/farmacologia , Micelas , Receptores Acoplados a Proteínas G/química , Detergentes/química , Células HEK293 , Humanos , Simulação de Dinâmica Molecular , Estrutura Molecular , Estabilidade Proteica/efeitos dos fármacos
3.
Nat Chem Biol ; 14(12): 1150-1158, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30420692

RESUMO

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.


Assuntos
Antagonistas Muscarínicos/metabolismo , Pirenzepina/análogos & derivados , Receptor Muscarínico M2/química , Receptor Muscarínico M2/metabolismo , Sítios de Ligação , Cristalografia por Raios X , Estabilidade Enzimática , Humanos , Simulação de Dinâmica Molecular , Antagonistas Muscarínicos/química , Mutação , N-Metilescopolamina/química , N-Metilescopolamina/metabolismo , Pirenzepina/química , Pirenzepina/metabolismo , Receptor Muscarínico M2/antagonistas & inibidores
4.
Biochemistry ; 57(45): 6387-6390, 2018 11 13.
Artigo em Inglês | MEDLINE | ID: mdl-30339352

RESUMO

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.


Assuntos
Trifosfato de Adenosina/metabolismo , Proteína Quinase C-alfa/antagonistas & inibidores , Proteína Quinase C-alfa/metabolismo , Inibidores de Proteínas Quinases/farmacologia , Regulação Alostérica , Sítio Alostérico , Sítios de Ligação , Humanos , Ligantes , Simulação de Dinâmica Molecular , Fosforilação , Serina/química , Serina/metabolismo , Treonina/química , Treonina/metabolismo
5.
Mol Pharmacol ; 93(4): 288-296, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29367258

RESUMO

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.


Assuntos
Desenho de Fármacos , Simulação de Dinâmica Molecular/tendências , Receptores Acoplados a Proteínas G/química , Receptores Acoplados a Proteínas G/metabolismo , Agonistas de Receptores Adrenérgicos beta 2/metabolismo , Agonistas de Receptores Adrenérgicos beta 2/farmacologia , Regulação Alostérica/efeitos dos fármacos , Regulação Alostérica/fisiologia , Sítios de Ligação/efeitos dos fármacos , Sítios de Ligação/fisiologia , Humanos , Ligantes , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Receptores Adrenérgicos beta 2/química , Receptores Adrenérgicos beta 2/metabolismo , Receptores Acoplados a Proteínas G/agonistas , Receptores Opioides kappa/agonistas , Receptores Opioides kappa/química , Receptores Opioides kappa/metabolismo
6.
J Biol Chem ; 292(39): 16300-16309, 2017 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-28821615

RESUMO

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.


Assuntos
Modelos Moleculares , Proteína Quinase C-alfa/metabolismo , Substituição de Aminoácidos , Animais , Biocatálise , Domínio Catalítico , Biologia Computacional , Transferência Ressonante de Energia de Fluorescência , Humanos , Cinética , Simulação de Dinâmica Molecular , Mutagênese Sítio-Dirigida , Mutação , Fosforilação , Conformação Proteica , Engenharia de Proteínas/métodos , Domínios e Motivos de Interação entre Proteínas , Proteína Quinase C-alfa/química , Proteína Quinase C-alfa/genética , Processamento de Proteína Pós-Traducional , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Células Sf9 , Spodoptera , Homologia Estrutural de Proteína
7.
J Am Chem Soc ; 138(47): 15425-15433, 2016 11 30.
Artigo em Inglês | MEDLINE | ID: mdl-27792324

RESUMO

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.


Assuntos
Detergentes/química , Simulação de Dinâmica Molecular , Receptor A2A de Adenosina/química , Mutação , Estabilidade Proteica , Receptor A2A de Adenosina/genética
8.
Opt Express ; 23(14): 18316-22, 2015 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-26191888

RESUMO

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.

9.
Biomacromolecules ; 16(8): 2265-75, 2015 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-26176305

RESUMO

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.


Assuntos
Catecóis/química , Cimentos Dentários/química , Metacrilatos/química , Polímeros/química , Catecóis/síntese química , Resinas Compostas/síntese química , Resinas Compostas/química , Colagem Dentária , Cimentos Dentários/síntese química , Dentina/química , Humanos , Teste de Materiais , Polímeros/síntese química , Propriedades de Superfície , Resistência à Tração
10.
Opt Express ; 22(7): 7865-74, 2014 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-24718162

RESUMO

We experimentally demonstrate a femtosecond mode-locked, all-fiberized laser that operates in the 2 µm region and that incorporates a saturable absorber based on a bulk-structured bismuth telluride (Bi(2)Te(3)) topological insulator (TI). Our fiberized saturable absorber was prepared by depositing a mechanically exfoliated, ~30 µm-thick Bi(2)Te(3) TI layer on a side-polished optical fiber platform. The bulk crystalline structure of the prepared Bi(2)Te(3) layer was confirmed by Raman and X-ray photoelectron spectroscopy measurements. The modulation depth of the prepared saturable absorber was measured to be ~20.6%. Using the saturable absorber, it is shown that stable, ultrafast pulses with a temporal width of ~795 fs could readily be generated at a wavelength of 1935 nm from a thulium/holmium co-doped fiber ring cavity. This experimental demonstration confirms that bulk structured, TI-based saturable absorbers can readily be used as an ultra-fast mode-locker for 2 µm lasers.

11.
J Nanosci Nanotechnol ; 14(10): 7847-54, 2014 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-25942879

RESUMO

We investigated whether a silver coating on an anodic oxidized titania (TiO2) nanotube surface would be useful for preventing infections in dental implants. We used a magnetron sputtering process to deposit Ag nanoparticles onto a TiO2 surface. We studied different sputtering input power densities and maintained other parameters constant. We used scanning electron microscopy, X-ray diffraction, and contact angle measurements to characterize the coated surfaces. Staphylococcus aureus was used to evaluate antibacterial activity. The X-ray diffraction analysis showed peaks that corresponded to metallic Ag, Ti, O, and biocompatible anatase phase TiO2 on the examined surfaces. The contact angles of the Ag nanoparticle-loaded surfaces were significantly lower at 2.5 W/cm2 input power under pulsed direct current mode compared to commercial, untreated Ti surfaces. In vitro antibacterial analysis indicated that a significantly reduced number of S. aureus were detected on an Ag nanoparticle-loaded TiO2 nanotube surface compared to control untreated surfaces. No cytotoxicity was noted, except in the group treated with 5 W/cm2 input power density, which was the highest input of power density we tested for the magnetron sputtering process. Overall, we concluded that it was feasible to create antibacterial Ag nanoparticle-loaded titanium nanotube surfaces with magnetron sputtering.


Assuntos
Antibacterianos/química , Materiais Revestidos Biocompatíveis/química , Implantes Dentários , Nanopartículas Metálicas/química , Nanotubos/química , Prata/química , Titânio/química , Animais , Antibacterianos/farmacologia , Antibacterianos/toxicidade , Linhagem Celular , Materiais Revestidos Biocompatíveis/farmacologia , Materiais Revestidos Biocompatíveis/toxicidade , Masculino , Camundongos , Pressão , Staphylococcus aureus/efeitos dos fármacos , Propriedades de Superfície , Titânio/farmacologia , Titânio/toxicidade
12.
Poult Sci ; 93(5): 1251-7, 2014 May.
Artigo em Inglês | MEDLINE | ID: mdl-24795319

RESUMO

The purpose of this study was to investigate the distribution of Salmonella species in an integrated broiler supply chain in Korea. A total of 1,214 samples from various steps of an integrated broiler production company including broiler breeder farms, broiler farms, broiler trucks, slaughterhouse, and retail chicken meats were collected and investigated. Salmonella was detected in 195 of the samples. The highest prevalence of Salmonella was observed in broiler transporting trucks (71.43%), followed by the slaughterhouse (63.89%) and broiler farms (16.05%). Salmonella Hadar was the most frequently isolated serotype (83.08%). All Salmonella Hadar isolates investigated in this study with pulsed-field gel electrophoresis showed the same XbaI pulsed-field gel electrophoresis pulsotype.


Assuntos
Galinhas , Doenças das Aves Domésticas/epidemiologia , Salmonelose Animal/epidemiologia , Salmonella/classificação , Salmonella/isolamento & purificação , Matadouros , Criação de Animais Domésticos , Animais , Eletroforese em Gel de Campo Pulsado/veterinária , Carne/microbiologia , Reação em Cadeia da Polimerase/veterinária , Doenças das Aves Domésticas/microbiologia , Prevalência , República da Coreia/epidemiologia , Salmonella/genética , Salmonelose Animal/microbiologia , Sorotipagem/veterinária , Especificidade da Espécie , Meios de Transporte
13.
Acta Odontol Scand ; 72(8): 618-22, 2014 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-24471730

RESUMO

OBJECTIVES: Vinyl polysiloxane (VPS) is elastomeric dental impression material which, despite having very few reports of adverse reactions, has shown high levels of cytotoxicity that is difficult to be interpreted without referencing to the positive control material. Therefore, in this study, positive control VPS was developed using sodium lauryl sulfate (SLS) for the reference of cytotoxicity test. MATERIALS AND METHODS: The positive control VPS with SLS was formed with a different proportion of SLS (0, 1, 2, 4, 8 and 16 wt%) added to the base. The cytotoxicity test was then carried out using the extractions or dilutions of the extractions from each of the test samples using murine fibroblast cells (L929). RESULTS: The final product of positive control VPS behaved similar to commercially available VPS; being initially liquid-like and then becoming rubber-like. Ion chromatography showed that the level of SLS released from the product increased as the proportion of added SLS increased, consequently resulting in an increased level of cytotoxicity. Also, the commercially available VPS was less cytotoxic than the positive control VPS with more or equal to 2 wt% of SLS. However, even the VPS with the highest SLS (16 wt%) did not cause oral mucosa irritation during the animal study. CONCLUSIONS: The positive control VPS was successfully produced using SLS, which will be useful in terms of providing references during in vitro cytotoxicity testing.


Assuntos
Materiais para Moldagem Odontológica/toxicidade , Polivinil/toxicidade , Siloxanas/toxicidade , Dodecilsulfato de Sódio/toxicidade , Tensoativos/toxicidade , Animais , Linhagem Celular , Cromatografia por Troca Iônica , Cricetinae , Materiais para Moldagem Odontológica/análise , Fibroblastos/efeitos dos fármacos , Teste de Materiais , Mesocricetus , Camundongos , Mucosa Bucal/efeitos dos fármacos , Polivinil/análise , Siloxanas/análise , Dodecilsulfato de Sódio/análise , Sulfatos/análise , Tensoativos/análise , Fatores de Tempo
14.
Opt Express ; 21(17): 20062-72, 2013 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-24105553

RESUMO

An in-depth experimental investigation was conducted into the use of a graphene oxide-based saturable absorber implemented on a side-polished fiber platform for femtosecond pulse generation in the 2 µm region. First, it was experimentally shown that an all-fiberized thulium-holmium (Tm-Ho)-codoped fiber ring laser with reduced cavity length can produce stable femtosecond pulses by incorporating a graphene oxide-deposited side-polished fiber. Second, the measurement accuracy issue in obtaining a precise pulse-width value by use of an autocorrelator together with a silica fiber-based 2 µm-band amplifier was investigated. It showed that the higher-order soliton compression effect caused by the combination of anomalous dispersion and Kerr nonlinearity can provide incorrect pulse-width information. Third, an experimental investigation into the precise role of the graphene oxide-deposited side-polished fiber was carried out to determine whether its polarization-dependent loss (PDL) can be a substantial contributor to mode-locking through nonlinear polarization rotation. By comparing its performance with that of a gold-deposited side-polished fiber, the PDL contribution to mode-locking was found to be insignificant, and the dominant mode-locking mechanism was shown to be saturable absorption due to mutual interaction between the evanescent field of the oscillated beam and the deposited graphene oxide particles.

15.
J Mol Graph Model ; 118: 108365, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36335829

RESUMO

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.


Assuntos
Angiotensina II , Receptor Tipo 1 de Angiotensina , Receptor Tipo 1 de Angiotensina/agonistas , Receptor Tipo 1 de Angiotensina/metabolismo , Angiotensina II/química , Angiotensina II/metabolismo , Angiotensina II/farmacologia , Espectroscopia de Ressonância de Spin Eletrônica , beta-Arrestinas/metabolismo , Ligantes , Conformação Proteica
16.
Acta Odontol Scand ; 70(6): 597-602, 2012 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-22182313

RESUMO

OBJECTIVE: Cytotoxicity evaluation is an important step in biocompatibility assessment of dental impression materials. Previously, cytotoxicity evaluations were carried out on already set ('set') impression materials for contact time or extraction time of 24 h or longer in duration. However, clinically, dental impression materials are in contact with oral tissue while they are being set ('polymerizing'), for no longer than 10 min. Hence, the aim of this study was to investigate the difference in results between 'polymerizing' and 'set' forms of impression materials as well as the difference in results between longer duration of contact or extraction time (12 or 24 h) and shorter duration of time (15 or 30 min). MATERIALS AND METHODS: Seven dental impression materials of different chemical compositions were tested. Two commonly used in vitro tests were used-test on extraction and test by direct contact. Both 'polymerizing' and 'set' forms of impression materials were used with different durations of extraction and contact (15 min, 30 min, 12 h and 24 h). RESULTS: There were significant (p < 0.05) differences of cell viability and cell proliferation between the 'polymerizing' and 'set' impression materials. Also, significant (p < 0.05) differences were noted with variance in duration of time. CONCLUSION: In light of the results, it is recommended to use a 'polymerizing' state of dental impression material for cytotoxicity evaluation, with 15 or 30 min of contact between cell and dental impression materials and an extraction time of 15 or 30 min that is more reflective of clinical situations.


Assuntos
Materiais Biocompatíveis , Materiais Dentários
17.
Nat Commun ; 13(1): 7428, 2022 12 02.
Artigo em Inglês | MEDLINE | ID: mdl-36460632

RESUMO

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.


Assuntos
Bioensaio , Simulação de Dinâmica Molecular , Projetos de Pesquisa
18.
Polymers (Basel) ; 14(1)2021 Dec 23.
Artigo em Inglês | MEDLINE | ID: mdl-35012059

RESUMO

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.

19.
J Am Chem Soc ; 132(21): 7252-3, 2010 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-20446682

RESUMO

X-ray crystallographic snapshots have shown that conformational changes of a tetraglycine loop in the active site of formyl-CoA:oxalate CoA transferase (FRC) play an important role in the catalytic cycle of the enzyme. Orthogonal space random walk (OSRW) simulations have been applied to obtain quantitative computational estimates of the relative free energy of the "open" and "closed" conformations of this loop together with the energetic barrier for interconversion of these states in wild type FRC. These OSRW calculations not only show that the two conformations have similar free energies but also predict a barrier that is consistent with the observed turnover number of the enzyme. In an effort to quantitate the importance of specific residues in the tetraglycine loop, OSRW simulations have also been performed on the G258A, G259A, G260A, and G261A FRC variants both to examine the energetic effects of replacing each glycine residue and to correlate the computed energies with kinetic and structural observations. In enzymes with substantially reduced catalytic efficiency (k(cat)/K(M)), the OSRW simulations reveal the adoption of additional low energy loop conformations. In the case of the G260A FRC variant, the new conformation identified by simulation is similar to that observed in the X-ray crystal structure of the protein. These results provide further evidence for the power of the OSRW method in sampling conformational space and, hence, in providing quantitative free energy estimates for the conformations adopted by functionally important active site loops. In addition, these simulations model the motions of side chains that are correlated with changes in loop conformation thereby permitting access to long time-scale motions through the use of nanosecond simulations.


Assuntos
Coenzima A-Transferases/química , Oxalatos/química , Domínio Catalítico , Coenzima A-Transferases/genética , Simulação por Computador , Cristalografia por Raios X , Entropia , Modelos Químicos , Movimento (Física) , Mutação , Estrutura Secundária de Proteína
20.
Mol Cancer Ther ; 7(7): 2133-41, 2008 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-18645023

RESUMO

The recombinant two kringle domain of human tissue-type plasminogen activator (TK1-2) has been shown to inhibit endothelial cell proliferation, angiogenesis, and tumor cell growth despite of sharing a low amino acid sequence homology with angiostatin. Here, we explored a possible inhibitory mechanism of action of TK1-2 by focusing on antimigratory effect. TK1-2 effectively inhibited endothelial cell migration induced by basic fibroblast growth factor or vascular endothelial growth factor in a dose-dependent manner and tube formation on Matrigel. It blocked basic fibroblast growth factor-induced or vascular endothelial growth factor-induced phosphorylation of extracellular signal-regulated kinase 1/2 and formation of actin stress fibers and focal adhesions. Interestingly, TK1-2 alone induced the weak phosphorylation of focal adhesion kinase, whereas it inhibited focal adhesion kinase phosphorylation induced by growth factors. When immobilized, TK1-2 promoted adhesion and spreading of endothelial cells compared with bovine serum albumin. However, treatment with anti-alpha(2)beta(1) blocking antibody markedly diminished endothelial cell adhesion to immobilized TK1-2 compared with anti-alpha(v)beta(3) or anti-alpha(5)beta(1) antibody. Pretreatment of soluble TK1-2 also altered the binding level of anti-alpha(2)beta(1) antibody to endothelial cells in fluorescence-activated cell sorting analysis. Indeed, a blocking antibody against integrin alpha(2)beta(1) or knocking down of integrin alpha(2) expression prevented the inhibitory effect of TK1-2 in cell migration. Therefore, these results suggest that TK1-2 inhibits endothelial cell migration through inhibition of signaling and cytoskeleton rearrangement in part by interfering with integrin alpha(2)beta(1).


Assuntos
Movimento Celular/efeitos dos fármacos , Integrina alfa2beta1/metabolismo , Peptídeos/farmacologia , Ativador de Plasminogênio Tecidual/química , Actinas/metabolismo , Anticorpos , Células Cultivadas , Regulação para Baixo/efeitos dos fármacos , Células Endoteliais/citologia , Células Endoteliais/efeitos dos fármacos , Células Endoteliais/enzimologia , Ativação Enzimática/efeitos dos fármacos , MAP Quinases Reguladas por Sinal Extracelular/metabolismo , Proteína-Tirosina Quinases de Adesão Focal/metabolismo , Adesões Focais/efeitos dos fármacos , Humanos , Neovascularização Fisiológica/efeitos dos fármacos , Ligação Proteica/efeitos dos fármacos , Estrutura Terciária de Proteína , Transdução de Sinais/efeitos dos fármacos , Fibras de Estresse/efeitos dos fármacos
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