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The Val34Met, Thr164Ile and Ser220Cys Polymorphisms of the β2-Adrenergic Receptor and Their Consequences on the Receptor Conformational Features: A Molecular Dynamics Simulation Study

Aneta Archala, Wojciech Plazinski, Anita Plazinska
2022 International Journal of Molecular Sciences  
The current study was focused on investigating to what extent the three polymorphisms of β2-AR (i.e., Val34Met, Thr164Ile and Ser220Cys) affect the interaction of β2-AR with its natural molecular environment  ...  The gene encoding the β2-adrenergic receptor (β2-AR) is polymorphic, which results in possible differences in a primary structure of this protein.  ...  The data were generated by using all-atom molecular dynamics simulations. AA Simulations (CHARMM) Interactions with Lipid Bilayer Gs Binding 9 ± 0.2 polymorph). Further details in the text.  ... 
doi:10.3390/ijms23105449 pmid:35628258 pmcid:PMC9141972 fatcat:lpklzn4h2jflnbtezjkjism5yy

2P270 Structural analysis of coupling element between β2 adrenergic receptor and G-protein(22A. Bioinformatics: Structural genomics,Poster)
2P270 β2アドレナリン受容体-Gas間の結合要素の解析(22A.生命情報科学:構造ゲノミクス,ポスター,日本生物物理学会年会第51回(2013年度))

Hidenori Sakaki, Masami Ikeda, Makiko Suwa
2013 Seibutsu Butsuri  
Based on the 3D structure of β2 adrenergic receptor ( βAR) with Gs type G-protein complex, we made several mutated structures ( βAR with non-Gs proteins), by comparative modeling, and optimized the side  ...  The respective ligand and pocket shape overlap was calculated. In addition, we addressed the effect of protein molecular dynamics on shape similarity between a protein pocket and its ligand.  ...  Based on the 3D structure of β2 adrenergic receptor ( βAR) with Gs type G-protein complex, we made several mutated structures ( βAR with non-Gs proteins), by comparative modeling, and optimized the side  ... 
doi:10.2142/biophys.53.s203_5 fatcat:v3ce75wa2bdalbl57xzup5izbi

2P267 Re-docking scheme for prediction of protein-protein interactions using interaction fingerprints(22A. Bioinformatics: Structural genomics,Poster)
2P267 相互作用プロファイルを用いたRe-docking法によるタンパク質間相互作用予測(22A.生命情報科学:構造ゲノミクス,ポスター,日本生物物理学会年会第51回(2013年度))

Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Takatsugu Hirokawa, Yutaka Akiyama
2013 Seibutsu Butsuri  
Based on the 3D structure of β2 adrenergic receptor ( βAR) with Gs type G-protein complex, we made several mutated structures ( βAR with non-Gs proteins), by comparative modeling, and optimized the side  ...  The respective ligand and pocket shape overlap was calculated. In addition, we addressed the effect of protein molecular dynamics on shape similarity between a protein pocket and its ligand.  ...  Based on the 3D structure of β2 adrenergic receptor ( βAR) with Gs type G-protein complex, we made several mutated structures ( βAR with non-Gs proteins), by comparative modeling, and optimized the side  ... 
doi:10.2142/biophys.53.s203_2 fatcat:ibrrl5k57betbpafu4hdnxcxdu

2P268 Protein binding pocket and ligand shape comparison(22A. Bioinformatics: Structural genomics,Poster)

Chie Motono, Takatsugu Hirokawa
2013 Seibutsu Butsuri  
Based on the 3D structure of β2 adrenergic receptor ( βAR) with Gs type G-protein complex, we made several mutated structures ( βAR with non-Gs proteins), by comparative modeling, and optimized the side  ...  The respective ligand and pocket shape overlap was calculated. In addition, we addressed the effect of protein molecular dynamics on shape similarity between a protein pocket and its ligand.  ...  Based on the 3D structure of β2 adrenergic receptor ( βAR) with Gs type G-protein complex, we made several mutated structures ( βAR with non-Gs proteins), by comparative modeling, and optimized the side  ... 
doi:10.2142/biophys.53.s203_3 fatcat:sa4bxazkbvhb3h2oq3udhsulyi

2P269 Construction of database for comparing structural data with microscopic image of transmembrane protein(22A. Bioinformatics: Structural genomics,Poster)
2P269 膜タンパク質の顕微鏡画像と立体構造データとの照合用データベースの構築(22A.生命情報科学:構造ゲノミクス,ポスター,日本生物物理学会年会第51回(2013年度))

Go Inoue, Masami Ikeda, Makiko Suwa
2013 Seibutsu Butsuri  
Based on the 3D structure of β2 adrenergic receptor ( βAR) with Gs type G-protein complex, we made several mutated structures ( βAR with non-Gs proteins), by comparative modeling, and optimized the side  ...  The respective ligand and pocket shape overlap was calculated. In addition, we addressed the effect of protein molecular dynamics on shape similarity between a protein pocket and its ligand.  ...  Based on the 3D structure of β2 adrenergic receptor ( βAR) with Gs type G-protein complex, we made several mutated structures ( βAR with non-Gs proteins), by comparative modeling, and optimized the side  ... 
doi:10.2142/biophys.53.s203_4 fatcat:gqpbnud5r5ak3hoxw6fnwjl4we

2P271 Flow cytometry identification of nanocyanobacteria and their limiting factors in the North Pacific Subtropical Gyre(23. Ecology & Environment,Poster)

Mathias Girault, Hisayuki Arakawa, Gerald Gregori, Fuminori Hashihama, Hyonchol Kim, Masao Odaka, Kenji Yasuda
2013 Seibutsu Butsuri  
Based on the 3D structure of β2 adrenergic receptor ( βAR) with Gs type G-protein complex, we made several mutated structures ( βAR with non-Gs proteins), by comparative modeling, and optimized the side  ...  The respective ligand and pocket shape overlap was calculated. In addition, we addressed the effect of protein molecular dynamics on shape similarity between a protein pocket and its ligand.  ...  Based on the 3D structure of β2 adrenergic receptor ( βAR) with Gs type G-protein complex, we made several mutated structures ( βAR with non-Gs proteins), by comparative modeling, and optimized the side  ... 
doi:10.2142/biophys.53.s203_6 fatcat:xbybqraw55dvblbtfzsr5uhq2i

2P266 Tertiary structure prediction of RNA-RNA complex structures using secondary structure information(22A. Bioinformatics: Structural genomics,Poster)

Satoshi Yamasaki, Kazuhiko Fukui
2013 Seibutsu Butsuri  
Based on the 3D structure of β2 adrenergic receptor ( βAR) with Gs type G-protein complex, we made several mutated structures ( βAR with non-Gs proteins), by comparative modeling, and optimized the side  ...  The respective ligand and pocket shape overlap was calculated. In addition, we addressed the effect of protein molecular dynamics on shape similarity between a protein pocket and its ligand.  ...  Based on the 3D structure of β2 adrenergic receptor ( βAR) with Gs type G-protein complex, we made several mutated structures ( βAR with non-Gs proteins), by comparative modeling, and optimized the side  ... 
doi:10.2142/biophys.53.s203_1 fatcat:flgpmoytofgdph5kybslv4epey

β2-adrenoceptor ligand efficacy is tuned by a two-stage interaction with the Gαs C terminus

Keehun Kim, Shayla Paulekas, Fredrik Sadler, Tejas M. Gupte, Michael Ritt, Matthew Dysthe, Nagarajan Vaidehi, Sivaraj Sivaramakrishnan
2021 Proceedings of the National Academy of Sciences of the United States of America  
A recent biophysical study has characterized a ligand "molecular efficacy" that quantifies the influence of ligand-dependent receptor conformation on G protein activation.  ...  Nonetheless, the structural translation of ligand molecular efficacy into G protein activation remains unclear and forms the focus of this study.  ...  We have previously reported that β2AR SPASM sensors probe ligand and receptor-dependent G protein selectivity by measuring the strength of the interaction between the receptor and the α5-helix of distinct  ... 
doi:10.1073/pnas.2017201118 pmid:33836582 fatcat:7mr5dit4gjcb3eeep6q6sjmrii

Cholesterol Modulates the Dimer Interface of the β2-Adrenergic Receptor via Cholesterol Occupancy Sites

Xavier Prasanna, Amitabha Chattopadhyay, Durba Sengupta
2014 Biophysical Journal  
We used MARTINI coarse-grained molecular-dynamics simulations to explore dimerization of the β2-adrenergic receptor in lipid bilayers containing cholesterol.  ...  The β2-adrenergic receptor is an important member of the G-protein-coupled receptor (GPCR) superfamily, whose stability and function are modulated by membrane cholesterol.  ...  If the receptor-Gs protein interaction includes a receptor dimer, the dimer interface observed in our simulations in POPC bilayers could lead to potential steric hindrance with the Gs protein since it  ... 
doi:10.1016/j.bpj.2014.02.002 pmid:24655504 pmcid:PMC3984991 fatcat:gy3r7lxgfjg2bo5s5y3artoe7m

Universal Properties and Specificities of the β2-Adrenergic Receptor-Gs Protein Complex Activation Mechanism Revealed by All-Atom Molecular Dynamics Simulations

Argha Mitra, Arijit Sarkar, Attila Borics
2021 International Journal of Molecular Sciences  
In this follow-up study, we have examined the β2-adrenergic receptor (β2AR) to see if our hypothesis drawn from an extensive study of the μ-opioid receptor (MOP) is fundamental and directly transferable  ...  We have found that there are some general similarities between the two receptors, in agreement with previous studies, and there are some receptor-specific differences that could be associated with different  ...  Acknowledgments: Computing resources were provided by the Government Agency of Information Technology Development, Hungary. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms221910423 pmid:34638767 pmcid:PMC8508748 fatcat:2pjvriythvdjbd3xxkzub2dvx4

Structural insight into G protein-coupled receptor signaling efficacy and bias between Gs and β-arrestin

Louis-Philippe picard, Anne-Marie Schönegge, Michel Bouvier
2019 ACS Pharmacology & Translational Science  
Using the β2-adrenergic receptor as a model, we identified a linker residue (L1243.43) between the known PIF and NPxxY structural motifs, that plays a central role in the differential efficacy of biased  ...  ligands toward the Gs and β-arrestin pathways.  ...  magnetic resonance spectroscopy, and molecular dynamic simulations. 12, 13 The β2-adrenergic receptor (β2AR) is a prototypical receptor for which ligands with different propensity to activate different  ... 
doi:10.1021/acsptsci.9b00012 pmid:32259053 pmcid:PMC7088954 fatcat:3rc3ergk4feydekiakndvkkl4y

Analysis of β2AR-Gs and β2AR-Gi complex formation by NMR spectroscopy

Xiuyan Ma, Yunfei Hu, Hossein Batebi, Jie Heng, Jun Xu, Xiangyu Liu, Xiaogang Niu, Hongwei Li, Peter W. Hildebrand, Changwen Jin, Brian K. Kobilka
2020 Proceedings of the National Academy of Sciences of the United States of America  
The β2-adrenergic receptor (β2AR) is a prototypical G protein-coupled receptor (GPCR) that preferentially couples to the stimulatory G protein Gs and stimulates cAMP formation.  ...  Here, we utilize solution nuclear magnetic resonance (NMR) spectroscopy and supporting molecular dynamics (MD) simulations to monitor the conformational changes in the G protein coupling interface of the  ...  All NMR spectra were obtained at the Beijing NMR Center and the NMR facility of the National Center for Protein Sciences at Peking University.  ... 
doi:10.1073/pnas.2009786117 pmid:32868434 fatcat:2xyer6ukbngzdcwbvjr52rksu4

Antibody Fragments Defining Biologically Relevant Conformations of Target Proteins

Alastair Lawson
2014 Antibodies  
protein conformational sampling.  ...  This review charts the progress being made in understanding function in the context of structure using this approach, and highlights new opportunities for drug discovery.  ...  Conflicts of Interest ADGL holds shares and share options in UCB.  ... 
doi:10.3390/antib3040289 fatcat:wog76krydndz5bbpzvvcg47aza

G protein coupled receptor interactions with cholesterol deep in the membrane

Samuel Genheden, Jonathan W. Essex, Anthony G. Lee
2017 Biochimica et Biophysica Acta - Biomembranes  
Simulations detect interactions between cholesterol and GPCRs deep in the membrane These interactions change on agonist binding Requirements for interaction are just a hydrogen bond partner and a hole  ...  We have detected a number of deep cholesterol binding sites on β 2 adrenergic and A 2A adenosine receptors, and shown changes in these sites on agonist binding.  ...  , as shown by neutron diffraction studies and full atomistic and coarse-grained molecular dynamic simulations and consistent with the reported high rate of flip-flop of cholesterol across the membrane  ... 
doi:10.1016/j.bbamem.2016.12.001 pmid:27919726 fatcat:bbjc7cjzorg6jljrr5zah4ffpm

Computational Study on the Different Ligands Induced Conformation Change of β2 Adrenergic Receptor-Gs Protein Complex

Qifeng Bai, Yang Zhang, Yihe Ban, Huanxiang Liu, Xiaojun Yao, Freddie Salsbury Jr
2013 PLoS ONE  
Here, we performed molecular dynamics (MD) simulations on the structures of b 2 AR-Gs protein in complex with different types of ligands.  ...  Citation: Bai Q, Zhang Y, Ban Y, Liu H, Yao X (2013) Computational Study on the Different Ligands Induced Conformation Change of b2 Adrenergic Receptor-Gs Protein Complex. PLoS ONE 8(7): e68138.  ...  Acknowledgments The authors wish to thank the Center of Communication and Network of Lanzhou University for supplying the graphics processing unit (GPU) workstation. Author Contributions  ... 
doi:10.1371/journal.pone.0068138 pmid:23922653 pmcid:PMC3726664 fatcat:5lyookbjmnc2dexbdh6h7kgnuq
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