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Items: 1 to 20 of 100

1.

Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs.

Tomobe K, Yamamoto E, Yasuoka K.

Methods Mol Biol. 2019;1947:21-30. doi: 10.1007/978-1-4939-9121-1_2.

PMID:
30969409
2.

Coarse-grained force fields for molecular simulations.

Barnoud J, Monticelli L.

Methods Mol Biol. 2015;1215:125-49. doi: 10.1007/978-1-4939-1465-4_7.

PMID:
25330962
3.

Cholesterol modulates the membrane effects and spatial organization of membrane-penetrating ligands for G-protein coupled receptors.

Khelashvili G, Mondal S, Andersen OS, Weinstein H.

J Phys Chem B. 2010 Sep 23;114(37):12046-57. doi: 10.1021/jp106373r.

4.

Molecular modeling and simulation of membrane lipid-mediated effects on GPCRs.

Sadiq SK, Guixa-Gonzalez R, Dainese E, Pastor M, De Fabritiis G, Selent J.

Curr Med Chem. 2013;20(1):22-38. Review.

PMID:
23151000
5.

G protein coupled receptor interactions with cholesterol deep in the membrane.

Genheden S, Essex JW, Lee AG.

Biochim Biophys Acta Biomembr. 2017 Feb;1859(2):268-281. doi: 10.1016/j.bbamem.2016.12.001. Epub 2016 Dec 3.

7.

Understanding the molecular basis of agonist/antagonist mechanism of GPER1/GPR30 through structural and energetic analyses.

Méndez-Luna D, Bello M, Correa-Basurto J.

J Steroid Biochem Mol Biol. 2016 Apr;158:104-116. doi: 10.1016/j.jsbmb.2016.01.001. Epub 2016 Jan 6.

PMID:
26772481
8.

Molecular dynamics simulations of GPCR-cholesterol interaction: An emerging paradigm.

Sengupta D, Chattopadhyay A.

Biochim Biophys Acta. 2015 Sep;1848(9):1775-82. doi: 10.1016/j.bbamem.2015.03.018. Epub 2015 Mar 25. Review.

9.

Molecular dynamics simulations of bovine rhodopsin: influence of protonation states and different membrane-mimicking environments.

Schlegel B, Sippl W, Höltje HD.

J Mol Model. 2005 Dec;12(1):49-64. Epub 2005 Oct 25.

PMID:
16247601
10.

The Molecular Switching Mechanism at the Conserved D(E)RY Motif in Class-A GPCRs.

Sandoval A, Eichler S, Madathil S, Reeves PJ, Fahmy K, Böckmann RA.

Biophys J. 2016 Jul 12;111(1):79-89. doi: 10.1016/j.bpj.2016.06.004.

11.

Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway.

Yuan S, Filipek S, Palczewski K, Vogel H.

Nat Commun. 2014 Sep 9;5:4733. doi: 10.1038/ncomms5733.

PMID:
25203160
12.

Key issues in the computational simulation of GPCR function: representation of loop domains.

Mehler EL, Periole X, Hassan SA, Weinstein H.

J Comput Aided Mol Des. 2002 Nov;16(11):841-53.

PMID:
12825797
13.

Characterization of the dynamic events of GPCRs by automated computational simulations.

Gutiérrez-de-Terán H, Bello X, Rodríguez D.

Biochem Soc Trans. 2013 Feb 1;41(1):205-12. doi: 10.1042/BST20120287. Review.

PMID:
23356284
14.

Internal hydration increases during activation of the G-protein-coupled receptor rhodopsin.

Grossfield A, Pitman MC, Feller SE, Soubias O, Gawrisch K.

J Mol Biol. 2008 Aug 29;381(2):478-86. doi: 10.1016/j.jmb.2008.05.036. Epub 2008 May 22.

15.

Coupled diffusion in lipid bilayers upon close approach.

Pronk S, Lindahl E, Kasson PM.

J Am Chem Soc. 2015 Jan 21;137(2):708-14. doi: 10.1021/ja508803d. Epub 2015 Jan 6.

16.

GPCRs: What Can We Learn from Molecular Dynamics Simulations?

Velgy N, Hedger G, Biggin PC.

Methods Mol Biol. 2018;1705:133-158. doi: 10.1007/978-1-4939-7465-8_6.

PMID:
29188561
17.

Molecular dynamics of water and monovalent-ions transportation mechanisms of pentameric sarcolipin.

Cao Y, Wu X, Lee I, Wang X.

Proteins. 2016 Jan;84(1):73-81. doi: 10.1002/prot.24956. Epub 2015 Nov 26.

PMID:
26522287
18.

Structure-based simulations reveal concerted dynamics of GPCR activation.

Leioatts N, Suresh P, Romo TD, Grossfield A.

Proteins. 2014 Oct;82(10):2538-51. doi: 10.1002/prot.24617. Epub 2014 Jun 9.

19.

Agonist-induced conformational changes in bovine rhodopsin: insight into activation of G-protein-coupled receptors.

Bhattacharya S, Hall SE, Vaidehi N.

J Mol Biol. 2008 Oct 3;382(2):539-55. doi: 10.1016/j.jmb.2008.06.084. Epub 2008 Jul 7.

PMID:
18638482
20.

Molecular dynamics simulations of lipid bilayers: simple recipe of how to do it.

Martinez-Seara H, Róg T.

Methods Mol Biol. 2013;924:407-29. doi: 10.1007/978-1-62703-017-5_15.

PMID:
23034757

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