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Items: 1 to 50 of 68

1.

Structural insights into binding specificity, efficacy and bias of a β2AR partial agonist.

Masureel M, Zou Y, Picard LP, van der Westhuizen E, Mahoney JP, Rodrigues JPGLM, Mildorf TJ, Dror RO, Shaw DE, Bouvier M, Pardon E, Steyaert J, Sunahara RK, Weis WI, Zhang C, Kobilka BK.

Nat Chem Biol. 2018 Nov;14(11):1059-1066. doi: 10.1038/s41589-018-0145-x. Epub 2018 Oct 16.

PMID:
30327561
2.

Structural basis for σ1 receptor ligand recognition.

Schmidt HR, Betz RM, Dror RO, Kruse AC.

Nat Struct Mol Biol. 2018 Oct;25(10):981-987. doi: 10.1038/s41594-018-0137-2. Epub 2018 Oct 5.

PMID:
30291362
3.

Molecular Dynamics Simulation for All.

Hollingsworth SA, Dror RO.

Neuron. 2018 Sep 19;99(6):1129-1143. doi: 10.1016/j.neuron.2018.08.011. Review.

PMID:
30236283
4.

Structural mechanisms of selectivity and gating in anion channelrhodopsins.

Kato HE, Kim YS, Paggi JM, Evans KE, Allen WE, Richardson C, Inoue K, Ito S, Ramakrishnan C, Fenno LE, Yamashita K, Hilger D, Lee SY, Berndt A, Shen K, Kandori H, Dror RO, Kobilka BK, Deisseroth K.

Nature. 2018 Sep;561(7723):349-354. doi: 10.1038/s41586-018-0504-5. Epub 2018 Aug 29.

PMID:
30158697
5.

Crystal structure of the natural anion-conducting channelrhodopsin GtACR1.

Kim YS, Kato HE, Yamashita K, Ito S, Inoue K, Ramakrishnan C, Fenno LE, Evans KE, Paggi JM, Dror RO, Kandori H, Kobilka BK, Deisseroth K.

Nature. 2018 Sep;561(7723):343-348. doi: 10.1038/s41586-018-0511-6. Epub 2018 Aug 29.

PMID:
30158696
6.

Entry from the Lipid Bilayer: A Possible Pathway for Inhibition of a Peptide G Protein-Coupled Receptor by a Lipophilic Small Molecule.

Bokoch MP, Jo H, Valcourt JR, Srinivasan Y, Pan AC, Capponi S, Grabe M, Dror RO, Shaw DE, DeGrado WF, Coughlin SR.

Biochemistry. 2018 Oct 2;57(39):5748-5758. doi: 10.1021/acs.biochem.8b00577. Epub 2018 Aug 27.

PMID:
30102523
7.

Structure of the µ-opioid receptor-Gi protein complex.

Koehl A, Hu H, Maeda S, Zhang Y, Qu Q, Paggi JM, Latorraca NR, Hilger D, Dawson R, Matile H, Schertler GFX, Granier S, Weis WI, Dror RO, Manglik A, Skiniotis G, Kobilka BK.

Nature. 2018 Jun;558(7711):547-552. doi: 10.1038/s41586-018-0219-7. Epub 2018 Jun 13.

PMID:
29899455
8.

Catalytic activation of β-arrestin by GPCRs.

Eichel K, Jullié D, Barsi-Rhyne B, Latorraca NR, Masureel M, Sibarita JB, Dror RO, von Zastrow M.

Nature. 2018 May;557(7705):381-386. doi: 10.1038/s41586-018-0079-1. Epub 2018 May 2.

PMID:
29720660
9.

Molecular mechanism of GPCR-mediated arrestin activation.

Latorraca NR, Wang JK, Bauer B, Townshend RJL, Hollingsworth SA, Olivieri JE, Xu HE, Sommer ME, Dror RO.

Nature. 2018 May;557(7705):452-456. doi: 10.1038/s41586-018-0077-3. Epub 2018 May 2.

PMID:
29720655
10.

Gi- and Gs-coupled GPCRs show different modes of G-protein binding.

Van Eps N, Altenbach C, Caro LN, Latorraca NR, Hollingsworth SA, Dror RO, Ernst OP, Hubbell WL.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2383-2388. doi: 10.1073/pnas.1721896115. Epub 2018 Feb 20.

11.

Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs.

McCorvy JD, Butler KV, Kelly B, Rechsteiner K, Karpiak J, Betz RM, Kormos BL, Shoichet BK, Dror RO, Jin J, Roth BL.

Nat Chem Biol. 2018 Feb;14(2):126-134. doi: 10.1038/nchembio.2527. Epub 2017 Dec 11.

12.

D4 dopamine receptor high-resolution structures enable the discovery of selective agonists.

Wang S, Wacker D, Levit A, Che T, Betz RM, McCorvy JD, Venkatakrishnan AJ, Huang XP, Dror RO, Shoichet BK, Roth BL.

Science. 2017 Oct 20;358(6361):381-386. doi: 10.1126/science.aan5468.

13.

Mechanism of intracellular allosteric β2AR antagonist revealed by X-ray crystal structure.

Liu X, Ahn S, Kahsai AW, Meng KC, Latorraca NR, Pani B, Venkatakrishnan AJ, Masoudi A, Weis WI, Dror RO, Chen X, Lefkowitz RJ, Kobilka BK.

Nature. 2017 Aug 24;548(7668):480-484. doi: 10.1038/nature23652. Epub 2017 Aug 16.

14.

Identification of Phosphorylation Codes for Arrestin Recruitment by G Protein-Coupled Receptors.

Zhou XE, He Y, de Waal PW, Gao X, Kang Y, Van Eps N, Yin Y, Pal K, Goswami D, White TA, Barty A, Latorraca NR, Chapman HN, Hubbell WL, Dror RO, Stevens RC, Cherezov V, Gurevich VV, Griffin PR, Ernst OP, Melcher K, Xu HE.

Cell. 2017 Jul 27;170(3):457-469.e13. doi: 10.1016/j.cell.2017.07.002.

15.

Structural and Functional Analysis of a β2-Adrenergic Receptor Complex with GRK5.

Komolov KE, Du Y, Duc NM, Betz RM, Rodrigues JPGLM, Leib RD, Patra D, Skiniotis G, Adams CM, Dror RO, Chung KY, Kobilka BK, Benovic JL.

Cell. 2017 Apr 20;169(3):407-421.e16. doi: 10.1016/j.cell.2017.03.047.

16.

Mechanism of Substrate Translocation in an Alternating Access Transporter.

Latorraca NR, Fastman NM, Venkatakrishnan AJ, Frommer WB, Dror RO, Feng L.

Cell. 2017 Mar 23;169(1):96-107.e12. doi: 10.1016/j.cell.2017.03.010.

17.

Crystal Structure of an LSD-Bound Human Serotonin Receptor.

Wacker D, Wang S, McCorvy JD, Betz RM, Venkatakrishnan AJ, Levit A, Lansu K, Schools ZL, Che T, Nichols DE, Shoichet BK, Dror RO, Roth BL.

Cell. 2017 Jan 26;168(3):377-389.e12. doi: 10.1016/j.cell.2016.12.033.

18.

Crystal Structure of a Full-Length Human Tetraspanin Reveals a Cholesterol-Binding Pocket.

Zimmerman B, Kelly B, McMillan BJ, Seegar TCM, Dror RO, Kruse AC, Blacklow SC.

Cell. 2016 Nov 3;167(4):1041-1051.e11. doi: 10.1016/j.cell.2016.09.056. Epub 2016 Oct 27.

19.

GPCR Dynamics: Structures in Motion.

Latorraca NR, Venkatakrishnan AJ, Dror RO.

Chem Rev. 2017 Jan 11;117(1):139-155. doi: 10.1021/acs.chemrev.6b00177. Epub 2016 Sep 13. Review.

20.

Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

Hertig S, Latorraca NR, Dror RO.

PLoS Comput Biol. 2016 Jun 10;12(6):e1004746. doi: 10.1371/journal.pcbi.1004746. eCollection 2016 Jun. Review.

21.

Molecular Basis of Ligand Dissociation from the Adenosine A2A Receptor.

Guo D, Pan AC, Dror RO, Mocking T, Liu R, Heitman LH, Shaw DE, IJzerman AP.

Mol Pharmacol. 2016 May;89(5):485-91. doi: 10.1124/mol.115.102657. Epub 2016 Feb 12.

22.

Structural insights into µ-opioid receptor activation.

Huang W, Manglik A, Venkatakrishnan AJ, Laeremans T, Feinberg EN, Sanborn AL, Kato HE, Livingston KE, Thorsen TS, Kling RC, Granier S, Gmeiner P, Husbands SM, Traynor JR, Weis WI, Steyaert J, Dror RO, Kobilka BK.

Nature. 2015 Aug 20;524(7565):315-21. doi: 10.1038/nature14886. Epub 2015 Aug 5.

23.

SIGNAL TRANSDUCTION. Structural basis for nucleotide exchange in heterotrimeric G proteins.

Dror RO, Mildorf TJ, Hilger D, Manglik A, Borhani DW, Arlow DH, Philippsen A, Villanueva N, Yang Z, Lerch MT, Hubbell WL, Kobilka BK, Sunahara RK, Shaw DE.

Science. 2015 Jun 19;348(6241):1361-5. doi: 10.1126/science.aaa5264.

24.

Identifying localized changes in large systems: Change-point detection for biomolecular simulations.

Fan Z, Dror RO, Mildorf TJ, Piana S, Shaw DE.

Proc Natl Acad Sci U S A. 2015 Jun 16;112(24):7454-9. doi: 10.1073/pnas.1415846112. Epub 2015 May 29.

25.

Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor.

Burg JS, Ingram JR, Venkatakrishnan AJ, Jude KM, Dukkipati A, Feinberg EN, Angelini A, Waghray D, Dror RO, Ploegh HL, Garcia KC.

Science. 2015 Mar 6;347(6226):1113-7. doi: 10.1126/science.aaa5026.

26.

Insights into the role of Asp79(2.50) in β2 adrenergic receptor activation from molecular dynamics simulations.

Ranganathan A, Dror RO, Carlsson J.

Biochemistry. 2014 Nov 25;53(46):7283-96. doi: 10.1021/bi5008723. Epub 2014 Nov 12.

PMID:
25347607
27.

Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure.

Lippert RA, Predescu C, Ierardi DJ, Mackenzie KM, Eastwood MP, Dror RO, Shaw DE.

J Chem Phys. 2013 Oct 28;139(16):164106. doi: 10.1063/1.4825247.

PMID:
24182003
28.

Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs.

Dror RO, Green HF, Valant C, Borhani DW, Valcourt JR, Pan AC, Arlow DH, Canals M, Lane JR, Rahmani R, Baell JB, Sexton PM, Christopoulos A, Shaw DE.

Nature. 2013 Nov 14;503(7475):295-9. doi: 10.1038/nature12595. Epub 2013 Oct 13.

PMID:
24121438
29.

Her2 activation mechanism reflects evolutionary preservation of asymmetric ectodomain dimers in the human EGFR family.

Arkhipov A, Shan Y, Kim ET, Dror RO, Shaw DE.

Elife. 2013 Jul 16;2:e00708. doi: 10.7554/eLife.00708.

30.

The role of ligands on the equilibria between functional states of a G protein-coupled receptor.

Kim TH, Chung KY, Manglik A, Hansen AL, Dror RO, Mildorf TJ, Shaw DE, Kobilka BK, Prosser RS.

J Am Chem Soc. 2013 Jun 26;135(25):9465-74. doi: 10.1021/ja404305k. Epub 2013 Jun 14.

31.

Molecular determinants of drug-receptor binding kinetics.

Pan AC, Borhani DW, Dror RO, Shaw DE.

Drug Discov Today. 2013 Jul;18(13-14):667-73. doi: 10.1016/j.drudis.2013.02.007. Epub 2013 Feb 27. Review.

PMID:
23454741
32.

The dynamic process of β(2)-adrenergic receptor activation.

Nygaard R, Zou Y, Dror RO, Mildorf TJ, Arlow DH, Manglik A, Pan AC, Liu CW, Fung JJ, Bokoch MP, Thian FS, Kobilka TS, Shaw DE, Mueller L, Prosser RS, Kobilka BK.

Cell. 2013 Jan 31;152(3):532-42. doi: 10.1016/j.cell.2013.01.008.

33.

High-resolution crystal structure of human protease-activated receptor 1.

Zhang C, Srinivasan Y, Arlow DH, Fung JJ, Palmer D, Zheng Y, Green HF, Pandey A, Dror RO, Shaw DE, Weis WI, Coughlin SR, Kobilka BK.

Nature. 2012 Dec 20;492(7429):387-92. doi: 10.1038/nature11701. Epub 2012 Dec 9.

34.

Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.

Piana S, Lindorff-Larsen K, Dirks RM, Salmon JK, Dror RO, Shaw DE.

PLoS One. 2012;7(6):e39918. doi: 10.1371/journal.pone.0039918. Epub 2012 Jun 29.

35.

Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization.

Shan Y, Eastwood MP, Zhang X, Kim ET, Arkhipov A, Dror RO, Jumper J, Kuriyan J, Shaw DE.

Cell. 2012 May 11;149(4):860-70. doi: 10.1016/j.cell.2012.02.063.

36.

Biomolecular simulation: a computational microscope for molecular biology.

Dror RO, Dirks RM, Grossman JP, Xu H, Shaw DE.

Annu Rev Biophys. 2012;41:429-52. doi: 10.1146/annurev-biophys-042910-155245. Review.

PMID:
22577825
37.

Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.

Raval A, Piana S, Eastwood MP, Dror RO, Shaw DE.

Proteins. 2012 Aug;80(8):2071-9. doi: 10.1002/prot.24098. Epub 2012 May 15.

PMID:
22513870
38.

Mechanism of voltage gating in potassium channels.

Jensen MØ, Jogini V, Borhani DW, Leffler AE, Dror RO, Shaw DE.

Science. 2012 Apr 13;336(6078):229-33. doi: 10.1126/science.1216533.

39.

Systematic validation of protein force fields against experimental data.

Lindorff-Larsen K, Maragakis P, Piana S, Eastwood MP, Dror RO, Shaw DE.

PLoS One. 2012;7(2):e32131. doi: 10.1371/journal.pone.0032131. Epub 2012 Feb 22. Erratum in: PLoS One. 2013;8(4). doi:10.1371/annotation/8301b5d4-1ba3-40e7-8fcd-3e169b967044.

40.

Structure and dynamics of the M3 muscarinic acetylcholine receptor.

Kruse AC, Hu J, Pan AC, Arlow DH, Rosenbaum DM, Rosemond E, Green HF, Liu T, Chae PS, Dror RO, Shaw DE, Weis WI, Wess J, Kobilka BK.

Nature. 2012 Feb 22;482(7386):552-6. doi: 10.1038/nature10867.

41.

How fast-folding proteins fold.

Lindorff-Larsen K, Piana S, Dror RO, Shaw DE.

Science. 2011 Oct 28;334(6055):517-20. doi: 10.1126/science.1208351.

PMID:
22034434
42.

Activation mechanism of the β2-adrenergic receptor.

Dror RO, Arlow DH, Maragakis P, Mildorf TJ, Pan AC, Xu H, Borhani DW, Shaw DE.

Proc Natl Acad Sci U S A. 2011 Nov 15;108(46):18684-9. doi: 10.1073/pnas.1110499108. Epub 2011 Oct 26.

43.

Pathway and mechanism of drug binding to G-protein-coupled receptors.

Dror RO, Pan AC, Arlow DH, Borhani DW, Maragakis P, Shan Y, Xu H, Shaw DE.

Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13118-23. doi: 10.1073/pnas.1104614108. Epub 2011 Jul 21.

44.

How does a drug molecule find its target binding site?

Shan Y, Kim ET, Eastwood MP, Dror RO, Seeliger MA, Shaw DE.

J Am Chem Soc. 2011 Jun 22;133(24):9181-3. doi: 10.1021/ja202726y. Epub 2011 May 13. Erratum in: J Am Chem Soc. 2014 Feb 26;136(8):3320.

45.

Structure and function of an irreversible agonist-β(2) adrenoceptor complex.

Rosenbaum DM, Zhang C, Lyons JA, Holl R, Aragao D, Arlow DH, Rasmussen SG, Choi HJ, Devree BT, Sunahara RK, Chae PS, Gellman SH, Dror RO, Shaw DE, Weis WI, Caffrey M, Gmeiner P, Kobilka BK.

Nature. 2011 Jan 13;469(7329):236-40. doi: 10.1038/nature09665.

46.

Atomic-level characterization of the structural dynamics of proteins.

Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W.

Science. 2010 Oct 15;330(6002):341-6. doi: 10.1126/science.1187409.

47.

Equipartition and the Calculation of Temperature in Biomolecular Simulations.

Eastwood MP, Stafford KA, Lippert RA, Jensen MØ, Maragakis P, Predescu C, Dror RO, Shaw DE.

J Chem Theory Comput. 2010 Jul 13;6(7):2045-58. doi: 10.1021/ct9002916.

PMID:
26615934
48.

Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations.

Dror RO, Jensen MØ, Borhani DW, Shaw DE.

J Gen Physiol. 2010 Jun;135(6):555-62. doi: 10.1085/jgp.200910373. No abstract available.

49.

Improved side-chain torsion potentials for the Amber ff99SB protein force field.

Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE.

Proteins. 2010 Jun;78(8):1950-8. doi: 10.1002/prot.22711.

50.

Principles of conduction and hydrophobic gating in K+ channels.

Jensen MØ, Borhani DW, Lindorff-Larsen K, Maragakis P, Jogini V, Eastwood MP, Dror RO, Shaw DE.

Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):5833-8. doi: 10.1073/pnas.0911691107. Epub 2010 Mar 15.

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