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Items: 1 to 50 of 64

1.

Identification of global and ligand-specific calcium sensing receptor activation mechanisms.

Keller AN, Kufareva I, Josephs TM, Diao J, Mai VT, Conigrave AD, Christopoulos A, Gregory KJ, Leach K.

Mol Pharmacol. 2018 Apr 10. pii: mol.118.112086. doi: 10.1124/mol.118.112086. [Epub ahead of print]

2.

Convergence of Wnt, growth factor, and heterotrimeric G protein signals on the guanine nucleotide exchange factor Daple.

Aznar N, Ear J, Dunkel Y, Sun N, Satterfield K, He F, Kalogriopoulos NA, Lopez-Sanchez I, Ghassemian M, Sahoo D, Kufareva I, Ghosh P.

Sci Signal. 2018 Feb 27;11(519). pii: eaao4220. doi: 10.1126/scisignal.aao4220.

3.

Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV.

Zheng Y, Han GW, Abagyan R, Wu B, Stevens RC, Cherezov V, Kufareva I, Handel TM.

Immunity. 2017 Jun 20;46(6):1005-1017.e5. doi: 10.1016/j.immuni.2017.05.002.

PMID:
28636951
4.

What Do Structures Tell Us About Chemokine Receptor Function and Antagonism?

Kufareva I, Gustavsson M, Zheng Y, Stephens BS, Handel TM.

Annu Rev Biophys. 2017 May 22;46:175-198. doi: 10.1146/annurev-biophys-051013-022942. Review.

PMID:
28532213
5.

The GAPs, GEFs, GDIs and…now, GEMs: New kids on the heterotrimeric G protein signaling block.

Ghosh P, Rangamani P, Kufareva I.

Cell Cycle. 2017 Apr 3;16(7):607-612. doi: 10.1080/15384101.2017.1282584. Epub 2017 Mar 13. Review.

6.

Structural basis of ligand interaction with atypical chemokine receptor 3.

Gustavsson M, Wang L, van Gils N, Stephens BS, Zhang P, Schall TJ, Yang S, Abagyan R, Chance MR, Kufareva I, Handel TM.

Nat Commun. 2017 Jan 18;8:14135. doi: 10.1038/ncomms14135.

7.

Orphan receptor ligand discovery by pickpocketing pharmacological neighbors.

Ngo T, Ilatovskiy AV, Stewart AG, Coleman JL, McRobb FM, Riek RP, Graham RM, Abagyan R, Kufareva I, Smith NJ.

Nat Chem Biol. 2017 Feb;13(2):235-242. doi: 10.1038/nchembio.2266. Epub 2016 Dec 19.

8.

Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists.

Zheng Y, Qin L, Zacarías NV, de Vries H, Han GW, Gustavsson M, Dabros M, Zhao C, Cherney RJ, Carter P, Stamos D, Abagyan R, Cherezov V, Stevens RC, IJzerman AP, Heitman LH, Tebben A, Kufareva I, Handel TM.

Nature. 2016 Dec 15;540(7633):458-461. doi: 10.1038/nature20605. Epub 2016 Dec 7.

9.

AMP-activated protein kinase fortifies epithelial tight junctions during energetic stress via its effector GIV/Girdin.

Aznar N, Patel A, Rohena CC, Dunkel Y, Joosen LP, Taupin V, Kufareva I, Farquhar MG, Ghosh P.

Elife. 2016 Nov 4;5. pii: e20795. doi: 10.7554/eLife.20795.

10.

Crystal Structure of the Human Cannabinoid Receptor CB1.

Hua T, Vemuri K, Pu M, Qu L, Han GW, Wu Y, Zhao S, Shui W, Li S, Korde A, Laprairie RB, Stahl EL, Ho JH, Zvonok N, Zhou H, Kufareva I, Wu B, Zhao Q, Hanson MA, Bohn LM, Makriyannis A, Stevens RC, Liu ZJ.

Cell. 2016 Oct 20;167(3):750-762.e14. doi: 10.1016/j.cell.2016.10.004.

11.

Chemokines and their receptors: insights from molecular modeling and crystallography.

Kufareva I.

Curr Opin Pharmacol. 2016 Oct;30:27-37. doi: 10.1016/j.coph.2016.07.006. Epub 2016 Jul 25. Review.

12.

Signal transmission through the CXC chemokine receptor 4 (CXCR4) transmembrane helices.

Wescott MP, Kufareva I, Paes C, Goodman JR, Thaker Y, Puffer BA, Berdougo E, Rucker JB, Handel TM, Doranz BJ.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9928-33. doi: 10.1073/pnas.1601278113. Epub 2016 Aug 19.

13.

Towards a structural understanding of allosteric drugs at the human calcium-sensing receptor.

Leach K, Gregory KJ, Kufareva I, Khajehali E, Cook AE, Abagyan R, Conigrave AD, Sexton PM, Christopoulos A.

Cell Res. 2016 May;26(5):574-92. doi: 10.1038/cr.2016.36. Epub 2016 Mar 22.

14.

Disulfide Trapping for Modeling and Structure Determination of Receptor: Chemokine Complexes.

Kufareva I, Gustavsson M, Holden LG, Qin L, Zheng Y, Handel TM.

Methods Enzymol. 2016;570:389-420. doi: 10.1016/bs.mie.2015.12.001. Epub 2016 Jan 13.

15.

Identifying ligands at orphan GPCRs: current status using structure-based approaches.

Ngo T, Kufareva I, Coleman JLj, Graham RM, Abagyan R, Smith NJ.

Br J Pharmacol. 2016 Oct;173(20):2934-51. doi: 10.1111/bph.13452. Epub 2016 Mar 5. Review.

16.

Inactivating mutations in GNA13 and RHOA in Burkitt's lymphoma and diffuse large B-cell lymphoma: a tumor suppressor function for the Gα13/RhoA axis in B cells.

O'Hayre M, Inoue A, Kufareva I, Wang Z, Mikelis CM, Drummond RA, Avino S, Finkel K, Kalim KW, DiPasquale G, Guo F, Aoki J, Zheng Y, Lionakis MS, Molinolo AA, Gutkind JS.

Oncogene. 2016 Jul 21;35(29):3771-80. doi: 10.1038/onc.2015.442. Epub 2015 Nov 30.

17.

Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily.

Lenoir M, Kufareva I, Abagyan R, Overduin M.

Membranes (Basel). 2015 Oct 23;5(4):646-63. doi: 10.3390/membranes5040646.

18.

Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs.

Kufareva I, Handel TM, Abagyan R.

Methods Mol Biol. 2015;1335:295-311. doi: 10.1007/978-1-4939-2914-6_19.

19.

Dual targeting of the chemokine receptors CXCR4 and ACKR3 with novel engineered chemokines.

Hanes MS, Salanga CL, Chowdry AB, Comerford I, McColl SR, Kufareva I, Handel TM.

J Biol Chem. 2015 Sep 11;290(37):22385-97. doi: 10.1074/jbc.M115.675108. Epub 2015 Jul 27.

20.

Structure-based predictions of activity cliffs.

Husby J, Bottegoni G, Kufareva I, Abagyan R, Cavalli A.

J Chem Inf Model. 2015 May 26;55(5):1062-76. doi: 10.1021/ci500742b. Epub 2015 May 11.

21.

Activation of Gαi at the Golgi by GIV/Girdin imposes finiteness in Arf1 signaling.

Lo IC, Gupta V, Midde KK, Taupin V, Lopez-Sanchez I, Kufareva I, Abagyan R, Randazzo PA, Farquhar MG, Ghosh P.

Dev Cell. 2015 Apr 20;33(2):189-203. doi: 10.1016/j.devcel.2015.02.009. Epub 2015 Apr 9.

22.

Chemokine and chemokine receptor structure and interactions: implications for therapeutic strategies.

Kufareva I, Salanga CL, Handel TM.

Immunol Cell Biol. 2015 Apr;93(4):372-83. doi: 10.1038/icb.2015.15. Epub 2015 Feb 24. Review.

23.

Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine.

Qin L, Kufareva I, Holden LG, Wang C, Zheng Y, Zhao C, Fenalti G, Wu H, Han GW, Cherezov V, Abagyan R, Stevens RC, Handel TM.

Science. 2015 Mar 6;347(6226):1117-22. doi: 10.1126/science.1261064. Epub 2015 Jan 22.

24.

Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: molecular modeling and experimental validation.

Kufareva I, Stephens BS, Holden LG, Qin L, Zhao C, Kawamura T, Abagyan R, Handel TM.

Proc Natl Acad Sci U S A. 2014 Dec 16;111(50):E5363-72. doi: 10.1073/pnas.1417037111. Epub 2014 Dec 2.

25.

Discovery of novel membrane binding structures and functions.

Kufareva I, Lenoir M, Dancea F, Sridhar P, Raush E, Bissig C, Gruenberg J, Abagyan R, Overduin M.

Biochem Cell Biol. 2014 Dec;92(6):555-63. doi: 10.1139/bcb-2014-0074. Epub 2014 Sep 18.

26.

Structural basis for activation of trimeric Gi proteins by multiple growth factor receptors via GIV/Girdin.

Lin C, Ear J, Midde K, Lopez-Sanchez I, Aznar N, Garcia-Marcos M, Kufareva I, Abagyan R, Ghosh P.

Mol Biol Cell. 2014 Nov 5;25(22):3654-71. doi: 10.1091/mbc.E14-05-0978. Epub 2014 Sep 3.

27.

Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges.

Kufareva I, Katritch V; Participants of GPCR Dock 2013, Stevens RC, Abagyan R.

Structure. 2014 Aug 5;22(8):1120-1139. doi: 10.1016/j.str.2014.06.012. Epub 2014 Jul 24.

28.

In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor α.

McRobb FM, Kufareva I, Abagyan R.

Toxicol Sci. 2014 Sep;141(1):188-97. doi: 10.1093/toxsci/kfu114. Epub 2014 Jun 13.

29.

Identification of novel serotonin transporter compounds by virtual screening.

Gabrielsen M, Kurczab R, Siwek A, Wolak M, Ravna AW, Kristiansen K, Kufareva I, Abagyan R, Nowak G, Chilmonczyk Z, Sylte I, Bojarski AJ.

J Chem Inf Model. 2014 Mar 24;54(3):933-43. doi: 10.1021/ci400742s. Epub 2014 Feb 26.

30.

A general method for site specific fluorescent labeling of recombinant chemokines.

Kawamura T, Stephens B, Qin L, Yin X, Dores MR, Smith TH, Grimsey N, Abagyan R, Trejo J, Kufareva I, Fuster MM, Salanga CL, Handel TM.

PLoS One. 2014 Jan 28;9(1):e81454. doi: 10.1371/journal.pone.0081454. eCollection 2014.

31.

PeptiSite: a structural database of peptide binding sites in 4D.

Acharya C, Kufareva I, Ilatovskiy AV, Abagyan R.

Biochem Biophys Res Commun. 2014 Mar 21;445(4):717-23. doi: 10.1016/j.bbrc.2013.12.132. Epub 2014 Jan 6.

32.

In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species.

McRobb FM, Sahagún V, Kufareva I, Abagyan R.

Environ Sci Technol. 2014;48(3):1964-72. doi: 10.1021/es404568a. Epub 2014 Jan 15.

33.

Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5).

Lindin I, Wuxiuer Y, Kufareva I, Abagyan R, Moens U, Sylte I, Ravna AW.

Theor Biol Med Model. 2013 Sep 14;10:56. doi: 10.1186/1742-4682-10-56.

34.

Structure of the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex.

Tan Q, Zhu Y, Li J, Chen Z, Han GW, Kufareva I, Li T, Ma L, Fenalti G, Li J, Zhang W, Xie X, Yang H, Jiang H, Cherezov V, Liu H, Stevens RC, Zhao Q, Wu B.

Science. 2013 Sep 20;341(6152):1387-90. doi: 10.1126/science.1241475. Epub 2013 Sep 12.

35.

Sulfopeptide probes of the CXCR4/CXCL12 interface reveal oligomer-specific contacts and chemokine allostery.

Ziarek JJ, Getschman AE, Butler SJ, Taleski D, Stephens B, Kufareva I, Handel TM, Payne RJ, Volkman BF.

ACS Chem Biol. 2013 Sep 20;8(9):1955-63. doi: 10.1021/cb400274z. Epub 2013 Jun 26.

36.

Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics.

Ilatovskiy AV, Abagyan R, Kufareva I.

Int J Quantum Chem. 2013 Jun 15;113(12):1669-1675.

37.

Viral infection controlled by a calcium-dependent lipid-binding module in ALIX.

Bissig C, Lenoir M, Velluz MC, Kufareva I, Abagyan R, Overduin M, Gruenberg J.

Dev Cell. 2013 May 28;25(4):364-73. doi: 10.1016/j.devcel.2013.04.003. Epub 2013 May 9.

38.

Pivotal role of P450-P450 interactions in CYP3A4 allostery: the case of α-naphthoflavone.

Davydov DR, Davydova NY, Sineva EV, Kufareva I, Halpert JR.

Biochem J. 2013 Jul 15;453(2):219-30. doi: 10.1042/BJ20130398.

39.

The emerging mutational landscape of G proteins and G-protein-coupled receptors in cancer.

O'Hayre M, Vázquez-Prado J, Kufareva I, Stawiski EW, Handel TM, Seshagiri S, Gutkind JS.

Nat Rev Cancer. 2013 Jun;13(6):412-24. doi: 10.1038/nrc3521. Epub 2013 May 3. Review.

40.

A structural snapshot of CYP2B4 in complex with paroxetine provides insights into ligand binding and clusters of conformational states.

Shah MB, Kufareva I, Pascual J, Zhang Q, Stout CD, Halpert JR.

J Pharmacol Exp Ther. 2013 Jul;346(1):113-20. doi: 10.1124/jpet.113.204776. Epub 2013 Apr 30.

41.

A novel approach to quantify G-protein-coupled receptor dimerization equilibrium using bioluminescence resonance energy transfer.

Kufareva I, Stephens B, Gilliland CT, Wu B, Fenalti G, Hamel D, Stevens RC, Abagyan R, Handel TM.

Methods Mol Biol. 2013;1013:93-127. doi: 10.1007/978-1-62703-426-5_7.

42.

Synthesis, antidepressant evaluation and docking studies of long-chain alkylnitroquipazines as serotonin transporter inhibitors.

Gabrielsen M, Wołosewicz K, Zawadzka A, Kossakowski J, Nowak G, Wolak M, Stachowicz K, Siwek A, Ravna AW, Kufareva I, Kozerski L, Bednarek E, Sitkowski J, Bocian W, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z.

Chem Biol Drug Des. 2013 Jun;81(6):695-706. doi: 10.1111/cbdd.12116. Epub 2013 Apr 11.

43.

Lapatinib-binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds.

Katiyar S, Kufareva I, Behera R, Thomas SM, Ogata Y, Pollastri M, Abagyan R, Mensa-Wilmot K.

PLoS One. 2013;8(2):e56150. doi: 10.1371/journal.pone.0056150. Epub 2013 Feb 20. Erratum in: PLoS One. 2014;9(3):e92488.

44.

Compound activity prediction using models of binding pockets or ligand properties in 3D.

Kufareva I, Chen YC, Ilatovskiy AV, Abagyan R.

Curr Top Med Chem. 2012;12(17):1869-82. Review.

45.

Molecular mechanisms deployed by virally encoded G protein-coupled receptors in human diseases.

Montaner S, Kufareva I, Abagyan R, Gutkind JS.

Annu Rev Pharmacol Toxicol. 2013;53:331-54. doi: 10.1146/annurev-pharmtox-010510-100608. Epub 2012 Oct 22. Review.

46.

Novel cGMP efflux inhibitors identified by virtual ligand screening (VLS) and confirmed by experimental studies.

Sager G, Ørvoll EØ, Lysaa RA, Kufareva I, Abagyan R, Ravna AW.

J Med Chem. 2012 Apr 12;55(7):3049-57. doi: 10.1021/jm2014666. Epub 2012 Mar 20.

47.

Methods of protein structure comparison.

Kufareva I, Abagyan R.

Methods Mol Biol. 2012;857:231-57. doi: 10.1007/978-1-61779-588-6_10.

48.

Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors.

Jarończyk M, Wołosewicz K, Gabrielsen M, Nowak G, Kufareva I, Mazurek AP, Ravna AW, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z.

Eur J Med Chem. 2012 Mar;49:200-10. doi: 10.1016/j.ejmech.2012.01.012. Epub 2012 Jan 15.

49.

Pocketome: an encyclopedia of small-molecule binding sites in 4D.

Kufareva I, Ilatovskiy AV, Abagyan R.

Nucleic Acids Res. 2012 Jan;40(Database issue):D535-40. doi: 10.1093/nar/gkr825. Epub 2011 Nov 12.

50.

Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol.

Gabrielsen M, Kurczab R, Ravna AW, Kufareva I, Abagyan R, Chilmonczyk Z, Bojarski AJ, Sylte I.

Eur J Med Chem. 2012 Jan;47(1):24-37. doi: 10.1016/j.ejmech.2011.09.056. Epub 2011 Oct 20.

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