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Items: 1 to 50 of 119

1.

Comparison of the molecular properties of retinitis pigmentosa P23H and N15S amino acid replacements in rhodopsin.

Mitchell J, Balem F, Tirupula K, Man D, Dhiman HK, Yanamala N, Ollesch J, Planas-Iglesias J, Jennings BJ, Gerwert K, Iannaccone A, Klein-Seetharaman J.

PLoS One. 2019 May 17;14(5):e0214639. doi: 10.1371/journal.pone.0214639. eCollection 2019.

2.

Towards personalised molecular feedback for weight loss.

Tejpal S, Sanghera N, Manoharan V, Planas-Iglesias J, Myler K, Klein-Seetharaman J.

BMC Obes. 2019 May 6;6:20. doi: 10.1186/s40608-019-0237-5. eCollection 2019.

3.

Characterisation of denatured states of sensory rhodopsin II by solution-state NMR.

Tan YL, Mitchell J, Klein-Seetharaman J, Nietlispach D.

J Mol Biol. 2019 Jul 12;431(15):2790-2809. doi: 10.1016/j.jmb.2019.04.039. Epub 2019 May 6.

PMID:
31071327
4.

Antimicrobial biopolymer formation from sodium alginate and algae extract using aminoglycosides.

Kumar L, Brice J, Toberer L, Klein-Seetharaman J, Knauss D, Sarkar SK.

PLoS One. 2019 Mar 26;14(3):e0214411. doi: 10.1371/journal.pone.0214411. eCollection 2019.

5.

Structural and Functional Consequences of the Weak Binding of Chlorin e6 to Bovine Rhodopsin.

Mitchell J, Yanamala N, Tan YL, Gardner EE, Tirupula KC, Balem F, Sheves M, Nietlispach D, Klein-Seetharaman J.

Photochem Photobiol. 2019 May;95(3):787-802. doi: 10.1111/php.13074. Epub 2019 Mar 12.

PMID:
30582615
6.

Characterization of Denatured States and Reversible Unfolding of Sensory Rhodopsin II.

Tan YL, Mitchell J, Klein-Seetharaman J, Nietlispach D.

J Mol Biol. 2018 Oct 19;430(21):4068-4086. doi: 10.1016/j.jmb.2018.07.031. Epub 2018 Aug 9.

PMID:
30098339
7.

Structural characterization of cardiolipin-driven activation of cytochrome c into a peroxidase and membrane perturbation.

Mohammadyani D, Yanamala N, Samhan-Arias AK, Kapralov AA, Stepanov G, Nuar N, Planas-Iglesias J, Sanghera N, Kagan VE, Klein-Seetharaman J.

Biochim Biophys Acta Biomembr. 2018 May;1860(5):1057-1068. doi: 10.1016/j.bbamem.2018.01.009. Epub 2018 Jan 6.

8.

Chlorophyll-Derivative Modulation of Rhodopsin Signaling Properties through Evolutionarily Conserved Interaction Pathways.

Woods KN, Pfeffer J, Klein-Seetharaman J.

Front Mol Biosci. 2017 Dec 12;4:85. doi: 10.3389/fmolb.2017.00085. eCollection 2017.

9.

Lipid bodies containing oxidatively truncated lipids block antigen cross-presentation by dendritic cells in cancer.

Veglia F, Tyurin VA, Mohammadyani D, Blasi M, Duperret EK, Donthireddy L, Hashimoto A, Kapralov A, Amoscato A, Angelini R, Patel S, Alicea-Torres K, Weiner D, Murphy ME, Klein-Seetharaman J, Celis E, Kagan VE, Gabrilovich DI.

Nat Commun. 2017 Dec 14;8(1):2122. doi: 10.1038/s41467-017-02186-9.

10.

Structure and dynamics of the insulin receptor: implications for receptor activation and drug discovery.

Ye L, Maji S, Sanghera N, Gopalasingam P, Gorbunov E, Tarasov S, Epstein O, Klein-Seetharaman J.

Drug Discov Today. 2017 Jul;22(7):1092-1102. doi: 10.1016/j.drudis.2017.04.011. Epub 2017 May 3. Review.

PMID:
28476537
11.

Multitask Matrix Completion for Learning Protein Interactions Across Diseases.

Kshirsagar M, Murugesan K, Carbonell JG, Klein-Seetharaman J.

J Comput Biol. 2017 Jun;24(6):501-514. doi: 10.1089/cmb.2016.0201. Epub 2017 Jan 27.

PMID:
28128642
12.

Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors.

Woods KN, Pfeffer J, Dutta A, Klein-Seetharaman J.

Sci Rep. 2016 Nov 16;6:37290. doi: 10.1038/srep37290.

13.

Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis.

Kagan VE, Mao G, Qu F, Angeli JP, Doll S, Croix CS, Dar HH, Liu B, Tyurin VA, Ritov VB, Kapralov AA, Amoscato AA, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Proneth B, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli RK, Stockwell BR, Tyurina YY, Conrad M, Bayır H.

Nat Chem Biol. 2017 Jan;13(1):81-90. doi: 10.1038/nchembio.2238. Epub 2016 Nov 14.

14.

Known unknowns of cardiolipin signaling: The best is yet to come.

Maguire JJ, Tyurina YY, Mohammadyani D, Kapralov AA, Anthonymuthu TS, Qu F, Amoscato AA, Sparvero LJ, Tyurin VA, Planas-Iglesias J, He RR, Klein-Seetharaman J, Bayır H, Kagan VE.

Biochim Biophys Acta Mol Cell Biol Lipids. 2017 Jan;1862(1):8-24. doi: 10.1016/j.bbalip.2016.08.001. Epub 2016 Aug 4. Review.

15.

Mitochondrial Redox Opto-Lipidomics Reveals Mono-Oxygenated Cardiolipins as Pro-Apoptotic Death Signals.

Mao G, Qu F, St Croix CM, Tyurina YY, Planas-Iglesias J, Jiang J, Huang Z, Amoscato AA, Tyurin VA, Kapralov AA, Cheikhi A, Maguire J, Klein-Seetharaman J, Bayır H, Kagan VE.

ACS Chem Biol. 2016 Feb 19;11(2):530-40. doi: 10.1021/acschembio.5b00737. Epub 2016 Jan 5.

16.

The brown adipocyte protein CIDEA promotes lipid droplet fusion via a phosphatidic acid-binding amphipathic helix.

Barneda D, Planas-Iglesias J, Gaspar ML, Mohammadyani D, Prasannan S, Dormann D, Han GS, Jesch SA, Carman GM, Kagan V, Parker MG, Ktistakis NT, Klein-Seetharaman J, Dixon AM, Henry SA, Christian M.

Elife. 2015 Nov 26;4:e07485. doi: 10.7554/eLife.07485.

17.

Dichotomous roles for externalized cardiolipin in extracellular signaling: Promotion of phagocytosis and attenuation of innate immunity.

Balasubramanian K, Maeda A, Lee JS, Mohammadyani D, Dar HH, Jiang JF, St Croix CM, Watkins S, Tyurin VA, Tyurina YY, Klöditz K, Polimova A, Kapralova VI, Xiong Z, Ray P, Klein-Seetharaman J, Mallampalli RK, Bayir H, Fadeel B, Kagan VE.

Sci Signal. 2015 Sep 22;8(395):ra95. doi: 10.1126/scisignal.aaa6179.

18.

Cardiolipin Interactions with Proteins.

Planas-Iglesias J, Dwarakanath H, Mohammadyani D, Yanamala N, Kagan VE, Klein-Seetharaman J.

Biophys J. 2015 Sep 15;109(6):1282-94. doi: 10.1016/j.bpj.2015.07.034. Epub 2015 Aug 20.

19.

Techniques for transferring host-pathogen protein interactions knowledge to new tasks.

Kshirsagar M, Schleker S, Carbonell J, Klein-Seetharaman J.

Front Microbiol. 2015 Feb 2;6:36. doi: 10.3389/fmicb.2015.00036. eCollection 2015.

20.

Comparing human-Salmonella with plant-Salmonella protein-protein interaction predictions.

Schleker S, Kshirsagar M, Klein-Seetharaman J.

Front Microbiol. 2015 Jan 28;6:45. doi: 10.3389/fmicb.2015.00045. eCollection 2015.

21.

Refining literature curated protein interactions using expert opinions.

Tastan O, Qi Y, Carbonell JG, Klein-Seetharaman J.

Pac Symp Biocomput. 2015:318-29.

22.

Cardiolipin signaling mechanisms: collapse of asymmetry and oxidation.

Kagan VE, Tyurina YY, Tyurin VA, Mohammadyani D, Angeli JP, Baranov SV, Klein-Seetharaman J, Friedlander RM, Mallampalli RK, Conrad M, Bayir H.

Antioxid Redox Signal. 2015 Jun 20;22(18):1667-80. doi: 10.1089/ars.2014.6219. Epub 2015 Mar 31. Review.

23.

Structural re-arrangement and peroxidase activation of cytochrome c by anionic analogues of vitamin E, tocopherol succinate and tocopherol phosphate.

Yanamala N, Kapralov AA, Djukic M, Peterson J, Mao G, Klein-Seetharaman J, Stoyanovsky DA, Stursa J, Neuzil J, Kagan VE.

J Biol Chem. 2014 Nov 21;289(47):32488-98. doi: 10.1074/jbc.M114.601377. Epub 2014 Oct 2.

24.

Differential dynamics of extracellular and cytoplasmic domains in denatured States of rhodopsin.

Dutta A, Altenbach C, Mangahas S, Yanamala N, Gardner E, Hubbell WL, Klein-Seetharaman J.

Biochemistry. 2014 Nov 25;53(46):7160-9. doi: 10.1021/bi401557e. Epub 2014 Nov 10.

25.

Mitochondrial NM23-H4/NDPK-D: a bifunctional nanoswitch for bioenergetics and lipid signaling.

Schlattner U, Tokarska-Schlattner M, Epand RM, Boissan M, Lacombe ML, Klein-Seetharaman J, Kagan VE.

Naunyn Schmiedebergs Arch Pharmacol. 2015 Feb;388(2):271-8. doi: 10.1007/s00210-014-1047-4. Epub 2014 Sep 18.

PMID:
25231795
26.

Early integration of the individual student in academic activities: a novel classroom concept for graduate education in molecular biophysics and structural biology.

Leuba SH, Carney SM, Dahlburg EM, Eells RJ, Ghodke H, Yanamala N, Schauer G, Klein-Seetharaman J.

BMC Biophys. 2014 Aug 5;7:6. doi: 10.1186/2046-1682-7-6. eCollection 2014.

27.

Molecular speciation and dynamics of oxidized triacylglycerols in lipid droplets: Mass spectrometry and coarse-grained simulations.

Mohammadyani D, Tyurin VA, O'Brien M, Sadovsky Y, Gabrilovich DI, Klein-Seetharaman J, Kagan VE.

Free Radic Biol Med. 2014 Nov;76:53-60. doi: 10.1016/j.freeradbiomed.2014.07.042. Epub 2014 Aug 10.

28.

A mitochondrial pathway for biosynthesis of lipid mediators.

Tyurina YY, Poloyac SM, Tyurin VA, Kapralov AA, Jiang J, Anthonymuthu TS, Kapralova VI, Vikulina AS, Jung MY, Epperly MW, Mohammadyani D, Klein-Seetharaman J, Jackson TC, Kochanek PM, Pitt BR, Greenberger JS, Vladimirov YA, Bayır H, Kagan VE.

Nat Chem. 2014 Jun;6(6):542-52. doi: 10.1038/nchem.1924. Epub 2014 Apr 20.

29.

Oxidized lipids block antigen cross-presentation by dendritic cells in cancer.

Ramakrishnan R, Tyurin VA, Veglia F, Condamine T, Amoscato A, Mohammadyani D, Johnson JJ, Zhang LM, Klein-Seetharaman J, Celis E, Kagan VE, Gabrilovich DI.

J Immunol. 2014 Mar 15;192(6):2920-31. doi: 10.4049/jimmunol.1302801. Epub 2014 Feb 19. Erratum in: J Immunol. 2014 May 15;192(10):4935. Tuyrin, Vladimir A [corrected to Tyurin, Vladimir A]; Cao, Wei [removed].

30.

Characterization of the simultaneous decay kinetics of metarhodopsin states II and III in rhodopsin by solution-state NMR spectroscopy.

Stehle J, Silvers R, Werner K, Chatterjee D, Gande S, Scholz F, Dutta A, Wachtveitl J, Klein-Seetharaman J, Schwalbe H.

Angew Chem Int Ed Engl. 2014 Feb 17;53(8):2078-84. doi: 10.1002/anie.201309581. Epub 2014 Feb 6.

PMID:
24505031
31.

X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes.

Boscia AL, Treece BW, Mohammadyani D, Klein-Seetharaman J, Braun AR, Wassenaar TA, Klösgen B, Tristram-Nagle S.

Chem Phys Lipids. 2014 Feb;178:1-10. doi: 10.1016/j.chemphyslip.2013.12.010. Epub 2013 Dec 28.

32.

Retinal proteins as model systems for membrane protein folding.

Tastan O, Dutta A, Booth P, Klein-Seetharaman J.

Biochim Biophys Acta. 2014 May;1837(5):656-63. doi: 10.1016/j.bbabio.2013.11.021. Epub 2013 Dec 12. Review.

33.

Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells.

Chu CT, Ji J, Dagda RK, Jiang JF, Tyurina YY, Kapralov AA, Tyurin VA, Yanamala N, Shrivastava IH, Mohammadyani D, Wang KZQ, Zhu J, Klein-Seetharaman J, Balasubramanian K, Amoscato AA, Borisenko G, Huang Z, Gusdon AM, Cheikhi A, Steer EK, Wang R, Baty C, Watkins S, Bahar I, Bayir H, Kagan VE.

Nat Cell Biol. 2013 Oct;15(10):1197-1205. doi: 10.1038/ncb2837. Epub 2013 Sep 15.

34.

Multitask learning for host-pathogen protein interactions.

Kshirsagar M, Carbonell J, Klein-Seetharaman J.

Bioinformatics. 2013 Jul 1;29(13):i217-26. doi: 10.1093/bioinformatics/btt245.

35.

Biodegradation of single-walled carbon nanotubes by eosinophil peroxidase.

Andón FT, Kapralov AA, Yanamala N, Feng W, Baygan A, Chambers BJ, Hultenby K, Ye F, Toprak MS, Brandner BD, Fornara A, Klein-Seetharaman J, Kotchey GP, Star A, Shvedova AA, Fadeel B, Kagan VE.

Small. 2013 Aug 26;9(16):2721-9, 2720. doi: 10.1002/smll.201202508. Epub 2013 Feb 27.

36.

Dual function of mitochondrial Nm23-H4 protein in phosphotransfer and intermembrane lipid transfer: a cardiolipin-dependent switch.

Schlattner U, Tokarska-Schlattner M, Ramirez S, Tyurina YY, Amoscato AA, Mohammadyani D, Huang Z, Jiang J, Yanamala N, Seffouh A, Boissan M, Epand RF, Epand RM, Klein-Seetharaman J, Lacombe ML, Kagan VE.

J Biol Chem. 2013 Jan 4;288(1):111-21. doi: 10.1074/jbc.M112.408633. Epub 2012 Nov 13.

37.

Specificity of lipoprotein-associated phospholipase A(2) toward oxidized phosphatidylserines: liquid chromatography-electrospray ionization mass spectrometry characterization of products and computer modeling of interactions.

Tyurin VA, Yanamala N, Tyurina YY, Klein-Seetharaman J, Macphee CH, Kagan VE.

Biochemistry. 2012 Dec 4;51(48):9736-50. doi: 10.1021/bi301024e. Epub 2012 Nov 19.

38.

Identification of motions in membrane proteins by elastic network models and their experimental validation.

Isin B, Tirupula KC, Oltvai ZN, Klein-Seetharaman J, Bahar I.

Methods Mol Biol. 2012;914:285-317. doi: 10.1007/978-1-62703-023-6_17.

39.

Techniques to cope with missing data in host-pathogen protein interaction prediction.

Kshirsagar M, Carbonell J, Klein-Seetharaman J.

Bioinformatics. 2012 Sep 15;28(18):i466-i472. doi: 10.1093/bioinformatics/bts375.

40.

In support of the BMRB.

Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay LE, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil RR, Ho C, Rule G, Gronenborn AM, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue ED, Mott H, Nietlispach D, Barsukov I, Lian LY, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis IJ, Watts A, Conte MR, Mason J, Pfuhl M, Sanderson MR, Craven J, Williamson M, Dominguez C, Roberts G, Günther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw DE, Steinbeck C, Vendruscolo M, Vuister GW, Walters KJ, Weinstein H, Wüthrich K, Yokoyama S.

Nat Struct Mol Biol. 2012 Sep;19(9):854-60. doi: 10.1038/nsmb.2371. No abstract available.

PMID:
22955930
41.

A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors.

Moitra S, Tirupula KC, Klein-Seetharaman J, Langmead CJ.

BMC Biophys. 2012 Jun 29;5:13. doi: 10.1186/2046-1682-5-13.

42.

BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference.

Garcia-Garcia J, Schleker S, Klein-Seetharaman J, Oliva B.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W147-51. doi: 10.1093/nar/gks553. Epub 2012 Jun 11.

43.

Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes.

Schleker S, Garcia-Garcia J, Klein-Seetharaman J, Oliva B.

Chem Biodivers. 2012 May;9(5):991-1018. doi: 10.1002/cbdv.201100392.

44.

Adsorption of surfactant lipids by single-walled carbon nanotubes in mouse lung upon pharyngeal aspiration.

Kapralov AA, Feng WH, Amoscato AA, Yanamala N, Balasubramanian K, Winnica DE, Kisin ER, Kotchey GP, Gou P, Sparvero LJ, Ray P, Mallampalli RK, Klein-Seetharaman J, Fadeel B, Star A, Shvedova AA, Kagan VE.

ACS Nano. 2012 May 22;6(5):4147-56. doi: 10.1021/nn300626q. Epub 2012 Apr 6.

45.

The current Salmonella-host interactome.

Schleker S, Sun J, Raghavan B, Srnec M, Müller N, Koepfinger M, Murthy L, Zhao Z, Klein-Seetharaman J.

Proteomics Clin Appl. 2012 Jan;6(1-2):117-33. doi: 10.1002/prca.201100083. Epub 2011 Dec 27. Review.

46.

Determining confidence of predicted interactions between HIV-1 and human proteins using conformal method.

Nouretdinov I, Gammerman A, Qi Y, Klein-Seetharaman J.

Pac Symp Biocomput. 2012:311-22.

47.

Isotope labeling in mammalian cells.

Dutta A, Saxena K, Schwalbe H, Klein-Seetharaman J.

Methods Mol Biol. 2012;831:55-69. doi: 10.1007/978-1-61779-480-3_4.

48.

Isotope labeling in insect cells.

Saxena K, Dutta A, Klein-Seetharaman J, Schwalbe H.

Methods Mol Biol. 2012;831:37-54. doi: 10.1007/978-1-61779-480-3_3.

49.

A mitochondria-targeted inhibitor of cytochrome c peroxidase mitigates radiation-induced death.

Atkinson J, Kapralov AA, Yanamala N, Tyurina YY, Amoscato AA, Pearce L, Peterson J, Huang Z, Jiang J, Samhan-Arias AK, Maeda A, Feng W, Wasserloos K, Belikova NA, Tyurin VA, Wang H, Fletcher J, Wang Y, Vlasova II, Klein-Seetharaman J, Stoyanovsky DA, Bayîr H, Pitt BR, Epperly MW, Greenberger JS, Kagan VE.

Nat Commun. 2011 Oct 11;2:497. doi: 10.1038/ncomms1499.

50.

The cytoplasmic rhodopsin-protein interface: potential for drug discovery.

Yanamala N, Gardner E, Riciutti A, Klein-Seetharaman J.

Curr Drug Targets. 2012 Jan;13(1):3-14. Review.

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