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Items: 1 to 50 of 183

1.

Effect of late endosomal DOBMP lipid and traditional model lipids of electrophysiology on the anthrax toxin channel activity.

Kalu N, Atsmon-Raz Y, Momben Abolfath S, Lucas L, Kenney C, Leppla SH, Tieleman DP, Nestorovich EM.

Biochim Biophys Acta Biomembr. 2018 Nov;1860(11):2192-2203. doi: 10.1016/j.bbamem.2018.08.011. Epub 2018 Aug 23.

PMID:
30409515
2.

Low- q Bicelles Are Mixed Micelles.

Caldwell TA, Baoukina S, Brock AT, Oliver RC, Root KT, Krueger JK, Glover KJ, Tieleman DP, Columbus L.

J Phys Chem Lett. 2018 Aug 2;9(15):4469-4473. doi: 10.1021/acs.jpclett.8b02079. Epub 2018 Jul 25.

PMID:
30024762
3.

Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins.

Corradi V, Mendez-Villuendas E, Ingólfsson HI, Gu RX, Siuda I, Melo MN, Moussatova A, DeGagné LJ, Sejdiu BI, Singh G, Wassenaar TA, Delgado Magnero K, Marrink SJ, Tieleman DP.

ACS Cent Sci. 2018 Jun 27;4(6):709-717. doi: 10.1021/acscentsci.8b00143. Epub 2018 Jun 13.

4.

Phospholipid Chain Interactions with Cholesterol Drive Domain Formation in Lipid Membranes.

Bennett WFD, Shea JE, Tieleman DP.

Biophys J. 2018 Jun 5;114(11):2595-2605. doi: 10.1016/j.bpj.2018.04.022.

PMID:
29874610
5.

Regulation of Shigella Effector Kinase OspG through Modulation of Its Dynamic Properties.

Grishin AM, Barber KR, Gu RX, Tieleman DP, Shaw GS, Cygler M.

J Mol Biol. 2018 Jul 6;430(14):2096-2112. doi: 10.1016/j.jmb.2018.05.015. Epub 2018 May 16.

PMID:
29777720
6.

Structure of Transmembrane Helix 8 and Possible Membrane Defects in CFTR.

Corradi V, Gu RX, Vergani P, Tieleman DP.

Biophys J. 2018 Apr 24;114(8):1751-1754. doi: 10.1016/j.bpj.2018.03.003.

7.

An auto-inhibitory helix in CTP:phosphocholine cytidylyltransferase hijacks the catalytic residue and constrains a pliable, domain-bridging helix pair.

Ramezanpour M, Lee J, Taneva SG, Tieleman DP, Cornell RB.

J Biol Chem. 2018 May 4;293(18):7070-7084. doi: 10.1074/jbc.RA118.002053. Epub 2018 Mar 8.

8.

Coarse-grained molecular dynamics simulations reveal lipid access pathways in P-glycoprotein.

Barreto-Ojeda E, Corradi V, Gu RX, Tieleman DP.

J Gen Physiol. 2018 Feb 6. pii: jgp.201711907. doi: 10.1085/jgp.201711907. [Epub ahead of print]

9.
10.

Composition Fluctuations in Lipid Bilayers.

Baoukina S, Rozmanov D, Tieleman DP.

Biophys J. 2017 Dec 19;113(12):2750-2761. doi: 10.1016/j.bpj.2017.10.009.

11.

Parameterization of Palmitoylated Cysteine, Farnesylated Cysteine, Geranylgeranylated Cysteine, and Myristoylated Glycine for the Martini Force Field.

Atsmon-Raz Y, Tieleman DP.

J Phys Chem B. 2017 Dec 14;121(49):11132-11143. doi: 10.1021/acs.jpcb.7b10175. Epub 2017 Dec 1.

PMID:
29144135
12.

Structural basis for antibacterial peptide self-immunity by the bacterial ABC transporter McjD.

Bountra K, Hagelueken G, Choudhury HG, Corradi V, El Omari K, Wagner A, Mathavan I, Zirah S, Yuan Wahlgren W, Tieleman DP, Schiemann O, Rebuffat S, Beis K.

EMBO J. 2017 Oct 16;36(20):3062-3079. doi: 10.15252/embj.201797278. Epub 2017 Sep 1.

13.

Antimicrobial Peptides in the Cross Hairs of Computer Simulations.

Tieleman DP.

Biophys J. 2017 Jul 11;113(1):1-3. doi: 10.1016/j.bpj.2017.06.004. No abstract available.

14.

Changes in the dynamics of the cardiac troponin C molecule explain the effects of Ca2+-sensitizing mutations.

Stevens CM, Rayani K, Singh G, Lotfalisalmasi B, Tieleman DP, Tibbits GF.

J Biol Chem. 2017 Jul 14;292(28):11915-11926. doi: 10.1074/jbc.M116.770776. Epub 2017 May 22.

15.

Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations.

Gu RX, Ingólfsson HI, de Vries AH, Marrink SJ, Tieleman DP.

J Phys Chem B. 2017 Apr 20;121(15):3262-3275. doi: 10.1021/acs.jpcb.6b07142. Epub 2016 Oct 4.

16.

Conformational flexibility of PL12 family heparinases: structure and substrate specificity of heparinase III from Bacteroides thetaiotaomicron (BT4657).

Ulaganathan T, Shi R, Yao D, Gu RX, Garron ML, Cherney M, Tieleman DP, Sterner E, Li G, Li L, Linhardt RJ, Cygler M.

Glycobiology. 2017 Jan;27(2):176-187. doi: 10.1093/glycob/cww096. Epub 2016 Sep 12.

17.

Biophysical experiments and simulation in nanoparticle-based drug delivery systems.

Thewalt J, Tieleman DP.

J Drug Target. 2016 Nov;24(9):768-773. Epub 2016 Sep 8.

PMID:
27608728
18.

Structural and Functional Basis for Lipid Synergy on the Activity of the Antibacterial Peptide ABC Transporter McjD.

Mehmood S, Corradi V, Choudhury HG, Hussain R, Becker P, Axford D, Zirah S, Rebuffat S, Tieleman DP, Robinson CV, Beis K.

J Biol Chem. 2016 Oct 7;291(41):21656-21668. Epub 2016 Aug 23.

19.

Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers.

Bennett WF, Hong CK, Wang Y, Tieleman DP.

J Chem Theory Comput. 2016 Sep 13;12(9):4524-33. doi: 10.1021/acs.jctc.6b00265. Epub 2016 Aug 30.

PMID:
27529120
20.

Characterization of Zebrafish Cardiac and Slow Skeletal Troponin C Paralogs by MD Simulation and ITC.

Stevens CM, Rayani K, Genge CE, Singh G, Liang B, Roller JM, Li C, Li AY, Tieleman DP, van Petegem F, Tibbits GF.

Biophys J. 2016 Jul 12;111(1):38-49. doi: 10.1016/j.bpj.2016.05.029.

21.

The Heterodimeric ABC Transporter EfrCD Mediates Multidrug Efflux in Enterococcus faecalis.

Hürlimann LM, Corradi V, Hohl M, Bloemberg GV, Tieleman DP, Seeger MA.

Antimicrob Agents Chemother. 2016 Aug 22;60(9):5400-11. doi: 10.1128/AAC.00661-16. Print 2016 Sep.

22.

Structure and Stability of Carbohydrate-Lipid Interactions. Methylmannose Polysaccharide-Fatty Acid Complexes.

Liu L, Siuda I, Richards MR, Renaud J, Kitova EN, Mayer PM, Tieleman DP, Lowary TL, Klassen JS.

Chembiochem. 2016 Aug 17;17(16):1571-8. doi: 10.1002/cbic.201600123. Epub 2016 Jul 13.

PMID:
27253157
23.

Probing catalytic rate enhancement during intramembrane proteolysis.

Arutyunova E, Smithers CC, Corradi V, Espiritu AC, Young HS, Tieleman DP, Lemieux MJ.

Biol Chem. 2016 Sep 1;397(9):907-19. doi: 10.1515/hsz-2016-0124.

PMID:
27071148
24.

Computational and experimental approaches for investigating nanoparticle-based drug delivery systems.

Ramezanpour M, Leung SS, Delgado-Magnero KH, Bashe BY, Thewalt J, Tieleman DP.

Biochim Biophys Acta. 2016 Jul;1858(7 Pt B):1688-709. doi: 10.1016/j.bbamem.2016.02.028. Epub 2016 Feb 27. Review.

25.

Computer simulations of lung surfactant.

Baoukina S, Tieleman DP.

Biochim Biophys Acta. 2016 Oct;1858(10):2431-2440. doi: 10.1016/j.bbamem.2016.02.030. Epub 2016 Feb 27. Review.

26.

Two-Dimensional Potentials of Mean Force of Nile Red in Intact and Damaged Model Bilayers. Application to Calculations of Fluorescence Spectra.

Singh G, Chamberlin AC, Zhekova HR, Noskov SY, Tieleman DP.

J Chem Theory Comput. 2016 Jan 12;12(1):364-71. doi: 10.1021/acs.jctc.5b00520. Epub 2015 Dec 4.

PMID:
26579726
27.

Martini Coarse-Grained Force Field: Extension to DNA.

Uusitalo JJ, Ingólfsson HI, Akhshi P, Tieleman DP, Marrink SJ.

J Chem Theory Comput. 2015 Aug 11;11(8):3932-45. doi: 10.1021/acs.jctc.5b00286. Epub 2015 Jul 23.

PMID:
26574472
28.

High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach.

Wassenaar TA, Pluhackova K, Moussatova A, Sengupta D, Marrink SJ, Tieleman DP, Böckmann RA.

J Chem Theory Comput. 2015 May 12;11(5):2278-91. doi: 10.1021/ct5010092. Epub 2015 Mar 26.

PMID:
26574426
29.

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations.

Wassenaar TA, Ingólfsson HI, Böckmann RA, Tieleman DP, Marrink SJ.

J Chem Theory Comput. 2015 May 12;11(5):2144-55. doi: 10.1021/acs.jctc.5b00209. Epub 2015 Apr 24.

PMID:
26574417
30.

Molecular models of nanodiscs.

Siuda I, Tieleman DP.

J Chem Theory Comput. 2015 Oct 13;11(10):4923-32. doi: 10.1021/acs.jctc.5b00668. Epub 2015 Sep 16.

PMID:
26574280
31.

Conformational Changes of the Antibacterial Peptide ATP Binding Cassette Transporter McjD Revealed by Molecular Dynamics Simulations.

Gu RX, Corradi V, Singh G, Choudhury HG, Beis K, Tieleman DP.

Biochemistry. 2015 Sep 29;54(38):5989-98. doi: 10.1021/acs.biochem.5b00753. Epub 2015 Sep 17.

PMID:
26334959
32.

Cystic Fibrosis Transmembrane Conductance Regulator (CFTR): CLOSED AND OPEN STATE CHANNEL MODELS.

Corradi V, Vergani P, Tieleman DP.

J Biol Chem. 2015 Sep 18;290(38):22891-906. doi: 10.1074/jbc.M115.665125. Epub 2015 Jul 30.

33.

Activation of the bacterial thermosensor DesK involves a serine zipper dimerization motif that is modulated by bilayer thickness.

Cybulski LE, Ballering J, Moussatova A, Inda ME, Vazquez DB, Wassenaar TA, de Mendoza D, Tieleman DP, Killian JA.

Proc Natl Acad Sci U S A. 2015 May 19;112(20):6353-8. doi: 10.1073/pnas.1422446112. Epub 2015 May 4.

34.

Density based visualization for molecular simulation.

Rozmanov D, Baoukina S, Tieleman DP.

Faraday Discuss. 2014;169:225-43. doi: 10.1039/c3fd00124e. Epub 2014 Jun 12.

PMID:
25341200
35.

Computer simulations of phase separation in lipid bilayers and monolayers.

Baoukina S, Tieleman DP.

Methods Mol Biol. 2015;1232:307-22. doi: 10.1007/978-1-4939-1752-5_21.

PMID:
25331143
36.

Microsecond molecular dynamics simulations of lipid mixing.

Hong C, Tieleman DP, Wang Y.

Langmuir. 2014 Oct 14;30(40):11993-2001. doi: 10.1021/la502363b. Epub 2014 Oct 1.

37.

Lipid organization of the plasma membrane.

Ingólfsson HI, Melo MN, van Eerden FJ, Arnarez C, Lopez CA, Wassenaar TA, Periole X, de Vries AH, Tieleman DP, Marrink SJ.

J Am Chem Soc. 2014 Oct 15;136(41):14554-9. doi: 10.1021/ja507832e. Epub 2014 Oct 1.

38.

The mechanism of collapse of heterogeneous lipid monolayers.

Baoukina S, Rozmanov D, Mendez-Villuendas E, Tieleman DP.

Biophys J. 2014 Sep 2;107(5):1136-1145. doi: 10.1016/j.bpj.2014.05.053.

39.

Oleic acid phase behavior from molecular dynamics simulations.

Janke JJ, Bennett WF, Tieleman DP.

Langmuir. 2014 Sep 9;30(35):10661-7. doi: 10.1021/la501962n. Epub 2014 Aug 22.

PMID:
25133680
40.

Effect of confinement on DNA, solvent and counterion dynamics in a model biological nanopore.

Markosyan S, De Biase PM, Czapla L, Samoylova O, Singh G, Cuervo J, Tieleman DP, Noskov SY.

Nanoscale. 2014 Aug 7;6(15):9006-16. doi: 10.1039/c3nr06559f.

PMID:
24968858
41.

The importance of membrane defects-lessons from simulations.

Bennett WF, Tieleman DP.

Acc Chem Res. 2014 Aug 19;47(8):2244-51. doi: 10.1021/ar4002729. Epub 2014 Jun 3.

PMID:
24892900
42.

The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations.

Pan J, Cheng X, Monticelli L, Heberle FA, Kučerka N, Tieleman DP, Katsaras J.

Soft Matter. 2014 Jun 7;10(21):3716-25. doi: 10.1039/c4sm00066h. Epub 2014 Feb 18.

PMID:
24807693
43.

Characterization of the immersion properties of the peripheral membrane anchor of the FATC domain of the kinase "target of rapamycin" by NMR, oriented CD spectroscopy, and MD simulations.

Sommer LA, Janke JJ, Bennett WF, Bürck J, Ulrich AS, Tieleman DP, Dames SA.

J Phys Chem B. 2014 May 8;118(18):4817-31. doi: 10.1021/jp501533d. Epub 2014 Apr 25.

PMID:
24725177
44.

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models.

Wassenaar TA, Pluhackova K, Böckmann RA, Marrink SJ, Tieleman DP.

J Chem Theory Comput. 2014 Feb 11;10(2):676-90. doi: 10.1021/ct400617g. Epub 2014 Jan 21.

PMID:
26580045
45.

The ryanodine receptor store-sensing gate controls Ca2+ waves and Ca2+-triggered arrhythmias.

Chen W, Wang R, Chen B, Zhong X, Kong H, Bai Y, Zhou Q, Xie C, Zhang J, Guo A, Tian X, Jones PP, O'Mara ML, Liu Y, Mi T, Zhang L, Bolstad J, Semeniuk L, Cheng H, Zhang J, Chen J, Tieleman DP, Gillis AM, Duff HJ, Fill M, Song LS, Chen SR.

Nat Med. 2014 Feb;20(2):184-92. doi: 10.1038/nm.3440. Epub 2014 Jan 19.

46.

Atomistic simulations of pore formation and closure in lipid bilayers.

Bennett WF, Sapay N, Tieleman DP.

Biophys J. 2014 Jan 7;106(1):210-9. doi: 10.1016/j.bpj.2013.11.4486.

47.

Structural basis for autoinhibition of CTP:phosphocholine cytidylyltransferase (CCT), the regulatory enzyme in phosphatidylcholine synthesis, by its membrane-binding amphipathic helix.

Lee J, Taneva SG, Holland BW, Tieleman DP, Cornell RB.

J Biol Chem. 2014 Jan 17;289(3):1742-55. doi: 10.1074/jbc.M113.526970. Epub 2013 Nov 25.

48.

Interaction of pristine and functionalized carbon nanotubes with lipid membranes.

Baoukina S, Monticelli L, Tieleman DP.

J Phys Chem B. 2013 Oct 10;117(40):12113-23. doi: 10.1021/jp405732k. Epub 2013 Sep 25.

PMID:
24024494
49.

Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations.

Bulacu M, Goga N, Zhao W, Rossi G, Monticelli L, Periole X, Tieleman DP, Marrink SJ.

J Chem Theory Comput. 2013 Aug 13;9(8):3282-92. doi: 10.1021/ct400219n. Epub 2013 Jul 16.

PMID:
26584087
50.

Computer simulations of the phase separation in model membranes.

Baoukina S, Mendez-Villuendas E, Bennett WF, Tieleman DP.

Faraday Discuss. 2013;161:63-75; discussion 113-50.

PMID:
23805738

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