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The energetics of protein-lipid interactions as viewed by molecular simulations.

Corey RA, Stansfeld PJ, Sansom MSP.

Biochem Soc Trans. 2019 Dec 24. pii: BST20190149. doi: 10.1042/BST20190149. [Epub ahead of print]


Lipid Interactions of a Ciliary Membrane TRP Channel: Simulation and Structural Studies of Polycystin-2.

Wang Q, Corey RA, Hedger G, Aryal P, Grieben M, Nasrallah C, Baronina A, Pike ACW, Shi J, Carpenter EP, Sansom MSP.

Structure. 2019 Nov 27. pii: S0969-2126(19)30389-2. doi: 10.1016/j.str.2019.11.005. [Epub ahead of print]


More Favorable Palmitic Acid Over Palmitoleic Acid Modification of Wnt3 Ensures Its Localization and Activity in Plasma Membrane Domains.

Azbazdar Y, Ozalp O, Sezgin E, Veerapathiran S, Duncan AL, Sansom MSP, Eggeling C, Wohland T, Karaca E, Ozhan G.

Front Cell Dev Biol. 2019 Nov 15;7:281. doi: 10.3389/fcell.2019.00281. eCollection 2019.


Structure and Dynamics of Cinnamycin-Lipid Complexes: Mechanisms of Selectivity for Phosphatidylethanolamine Lipids.

Vestergaard M, Berglund NA, Hsu PC, Song C, Koldsø H, Schiøtt B, Sansom MSP.

ACS Omega. 2019 Oct 28;4(20):18889-18899. doi: 10.1021/acsomega.9b02949. eCollection 2019 Nov 12.


The morphogen Sonic hedgehog inhibits its receptor Patched by a pincer grasp mechanism.

Rudolf AF, Kinnebrew M, Kowatsch C, Ansell TB, El Omari K, Bishop B, Pardon E, Schwab RA, Malinauskas T, Qian M, Duman R, Covey DF, Steyaert J, Wagner A, Sansom MSP, Rohatgi R, Siebold C.

Nat Chem Biol. 2019 Oct;15(10):975-982. doi: 10.1038/s41589-019-0370-y. Epub 2019 Sep 23.


Lipid-Dependent Regulation of Ion Channels and G Protein-Coupled Receptors: Insights from Structures and Simulations.

Duncan AL, Song W, Sansom MSP.

Annu Rev Pharmacol Toxicol. 2020 Jan 6;60:31-50. doi: 10.1146/annurev-pharmtox-010919-023411. Epub 2019 Sep 10.


Insights into Membrane Protein-Lipid Interactions from Free Energy Calculations.

Corey RA, Vickery ON, Sansom MSP, Stansfeld PJ.

J Chem Theory Comput. 2019 Oct 8;15(10):5727-5736. doi: 10.1021/acs.jctc.9b00548. Epub 2019 Sep 17.


Computational Virology: Molecular Simulations of Virus Dynamics and Interactions.

Jefferys EE, Sansom MSP.

Adv Exp Med Biol. 2019;1215:201-233. doi: 10.1007/978-3-030-14741-9_10.


A heuristic derived from analysis of the ion channel structural proteome permits the rapid identification of hydrophobic gates.

Rao S, Klesse G, Stansfeld PJ, Tucker SJ, Sansom MSP.

Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):13989-13995. doi: 10.1073/pnas.1902702116. Epub 2019 Jun 24.


CHAP: A Versatile Tool for the Structural and Functional Annotation of Ion Channel Pores.

Klesse G, Rao S, Sansom MSP, Tucker SJ.

J Mol Biol. 2019 Aug 9;431(17):3353-3365. doi: 10.1016/j.jmb.2019.06.003. Epub 2019 Jun 17.


Membrane Recognition and Binding by the Phosphatidylinositol Phosphate Kinase PIP5K1A: A Multiscale Simulation Study.

Amos STA, Kalli AC, Shi J, Sansom MSP.

Structure. 2019 Aug 6;27(8):1336-1346.e2. doi: 10.1016/j.str.2019.05.004. Epub 2019 Jun 13.


Structures of the otopetrin proton channels Otop1 and Otop3.

Saotome K, Teng B, Tsui CCA, Lee WH, Tu YH, Kaplan JP, Sansom MSP, Liman ER, Ward AB.

Nat Struct Mol Biol. 2019 Jun;26(6):518-525. doi: 10.1038/s41594-019-0235-9. Epub 2019 Jun 3.


Lipid Bilayer Composition Influences the Activity of the Antimicrobial Peptide Dermcidin Channel.

Song C, de Groot BL, Sansom MSP.

Biophys J. 2019 May 7;116(9):1658-1666. doi: 10.1016/j.bpj.2019.03.033. Epub 2019 Apr 5.


A lipid gating mechanism for the channel-forming O antigen ABC transporter.

Caffalette CA, Corey RA, Sansom MSP, Stansfeld PJ, Zimmer J.

Nat Commun. 2019 Feb 18;10(1):824. doi: 10.1038/s41467-019-08646-8.


Computational Modeling of Realistic Cell Membranes.

Marrink SJ, Corradi V, Souza PCT, Ingólfsson HI, Tieleman DP, Sansom MSP.

Chem Rev. 2019 May 8;119(9):6184-6226. doi: 10.1021/acs.chemrev.8b00460. Epub 2019 Jan 9.


Cholesterol Interaction Sites on the Transmembrane Domain of the Hedgehog Signal Transducer and Class F G Protein-Coupled Receptor Smoothened.

Hedger G, Koldsø H, Chavent M, Siebold C, Rohatgi R, Sansom MSP.

Structure. 2019 Mar 5;27(3):549-559.e2. doi: 10.1016/j.str.2018.11.003. Epub 2018 Dec 27.


State-dependent Lipid Interactions with the A2a Receptor Revealed by MD Simulations Using In Vivo-Mimetic Membranes.

Song W, Yen HY, Robinson CV, Sansom MSP.

Structure. 2019 Feb 5;27(2):392-403.e3. doi: 10.1016/j.str.2018.10.024. Epub 2018 Dec 20.


The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions.

Newport TD, Sansom MSP, Stansfeld PJ.

Nucleic Acids Res. 2019 Jan 8;47(D1):D390-D397. doi: 10.1093/nar/gky1047.


Cryo-EM reveals two distinct serotonin-bound conformations of full-length 5-HT3A receptor.

Basak S, Gicheru Y, Rao S, Sansom MSP, Chakrapani S.

Nature. 2018 Nov;563(7730):270-274. doi: 10.1038/s41586-018-0660-7. Epub 2018 Oct 31.


Cryo-EM structure of the mechanically activated ion channel OSCA1.2.

Jojoa-Cruz S, Saotome K, Murthy SE, Tsui CCA, Sansom MS, Patapoutian A, Ward AB.

Elife. 2018 Nov 1;7. pii: e41845. doi: 10.7554/eLife.41845.


Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network.

Esque J, Sansom MSP, Baaden M, Oguey C.

Sci Rep. 2018 Sep 10;8(1):13540. doi: 10.1038/s41598-018-31422-5.


How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins.

Chavent M, Duncan AL, Rassam P, Birkholz O, Hélie J, Reddy T, Beliaev D, Hambly B, Piehler J, Kleanthous C, Sansom MSP.

Nat Commun. 2018 Jul 20;9(1):2846. doi: 10.1038/s41467-018-05255-9.


PtdIns(4,5)P2 stabilizes active states of GPCRs and enhances selectivity of G-protein coupling.

Yen HY, Hoi KK, Liko I, Hedger G, Horrell MR, Song W, Wu D, Heine P, Warne T, Lee Y, Carpenter B, Plückthun A, Tate CG, Sansom MSP, Robinson CV.

Nature. 2018 Jul;559(7714):423-427. doi: 10.1038/s41586-018-0325-6. Epub 2018 Jul 11.


Electric-Field-Driven Translocation of ssDNA through Hydrophobic Nanopores.

Haynes T, Smith IPS, Wallace EJ, Trick JL, Sansom MSP, Khalid S.

ACS Nano. 2018 Aug 28;12(8):8208-8213. doi: 10.1021/acsnano.8b03365. Epub 2018 Jul 19.


Water and hydrophobic gates in ion channels and nanopores.

Rao S, Lynch CI, Klesse G, Oakley GE, Stansfeld PJ, Tucker SJ, Sansom MSP.

Faraday Discuss. 2018 Sep 28;209(0):231-247. doi: 10.1039/c8fd00013a.


Interactions of a Bacterial Cu(I)-ATPase with a Complex Lipid Environment.

Autzen HE, Koldsø H, Stansfeld PJ, Gourdon P, Sansom MSP, Nissen P.

Biochemistry. 2018 Jul 17;57(28):4063-4073. doi: 10.1021/acs.biochem.8b00326. Epub 2018 Jun 27.


Interactions of the EphA2 Kinase Domain with PIPs in Membranes: Implications for Receptor Function.

Chavent M, Karia D, Kalli AC, Domański J, Duncan AL, Hedger G, Stansfeld PJ, Seiradake E, Jones EY, Sansom MSP.

Structure. 2018 Jul 3;26(7):1025-1034.e2. doi: 10.1016/j.str.2018.05.003. Epub 2018 Jun 7.


Distinctive phosphoinositide- and Ca2+-binding properties of normal and cognitive performance-linked variant forms of KIBRA C2 domain.

Posner MG, Upadhyay A, Ishima R, Kalli AC, Harris G, Kremerskothen J, Sansom MSP, Crennell SJ, Bagby S.

J Biol Chem. 2018 Jun 15;293(24):9335-9344. doi: 10.1074/jbc.RA118.002279. Epub 2018 May 3.


Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association.

Domański J, Sansom MSP, Stansfeld PJ, Best RB.

J Chem Theory Comput. 2018 Mar 13;14(3):1706-1715. doi: 10.1021/acs.jctc.7b00983. Epub 2018 Feb 9.


Modes of Interaction of Pleckstrin Homology Domains with Membranes: Toward a Computational Biochemistry of Membrane Recognition.

Naughton FB, Kalli AC, Sansom MSP.

J Mol Biol. 2018 Feb 2;430(3):372-388. doi: 10.1016/j.jmb.2017.12.011. Epub 2017 Dec 20.


Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes.

Duncan AL, Reddy T, Koldsø H, Hélie J, Fowler PW, Chavent M, Sansom MSP.

Sci Rep. 2017 Nov 30;7(1):16647. doi: 10.1038/s41598-017-16865-6.


Peptide-surfactant interactions: A combined spectroscopic and molecular dynamics simulation approach.

Roussel G, Caudano Y, Matagne A, Sansom MS, Perpète EA, Michaux C.

Spectrochim Acta A Mol Biomol Spectrosc. 2018 Feb 5;190:464-470. doi: 10.1016/j.saa.2017.09.056. Epub 2017 Sep 21.


Asymmetric mechanosensitivity in a eukaryotic ion channel.

Clausen MV, Jarerattanachat V, Carpenter EP, Sansom MSP, Tucker SJ.

Proc Natl Acad Sci U S A. 2017 Oct 3;114(40):E8343-E8351. doi: 10.1073/pnas.1708990114. Epub 2017 Sep 18.


The effect of mutations in the lid region of Thermomyces lanuginosus lipase on interactions with triglyceride surfaces: A multi-scale simulation study.

Willems N, Lelimousin M, Skjold-Jørgensen J, Svendsen A, Sansom MSP.

Chem Phys Lipids. 2018 Mar;211:4-15. doi: 10.1016/j.chemphyslip.2017.08.004. Epub 2017 Aug 15.


The effects of stretch activation on ionic selectivity of the TREK-2 K2P K+ channel.

Nematian-Ardestani E, Jarerattanachat V, Aryal P, Sansom MSP, Tucker SJ.

Channels (Austin). 2017 Sep 3;11(5):482-486. doi: 10.1080/19336950.2017.1356955. Epub 2017 Jul 19.


Dynamic role of the tether helix in PIP2-dependent gating of a G protein-gated potassium channel.

Lacin E, Aryal P, Glaaser IW, Bodhinathan K, Tsai E, Marsh N, Tucker SJ, Sansom MSP, Slesinger PA.

J Gen Physiol. 2017 Jul 18. pii: jgp.201711801. doi: 10.1085/jgp.201711801. [Epub ahead of print]


Bilayer-Mediated Structural Transitions Control Mechanosensitivity of the TREK-2 K2P Channel.

Aryal P, Jarerattanachat V, Clausen MV, Schewe M, McClenaghan C, Argent L, Conrad LJ, Dong YY, Pike ACW, Carpenter EP, Baukrowitz T, Sansom MSP, Tucker SJ.

Structure. 2017 May 2;25(5):708-718.e2. doi: 10.1016/j.str.2017.03.006. Epub 2017 Apr 6.


A BEST example of channel structure annotation by molecular simulation.

Rao S, Klesse G, Stansfeld PJ, Tucker SJ, Sansom MSP.

Channels (Austin). 2017 Jul 4;11(4):347-353. doi: 10.1080/19336950.2017.1306163. Epub 2017 Mar 20.


Stability and dynamics of membrane-spanning DNA nanopores.

Maingi V, Burns JR, Uusitalo JJ, Howorka S, Marrink SJ, Sansom MS.

Nat Commun. 2017 Mar 20;8:14784. doi: 10.1038/ncomms14784.


Biomimetic Phospholipid Membrane Organization on Graphene and Graphene Oxide Surfaces: A Molecular Dynamics Simulation Study.

Willems N, Urtizberea A, Verre AF, Iliut M, Lelimousin M, Hirtz M, Vijayaraghavan A, Sansom MS.

ACS Nano. 2017 Feb 28;11(2):1613-1625. doi: 10.1021/acsnano.6b07352. Epub 2017 Feb 14.


Voltage Gating of a Biomimetic Nanopore: Electrowetting of a Hydrophobic Barrier.

Trick JL, Song C, Wallace EJ, Sansom MS.

ACS Nano. 2017 Feb 28;11(2):1840-1847. doi: 10.1021/acsnano.6b07865. Epub 2017 Feb 6.


Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity.

Yamamoto E, Akimoto T, Kalli AC, Yasuoka K, Sansom MS.

Sci Adv. 2017 Jan 20;3(1):e1601871. doi: 10.1126/sciadv.1601871. eCollection 2017 Jan.


Effect of the Southeast Asian Ovalocytosis Deletion on the Conformational Dynamics of Signal-Anchor Transmembrane Segment 1 of Red Cell Anion Exchanger 1 (AE1, Band 3, or SLC4A1).

Fowler PW, Sansom MS, Reithmeier RA.

Biochemistry. 2017 Feb 7;56(5):712-722. doi: 10.1021/acs.biochem.6b00966. Epub 2017 Jan 23.


Interfacial activation of M37 lipase: A multi-scale simulation study.

Willems N, Lelimousin M, Koldsø H, Sansom MS.

Biochim Biophys Acta Biomembr. 2017 Mar;1859(3):340-349. doi: 10.1016/j.bbamem.2016.12.012. Epub 2016 Dec 18.


Structure and lipid-binding properties of the kindlin-3 pleckstrin homology domain.

Ni T, Kalli AC, Naughton FB, Yates LA, Naneh O, Kozorog M, Anderluh G, Sansom MS, Gilbert RJ.

Biochem J. 2017 Feb 15;474(4):539-556. doi: 10.1042/BCJ20160791. Epub 2016 Dec 14.


On the interpretation of reflectivity data from lipid bilayers in terms of molecular-dynamics models.

Hughes AV, Ciesielski F, Kalli AC, Clifton LA, Charlton TR, Sansom MS, Webster JR.

Acta Crystallogr D Struct Biol. 2016 Dec 1;72(Pt 12):1227-1240. Epub 2016 Nov 29.


Functional Annotation of Ion Channel Structures by Molecular Simulation.

Trick JL, Chelvaniththilan S, Klesse G, Aryal P, Wallace EJ, Tucker SJ, Sansom MSP.

Structure. 2016 Dec 6;24(12):2207-2216. doi: 10.1016/j.str.2016.10.005. Epub 2016 Nov 17.


Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association.

Domański J, Hedger G, Best RB, Stansfeld PJ, Sansom MSP.

J Phys Chem B. 2017 Apr 20;121(15):3364-3375. doi: 10.1021/acs.jpcb.6b08445. Epub 2016 Nov 17.


Lipid-Loving ANTs: Molecular Simulations of Cardiolipin Interactions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes.

Hedger G, Rouse SL, Domański J, Chavent M, Koldsø H, Sansom MS.

Biochemistry. 2016 Nov 15;55(45):6238-6249. Epub 2016 Nov 4.


Membrane stiffness is modified by integral membrane proteins.

Fowler PW, Hélie J, Duncan A, Chavent M, Koldsø H, Sansom MS.

Soft Matter. 2016 Sep 20;12(37):7792-7803.

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