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pyHVis3D: Visualising Molecular Simulation deduced H-bond networks in 3D: Application to T-cell receptor interactions.

Knapp B, Alcala M, Zhang H, West C, van der Merwe PA, Deane CM.

Bioinformatics. 2018 Jan 10. doi: 10.1093/bioinformatics/btx842. [Epub ahead of print]


Architecture of a minimal signaling pathway explains the T-cell response to a 1 million-fold variation in antigen affinity and dose.

Lever M, Lim HS, Kruger P, Nguyen J, Trendel N, Abu-Shah E, Maini PK, van der Merwe PA, Dushek O.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):E6630-E6638. Epub 2016 Oct 4. Erratum in: Proc Natl Acad Sci U S A. 2017 Jan 3;:.


The contribution of major histocompatibility complex contacts to the affinity and kinetics of T cell receptor binding.

Zhang H, Lim HS, Knapp B, Deane CM, Aleksic M, Dushek O, van der Merwe PA.

Sci Rep. 2016 Oct 13;6:35326. doi: 10.1038/srep35326.


Homodimerization of the Lymph Vessel Endothelial Receptor LYVE-1 through a Redox-labile Disulfide Is Critical for Hyaluronan Binding in Lymphatic Endothelium.

Banerji S, Lawrance W, Metcalfe C, Briggs DC, Yamauchi A, Dushek O, van der Merwe PA, Day AJ, Jackson DG.

J Biol Chem. 2016 Nov 25;291(48):25004-25018. Epub 2016 Oct 12.


Multisite Phosphorylation Modulates the T Cell Receptor ζ-Chain Potency but not the Switchlike Response.

Mukhopadhyay H, de Wet B, Clemens L, Maini PK, Allard J, van der Merwe PA, Dushek O.

Biophys J. 2016 Apr 26;110(8):1896-1906. doi: 10.1016/j.bpj.2016.03.024.


Integrins Form an Expanding Diffusional Barrier that Coordinates Phagocytosis.

Freeman SA, Goyette J, Furuya W, Woods EC, Bertozzi CR, Bergmeier W, Hinz B, van der Merwe PA, Das R, Grinstein S.

Cell. 2016 Jan 14;164(1-2):128-140. doi: 10.1016/j.cell.2015.11.048.


Costimulation of IL-2 Production through CD28 Is Dependent on the Size of Its Ligand.

Lim HS, Cordoba SP, Dushek O, Goyette J, Taylor A, Rudd CE, van der Merwe PA.

J Immunol. 2015 Dec 1;195(11):5432-9. doi: 10.4049/jimmunol.1500707. Epub 2015 Oct 23.


T lymphocytes need less than 3 min to discriminate between peptide MHCs with similar TCR-binding parameters.

Brodovitch A, Shenderov E, Cerundolo V, Bongrand P, Pierres A, van der Merwe PA.

Eur J Immunol. 2015 Jun;45(6):1635-42. doi: 10.1002/eji.201445214. Epub 2015 Apr 21.


Phenotypic models of T cell activation.

Lever M, Maini PK, van der Merwe PA, Dushek O.

Nat Rev Immunol. 2014 Sep;14(9):619-29. doi: 10.1038/nri3728. Review.


SpyAvidin hubs enable precise and ultrastable orthogonal nanoassembly.

Fairhead M, Veggiani G, Lever M, Yan J, Mesner D, Robinson CV, Dushek O, van der Merwe PA, Howarth M.

J Am Chem Soc. 2014 Sep 3;136(35):12355-63. doi: 10.1021/ja505584f. Epub 2014 Aug 21.


An induced rebinding model of antigen discrimination.

Dushek O, van der Merwe PA.

Trends Immunol. 2014 Apr;35(4):153-8. doi: 10.1016/ Epub 2014 Mar 15. Review.


Saposins modulate human invariant Natural Killer T cells self-reactivity and facilitate lipid exchange with CD1d molecules during antigen presentation.

Salio M, Ghadbane H, Dushek O, Shepherd D, Cypen J, Gileadi U, Aichinger MC, Napolitani G, Qi X, van der Merwe PA, Wojno J, Veerapen N, Cox LR, Besra GS, Yuan W, Cresswell P, Cerundolo V.

Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):E4753-61. doi: 10.1073/pnas.1310050110. Epub 2013 Nov 18.


Mutant prolactin receptor and familial hyperprolactinemia.

Newey PJ, Gorvin CM, Cleland SJ, Willberg CB, Bridge M, Azharuddin M, Drummond RS, van der Merwe PA, Klenerman P, Bountra C, Thakker RV.

N Engl J Med. 2013 Nov 21;369(21):2012-2020. doi: 10.1056/NEJMoa1307557. Epub 2013 Nov 6.


The large ectodomains of CD45 and CD148 regulate their segregation from and inhibition of ligated T-cell receptor.

Cordoba SP, Choudhuri K, Zhang H, Bridge M, Basat AB, Dustin ML, van der Merwe PA.

Blood. 2013 May 23;121(21):4295-302. doi: 10.1182/blood-2012-07-442251. Epub 2013 Apr 11.


Systems model of T cell receptor proximal signaling reveals emergent ultrasensitivity.

Mukhopadhyay H, Cordoba SP, Maini PK, van der Merwe PA, Dushek O.

PLoS Comput Biol. 2013;9(3):e1003004. doi: 10.1371/journal.pcbi.1003004. Epub 2013 Mar 28.


Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms.

Stewart-Jones GB, Simpson P, van der Merwe PA, Easterbrook P, McMichael AJ, Rowland-Jones SL, Jones EY, Gillespie GM.

Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):E3483-92. doi: 10.1073/pnas.1207896109. Epub 2012 Nov 16.


Non-catalytic tyrosine-phosphorylated receptors.

Dushek O, Goyette J, van der Merwe PA.

Immunol Rev. 2012 Nov;250(1):258-76. doi: 10.1111/imr.12008. Review.


Why do some T cell receptor cytoplasmic domains associate with the plasma membrane?

van der Merwe PA, Zhang H, Cordoba SP.

Front Immunol. 2012 Feb 23;3:29. doi: 10.3389/fimmu.2012.00029. eCollection 2012.


Mechanical modulation of receptor-ligand interactions at cell-cell interfaces.

Allard JF, Dushek O, Coombs D, van der Merwe PA.

Biophys J. 2012 Mar 21;102(6):1265-73. doi: 10.1016/j.bpj.2012.02.006. Epub 2012 Mar 20.


Kinetics and mechanics of two-dimensional interactions between T cell receptors and different activating ligands.

Robert P, Aleksic M, Dushek O, Cerundolo V, Bongrand P, van der Merwe PA.

Biophys J. 2012 Jan 18;102(2):248-57. doi: 10.1016/j.bpj.2011.11.4018. Erratum in: Biophys J. 2014 Oct 7;107(7):1773.


Basic residues in the T-cell receptor ζ cytoplasmic domain mediate membrane association and modulate signaling.

Zhang H, Cordoba SP, Dushek O, van der Merwe PA.

Proc Natl Acad Sci U S A. 2011 Nov 29;108(48):19323-8. doi: 10.1073/pnas.1108052108. Epub 2011 Nov 14.


Boltzmann energy-based image analysis demonstrates that extracellular domain size differences explain protein segregation at immune synapses.

Burroughs NJ, Köhler K, Miloserdov V, Dustin ML, van der Merwe PA, Davis DM.

PLoS Comput Biol. 2011 Aug;7(8):e1002076. doi: 10.1371/journal.pcbi.1002076. Epub 2011 Aug 4.


Antigen potency and maximal efficacy reveal a mechanism of efficient T cell activation.

Dushek O, Aleksic M, Wheeler RJ, Zhang H, Cordoba SP, Peng YC, Chen JL, Cerundolo V, Dong T, Coombs D, van der Merwe PA.

Sci Signal. 2011 Jun 7;4(176):ra39. doi: 10.1126/scisignal.2001430.


Ultrasensitivity in multisite phosphorylation of membrane-anchored proteins.

Dushek O, van der Merwe PA, Shahrezaei V.

Biophys J. 2011 Mar 2;100(5):1189-97. doi: 10.1016/j.bpj.2011.01.060.


Late arrival: recruiting coreceptors to the T cell receptor complex.

van der Merwe PA, Cordoba SP.

Immunity. 2011 Jan 28;34(1):1-3. doi: 10.1016/j.immuni.2011.01.001.


Lck and the nature of the T cell receptor trigger.

Davis SJ, van der Merwe PA.

Trends Immunol. 2011 Jan;32(1):1-5. doi: 10.1016/ Epub 2010 Dec 27.


Matched sizes of activating and inhibitory receptor/ligand pairs are required for optimal signal integration by human natural killer cells.

Köhler K, Xiong S, Brzostek J, Mehrabi M, Eissmann P, Harrison A, Cordoba SP, Oddos S, Miloserdov V, Gould K, Burroughs NJ, van der Merwe PA, Davis DM.

PLoS One. 2010 Nov 5;5(11):e15374. doi: 10.1371/journal.pone.0015374.


Mechanisms for T cell receptor triggering.

van der Merwe PA, Dushek O.

Nat Rev Immunol. 2011 Jan;11(1):47-55. doi: 10.1038/nri2887. Epub 2010 Dec 3. Review.


What controls T cell receptor phosphorylation?

Fernandes RA, Yu C, Carmo AM, Evans EJ, van der Merwe PA, Davis SJ.

Cell. 2010 Sep 3;142(5):668-9. doi: 10.1016/j.cell.2010.08.018. No abstract available.


Ligand dimensions are important in controlling NK-cell responses.

Brzostek J, Chai JG, Gebhardt F, Busch DH, Zhao R, van der Merwe PA, Gould KG.

Eur J Immunol. 2010 Jul;40(7):2050-9. doi: 10.1002/eji.201040335.


Dependence of T cell antigen recognition on T cell receptor-peptide MHC confinement time.

Aleksic M, Dushek O, Zhang H, Shenderov E, Chen JL, Cerundolo V, Coombs D, van der Merwe PA.

Immunity. 2010 Feb 26;32(2):163-74. doi: 10.1016/j.immuni.2009.11.013. Epub 2010 Feb 4.


Ca2+ release from the endoplasmic reticulum of NY-ESO-1-specific T cells is modulated by the affinity of TCR and by the use of the CD8 coreceptor.

Chen JL, Morgan AJ, Stewart-Jones G, Shepherd D, Bossi G, Wooldridge L, Hutchinson SL, Sewell AK, Griffiths GM, van der Merwe PA, Jones EY, Galione A, Cerundolo V.

J Immunol. 2010 Feb 15;184(4):1829-1839. doi: 10.4049/jimmunol.0902103. Epub 2010 Jan 6.


Taking T cells beyond the diffraction limit.

van der Merwe PA, Dunne PD, Klenerman D, Davis SJ.

Nat Immunol. 2010 Jan;11(1):51-2. doi: 10.1038/ni0110-51. No abstract available.


Peptide-major histocompatibility complex dimensions control proximal kinase-phosphatase balance during T cell activation.

Choudhuri K, Parker M, Milicic A, Cole DK, Shaw MK, Sewell AK, Stewart-Jones G, Dong T, Gould KG, van der Merwe PA.

J Biol Chem. 2009 Sep 18;284(38):26096-105. doi: 10.1074/jbc.M109.039966. Epub 2009 Jul 23.


A single-chain H-2Db molecule presenting an influenza virus nucleoprotein epitope shows enhanced ability at stimulating CD8+ T cell responses in vivo.

Palmowski MJ, Parker M, Choudhuri K, Chiu C, Callan MF, van der Merwe PA, Cerundolo V, Gould KG.

J Immunol. 2009 Apr 15;182(8):4565-71. doi: 10.4049/jimmunol.0803893.


T cell-mediated autoimmune disease due to low-affinity crossreactivity to common microbial peptides.

Harkiolaki M, Holmes SL, Svendsen P, Gregersen JW, Jensen LT, McMahon R, Friese MA, van Boxel G, Etzensperger R, Tzartos JS, Kranc K, Sainsbury S, Harlos K, Mellins ED, Palace J, Esiri MM, van der Merwe PA, Jones EY, Fugger L.

Immunity. 2009 Mar 20;30(3):348-57. doi: 10.1016/j.immuni.2009.01.009. Erratum in: Immunity. 2009 Apr;30(4):610.


Nanoscale increases in CD2-CD48-mediated intermembrane spacing decrease adhesion and reorganize the immunological synapse.

Milstein O, Tseng SY, Starr T, Llodra J, Nans A, Liu M, Wild MK, van der Merwe PA, Stokes DL, Reisner Y, Dustin ML.

J Biol Chem. 2008 Dec 5;283(49):34414-22. doi: 10.1074/jbc.M804756200. Epub 2008 Sep 30.


Localization of the delta-like-1-binding site in human Notch-1 and its modulation by calcium affinity.

Cordle J, Redfieldz C, Stacey M, van der Merwe PA, Willis AC, Champion BR, Hambleton S, Handford PA.

J Biol Chem. 2008 Apr 25;283(17):11785-93. doi: 10.1074/jbc.M708424200. Epub 2008 Feb 22.


Rational design of a novel calcium-binding site adjacent to the ligand-binding site on CD2 increases its CD48 affinity.

Jones LM, Yang W, Maniccia AW, Harrison A, van der Merwe PA, Yang JJ.

Protein Sci. 2008 Mar;17(3):439-49. doi: 10.1110/ps.073328208.


Structure of a tyrosine phosphatase adhesive interaction reveals a spacer-clamp mechanism.

Aricescu AR, Siebold C, Choudhuri K, Chang VT, Lu W, Davis SJ, van der Merwe PA, Jones EY.

Science. 2007 Aug 31;317(5842):1217-20.


Molecular mechanisms involved in T cell receptor triggering.

Choudhuri K, van der Merwe PA.

Semin Immunol. 2007 Aug;19(4):255-61. Epub 2007 Jun 7. Review.


The length of lipids bound to human CD1d molecules modulates the affinity of NKT cell TCR and the threshold of NKT cell activation.

McCarthy C, Shepherd D, Fleire S, Stronge VS, Koch M, Illarionov PA, Bossi G, Salio M, Denkberg G, Reddington F, Tarlton A, Reddy BG, Schmidt RR, Reiter Y, Griffiths GM, van der Merwe PA, Besra GS, Jones EY, Batista FD, Cerundolo V.

J Exp Med. 2007 May 14;204(5):1131-44. Epub 2007 May 7.


Stochasticity and spatial heterogeneity in T-cell activation.

Burroughs NJ, van der Merwe PA.

Immunol Rev. 2007 Apr;216:69-80. Review.


How much can a T-cell antigen receptor adapt to structurally distinct antigenic peptides?

Mazza C, Auphan-Anezin N, Gregoire C, Guimezanes A, Kellenberger C, Roussel A, Kearney A, van der Merwe PA, Schmitt-Verhulst AM, Malissen B.

EMBO J. 2007 Apr 4;26(7):1972-83. Epub 2007 Mar 15.


The contribution of conformational adjustments and long-range electrostatic forces to the CD2/CD58 interaction.

Kearney A, Avramovic A, Castro MA, Carmo AM, Davis SJ, van der Merwe PA.

J Biol Chem. 2007 May 4;282(18):13160-6. Epub 2007 Mar 7.


Impact of salt bridges on the equilibrium binding and adhesion of human CD2 and CD58.

Bayas MV, Kearney A, Avramovic A, van der Merwe PA, Leckband DE.

J Biol Chem. 2007 Feb 23;282(8):5589-96. Epub 2006 Dec 15.


alphaVbeta6 is a novel receptor for human fibrillin-1. Comparative studies of molecular determinants underlying integrin-rgd affinity and specificity.

Jovanovic J, Takagi J, Choulier L, Abrescia NG, Stuart DI, van der Merwe PA, Mardon HJ, Handford PA.

J Biol Chem. 2007 Mar 2;282(9):6743-51. Epub 2006 Dec 11.


The kinetic-segregation model: TCR triggering and beyond.

Davis SJ, van der Merwe PA.

Nat Immunol. 2006 Aug;7(8):803-9. Review.


Crystal structure and binding properties of the CD2 and CD244 (2B4)-binding protein, CD48.

Evans EJ, Castro MA, O'Brien R, Kearney A, Walsh H, Sparks LM, Tucknott MG, Davies EA, Carmo AM, van der Merwe PA, Stuart DI, Jones EY, Ladbury JE, Ikemizu S, Davis SJ.

J Biol Chem. 2006 Sep 29;281(39):29309-20. Epub 2006 Jun 27.


Ligand detection and discrimination by spatial relocalization: A kinase-phosphatase segregation model of TCR activation.

Burroughs NJ, Lazic Z, van der Merwe PA.

Biophys J. 2006 Sep 1;91(5):1619-29. Epub 2006 Jun 2.

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