Publications

Preprints

• HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes.

  Gupta, S. ^†; Nerli, S. ^†; Kandy, S. K.; Mersky, G. L.; Sgourakis, N. G. bioRxiv March 21, 2023.

• Universal open MHC-I molecules for rapid peptide loading and enhanced complex stability across HLA allotypes.

  Sun, Y. ^†; Young, M. C. ^†; Woodward, C. H. ^†; Danon, J. N.; Truong, H.; Gupta, S.; Winters, T. J.; Burslem, G.; Sgourakis, N. G. bioRxiv March 18, 2023.

• Structure-based modeling of SARS-CoV-2 peptide/HLA-A02 antigens.

  Nerli S, Sgourakis NG. bioRxiv. 2020 Mar 27:2020.03.23.004176. Preprint.  

2023

• Xeno interactions between MHC-I proteins and molecular chaperones enable ligand exchange on a broad repertoire of HLA allotypes

  Yi Sun,  Georgia F. Papadaki, Christine A. Devlin, Julia N. Danon, Michael C. Young,  Trenton J. Winters, George M. Burslem  Erik Procko, and Nikolaos G. Sgourakis, Science Advances 2023, 9: 8

• Decoupling peptide binding from T cell receptor recognition with engineered chimeric MHC-I molecules

  Papadaki GF, Ani O, Florio TJ, Young MC, Danon JN, Sun Y, Dersh D, Sgourakis Frontiers in Immunology 2023 In Press

2022

• Editorial: Computational approaches for interpreting experimental data and understanding protein structure, dynamics and function relationships

  Hu Kaifeng, Lee Woonghee, Montelione Gaetano T., Sgourakis Nikolaos G., Vögeli Beat. Frontiers in Molecular Biosciences. 2022; 9.

• Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation

  Jiang, J., Taylor, D.K., Kim, E.J. et al. Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation. Nature Communications. 2022 Sept; 13, 5470.

• Global protein dynamics as communication sensors in peptide synthetase domains

  Mishra SH, Kancherla AK, Marincin KA, Bouvignies G, Nerli S, Sgourakis N, Dowling DP, Frueh DP. Science Advances. 2022 Jul 15;8(28):eabn6549.

• TAPBPR employs a ligand-independent docking mechanism to chaperone MR1 molecules

  McShan AC, Devlin CA, Papadaki GF, Sun Y, Green AI, Burslem GM, Prock E, Sgourakis NG Nature Chemical Biology. 2022, 18, pages 859–868

2021

• Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs

  Yarmarkovich M, Marshall QF, Warrington JM, Premaratne R, Farrel A, Groff D, Li W, di Marco M, Runbeck E, Truong H, Toor JS, Tripathi S, Nguyen S, Shen H, Noel T, Church NL, Weiner A, Kendsersky N, Martinez D, Weisberg R, Christie M, Eisenlohr L, Bosse KR, Dimitrov DS, Stevanovic S, Sgourakis NG, Kiefel BR, Maris JM. Nature. 2021 Nov;599(7885):477-484.

• Dynamics of MHC-I molecules in the antigen processing and presentation pathway

  Truong HV, Sgourakis NG. Current Opinion in Immunology. 2021 Jun;70:122-128.

• TAPBPR promotes antigen loading on MHC-I molecules using a peptide trap.

  McShan AC, Devlin CA, Morozov GI, Overall SA, Moschidi D, Akella N, Procko E, Sgourakis NG. Nature Communications. 2021 May 26;12(1):3174.

• Backbone-independent NMR resonance assignments of methyl probes in large proteins.

  Nerli S, De Paula VS, McShan AC, Sgourakis NG. Nature Communications. 2021 Jan 29;12(1):691.

2020

• Interleukin-2 druggability is modulated by global conformational transitions controlled by a helical capping switch.

  De Paula VS, Jude KM, Nerli S, Glassman CR, Garcia KC, Sgourakis NG. Proceedings of the National Academy of Sciences of the United States of America. 2020 Mar 31;117(13):7183-7192.

• Computational design of closely related proteins that adopt two well-defined but structurally divergent folds.

  Wei KY, Moschidi D, Bick MJ, Nerli S, McShan AC, Carter LP, Huang PS, Fletcher DA, Sgourakis NG, Boyken SE, Baker D. Proceedings of the National Academy of Sciences of the United States of America. 2020 Mar 31;117(13):7208-7215.

• High throughput pMHC-I tetramer library production using chaperone-mediated peptide exchange.

  Overall SA, Toor JS, Hao S, Yarmarkovich M, Sara M O’Rourke, Morozov GI, Nguyen S, Japp AS, Gonzalez N, Moschidi D, Betts MR, Maris JM, Smibert P, Sgourakis NG. Nature Communications. 2020 Apr 20;11(1):1909.  

• Macromolecular modeling and design in Rosetta: recent methods and frameworks.

  Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó’Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. Nature Methods. 2020 Jul;17(7):665-680.

• Structure-based modeling of SARS-CoV-2 peptide/HLA-A02 antigens.

  Nerli S, Sgourakis NG. bioRxiv. 2020 Mar 27:2020.03.23.004176. Preprint.  

• Nearest-neighbor NMR spectroscopy: categorizing spectral peaks by their adjacent nuclei.

  Behera SP, Dubey A, Chen WN, De Paula VS, Zhang M, Sgourakis NG, Bermel W, Wagner G, Coote PW, Arthanari H. Nature Communications. 2020 Nov 3;11(1):5547.

• Structure-Based Modeling of SARS-CoV-2 Peptide/HLA-A02 Antigens.

  Nerli S, Sgourakis NG. Frontiers in Medical Technology. 2020 Nov 17;2:553478.

2019

• NMR structure determination of Ixolaris and factor X(a) interaction reveals a noncanonical mechanism of Kunitz inhibition.

  De Paula VS, Sgourakis NG, Francischetti IMB, Almeida FCL, Monteiro RQ, Valente AP. Blood. 2019 Aug 22;134(8):699-708.

• An order-to-disorder structural switch activates the FoxM1 transcription factor.

  Marceau AH, Brison CM, Nerli S, Arsenault HE, McShan AC, Chen E, Lee HW, Benanti JA, Sgourakis NG, Rubin SM. eLife. 2019 May 28;8:e46131.

• Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection.

  McShan AC, Devlin CA, Overall SA, Park J, Toor JS, Moschidi D, Flores-Solis D, Choi H, Tripathi S, Procko E, Sgourakis NG. Proceedings of the National Academy of Sciences of the United States of America. 2019 Dec 17;116(51):25602-25613.

• De novo design of a homo-trimeric amantadine-binding protein.

  Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DA, Baker D. eLife. 2019 Dec 19;8:e47839.

• Production of soluble pMHC-I molecules in mammalian cells using the molecular chaperone TAPBPR.

  O’Rourke SM, Morozov GI, Roberts JT, Barb AW, Sgourakis NG. Protein Engineering Design & Selection. 2019 Dec 31;32(12):525-532.

2018

• Filamentous Bacteriophage Viruses: Preparation, Magic-Angle Spinning Solid-State NMR Experiments, and Structure Determination.

  Morag O, Sgourakis NG, Abramov G, Goldbourt A. Methods in Molecular Biology. 2018;1688:67-97.

• Chemical shift-based methods in NMR structure determination.

  Nerli S, McShan AC, Sgourakis NG. Progress in Nuclear Magnetic Resonance Spectroscopy. 2018 Jun-Aug;106-107:1-25.

• Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra.

  Evangelidis T, Nerli S, Nováček J, Brereton AE, Karplus PA, Dotas RR, Venditti V, Sgourakis NG, Tripsianes K. Nature Communications. 2018 Jan 26;9(1):384.

• A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations.

  Toor JS, Rao AA, McShan AC, Yarmarkovich M, Nerli S, Yamaguchi K, Madejska AA, Nguyen S, Tripathi S, Maris JM, Salama SR, Haussler D, Sgourakis NG. Frontiers in Immunology. 2018 Jan 30;9:99.

• Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle.

  McShan AC, Natarajan K, Kumirov VK, Flores-Solis D, Jiang J, Badstübner M, Toor JS, Bagshaw CR, Kovrigin EL, Margulies DH, Sgourakis NG. Nature Chemical Biology. 2018 Aug;14(8):811-820.

• The Role of Molecular Flexibility in Antigen Presentation and T Cell Receptor-Mediated Signaling.

  Natarajan K, Jiang J, May NA, Mage MG, Boyd LF, McShan AC, Sgourakis NG, Bax A, Margulies DH. Frontiers in Immunology. 2018 Jul 17;9:1657.

• De novo design of a non-local β-sheet protein with high stability and accuracy.

  Marcos E, Chidyausiku TM, McShan AC, Evangelidis T, Nerli S, Carter L, Nivón LG, Davis A, Oberdorfer G, Tripsianes K, Sgourakis NG, Baker D. Nature Structural & Molecular Biology. 2018 Nov;25(11):1028-1034.

• Programmable design of orthogonal protein heterodimers.

  Chen Z, Boyken SE, Jia M, Busch F, Flores-Solis D, Bick MJ, Lu P, VanAernum ZL, Sahasrabuddhe A, Langan RA, Bermeo S, Brunette TJ, Mulligan VK, Carter LP, DiMaio F, Sgourakis NG, Wysocki VH, Baker D. Nature. 2019 Jan;565(7737):106-111.

• CS-ROSETTA.

  Nerli S, Sgourakis NG. Methods in Enzymology. 2019;614:321-362.

2017

• An allosteric site in the T-cell receptor Cβ domain plays a critical signalling role.

  Natarajan K, McShan AC, Jiang J, Kumirov VK, Wang R, Zhao H, Schuck P, Tilahun ME, Boyd LF, Ying J, Bax A, Margulies DH, Sgourakis NG. Nature Communications. 2017 May 16;8:15260.

2015

• A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta.

  Rossi P, Shi L, Liu G, Barbieri CM, Lee HW, Grant TD, Luft JR, Xiao R, Acton TB, Snell EH, Montelione GT, Baker D, Lange OF, Sgourakis NG. Proteins. 2015 Feb;83(2):309-17. 

• The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body.

  Bergeron JRC, Worrall LJ, De S, Sgourakis NG, Cheung AH, Lameignere E, Okon M, Wasney GA, Baker D, McIntosh LP, Strynadka NCJ. Structure. 2015 Jan 6;23(1):161-172.

• The NMR-Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope.

  Morag O, Sgourakis NG, Baker D, Goldbourt A. Proceedings of the National Academy of Sciences of the United States of America. 2015 Jan 27;112(4):971-6.

• Type IV pilus: one architectural problem, many structural solutions.

  Bergeron JR, Sgourakis NG. Structure. 2015 Feb 3;23(2):253-5.

• A Novel MHC-I Surface Targeted for Binding by the MCMV m06 Immunoevasin Revealed by Solution NMR.

  Sgourakis NG, May NA, Boyd LF, Ying J, Bax A, Margulies DH. Journal of Biological Chemistry. 2015 Nov 27;290(48):28857-68.

2014

• The structure of mouse cytomegalovirus m04 protein obtained from sparse NMR data reveals a conserved fold of the m02-m06 viral immune modulator family.

  Sgourakis NG, Natarajan K, Ying J, Vogeli B, Boyd LF, Margulies DH, Bax A. Structure. 2014 Sep 2;22(9):1263-1273.

• High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy.

  Demers JP, Habenstein B, Loquet A, Kumar Vasa S, Giller K, Becker S, Baker D, Lange A, Sgourakis NG. Nature Communications. 2014 Sep 29;5:4976.

• Modeling an in-register, parallel “iowa” aβ fibril structure using solid-state NMR data from labeled samples with rosetta.

  Sgourakis NG, Yau WM, Qiang W. Structure. 2015 Jan 6;23(1):216-227.

2013

• The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles.

  Demers JP, Sgourakis NG, Gupta R, Loquet A, Giller K, Riedel D, Laube B, Kolbe M, Baker D, Becker S, Lange A. PLOS Pathogens. 2013 Mar;9(3):e1003245.

• A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly.

  Bergeron JR, Worrall LJ, Sgourakis NG, DiMaio F, Pfuetzner RA, Felise HB, Vuckovic M, Yu AC, Miller SI, Baker D, Strynadka NC. PLOS Pathogens. 2013;9(4):e1003307. 

2012

• Accurate protein structure modeling using sparse NMR data and homologous structure information.

  Thompson JM, Sgourakis NG, Liu G, Rossi P, Tang Y, Mills JL, Szyperski T, Montelione GT, Baker D. Proceedings of the National Academy of Sciences of the United States of America. 2012 Jun 19;109(25):9875-80. 

• Atomic model of the type III secretion system needle.

  Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M, Baker D, Becker S, Lange A. Nature. 2012 May 20;486(7402):276-9. 

• Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.

  Lange OF, Rossi P, Sgourakis NG, Song Y, Lee HW, Aramini JM, Ertekin A, Xiao R, Acton TB, Montelione GT, Baker D. Proceedings of the National Academy of Sciences of the United States of America. 2012 Jul 3;109(27):10873-8. 

2011

• Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms.

  Sgourakis NG, Merced-Serrano M, Boutsidis C, Drineas P, Du Z, Wang C, Garcia AE. Journal of Molecular Biology. 2011 Jan 14;405(2):570-83.

• Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings.

  Sgourakis NG, Lange OF, DiMaio F, André I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D. Journal of the American Chemical Society. 2011 Apr 27;133(16):6288-98.

2010

• Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain.

  Sgourakis NG, Patel MM, Garcia AE, Makhatadze GI, McCallum SA. Journal of Molecular Biology. 2010 Mar 5;396(4):1128-44.

• The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations.

  Sgourakis NG, Garcia AE. Journal of Molecular Biology. 2010 Apr 23;398(1):161-73.

• Discriminating early stage A{beta}42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study.

  Zhuang W, Sgourakis NG, Li Z, Garcia AE, Mukamel S. Proceedings of the National Academy of Sciences of the United States of America. 2010 Sep 7;107(36):15687-92.

• Experimental test of the thermodynamic model of protein cooperativity using temperature-induced unfolding of a Ubq-UIM fusion protein.

  Patel MM, Sgourakis NG, Garcia AE, Makhatadze GI. Biochemistry. 2010 Oct 5;49(39):8455-67.

2008

• Pressure effects on the ensemble dynamics of ubiquitin inspected with molecular dynamics simulations and isotropic reorientational eigenmode dynamics.

  Sgourakis NG, Day R, McCallum SA, Garcia AE. Biophysical Journal. 2008 Oct;95(8):3943-55.

2007

• The Alzheimer’s peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study.

  Sgourakis NG, Yan Y, McCallum SA, Wang C, Garcia AE. Journal of Molecular Biology. 2007 May 18;368(5):1448-57. 

2005

• A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models.

  Sgourakis NG, Bagos PG, Papasaikas PK, Hamodrakas SJ. BMC Bioinformatics. 2005 Apr 22;6:104. 

• Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks.

  Sgourakis NG, Bagos PG, Hamodrakas SJ. Bioinformatics. 2005 Nov 15;21(22):4101-6.