Publications
See publications on Google Scholar or PubMed.
See publications on Google Scholar or PubMed.
Sun Y, Florio TJ, Gupta S, Young MC, Marshall QF, Garfinkle SE, Papadaki GF, Truong HV, Mycek E, Li P, Farrel A, Church NL, Jabar S, Beasley MD, Kiefel BR, Yarmarkovich M, Mallik L, Maris JM, Sgourakis NG. bioRxiv. 2023 May 24:2023.05.24.542108. doi: 10.1101/2023.05.24.542108. Preprint.
Gupta, S. †; Nerli, S. †; Kandy, S. K.; Mersky, G. L.; Sgourakis, N. G. bioRxiv March 21, 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.
A Chicken Tapasin ortholog can chaperone empty HLA-B*37:01 molecules independent of other peptide-loading components. Papadaki GF, Woodward CH, Young MC, Winters TJ, Burslem GM, Sgourakis NG.J Biol Chem. 2023 Aug 3:105136. doi: 10.1016/j.jbc.2023.105136. Online ahead of print.PMID: 37543367
Sun Y, Young MC, Woodward CH, Danon JN, Truong HV, Gupta S, Winters TJ, Font-Burgada J, Burslem GM, Sgourakis NG. Proc Natl Acad Sci U S A. 2023 Jun 20;120(25):e2304055120. doi: 10.1073/pnas.2304055120. Epub 2023 Jun 13.
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
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
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.
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.
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.
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.
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.
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.
Nerli S, Sgourakis NG. Methods in Enzymology. 2019;614:321-362.
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.
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.
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.
Sgourakis NG, Natarajan K, Ying J, Vogeli B, Boyd LF, Margulies DH, Bax A. Structure. 2014 Sep 2;22(9):1263-1273.
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.
Sgourakis NG, Yau WM, Qiang W. Structure. 2015 Jan 6;23(1):216-227.
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.
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.
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.
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.
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.
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.
Sgourakis NG, Patel MM, Garcia AE, Makhatadze GI, McCallum SA. Journal of Molecular Biology. 2010 Mar 5;396(4):1128-44.
Sgourakis NG, Garcia AE. Journal of Molecular Biology. 2010 Apr 23;398(1):161-73.
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.
Patel MM, Sgourakis NG, Garcia AE, Makhatadze GI. Biochemistry. 2010 Oct 5;49(39):8455-67.
Sgourakis NG, Day R, McCallum SA, Garcia AE. Biophysical Journal. 2008 Oct;95(8):3943-55.
Sgourakis NG, Yan Y, McCallum SA, Wang C, Garcia AE. Journal of Molecular Biology. 2007 May 18;368(5):1448-57.
Sgourakis NG, Bagos PG, Papasaikas PK, Hamodrakas SJ. BMC Bioinformatics. 2005 Apr 22;6:104.
Sgourakis NG, Bagos PG, Hamodrakas SJ. Bioinformatics. 2005 Nov 15;21(22):4101-6.