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Items: 34

1.

Rapid and Focused Maturation of a VRC01-Class HIV Broadly Neutralizing Antibody Lineage Involves Both Binding and Accommodation of the N276-Glycan.

Umotoy J, Bagaya BS, Joyce C, Schiffner T, Menis S, Saye-Francisco KL, Biddle T, Mohan S, Vollbrecht T, Kalyuzhniy O, Madzorera S, Kitchin D, Lambson B, Nonyane M, Kilembe W; IAVI Protocol C Investigators; IAVI African HIV Research Network, Poignard P, Schief WR, Burton DR, Murrell B, Moore PL, Briney B, Sok D, Landais E.

Immunity. 2019 Jul 16;51(1):141-154.e6. doi: 10.1016/j.immuni.2019.06.004.

2.

Glycan Masking Focuses Immune Responses to the HIV-1 CD4-Binding Site and Enhances Elicitation of VRC01-Class Precursor Antibodies.

Duan H, Chen X, Boyington JC, Cheng C, Zhang Y, Jafari AJ, Stephens T, Tsybovsky Y, Kalyuzhniy O, Zhao P, Menis S, Nason MC, Normandin E, Mukhamedova M, DeKosky BJ, Wells L, Schief WR, Tian M, Alt FW, Kwong PD, Mascola JR.

Immunity. 2018 Aug 21;49(2):301-311.e5. doi: 10.1016/j.immuni.2018.07.005. Epub 2018 Jul 31.

3.

The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen.

Havenar-Daughton C, Sarkar A, Kulp DW, Toy L, Hu X, Deresa I, Kalyuzhniy O, Kaushik K, Upadhyay AA, Menis S, Landais E, Cao L, Diedrich JK, Kumar S, Schiffner T, Reiss SM, Seumois G, Yates JR, Paulson JC, Bosinger SE, Wilson IA, Schief WR, Crotty S.

Sci Transl Med. 2018 Jul 4;10(448). pii: eaat0381. doi: 10.1126/scitranslmed.aat0381.

4.

Structural and immunologic correlates of chemically stabilized HIV-1 envelope glycoproteins.

Schiffner T, Pallesen J, Russell RA, Dodd J, de Val N, LaBranche CC, Montefiori D, Tomaras GD, Shen X, Harris SL, Moghaddam AE, Kalyuzhniy O, Sanders RW, McCoy LE, Moore JP, Ward AB, Sattentau QJ.

PLoS Pathog. 2018 May 10;14(5):e1006986. doi: 10.1371/journal.ppat.1006986. eCollection 2018 May.

5.

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design.

Adolf-Bryfogle J, Kalyuzhniy O, Kubitz M, Weitzner BD, Hu X, Adachi Y, Schief WR, Dunbrack RL Jr.

PLoS Comput Biol. 2018 Apr 27;14(4):e1006112. doi: 10.1371/journal.pcbi.1006112. eCollection 2018 Apr.

6.

Precursor Frequency and Affinity Determine B Cell Competitive Fitness in Germinal Centers, Tested with Germline-Targeting HIV Vaccine Immunogens.

Abbott RK, Lee JH, Menis S, Skog P, Rossi M, Ota T, Kulp DW, Bhullar D, Kalyuzhniy O, Havenar-Daughton C, Schief WR, Nemazee D, Crotty S.

Immunity. 2018 Jan 16;48(1):133-146.e6. doi: 10.1016/j.immuni.2017.11.023. Epub 2017 Dec 26.

7.

Structure-based design of native-like HIV-1 envelope trimers to silence non-neutralizing epitopes and eliminate CD4 binding.

Kulp DW, Steichen JM, Pauthner M, Hu X, Schiffner T, Liguori A, Cottrell CA, Havenar-Daughton C, Ozorowski G, Georgeson E, Kalyuzhniy O, Willis JR, Kubitz M, Adachi Y, Reiss SM, Shin M, de Val N, Ward AB, Crotty S, Burton DR, Schief WR.

Nat Commun. 2017 Nov 21;8(1):1655. doi: 10.1038/s41467-017-01549-6.

8.

Lipid interactions and angle of approach to the HIV-1 viral membrane of broadly neutralizing antibody 10E8: Insights for vaccine and therapeutic design.

Irimia A, Serra AM, Sarkar A, Jacak R, Kalyuzhniy O, Sok D, Saye-Francisco KL, Schiffner T, Tingle R, Kubitz M, Adachi Y, Stanfield RL, Deller MC, Burton DR, Schief WR, Wilson IA.

PLoS Pathog. 2017 Feb 22;13(2):e1006212. doi: 10.1371/journal.ppat.1006212. eCollection 2017 Feb.

9.

Structural basis for nonneutralizing antibody competition at antigenic site II of the respiratory syncytial virus fusion protein.

Mousa JJ, Sauer MF, Sevy AM, Finn JA, Bates JT, Alvarado G, King HG, Loerinc LB, Fong RH, Doranz BJ, Correia BE, Kalyuzhniy O, Wen X, Jardetzky TS, Schief WR, Ohi MD, Meiler J, Crowe JE Jr.

Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):E6849-E6858. Epub 2016 Oct 17.

10.

Correction: Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design.

Jardine JG, Sok D, Julien JP, Briney B, Sarkar A, Liang CH, Scherer EM, Henry Dunand CJ, Adachi Y, Diwanji D, Hsueh J, Jones M, Kalyuzhniy O, Kubitz M, Spencer S, Pauthner M, Saye-Francisco KL, Sesterhenn F, Wilson PC, Galloway DA, Stanfield RL, Wilson IA, Burton DR, Schief WR.

PLoS Pathog. 2016 Sep 14;12(9):e1005905. doi: 10.1371/journal.ppat.1005905. eCollection 2016 Sep.

11.

HIV Vaccine Design to Target Germline Precursors of Glycan-Dependent Broadly Neutralizing Antibodies.

Steichen JM, Kulp DW, Tokatlian T, Escolano A, Dosenovic P, Stanfield RL, McCoy LE, Ozorowski G, Hu X, Kalyuzhniy O, Briney B, Schiffner T, Garces F, Freund NT, Gitlin AD, Menis S, Georgeson E, Kubitz M, Adachi Y, Jones M, Mutafyan AA, Yun DS, Mayer CT, Ward AB, Burton DR, Wilson IA, Irvine DJ, Nussenzweig MC, Schief WR.

Immunity. 2016 Sep 20;45(3):483-496. doi: 10.1016/j.immuni.2016.08.016. Epub 2016 Sep 8.

12.

Tailored Immunogens Direct Affinity Maturation toward HIV Neutralizing Antibodies.

Briney B, Sok D, Jardine JG, Kulp DW, Skog P, Menis S, Jacak R, Kalyuzhniy O, de Val N, Sesterhenn F, Le KM, Ramos A, Jones M, Saye-Francisco KL, Blane TR, Spencer S, Georgeson E, Hu X, Ozorowski G, Adachi Y, Kubitz M, Sarkar A, Wilson IA, Ward AB, Nemazee D, Burton DR, Schief WR.

Cell. 2016 Sep 8;166(6):1459-1470.e11. doi: 10.1016/j.cell.2016.08.005.

13.

Priming HIV-1 broadly neutralizing antibody precursors in human Ig loci transgenic mice.

Sok D, Briney B, Jardine JG, Kulp DW, Menis S, Pauthner M, Wood A, Lee EC, Le KM, Jones M, Ramos A, Kalyuzhniy O, Adachi Y, Kubitz M, MacPherson S, Bradley A, Friedrich GA, Schief WR, Burton DR.

Science. 2016 Sep 30;353(6307):1557-1560. Epub 2016 Sep 8.

14.

Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design.

Jardine JG, Sok D, Julien JP, Briney B, Sarkar A, Liang CH, Scherer EA, Henry Dunand CJ, Adachi Y, Diwanji D, Hsueh J, Jones M, Kalyuzhniy O, Kubitz M, Spencer S, Pauthner M, Saye-Francisco KL, Sesterhenn F, Wilson PC, Galloway DM, Stanfield RL, Wilson IA, Burton DR, Schief WR.

PLoS Pathog. 2016 Aug 25;12(8):e1005815. doi: 10.1371/journal.ppat.1005815. eCollection 2016 Aug. Erratum in: PLoS Pathog. 2016 Sep;12(9):e1005905.

15.

HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen.

Jardine JG, Kulp DW, Havenar-Daughton C, Sarkar A, Briney B, Sok D, Sesterhenn F, Ereño-Orbea J, Kalyuzhniy O, Deresa I, Hu X, Spencer S, Jones M, Georgeson E, Adachi Y, Kubitz M, deCamp AC, Julien JP, Wilson IA, Burton DR, Crotty S, Schief WR.

Science. 2016 Mar 25;351(6280):1458-63. doi: 10.1126/science.aad9195.

16.

HIV-1 VACCINES. Priming a broadly neutralizing antibody response to HIV-1 using a germline-targeting immunogen.

Jardine JG, Ota T, Sok D, Pauthner M, Kulp DW, Kalyuzhniy O, Skog PD, Thinnes TC, Bhullar D, Briney B, Menis S, Jones M, Kubitz M, Spencer S, Adachi Y, Burton DR, Schief WR, Nemazee D.

Science. 2015 Jul 10;349(6244):156-61. doi: 10.1126/science.aac5894. Epub 2015 Jun 18.

17.

Proof of principle for epitope-focused vaccine design.

Correia BE, Bates JT, Loomis RJ, Baneyx G, Carrico C, Jardine JG, Rupert P, Correnti C, Kalyuzhniy O, Vittal V, Connell MJ, Stevens E, Schroeter A, Chen M, Macpherson S, Serra AM, Adachi Y, Holmes MA, Li Y, Klevit RE, Graham BS, Wyatt RT, Baker D, Strong RK, Crowe JE Jr, Johnson PR, Schief WR.

Nature. 2014 Mar 13;507(7491):201-6. doi: 10.1038/nature12966. Epub 2014 Feb 5.

18.

Rational HIV immunogen design to target specific germline B cell receptors.

Jardine J, Julien JP, Menis S, Ota T, Kalyuzhniy O, McGuire A, Sok D, Huang PS, MacPherson S, Jones M, Nieusma T, Mathison J, Baker D, Ward AB, Burton DR, Stamatatos L, Nemazee D, Wilson IA, Schief WR.

Science. 2013 May 10;340(6133):711-6. doi: 10.1126/science.1234150. Epub 2013 Mar 28.

19.

Coagulation factor X activates innate immunity to human species C adenovirus.

Doronin K, Flatt JW, Di Paolo NC, Khare R, Kalyuzhniy O, Acchione M, Sumida JP, Ohto U, Shimizu T, Akashi-Takamura S, Miyake K, MacDonald JW, Bammler TK, Beyer RP, Farin FM, Stewart PL, Shayakhmetov DM.

Science. 2012 Nov 9;338(6108):795-8. doi: 10.1126/science.1226625. Epub 2012 Sep 27.

20.

Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope.

Azoitei ML, Ban YE, Julien JP, Bryson S, Schroeter A, Kalyuzhniy O, Porter JR, Adachi Y, Baker D, Pai EF, Schief WR.

J Mol Biol. 2012 Jan 6;415(1):175-92. doi: 10.1016/j.jmb.2011.10.003. Epub 2011 Oct 31.

PMID:
22061265
21.

Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.

Azoitei ML, Correia BE, Ban YE, Carrico C, Kalyuzhniy O, Chen L, Schroeter A, Huang PS, McLellan JS, Kwong PD, Baker D, Strong RK, Schief WR.

Science. 2011 Oct 21;334(6054):373-6. doi: 10.1126/science.1209368.

22.

Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope.

Correia BE, Ban YE, Holmes MA, Xu H, Ellingson K, Kraft Z, Carrico C, Boni E, Sather DN, Zenobia C, Burke KY, Bradley-Hewitt T, Bruhn-Johannsen JF, Kalyuzhniy O, Baker D, Strong RK, Stamatatos L, Schief WR.

Structure. 2010 Sep 8;18(9):1116-26. doi: 10.1016/j.str.2010.06.010.

23.

A global benchmark study using affinity-based biosensors.

Rich RL, Papalia GA, Flynn PJ, Furneisen J, Quinn J, Klein JS, Katsamba PS, Waddell MB, Scott M, Thompson J, Berlier J, Corry S, Baltzinger M, Zeder-Lutz G, Schoenemann A, Clabbers A, Wieckowski S, Murphy MM, Page P, Ryan TE, Duffner J, Ganguly T, Corbin J, Gautam S, Anderluh G, Bavdek A, Reichmann D, Yadav SP, Hommema E, Pol E, Drake A, Klakamp S, Chapman T, Kernaghan D, Miller K, Schuman J, Lindquist K, Herlihy K, Murphy MB, Bohnsack R, Andrien B, Brandani P, Terwey D, Millican R, Darling RJ, Wang L, Carter Q, Dotzlaf J, Lopez-Sagaseta J, Campbell I, Torreri P, Hoos S, England P, Liu Y, Abdiche Y, Malashock D, Pinkerton A, Wong M, Lafer E, Hinck C, Thompson K, Primo CD, Joyce A, Brooks J, Torta F, Bagge Hagel AB, Krarup J, Pass J, Ferreira M, Shikov S, Mikolajczyk M, Abe Y, Barbato G, Giannetti AM, Krishnamoorthy G, Beusink B, Satpaev D, Tsang T, Fang E, Partridge J, Brohawn S, Horn J, Pritsch O, Obal G, Nilapwar S, Busby B, Gutierrez-Sanchez G, Gupta RD, Canepa S, Witte K, Nikolovska-Coleska Z, Cho YH, D'Agata R, Schlick K, Calvert R, Munoz EM, Hernaiz MJ, Bravman T, Dines M, Yang MH, Puskas A, Boni E, Li J, Wear M, Grinberg A, Baardsnes J, Dolezal O, Gainey M, Anderson H, Peng J, Lewis M, Spies P, Trinh Q, Bibikov S, Raymond J, Yousef M, Chandrasekaran V, Feng Y, Emerick A, Mundodo S, Guimaraes R, McGirr K, Li YJ, Hughes H, Mantz H, Skrabana R, Witmer M, Ballard J, Martin L, Skladal P, Korza G, Laird-Offringa I, Lee CS, Khadir A, Podlaski F, Neuner P, Rothacker J, Rafique A, Dankbar N, Kainz P, Gedig E, Vuyisich M, Boozer C, Ly N, Toews M, Uren A, Kalyuzhniy O, Lewis K, Chomey E, Pak BJ, Myszka DG.

Anal Biochem. 2009 Mar 15;386(2):194-216. doi: 10.1016/j.ab.2008.11.021. Epub 2008 Nov 27.

24.

Adenovirus serotype 5 hexon is critical for virus infection of hepatocytes in vivo.

Kalyuzhniy O, Di Paolo NC, Silvestry M, Hofherr SE, Barry MA, Stewart PL, Shayakhmetov DM.

Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5483-8. doi: 10.1073/pnas.0711757105. Epub 2008 Apr 7.

25.

Characterization of Trypanosoma brucei dihydroorotate dehydrogenase as a possible drug target; structural, kinetic and RNAi studies.

Arakaki TL, Buckner FS, Gillespie JR, Malmquist NA, Phillips MA, Kalyuzhniy O, Luft JR, Detitta GT, Verlinde CL, Van Voorhis WC, Hol WG, Merritt EA.

Mol Microbiol. 2008 Apr;68(1):37-50. doi: 10.1111/j.1365-2958.2008.06131.x. Epub 2008 Feb 26.

26.

Identification of CD46 binding sites within the adenovirus serotype 35 fiber knob.

Wang H, Liaw YC, Stone D, Kalyuzhniy O, Amiraslanov I, Tuve S, Verlinde CL, Shayakhmetov D, Stehle T, Roffler S, Lieber A.

J Virol. 2007 Dec;81(23):12785-92. Epub 2007 Sep 26.

27.

Fiber shaft-chimeric adenovirus vectors lacking the KKTK motif efficiently infect liver cells in vivo.

Di Paolo NC, Kalyuzhniy O, Shayakhmetov DM.

J Virol. 2007 Nov;81(22):12249-59. Epub 2007 Sep 12.

28.

Using fragment cocktail crystallography to assist inhibitor design of Trypanosoma brucei nucleoside 2-deoxyribosyltransferase.

Bosch J, Robien MA, Mehlin C, Boni E, Riechers A, Buckner FS, Van Voorhis WC, Myler PJ, Worthey EA, DeTitta G, Luft JR, Lauricella A, Gulde S, Anderson LA, Kalyuzhniy O, Neely HM, Ross J, Earnest TN, Soltis M, Schoenfeld L, Zucker F, Merritt EA, Fan E, Verlinde CL, Hol WG.

J Med Chem. 2006 Oct 5;49(20):5939-46.

PMID:
17004709
29.

Structure of ribose 5-phosphate isomerase from Plasmodium falciparum.

Holmes MA, Buckner FS, Van Voorhis WC, Verlinde CL, Mehlin C, Boni E, DeTitta G, Luft J, Lauricella A, Anderson L, Kalyuzhniy O, Zucker F, Schoenfeld LW, Earnest TN, Hol WG, Merritt EA.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 May 1;62(Pt 5):427-31. Epub 2006 Apr 12.

30.

Structure of the conserved hypothetical protein MAL13P1.257 from Plasmodium falciparum.

Holmes MA, Buckner FS, Van Voorhis WC, Mehlin C, Boni E, Earnest TN, DeTitta G, Luft J, Lauricella A, Anderson L, Kalyuzhniy O, Zucker F, Schoenfeld LW, Hol WG, Merritt EA.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Mar 1;62(Pt 3):180-5. Epub 2006 Feb 24.

31.

Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major.

Arakaki T, Le Trong I, Phizicky E, Quartley E, DeTitta G, Luft J, Lauricella A, Anderson L, Kalyuzhniy O, Worthey E, Myler PJ, Kim D, Baker D, Hol WG, Merritt EA.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Mar 1;62(Pt 3):175-9. Epub 2006 Feb 24.

32.

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 A resolution reveals intriguing extra electron density in the active site.

Robien MA, Bosch J, Buckner FS, Van Voorhis WC, Worthey EA, Myler P, Mehlin C, Boni EE, Kalyuzhniy O, Anderson L, Lauricella A, Gulde S, Luft JR, DeTitta G, Caruthers JM, Hodgson KO, Soltis M, Zucker F, Verlinde CL, Merritt EA, Schoenfeld LW, Hol WG.

Proteins. 2006 Mar 15;62(3):570-7.

PMID:
16345073
33.

Structure of a ribulose 5-phosphate 3-epimerase from Plasmodium falciparum.

Caruthers J, Bosch J, Buckner F, Van Voorhis W, Myler P, Worthey E, Mehlin C, Boni E, DeTitta G, Luft J, Lauricella A, Kalyuzhniy O, Anderson L, Zucker F, Soltis M, Hol WG.

Proteins. 2006 Feb 1;62(2):338-42.

PMID:
16304640
34.

Synthetic RGD-containing alpha-helical coiled coil peptides promote integrin-dependent cell adhesion.

Villard V, Kalyuzhniy O, Riccio O, Potekhin S, Melnik TN, Kajava AV, Rüegg C, Corradin G.

J Pept Sci. 2006 Mar;12(3):206-12.

PMID:
16103993

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