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156 results on '"Borbulevych, Oleg"'

4. 11th German Conference on Chemoinformatics (GCC 2015): Fulda, Germany. 8–10 November 2015

Author

Fechner, Uli, de Graaf, Chris, Torda, Andrew E., Güssregen, Stefan, Evers, Andreas, Matter, Hans, Hessler, Gerhard, Richmond, Nicola J., Schmidtke, Peter, Segler, Marwin H. S., Waller, Mark P., Pleik, Stefanie, Shea, Joan-Emma, Levine, Zachary, Mullen, Ryan, van den Broek, Karina, Epple, Matthias, Kuhn, Hubert, Truszkowski, Andreas, Zielesny, Achim, Fraaije, Johannes (Hans), Gracia, Ruben Serral, Kast, Stefan M., Bulusu, Krishna C., Bender, Andreas, Yosipof, Abraham, Nahum, Oren, Senderowitz, Hanoch, Krotzky, Timo, Schulz, Robert, Wolber, Gerhard, Bietz, Stefan, Rarey, Matthias, Zimmermann, Markus O., Lange, Andreas, Ruff, Manuel, Heidrich, Johannes, Onlia, Ionut, Exner, Thomas E., Boeckler, Frank M., Bermudez, Marcel, Firaha, Dzmitry S., Hollóczki, Oldamur, Kirchner, Barbara, Tautermann, Christofer S., Volkamer, Andrea, Eid, Sameh, Turk, Samo, Rippmann, Friedrich, Fulle, Simone, Saleh, Noureldin, Saladino, Giorgio, Gervasio, Francesco L., Haensele, Elke, Banting, Lee, Whitley, David C., Oliveira Santos, Jana Sopkova-de, Bureau, Ronan, Clark, Timothy, Sandmann, Achim, Lanig, Harald, Kibies, Patrick, Heil, Jochen, Hoffgaard, Franziska, Frach, Roland, Engel, Julian, Smith, Steven, Basu, Debjit, Rauh, Daniel, Kohlbacher, Oliver, Boeckler, Frank M., Essex, Jonathan W., Bodnarchuk, Michael S., Ross, Gregory A., Finkelmann, Arndt R., Göller, Andreas H., Schneider, Gisbert, Husch, Tamara, Schütter, Christoph, Balducci, Andrea, Korth, Martin, Ntie-Kang, Fidele, Günther, Stefan, Sippl, Wolfgang, Mbaze, Luc Meva’a, Ntie-Kang, Fidele, Simoben, Conrad V., Lifongo, Lydia L., Ntie-Kang, Fidele, Judson, Philip, Barilla, Jiří, Lokajíček, Miloš V., Pisaková, Hana, Simr, Pavel, Kireeva, Natalia, Petrov, Alexandre, Ostroumov, Denis, Solovev, Vitaly P., Pervov, Vladislav S., Friedrich, Nils-Ole, Sommer, Kai, Rarey, Matthias, Kirchmair, Johannes, Proschak, Eugen, Weber, Julia, Moser, Daniel, Kalinowski, Lena, Achenbach, Janosch, Mackey, Mark, Cheeseright, Tim, Renner, Gerrit, Renner, Gerrit, Schmidt, Torsten C., Schram, Jürgen, Egelkraut-Holtus, Marion, van Oeyen, Albert, Kalliokoski, Tuomo, Fourches, Denis, Ibezim, Akachukwu, Mbah, Chika J., Adikwu, Umale M., Nwodo, Ngozi J., Steudle, Alexander, Masek, Brian B., Nagy, Stephan, Baker, David, Soltanshahi, Fred, Dorfman, Roman, Dubrucq, Karen, Patel, Hitesh, Koch, Oliver, Mrugalla, Florian, Kast, Stefan M., Ain, Qurrat U., Fuchs, Julian E., Owen, Robert M., Omoto, Kiyoyuki, Torella, Rubben, Pryde, David C., Glen, Robert, Bender, Andreas, Hošek, Petr, Spiwok, Vojtěch, Mervin, Lewis H., Barrett, Ian, Firth, Mike, Murray, David C., McWilliams, Lisa, Cao, Qing, Engkvist, Ola, Warszycki, Dawid, Śmieja, Marek, Bojarski, Andrzej J., Aniceto, Natalia, Freitas, Alex, Ghafourian, Taravat, Herrmann, Guido, Eigner-Pitto, Valentina, Naß, Alexandra, Kurczab, Rafał, Bojarski, Andrzej J., Lange, Andreas, Günther, Marcel B., Hennig, Susanne, Büttner, Felix M., Schall, Christoph, Sievers-Engler, Adrian, Ansideri, Francesco, Koch, Pierre, Stehle, Thilo, Laufer, Stefan, Böckler, Frank M., Zdrazil, Barbara, Montanari, Floriane, Ecker, Gerhard F., Grebner, Christoph, Hogner, Anders, Ulander, Johan, Edman, Karl, Guallar, Victor, Tyrchan, Christian, Ulander, Johan, Tyrchan, Christian, Klute, Wolfgang, Bergström, Fredrik, Kramer, Christian, Nguyen, Quoc Dat, Frach, Roland, Kibies, Patrick, Strohfeldt, Steven, Böttcher, Saraphina, Pongratz, Tim, Horinek, Dominik, Kast, Stefan M., Rupp, Bernd, Al-Yamori, Raed, Lisurek, Michael, Kühne, Ronald, Furtado, Filipe, van den Broek, Karina, Wessjohann, Ludger, Mathea, Miriam, Baumann, Knut, Mohamad-Zobir, Siti Zuraidah, Fu, Xianjun, Fan, Tai-Ping, Bender, Andreas, Kuhn, Maximilian A., Sotriffer, Christoph A., Zoufir, Azedine, Li, Xitong, Mervin, Lewis, Berg, Ellen, Polokoff, Mark, Ihlenfeldt, Wolf D., Ihlenfeldt, Wolf D., Pretzel, Jette, Alhalabi, Zayan, Fraczkiewicz, Robert, Waldman, Marvin, Clark, Robert D., Shaikh, Neem, Garg, Prabha, Kos, Alexander, Himmler, Hans-Jürgen, Sandmann, Achim, Jardin, Christophe, Sticht, Heinrich, Steinbrecher, Thomas B., Dahlgren, Markus, Cappel, Daniel, Lin, Teng, Wang, Lingle, Krilov, Goran, Abel, Robert, Friesner, Richard, Sherman, Woody, Pöhner, Ina A., Panecka, Joanna, Wade, Rebecca C., Bietz, Stefan, Schomburg, Karen T., Hilbig, Matthias, Rarey, Matthias, Jäger, Christian, Wieczorek, Vivien, Westerhoff, Lance M., Borbulevych, Oleg Y., Demuth, Hans-Ulrich, Buchholz, Mirko, Schmidt, Denis, Rickmeyer, Thomas, Krotzky, Timo, Kolb, Peter, Mittal, Sumit, Sánchez-García, Elsa, Nogueira, Mauro S., Oliveira, Tiago B., da Costa, Fernando B., and Schmidt, Thomas J.

Published
2016
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26. X-ray diffraction and ab initio quantum-chemical study of the charge density in the crystals of Meisenheimer complexes-derivatives of 2, 4, 6-trinitrobenzene and 5, 7-dinitroquinoline

Author

Borbulevych, Oleg Ya., Shishkin, Oleg V., and Antipin, Mikhail Yu.

Subjects
Potassium -- Chemical properties, Potassium -- Research, Molecular crystals -- Analysis, X-rays -- Diffraction, X-rays -- Usage, Chemicals, plastics and rubber industries
Abstract

The experimental charge density in the crystals of Meisenheimer complexes, derivatives of 2, 4, 6-trinitrobenzene and 5, 7-dinitroquinoline is studied. The findings indicate that the potassium cations coordinated with sigma-complex in the crystals considerably affect the charge density distribution.

Published
2002

29. High‐throughput quantum‐mechanics/molecular‐mechanics (ONIOM) macromolecular crystallographic refinement with PHENIX/DivCon: the impact of mixed Hamiltonian methods on ligand and protein structure.

Author

Borbulevych, Oleg, Martin, Roger I., and Westerhoff, Lance M.

Subjects
*CRYSTAL defects, *MACROMOLECULAR dynamics, *HAMILTONIAN systems
Abstract

Conventional macromolecular crystallographic refinement relies on often dubious stereochemical restraints, the preparation of which often requires human validation for unusual species, and on rudimentary energy functionals that are devoid of nonbonding effects owing to electrostatics, polarization, charge transfer or even hydrogen bonding. While this approach has served the crystallographic community for decades, as structure‐based drug design/discovery (SBDD) has grown in prominence it has become clear that these conventional methods are less rigorous than they need to be in order to produce properly predictive protein–ligand models, and that the human intervention that is required to successfully treat ligands and other unusual chemistries found in SBDD often precludes high‐throughput, automated refinement. Recently, plugins to the Python‐based Hierarchical ENvironment for Integrated Xtallography (PHENIX) crystallographic platform have been developed to augment conventional methods with the in situ use of quantum mechanics (QM) applied to ligand(s) along with the surrounding active site(s) at each step of refinement [Borbulevych et al. (2014), Acta Cryst D70, 1233–1247]. This method (Region‐QM) significantly increases the accuracy of the X‐ray refinement process, and this approach is now used, coupled with experimental density, to accurately determine protonation states, binding modes, ring‐flip states, water positions and so on. In the present work, this approach is expanded to include a more rigorous treatment of the entire structure, including the ligand(s), the associated active site(s) and the entire protein, using a fully automated, mixed quantum‐mechanics/molecular‐mechanics (QM/MM) Hamiltonian recently implemented in the DivCon package. This approach was validated through the automatic treatment of a population of 80 protein–ligand structures chosen from the Astex Diverse Set. Across the entire population, this method results in an average 3.5‐fold reduction in ligand strain and a 4.5‐fold improvement in MolProbity clashscore, as well as improvements in Ramachandran and rotamer outlier analyses. Overall, these results demonstrate that the use of a structure‐wide QM/MM Hamiltonian exhibits improvements in the local structural chemistry of the ligand similar to Region‐QM refinement but with significant improvements in the overall structure beyond the active site. Quantum‐mechanics/molecular‐mechanics (ONIOM) X‐ray macromolecular refinement using the program DivCon integrated with PHENIX is reported. [ABSTRACT FROM AUTHOR]

Published
2018
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30. T cell receptors used in cancer gene therapy cross-react with MART-1/Melan-A tumor antigens via distinct mechanisms1

Author

Borbulevych, Oleg Y., Santhanagopolan, Sujatha M., Hossain, Moushumi, and Baker, Brian M.

Subjects
T-Lymphocytes, Receptors, Antigen, T-Cell, chemical and pharmacologic phenomena, Genetic Therapy, Cross Reactions, Crystallography, X-Ray, Article, Protein Structure, Secondary, MART-1 Antigen, Neoplasms, HLA-A2 Antigen, Animals, Humans, Immunotherapy, Protein Structure, Quaternary, Protein Binding
Abstract

T cells engineered to express T cell receptors (TCRs) specific for tumor antigens can drive cancer regression. The first TCRs used in cancer gene therapy, DMF4 and DMF5, recognize two structurally distinct peptide epitopes of the melanoma-associated MART-1/Melan-A protein, both presented by the class I MHC protein HLA-A*0201. To help understand the mechanisms of TCR cross-reactivity and provide a foundation for the further development of immunotherapy, we determined the crystallographic structures of DMF4 and DMF5 in complex with both of the MART-1/Melan-A epitopes. The two TCRs use different mechanisms to accommodate the two ligands. Whereas DMF4 binds the two with a different orientation, altering its position over the peptide/MHC, DMF5 binds them both identically. The simpler mode of cross-reactivity by DMF5 is associated with higher affinity towards both ligands, consistent with the superior functional avidity of DMF5. More generally, the observation of two diverging mechanisms of cross-reactivity with the same antigens and the finding that TCR binding orientation can be determined by peptide alone extend our understanding of the mechanisms underlying TCR cross-reactivity.

Published
2011

31. Increased Immunogenicity of an Anchor-Modified Tumor-Associated Antigen Is Due to the Enhanced Stability of the Peptide/MHC Complex: Implications for Vaccine Design1

Author

Borbulevych, Oleg Y., Baxter, Tiffany K., Yu, Zhiya, Restifo, Nicholas P., and Baker, Brian M.

Subjects
Models, Molecular, Membrane Glycoproteins, HLA-A Antigens, Protein Conformation, T-Lymphocytes, In Vitro Techniques, Crystallography, X-Ray, Cancer Vaccines, Article, Neoplasm Proteins, Drug Stability, Antigens, Neoplasm, Drug Design, Multiprotein Complexes, HLA-A2 Antigen, Humans, Thermodynamics, Melanoma, gp100 Melanoma Antigen
Abstract

The use of "anchor-fixed" altered peptide ligands is of considerable interest in the development of therapeutic vaccines for cancer and infectious diseases, but the mechanism by which successful altered peptide ligands elicit enhanced immunity is unclear. In this study, we have determined the crystallographic structure of a major tumor rejection Ag, gp100(209-217), in complex with the HLA-A*0201 (HLA-A2) molecule, as well as the structure of a modified version of the peptide which substitutes methionine for threonine at position 2 (T2M; gp100(209-2M)). The T2M-modified peptide, which is more immunogenic in vitro and in vivo, binds HLA-A2 with a approximately 9-fold greater affinity and has a approximately 7-fold slower dissociation rate at physiological temperature. Within the limit of the crystallographic data, the T2M substitution does not alter the structure of the peptide/HLA-A2 complex. Consistent with this finding, in peripheral blood from 95 human subjects, we were unable to identify higher frequencies of T cells specific for either the native or modified peptide. These data strongly support the conclusion that the greater immunogenicity of the gp100(209-2M) peptide is due to the enhanced stability of the peptide/MHC complex, validating the anchor-fixing approach for generating therapeutic vaccine candidates. Thermodynamic data suggest that the enhanced stability of the T2M-modified peptide/HLA-A2 complex is attributable to the increased hydrophobicity of the modified peptide, but the gain due to hydrophobicity is offset considerably by the loss of a hydrogen bond made by the native peptide to the HLA-A2 molecule. Our findings have broad implications for the optimization of current vaccine-design strategies.

Published
2005

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