Таблица заданий для самостоятельной работы

ФИО Статья Зачет
1 Алла Федорова Hu, C., & Wang, J. (2016). Chapter Five-Method for Enzyme Design with Genetically Encoded Unnatural Amino Acids. Methods in Enzymology, 580, 109-133. Устный ответ (23-12-2016)
2 Азамат Гафуров Rahimi, M., van der Meer, J. Y., Geertsema, E. M., Poddar, H., Baas, B. J., & Poelarends, G. J. (2016). Mutations Closer to the Active Site Improve the Promiscuous Aldolase Activity of 4‐Oxalocrotonate Tautomerase More Effectively than Distant Mutations. ChemBioChem. Да (8-12-2016)
3 Екатерина Носикова Jacobs, T. M., Williams, B., Williams, T., Xu, X., Eletsky, A., Federizon, J. F., ... & Kuhlman, B. (2016). Design of structurally distinct proteins using strategies inspired by evolution. Science, 352(6286), 687-690. Устный ответ (23-12-2016)
4 Алексей Елисеев Kan, S. J., Lewis, R. D., Chen, K., & Arnold, F. H. (2016). Directed evolution of cytochrome c for carbon–silicon bond formation: Bringing silicon to life. Science, 354(6315), 1048-1051. Устный ответ (23-12-2016)
5 Михаил Кунин Cahn, J. K. B., Baumschlager, A., Brinkmann-Chen, S., & Arnold, F. H. (2015). Mutations in adenine-binding pockets enhance catalytic properties of NAD (P) H-dependent enzymes. Protein Engineering Design and Selection, gzv057.
6 Филипп Гусев Sauer, D. B., Karpowich, N. K., Song, J. M., & Wang, D. N. (2015). Rapid bioinformatic identification of thermostabilizing mutations. Biophysical journal, 109(7), 1420-1428. Устный ответ (23-12-2016)
7 Баина Босхомджиева Lin, Y. W., Nagao, S., Zhang, M., Shomura, Y., Higuchi, Y., & Hirota, S. (2015). Rational design of heterodimeric protein using domain swapping for myoglobin. Angewandte Chemie International Edition, 54(2), 511-515.
8 Юлия Вакуленко Hsia, Y., Bale, J. B., Gonen, S., Shi, D., Sheffler, W., Fong, K. K., ... & Yi, S. (2016). Design of a hyperstable 60-subunit protein icosahedron. Nature, 535(7610), 136-139. Доклад 20-12-2016
9 Елизавета Беседина Parmeggiani, F., Huang, P. S., Vorobiev, S., Xiao, R., Park, K., Caprari, S., ... & Montelione, G. T. (2015). A general computational approach for repeat protein design. Journal of molecular biology, 427(2), 563-575.
10 Мария Новикова Aprile, F. A., Sormanni, P., & Vendruscolo, M. (2015). A rational design strategy for the selective activity enhancement of a molecular chaperone toward a target substrate. Biochemistry, 54(32), 5103-5112.
11 Евгения Панкевич Carlin, D. A., Caster, R. W., Wang, X., Betzenderfer, S. A., Chen, C. X., Duong, V. M., ... & Kim, N. (2016). Kinetic Characterization of 100 Glycoside Hydrolase Mutants Enables the Discovery of Structural Features Correlated with Kinetic Constants. PloS one, 11(1), e0147596.
12 Анна Желудкевич Hart, K. M., Ho, C. M., Dutta, S., Gross, M. L., & Bowman, G. R. (2016). Modelling proteins' hidden conformations to predict antibiotic resistance. Nature Communications, 7, 12965.
13 Соня Тишина Chen, Qi, et al. "Rational design of a carboxylic esterase RhEst1 based on computational analysis of substrate binding." Journal of Molecular Graphics and Modelling 62 (2015): 319-324.
14 Ярослав Попов Choi, J. H., Laurent, A. H., Hilser, V. J., & Ostermeier, M. (2015). Design of protein switches based on an ensemble model of allostery. Nature communications, 6. Доклад 20-12-2016
15 Дмитрий Медведев Dunn, M.R., Otto, C., Fenton, K.E. and Chaput, J.C., 2016. Improving polymerase activity with unnatural substrates by sampling mutations in homologous protein architectures. ACS chemical biology. Доклад 20-12-2016
16 Наталья Ходыкина Del Giudice, I., Coppolecchia, R., Merone, L., Porzio, E., Carusone, T. M., Mandrich, L., ... & Manco, G. (2015). An efficient thermostable organophosphate hydrolase and its application in pesticide decontamination. Biotechnology and bioengineering.
17 Дмитрий Травин Protein engineering of Bacillus acidopullulyticus pullulanase for enhanced thermostability using in silico data driven rational design methods Доклад 20-12-2016
18 Александра Анисимова Alexandra Holinski, Kristina Heyn, Rainer Merkl, Reinhard Sterner (2016) Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex. Proteins 10.1002/prot.25225
19 Нуждина Катя Reeve, S. M., Gainza, P., Frey, K. M., Georgiev, I., Donald, B. R., & Anderson, A. C. (2015). Protein design algorithms predict viable resistance to an experimental antifolate. Proceedings of the National Academy of Sciences, 112(3), 749-754.
20 Наталия Трушина Amol V. Shivange, Hans Wolfgang Hoeffken, Stefan Haefner and Ulrich Schwaneberg (2016) Protein consensus-based surface engineering (ProCoS): a computer-assisted method for directed protein evolution. BioTechniques
21 Анна Образцова Serna, N., Céspedes, M. V., Saccardo, P., Xu, Z., Unzueta, U., Álamo, P., ... & Vázquez, E. (2016). Rational engineering of single-chain polypeptides into protein-only, BBB-targeted nanoparticles. Nanomedicine: Nanotechnology, Biology and Medicine, 12(5), 1241-1251.
22 Марк Меерсон Juillerat, A., Marechal, A., Filhol, J. M., Valton, J., Duclert, A., Poirot, L., & Duchateau, P. (2016). Design of chimeric antigen receptors with integrated controllable transient functions. Scientific reports, 6.
23 Радик Шафиков Bhardwaj, G., Mulligan, V. K., Bahl, C. D., Gilmore, J. M., Harvey, P. J., Cheneval, O., ... & Huang, P. S. (2016). Accurate de novo design of hyperstable constrained peptides. Nature.
24 Анна Андреева Deng, J., Yao, Z., Chen, K., Yuan, Y. A., Lin, J., & Wei, D. (2016). Towards the computational design and engineering of enzyme enantioselectivity: a case study by a carbonyl reductase from Gluconobacter oxydans. Journal of biotechnology, 217, 31-40.
25 Федор Галкин Votteler, J., Ogohara, C., Yi, S., Hsia, Y., Nattermann, U., Belnap, D. M., ... & Sundquist, W. I. (2016). Designed proteins induce the formation of nanocage-containing extracellular vesicles. Nature, 540(7632), 292-295.
26 Адалят Мамедов Ece, S., Evran, S., Janda, J. O., Merkl, R., & Sterner, R. (2015). Improving thermal and detergent stability of Bacillus stearothermophilus neopullulanase by rational enzyme design. Protein Engineering Design and Selection, gzv001.
27 Диана Евстафьева Shivange, A. V., Roccatano, D., & Schwaneberg, U. (2016). Iterative key-residues interrogation of a phytase with thermostability increasing substitutions identified in directed evolution. Applied microbiology and biotechnology, 100(1), 227-242.
28 Александра Малеева Wright, A. V., Sternberg, S. H., Taylor, D. W., Staahl, B. T., Bardales, J. A., Kornfeld, J. E., & Doudna, J. A. (2015). Rational design of a split-Cas9 enzyme complex. Proceedings of the National Academy of Sciences, 112(10), 2984-2989.
29 Алибек Абдрахманов Agah, S., Poulos, S., Yu, A., Kucharska, I., & Faham, S. (2016). Protein rethreading: A
novel approach to protein design. Scientific reports, 6.