Лаборатория биомолекулярного ЯМР

В лаборатории. Самохвалов А.Н. (холст, масло)

Опубликовано: 13.01.2024

Тэги: Вологда, Скрынников

X-ray Crystallography Module in MD Simulation Program Amber 2023. Refining the Models of Protein Crystals

Опубликовано: 26.12.2023

Here, we present the new crystallography module xray, released as a part of the Amber 2023 package.

Oleg Mikhailovskii, Sergei A. Izmailov, Yi Xue, David A. Case, and Nikolai R. Skrynnikov

https://pubs.acs.org/doi/10.1021/acs.jcim.3c01531

Тэги: Измайлов, Михайловский, Скрынников

Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4

Опубликовано: 20.11.2023

Here, we investigate, both experimentally and via the MD modeling, the translational diffusion of a 25-residue N-terminal fragment from histone H4 (N-H4).

Olga O Lebedenko, Vladislav A Salikov, Sergei A Izmailov, Ivan S Podkorytov, Nikolai R Skrynnikov

https://www.sciencedirect.com/science/article/abs/pii/S0006349523007208

Тэги: Измайлов, Лебеденко, Подкорытов, Саликов, Скрынников

Conformational and Interaction Landscape of Histone H4 Tails in Nucleosomes Probed by Paramagnetic NMR Spectroscopy

Опубликовано: 09.11.2023

Here we investigate the conformational ensemble and interactions of the H4 tail in nucleosomes by means of solution NMR measurements of paramagnetic relaxation enhancements (PREs) in recombinant samples reconstituted with ¹⁵N-enriched H4 and nitroxide spin-label tagged H3.

Wenjun Sun, Olga O. Lebedenko, Nicole Gonzalez Salguero, Matthew D. Shannon, Mohamad Zandian, Michael G. Poirier, Nikolai R. Skrynnikov, and Christopher P. Jaroniec

https://pubs.acs.org/doi/full/10.1021/jacs.3c10340

Тэги: Лебеденко, Скрынников

Лаборатории биомолекулярного ЯМР исполнилось 10 лет!

Опубликовано: 04.10.2023

Поздравляем всех нас и особенно Николая с десятилетним юбилеем!

Приказ об утверждении результатов конкурса на создание научных лабораторий

Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD

Опубликовано: 12.01.2023

Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips.

Diego F. Gauto, Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, Paul Schanda

https://www.sciencedirect.com/science/article/pii/S2590152422000204?via%3Dihub

Тэги: Лебеденко, Скрынников

Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography

Опубликовано: 11.01.2023

In this work, we have simulated diffraction photographs based on MD simulations of a supercell comprised of 125 unit cells of tetragonal lysozyme. The calculations were conducted using the fundamental Huygens–Fresnel principle.

Ning Liu, Oleg Mikhailovskii, Nikolai R. Skrynnikovb, and Yi Xue

https://journals.iucr.org/m/issues/2023/01/00/lz5062/index.html

Тэги: Mikhailovskii, Ning Liu, Skrynnikov, Yi Xue

Effect of rotation in NMR diffusion experiments on micron-sized particles: A generalized theoretical treatment

Опубликовано: 17.11.2022

A theory is developed to describe the effect of particle rotation in PFG NMR experiments. The rotation can produce 1.5-fold or even greater acceleration of apparent diffusion rates. Large macromolecular assemblies always diffuse much more slowly than their constituent monomers.

Ivan S.Podkorytov, Nikolai R.Skrynnikov

https://doi.org/10.1016/j.jmr.2022.107303

Тэги: Подкорытов, Скрынников

Ежегодная конференция Института Трансляционной Биомедицины СПбГУ (ИТБМ СПбГУ) «Актуальные проблемы трансляционной биомедицины 2022»

Опубликовано: 26.07.2022

Кто-то выступал с докладом, кто-то слушал, а Борис летал на воздушном змее.

Б.Б. Харьков

https://events.spbu.ru/events/translational-biomedicine-2022

https://events.spbu.ru/eventsContent/events/2022/%D0%A1%D0%B1%D0%BE%D1%80%D0%BD%D0%B8%D0%BA%20%D1%82%D0%B5%D0%B7%D0%B8%D1%81%D0%BE%D0%B2%20%D0%BA%D0%BE%D0%BD%D1%84%20%D0%98%D0%A2%D0%91%D0%9C%202022.pdf

Тэги: Харьков

Amber22 is now available!

Опубликовано: 27.04.2022

Version 22 of the Amber software suite represents a significant update from version 20.

D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman

https://ambermd.org/doc12/Amber22.pdf

Тэги: Mikhailovskii, Yi Xue, Измайлов, Скрынников

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