Laboratory of Biomolecular NMR

In the laboratory. Samokhvalov A.N. (oil on canvas)

Posted: 13.01.2024

Tags: Skrynnikov, Vologda

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

Posted: 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

Tags: Izmailov, Mikhailovskii, Skrynnikov

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

Posted: 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

Tags: Izmailov, Podkorytov, Salikov, Skrynnikov

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

Posted: 09.11.2023

Это изображение имеет пустой атрибут alt; его имя файла - ja3c10340_0003.gif — 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

Tags: Lebedenko, Skrynnikov

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

Posted: 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

Tags: Lebedenko, Skrynnikov

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

Posted: 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

Tags: Mikhailovskii, Ning Liu, Skrynnikov, Yi Xue

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

Posted: 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

Tags: Podkorytov, Skrynnikov

Annual conference of the Institute of Translational Biomedicine of St. Petersburg State University (ITBM SPbU) “Actual problems of translational biomedicine 2022”

Posted: 26.07.2022

Someone made a presentation, someone listened, and Boris flew a kite.

Boris B. Kharkov

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

Tags: Kharkov

Amber22 is now available!

Posted: 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

Tags: Izmailov, Mikhailovskii, Skrynnikov, Yi Xue