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Posts tagged ‘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



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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




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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



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Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber

Posted: 23.12.2021
Flowchart illustrating the functionalities and interactions of the new Amber module kXrayEnergy.

Oleg Mikhailovskii, Yi Xue, and Nikolai R. Skrynnikov.



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The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils

Posted: 23.04.2021

Dr. Boris B. Kharkov, Ivan S. Podkorytov, Dr. Stanislav A. Bondarev, Dr. Mikhail V. Belousov, Vladislav A. Salikov, Prof. Dr. Galina A. Zhouravleva, Prof. Dr. Nikolai R. Skrynnikov



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Histone H4 tails in nucleosomes: a fuzzy interaction with DNA

Posted: 24.02.2021

Sevastyan O. Rabdano, Matthew D. Shannon, Sergei A. Izmailov, Nicole Gonzalez Salguero, Mohamad Zandian, Rudra N. Purusottam, Michael G. Poirier, Nikolai R. Skrynnikov and Christopher P. Jaroniec



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Structural and dynamic origins of ESR lineshapes in spin-labeled GB1 domain: the insights from spin dynamics simulations based on long MD trajectories

Posted: 20.01.2020

Izmailov, S.A, Rabdano, S.O., Hasanbasri, Z., Podkorytov, I.S., Saxena, S., Skrynnikov, N.R. Structural and dynamic origins of ESR lineshapes in spin-labeled GB1 domain: the insights from spin dynamics simulations based on long MD trajectories. Scientific Reports 2020.

DOI: 10.1038/s41598-019-56750-y


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Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2

Posted: 26.12.2019

Luzik, D.A., Rogacheva, O.N., Izmailov, S.A., Indeykina, M.I., Kononikhin, A.S., Skrynnikov, N.R. Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2. Scientific Reports 2019.



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4-th annual meeting of Institute of Translational Biomedicine of SPbSU, Saint Petersburg, Russia

Posted: 20.07.2018

Boris Kharkov, Sergey Izmailov, Sevastyan Rabdano, Nikolai Skrynnikov, Dmitry Luzik, Olga Rogacheva and Ivan Podkorytov took part in the fourth annual conference of the Institute of Translational Biomedicine, which was held on July 20-22, 2018 in St. Petersburg.

Sergei Izmailov presented the report “EPR tags as a probe for studying protein systems: what the spectra say.”

Ivan Podkorytov presented the report “Research of mobile Sup35NM protein sites in monomers and in the composition of fibrils by NMR with diffusion filter”.

Olga Rogacheva presented the report “Bioconjugation of peptides in the context of targeted therapy: modeling and experiment.”

Dmitry Luzik presented the report “Covalent binding of modified Sos1-derived peptide and N-terminal SH3-domain of adapter protein Grb2”.

Sevastyan Rabdano presented the report “ESR spectroscopy as a probe of protein dynamics: an insight from long MD simulations”.

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15-th International School-Conference Magnetic resonance and its applications Spinus 2018

Posted: 01.04.2018

Sergey Izmailov, Sevastyan Rabdano, Nikolai Skrynnikov, Boris Kharkov and Vladislav Salikov took part in the 15th international school-conference “Magnetic Resonance and Its Applications, Spinus” held on April 1-6, 2018.

Sergey Izmailov presented the report “EPR spectra simulation from MD data using Redfield theory and direct propagation method”.

Sevastyan Rabdano presented the report “Dynamic modes in spin-labeled protein revealed by MD simulations: experimental and computed EPR spectra”.

Nikolai Skrynnikov presented the lecture “Many faces of disulfide bond”.

Boris Kharkov presented the report “Skin-Effect Compensated Optimal Control Pulses for Excitation in a Conductive Medium”.

Vladislav Salikov presented the poster “Optimization of bacterial expression of MdmX N-terminal domain for NMR studies”.

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