Rabdano, S. O.; Izmailov, S. A.; Luzik, D. A.; Groves, A.; Podkorytov, I. S.; Skrynnikov, N. R. Onset of Disorder and Protein Aggregation due to Oxidation-Induced Intermolecular Disulfide Bonds: Case Study of RRM2 Domain from TDP-43. Scientific Reports 2017, 7 (1), 11161.
DOI: 10.1038/s41598-017-10574-w.
Tags: Izmailov, Luzik, Podkorytov, Rabdano, Skrynnikov
Rogacheva, O. N.; Izmailov, S. A.; Slipchenko, L. V.; Skrynnikov, N. R. Non-Native Disulfide Bridges in Protein-Peptide Complex and in Protein Homodimers Trigger Unfolding and Aggregation. The FEBS Journal 2017, 284 (Suppl. 1), 311.
DOI: 10.1111/febs.14174.
Tags: Izmailov, Rogacheva, Skrynnikov
Kaempf, K.; Rabdano, S. O.; Izmailov, S. A.; Groves, A.; Podkorytov, I. S.; Skrynnikov, N. R. Local and Global Dynamics of Intrinsically Disordered Proteins: A Case Study of H4 Histone Tail. The FEBS Journal 2017, 284 (Suppl. 1), 95.
DOI: 10.1111/febs.14171.
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Tags: Izmailov, Kaempf, Podkorytov, Rabdano, Skrynnikov
Izmailov, S. A.; Podkorytov, I. S.; Skrynnikov, N. R. Simple MD-Based Model for Oxidative Folding of Peptides and Proteins. Scientific Reports 2017, 7 (1).
DOI: 10.1038/s41598-017-09229-7.
Tags: Izmailov, Podkorytov, Skrynnikov
Kurauskas, V.; Izmailov, S. A.; Rogacheva, O. N.; Hessel, A.; Ayala, I.; Woodhouse, J.; Shilova, A.; Xue, Y.; Yuwen, T.; Coquelle, N.; Colletier, J.-P.; Skrynnikov, N. R.; Schanda, P. Slow Conformational Exchange and Overall Rocking Motion in Ubiquitin Protein Crystals. Nature Communications 2017, 8 (1).
DOI: 10.1038/s41467-017-00165-8.
Tags: Izmailov, Rogacheva, Skrynnikov
Nikolai Skrynnikov, Ivan Podkorytov, Dmitry Luzik, Olga Rogacheva, Sevastyan Rabdano, Sergei Izmailov, Ali Shaban and Oleg Mikhailovsky attended the conference of Institute of Translational Biomedicine of SPbSU “Actual Problems of Translational Biomedicine – 2017”, St. Petersburg.
Tags: Izmailov, Luzik, Podkorytov, Rabdano, Rogacheva, Skrynnikov
Sevastyan Rabdano, Sergei Izmailov and Dmitri Luzik took part in bioinformatics hackathon BioHack 2017.
Sergei Izmailov was a leader of a team that worked on the project “Identification of oncogene proteins as targets for covalently binding peptides”.
Dmitry Luzik was in team that worked on the project “Interactome of human proteoforms”.
Sevastyan Rabdano was in team that worked on the project “Research of bound states of water molecules at the interfaces of biomolecules”. His team took third place and received award from organizers.
O. N. Rogacheva , S. A. Izmailov , V. Kurauskas , A. Shilova , P. Ma, Y. Xue, N. Coquelle, J. D. Haller, T. Yuwen, I. Ayala, A. Hessel, J. Woodhouse, O. Mikhailovskii, D. Willbold, J. Colletier, N. R. Skrynnikov, P. Schanda “Dynamics in protein crystals: insights from MD simulations complement new solid-state NMR and X-ray data” The FEBS Journal 283 (Suppl. 1), 237 (2016).
DOI: 10.1111/febs.13808
Tags: Izmailov, Rogacheva, Skrynnikov
Nikolai Skrynnikov, Ivan Podkorytov, Sergei Izmailov, Olga Rogacheva, Kerstin Kaempf and Sevastyan Rabdano attended XXXVIII Finnish NMR Symposium, Jyvaskyla, Finland.
Nikolai Skrynnikov presented lecture “Dynamics in Protein Crystals: Insights From MD Simulations Complement New Solid-State NMR And X-Ray Data”.
Kerstin Kaempf presented oral talk “Local and global dynamics of intrinsically disordered proteins: a case study of H4 histone tail“.
Ivan Podkorytov presented poster “Diffusion-filtered experiment to detect flexible portion of protein chain in amyloid fibrils: application to Sup35NM“.
Sergei Izmailov presented poster “Simple MD-based model for oxidative folding of peptides and proteins”.
Olga Rogacheva presented poster “Using molecular dynamics simulation and chemical shift prediction to unravel dynamics in different crystal forms of ubiquitin”.
Sevastyan Rabdano presented poster “Loss of protein stability due to formation of intermolecular disulfide bonds under the effect of oxidative stress: case study of the RRM2 domain from neuropathological protein TDP-43”.
Tags: Finland, Izmailov, Jyvaskyla, Kaempf, Podkorytov, Rabdano, Rogacheva, Skrynnikov
We have investigated dynamics in two crystal forms of ubiquitin (PDB entries 3ONS and 3N30) with particular emphasis on (i) conformational exchange between β turn type I and II in the region 51-54 and (ii) rocking dynamics where protein molecules as a whole undergo subtle reorientational motion within the confines of the crystal lattice. Experimentally, both motional processes have been probed using relaxation dispersion solid state NMR techniques and showed similar or identical characteristic times (tens of microseconds) in 3N30 crystals. This raise a question: is this merely a coincidence or, otherwise, are these two motional modes coupled? To answer this question we performed MD simulations of 3ONS and 3N30 crystals. To quantify the effect of rocking motion we have used temporal correlation functions.
Crystal MD simulations provide useful insight into rocking motion. We demonstrated that 3N30 crystal is prone to rocking and observed a weak coupling between rocking motion and βI↔βII exchange. Our data are also supported by X-Ray and ssNMR evidence and appear to be quite accurate in explaining the population balance between different conformations.
Tags: Izmailov, Rogacheva, Skrynnikov, Ubiquitin
