Laboratory of Biomolecular NMR

Spinus 2017 – Magnetic Resonance and Its Applications

Posted: 29.04.2017

spinus

Nikolai Skrynnikov, Vladislav Salikov and Sevastyan Rabdano attended the Spinus 2017 conference “Magnetic Resonance and Its Applications”.

Nikolai Skrynnikov presented the lecture “Recent results from the Laboratory of biomolecular NMR @ SPbGU: from mechanism of anti-cancer peptides to characterization of flexible tails in amyloid fibrils”.

Sevastyan Rabdano presented the oral talk “Reconstruction of particle size-distribution from conjunction of NMR and DLS diffusion data”.

Vladislav Salikov presented porster “Analysis of NMR spectra of alizarin and alizarin red S”.

Tags: Rabdano, Salikov, Skrynnikov

TEDxSPBU

Posted: 22.04.2017

Sevastyan Rabdano was invited to give a talk at locally organized TED event TEDxSPBU. The topic of talk was “Can we use negative impact of oxidants in positive way?”

Tags: Rabdano

BioHack 2017

Posted: 05.03.2017

PogC4n9AZHE

XVJGuOFwPwM

0PCqt-a8DTU

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.

Tags: Izmailov, Luzik, Rabdano

Origin of anti-tumor activity of the cysteine-containing GO peptides and further optimization of their cytotoxic properties

Posted: 20.01.2017

srep40217-f8

Tyuryaeva, I. I., Lyublinskaya, O. G., Podkorytov, I. S. & Skrynnikov, N. R. “Origin of anti-tumor activity of the cysteine-containing GO peptides and further optimization of their cytotoxic properties” Scientific Reports 7, 40217 (2017).

DOI: 10.1038/srep40217

Tags: Lyublinskaya, Podkorytov, Skrynnikov, Tyuryaeva

Expert council of NIH

Posted: 15.11.2016

Nikolai Skrynnikov participated in expert council of NIH, Washington, USA, 15-17 Nov, 2016.

Tags: Skrynnikov

Chicago Areа NMR Discussion Group (CANMRDG)

Posted: 07.11.2016

Nikolai Skrynnikov organized the conference with 120 attendees “Chicago Areа NMR Discussion Group (CANMRDG)”, Milwaukie, USA, 5 Nov, 2016.

Tags: Skrynnikov

Dynamics in protein crystals: insights from MD simulations complement new solid-state NMR and X-ray data

Posted: 03.09.2016

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

Gordon Research Conference on Diffraction Methods

Posted: 17.07.2016

Pictur32

Nikolai Skrynnikov presented talk “Motions of Protein Molecules Within the Crystalline Lattice” at the Gordon Research Conference on Diffraction Methods, Bates College, ME, USA, 17-22 Jul 2016.

Tags: Skrynnikov

XXXVIII Finnish NMR Symposium

Posted: 13.06.2016

Finnish NMR symposium

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

Dynamics in Protein Crystals

Posted: 01.06.2016

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.

screen-shot-2016-09-07-at-23-49-51

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

Links

Tags