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Posts tagged ‘Luzik’

Crystal structure of the SH3 domain of growth factor receptor-bound protein 2

Posted: 29.05.2020

Bolgov, A., Korban, S., Luzik, D., Zhemkov, V., Kim, M., Rogacheva, O., & Bezprozvanny, I. Crystal structure of the SH3 domain of growth factor receptor-bound protein 2. Acta Crystallographica Section F: Structural Biology Communications, 76(6), 263-270, 2020.

This study presents the crystal structure of the N-terminal SH3 (SH3N) domain of growth factor receptor-bound protein 2 (Grb2) at 2.5 Å resolution. Grb2 is a small (215-amino-acid) adaptor protein that is widely expressed and involved in signal transduction/cell communication. The crystal structure of full-length Grb2 has previously been reported (PDB entry 1gri). The structure of the isolated SH3N domain is consistent with the full-length structure. The structure of the isolated SH3N domain was solved at a higher resolution (2.5 Å compared with 3.1 Å for the previously deposited structure) and made it possible to resolve some of the loops that were missing in the full-length structure. In addition, interactions between the carboxy-terminal region of the SH3N domain and the Sos1-binding sites were observed in the structure of the isolated domain. Analysis of these interactions provided new information about the ligand-binding properties of the SH3N domain of Grb2.

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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.

DOI:

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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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FEBS congress, Jerusalem, Israel

Posted: 14.09.2017

Ivan Podkorytov, Sevastyan Rabdano, Olga Rogacheva, Kerstin Kaempf and Dmitri Luzik attended the FEBS congress in Jerusalem, Israel.

Kerstin Kaempf presented short oral talk “Local and global dynamics of intrinsically disordered proteins: a case study of H4 histone tail”.

Ivan Podkorytov presented poster “Detection of flexible portion of protein chain in Sup35NM amyloid fibrils by means of diffusion-filtered NMR experiment”.

Sevastyan Rabdano presented poster “Characterizing the Size of Protein Aggregate Particles Using a Combination of NMR Diffusion Measurements and Dynamic Light Scattering: Case Study of RRM2 Domain from Protein TDP-43”.

Olga Rogacheva presented poster “New linear interaction between charged lysine side chain and carbonyl group in protein structures”.

Dmitry Luzik presented poster “Non-native disulfide bridges in protein-peptide complex and in protein homodimers trigger unfolding and aggregation”.

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Onset of disorder and protein aggregation due to oxidation-induced intermolecular disulfide bonds: case study of RRM2 domain from TDP-43

Posted: 11.09.2017

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 20177 (1), 11161.

DOI: 10.1038/s41598-017-10574-w.

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Non-Native Disulfide Bridges in Protein-Peptide Complex and in Protein Homodimers Trigger Unfolding and Aggregation

Posted: 08.09.2017

Luzik, D. A.; Rabdano, S. O.; Skrynnikov, N. R. Non-Native Disulfide Bridges in Protein-Peptide Complex and in Protein Homodimers Trigger Unfolding and Aggregation. The FEBS Journal 2017284 (Suppl. 1), 212.

DOI: 10.1111/febs.14174.

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Characterizing the size of protein aggregate particles using a combination of NMR diffusion measurements and dynamic light scattering: case study of RRM2 domain from protein TDP-43

Posted: 08.09.2017

Rabdano, S.; Podkorytov, I.; Luzik, D.; Skrynnikov, N. Characterizing the Size of Protein Aggregate Particles Using a Combination of NMR Diffusion Measurements and Dynamic Light Scattering: Case Study of RRM2 Domain from Protein TDP-43. The FEBS Journal 2017284 (Suppl. 1), 212.

DOI: 10.1111/febs.14174.

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Conference of Institute of Translational Biomedicine of SPbSU “Actual Problems of Translational Biomedicine – 2017”

Posted: 16.07.2017

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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.

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BioHack 2017

Posted: 05.03.2017

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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.

 

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