Dr. Alex Volkov

 

Contact Details

Jean Jeener NMR Centre
Vrije Universiteit Brussel
Pleinlaan 2
1050 Brussels
Belgium

E-mail: ovolkov@vub.ac.be

Phone: +32 (0)2 629 3553
Fax: +32 (0)2 629 1963

 

 

Biography

 

2015 – present   VIB Staff Scientist (Structural Biology Research Centre, VIB-VUB, Belgium)
2009 – 2015       Post Doc (Prof. Nico van Nuland, Vrije Universiteit Brussel - VIB, Belgium)
2008 – 2009       Post Doc (Dr. Chun Tang, University of Missouri - Columbia, MO USA)
2007 – 2008       Post Doc (Prof. Jacques Fastrez, Université Catholique de Louvain, Belgium)
2002 – 2007       PhD (Dr. Marcellus Ubbink, Leiden University, the Netherlands)
2000 – 2001       MSc in biochemistry (Leiden University, the Netherlands)
1998 – 2000       MSc in inorganic chemistry (National Taras Shevchenko University of Kiev, Ukraine)
1995 – 1998       BSc in chemistry (National Taras Shevchenko University of Kiev, Ukraine)
 
My PhD thesis is freely available from the website of the Leiden University Repository.

 

Publications

 

25.  Contreras-Martos, S., Piai, A., Kosol, S., Varadi, M., Bekesi, A., Lebrun, P., Volkov, A.N., Gevaert, K., Pierattelli, R., Felli, I. & Tompa, P. Linking functions: an additional role for an intrinsically disordered linker domain in the transcriptional coactivator CBP. Sci. Rep. 7, 4676 (2017). PDF(2.7 MB)

24.  Boeynaems, S., Bogaert, E., Kovacs, D., Konijnenberg, A., Timmerman, E., Volkov, A., Guharoy, M., De Decker, M., Jaspers, T., Ryan, V.H., Janke, A.M., Baatsen, P., Vercruysse, T., Kolaitis, R.M., Daelemans, D., Taylor, J.P., Kedersha, N., Anderson, P., Impens, F., Sobott, F., Schymkowitz, J., Rousseau, F., Fawzi, N.L., Robberecht, W., Van Damme, P., Tompa, P. & Van Den Bosch, L. Phase Separation of C9orf72 Dipeptide Repeats Perturbs Stress Granule Dynamics. Mol. Cell 65, 1044-1055 (2017). PDF(3.6 MB)

23.  Antonik, P.M.*, Volkov, A.N.*, Broder, U.N., Lo Re, D., van Nuland, N.A.J. & Crowley, P.B. Anomer-specific recognition and dynamics in a fucose-binding lectin. Biochemistry 55, 1195-203 (2016). *contributed equally

22. Volkov, A.N. Structure and function of transient encounters of redox proteins. Acc. Chem. Res. 48, 3036-43 (2015). PDF(2.9 MB)

21. Van de Water, K., Sterckx, Y.G.J. & Volkov, A.N. The low-affinity complex of cytochrome c and its peroxidase. Nat. Commun. 6, 7073 (2015). PDF(1.6 MB) SupplementaryMaterial(1.0 MB)

20. Van de Water, K., van Nuland, N.A.J & Volkov, A.N. Transient protein encounters characterized by paramagnetic NMR. Chem. Sci. 5, 4227-36 (2014). PDF(1.2 MB) SupplementaryMaterial(1.1 MB)

19. Sterckx, Y.G.J. & Volkov, A.N. Cofactor-dependent structural and binding properties of yeast cytochrome c peroxidase. Biochemistry 53, 4526-36 (2014).

18. Sterckx, Y.G.J., Volkov, A.N., Vranken, W.F., Kragelj, J., Ringkjøbing-Jensen, M., Buts, L., Garcia-Pino, A., Jové, T., Van Melderen, L., Blackledge, M., van Nuland, N.A.J. & Loris, R. SAXS and NMR-derived conformational ensemble of the highly flexible antitoxin PaaA2. Structure 22, 854-65 (2014). PDB(3ZBE) BMRB(18841)

17. Vanwetswinkel, S., Volkov, A.N., Sterckx, Y.G.J., Garcia-Pino, A., Buts, L., Vranken, W.F., Bouckaert, J., Roy, R., Wyns, L. & van Nuland, N.A.J. Study of the structural and dynamic effects in the FimH adhesin upon α-D-heptyl mannose binding. J. Med. Chem. 57, 1416-27 (2014). PDB(3ZPD) PDB(4LOV) BMRB(19066) BMRB(19254) BMRB(19255) BMRB(19256)

16. Vanwetswinkel, S., van Nuland, N.A.J. & Volkov, A.N. Paramagnetic properties of the low- and high-spin states of yeast cytochrome c peroxidase. J. Biomol. NMR 57, 21-6 (2013). PDF(0.2 MB) BMRB(19075) BMRB(19076)

15. Volkov, A.N. & van Nuland, N.A.J. Solution NMR study of the yeast cytochrome c peroxidase - cytochrome c interaction. J. Biomol. NMR 56, 255-63 (2013). PDF(0.8 MB)

14. Volkov, A.N., Wohlkonig, A., Soror, S.H. & van Nuland, N.A.J. Expression, purification, characterization, and solution nuclear magnetic resonance study of highly deuterated yeast cytochrome c peroxidase with enhanced solubility. Biochemistry 52, 2165-75 (2013). PDF(2.2 MB) SupplementaryMaterial(1.7 MB) PDB(4JB4) BMRB(19004) BMRB(19005)

13. Volkov, A.N. & van Nuland, N.A.J. Electron transfer interactome of cytochrome c. PLoS Comput. Biol. 8, e1002807 (2012). PDF(0.9 MB) SupplementaryMaterial(1.3 MB) VideoS1(QuickTime, 9.5 MB) VideoS2(QuickTime, 9.3 MB) VideoS3(QuickTime, 9.5 MB) VideoS4(QuickTime, 9.8 MB) VideoS5(QuickTime, 7.1 MB) VideoS6(QuickTime, 6.6 MB) VideoS7(QuickTime, 9.7 MB) VideoS8(QuickTime, 8.1 MB) SupplementaryScriptFiles(.tar.bz2, 0.9 MB)

12. Volkov, A.N., Vanwetswinkel, S., Van de Water, K. & van Nuland, N.A.J. Redox-dependent conformational changes in eukaryotic cytochromes revealed by paramagnetic NMR spectroscopy. J. Biomol. NMR. 52, 245-56 (2012). PDF(0.8 MB) SupplementaryMaterial(1.0 MB) BMRB(17845) BMRB(17846) BMRB(17847) BMRB(17848)

11. Volkov, A.N., Nicholls, P. & Worrall, J.A.R. The complex of cytochrome c and cytochrome c peroxidase: the end of the road? Biochim. Biophys. Acta 1807, 1482-503 (2011). PDF(1.9 MB)

10. Van de Water, K., Soror, S.H., Wohlkonig, A., van Nuland, N.A.J. & Volkov, A.N. Crystallization and preliminary X-ray diffraction analysis of kanamycin-binding beta-lactamase in complex with its ligand. Acta Crystallogr. F. 67, 703-6 (2011). PDF(0.3 MB)

9. Volkov, A.N., Barrios, H., Mathonet, M., Evrard, C., Ubbink, M., Declercq, J.P., Soumillion, P. & Fastrez, J. Engineering an allosteric binding site for aminoglycosides into the TEM-1 beta-lactamase. Chem.Bio.Chem. 12, 904-13 (2011). PDF(1.0 MB) SupplementaryMaterial(0.7 MB) PDB(2V1Z) PDB(2V20) BMRB(15917)

 
 
 
 
4. Volkov, A.N., Bashir, Q., Worrall, J.A.R. & Ubbink, M. Binding hot spot in the weak protein complex of physiological redox partners yeast cytochrome c and cytochrome c peroxidase. J.Mol.Biol. 385, 1003-13 (2009). PDF(0.7 MB)
 
 
2. Volkov, A.N., Ferrari, D., Worrall, J.A.R., Bonvin, A.M.J.J. & Ubbink, M. The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK. Prot.Sci. 14, 799-811 (2005). PDF(0.4 MB) SupplementaryMaterial(0.7 MB)
Correction in Prot.Sci. 15, 1563 (2006) PDF(0.1 MB)
 
1. Zaitsev, V.N., Volkov, A.N., Zub, V.Ya. & Zaitseva, G.N. A study of the interaction of diethylenetriamine complexes of copper fixed on silica with reagents of different nature by the ESR method. Ukrainskij Khimicheskij Zhurnal (Russian Edition) 64, 12-7 (1998).
 

Scripts

 

 
Functional epitope mapping in electron transfer protein complexes (XPLOR-NIH and Python 2.x; .tar.bz2, 0.9 MB)
Volkov, A. N. & van Nuland, N. A. J. (2012) Electron transfer interactome of cytochrome c. PLoS Comput. Biol. 8, e1002807. PDF(0.9 MB) SupplementaryMaterial(1.3 MB)
 

Spatiotemporal encounter state mapping from PRE data (XPLOR-NIH and Python 2.x; .tar.gz, 0.5 MB)
Volkov, A. N., Ubbink, M. & van Nuland, N. A. J. (2010) Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy. J.Biomol.NMR. 48, 225-236. PDF(1.0 MB) SupplementaryMaterial(0.5 MB)

 

Generating polar contour plots for an ensemble of centers of mass in spherical coordinates (Matlab; .zip, 0.1 MB)
Volkov, A. N., Bashir, Q., Worrall, J. A. R., Ullmann, G. M. & Ubbink, M. (2010) Shifting the equilibrium between the encounter state and the specific form of a protein complex by interfacial point mutations. J.Am.Chem.Soc. 132, 11487-11495. PDF(4.0 MB) SupplementaryMaterial(2.3 MB)

Calculating 1GPREs from peak intensities in paramagnetic and diamagnetic HSQC spectra (Python 2.x; .zip, 9 KB)
Volkov, A. N., Bashir, Q., Worrall, J. A. R., Ullmann, G. M. & Ubbink, M. (2010) Shifting the equilibrium between the encounter state and the specific form of a protein complex by interfacial point mutations. J.Am.Chem.Soc. 132, 11487-11495. PDF(4.0 MB) SupplementaryMaterial(2.3 MB)