Alexander V. Shkumatov

PhD student, postdoc

Address

Tel: +49 [0] 40 89902 178
Fax: +49 [0] 40 89902 149
ashkumat@embl-hamburg.de

Biography

Research fields

Biological small-angle X-ray scattering (SAXS): analysis of biological systems with different levels of flexibility

Computational biology: sequence analysis, protein structure/function prediction, docking, development/support of tools for analysis of SAXS data

Research interests

Application of hybrid methods to solve biological problems. Read more on my wikipedia article

Responsibilities and activities

• Local contact at small angle X-ray scattering beamline X33 at DESY, Hamburg
• Collaborative projects dealing with the analysis of scattering data for biological systems with different levels of flexibility
• Support and further development of the tools for analysis of biological SAXS data: CRYSOL, CRYSON, EM2DAM, RANLOGS
• Development of NMADREFS (Normal Mode Analysis Driven REFinement using SAXS constraint)

Publications

• Extracellular complexes of the hematopoietic human and mouse CSF-1 receptor are driven by common assembly principles.
  Elegheert J, Desfosses A, Shkumatov AV, Wu X, Bracke N, Verstraete K, Craenenbroeck K, Brooks BR, Svergun DI, Vergauwen B, Gutsche I, Savvides SN.
  Structure. 2011 Dec 7;19(12):1762-1772 PubMed
• A flexible brace maintains the assembly of a hexameric replicative helicase during DNA unwinding
  Shkumatov* AV, Whelan* F, Stead* J, Svergun D, Sanders C, and Antson F.
  Nucleic Acids Research. 2011 Epub Nov 8. PubMed
• Oligomerization propensity and flexibility of yeast frataxin studied by X-ray crystallography and small-angle X-ray scattering.
  Shkumatov* AV, Söderberg* CAG, Rajana S, Gakh O, Svergun DI, Isaya G, and Al-Karadaghi S.
  Journal of Molecular Biology. 2011 Dec 16;414(5):783-97 PubMed
• Insights into the molecular activation mechanism of the RhoA-specific guanine nucleotide exchange factor, PDZRhoGEF.
  Shkumatov* AV, Bielnicki* J, Derewenda U, Somlyo A, Svergun D, and Derewenda Z.
  Journal of Biological Chemistry. 2011 Oct 7;286(40):35163-75 PubMed
• Structural memory of natively unfolded tau protein detected by small-angle X-ray scattering.
  Shkumatov* AV, Chinnathambi* S, Mandelkow E, Svergun DI.
  Proteins. 2011 Mar 22; 79(7):2122-31 PubMed
• Structural insights into the extracellular assembly of the hematopoietic Flt3 signaling complex.
  Verstraete K, Vandriessche G, Januar M, Elegheert J, Shkumatov AV, Desfosses A, Van Craenenbroeck K, Svergun DI, Gutsche I, Vergauwen B, Savvides SN.
  Blood. 2011 Mar 9; 118(1):60-8 PubMed
• Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades.
  Shkumatov* A, Förster* F, Liang* C, Beisser D, Engelmann JC, Schnölzer M, Frohme M, Müller T, Schill RO, Dandekar T.
  BMC Genomics. 2009 Oct 12; 10:469 PubMed
• Finding functional sites in structural genomics proteins.
  Stark A, Shkumatov A, Russell RB.
  Structure. 2004 Aug; 12(8):1405-12 PubMed

* equal contributors

Collaborations

Structure and conformation of tau protein in solution E. Mandelkow, DZNE, German Center for Neurodegenerative Diseases, c/o CAESAR, 53175 Bonn, Germany

Hematopoietic cytokine-receptor complexes important for the human hematopoietic and immune systems S. Savvides, Ghent University, Ghent, Belgium

The supramodular architecture of the RGSL family of multidomain nucleotide exchange factors Z. Derewenda, University of Virginia, USA

Assembly and dynamics of yeast frataxin and cobaltochelatase S. Al-Karadaghi, Lund University, Chemistry Centre, Sweden

Oligomerisation of human frataxin S. Al-Karadaghi, Lund University, Chemistry Centre, Lund, Sweden

Structural Investigation of the mechanism of a papillomavirus E1 Helicase A. Antson, York Structural Biology Laboratory, UK

Self-assembly and structural organization of spider silk proteins S. Knight, Swedish University of Agricultural Sciences, Uppsala, Sweden