ELENA YAKUBOVSKAYA, PH.D.

** ***** ***** ******* **** E. Setauket, NY 11733 T: +1-631-***-**** ac0cwm@r.postjobfree.com; ac0cwm@r.postjobfree.com PROFILE

Highly motivated scientist with extensive academic and industrial research experience in protein biochemistry, biophysics, and structural biology. Proven ability to solve complex problems confirmed by a strong publication record.

CORE EXPERTI SE

Molecular Cloning Restriction enzyme cloning, ligation independent cloning, site-directed mutagenesis. Protein Expression

& Purification

Recombinant protein expression in e-coli and insect cell, solubility and expression optimization. Proteins and protein complexes purification utilizing affinity, hydrophobic interaction, gel filtration, ion exchange, and dye-binding chromatography using FPLC (AKTA system). Membrane protein purification and refolding. Protein purification from native tissues. Antibody and Fab purification. Protein Analysis &

Characterization

Biochemistry and Molecular Biology: DNA/RNA polymerization, transcription, metiltransferase and topoisomerase assays. Electrophoresis, mobility shift assay, immunoblotting, crosslinking, footprinting, limited proteolysis, pull-down assay. Biophysics: Surface Plasmon Resonance (ex: Biacore), Isothermal Ttitration Calorimetry (ex: VP-ITC), Linear and Circular Dichroism, Thermophoresis, Fluorescent Resonance Energy Transfer, dynamic light scattering. Structural Biology

X-Ray Crystallography: De novo crystallization and optimization (including protein and protein-ligand complexes), seeding techniques, automated screening

(Mosquito), crystal mounting and synchrotron X-ray data collection, solving protein structures by heavy atom phasing and molecular replacement. Cryo-EM and negative staining EM. Grid preparation and freezing, data collection (FET Technai F20, JEOL 1230, FEI Titan Krios), single particle reconstruction (EMAN, Spider, Appion). Docking of X-ray structures in the Cryo EM envelope. Other structural techniques: AFM, TEM, SAXS, NMR.

LEADERSHIP, MENTORING, & COLLABORATIVE WORK

Mentoring &

Collaboration

Established extensive and productive collaborations, both internal and external, with chemists and structural and computation biologists from five different institutions. Trained 15+ graduate students and postdocs in protein purification, enzymatic assays, crystallographic experiment and biophysics techniques. Maintained AKTA FPLC purification systems, VP-ITC, and Biacore systems and trained faculty and students of Pharmacology Department at Stony Brook University to operate the equipment.

Communication Published 20+ papers in peer-reviewed journals. Presented results at 10+ national and international conferences. Intensive grants and proposal writing experience. Outreach Founding director of SigmaCamp, a science camp for middle and high school students, which has 50 faculty and staff members.

Elena Yakubovskaya, Ph.D. Page 2

RESEARCH EXPERIENCE

SUNY Pharmacology Dept., Stony Brook, New York, Research Scientist 2009 – Present

Discovered the organization of the human mitochondrial multiprotein transcription initiation complex and demonstrated the mechanism of its assembly on DNA using a combination of different experimental and computational methods, including electron microscopy, X-ray crystallography, SAXS, ITC, docking, and molecular dynamics (Yakubovskaya E., et al. Nucleic Acids Res. (2014) 42(6):4100–12).

Solved the 2.0 Å resolution crystal structure of the MTERF4:NSUN4 protein complex, and suggests a model for RNA binding, providing insight into the mechanism by which an MTERF family member facilitates rRNA methylation. (Yakubovskaya E., et al. Structure. (2012) 20(11):1940–7).

Determined the unique binding mechanism of mitochondrial transcription termination factor (MTERF1) to DNA by solving X-ray structure of MTERF1/DNA complex and set of biophysics techniques. Results explain the mechanism of transcription termination in human mitochondria and a possible role of some pathogenic mutations in mitochondrial DNA (Yakubovskaya E., et al. Cell. (2010) 41(6):982–93). SUNY Pharmacology Dept., Stony Brook, New York, Postdoctoral Research Associate 2004 – 2009

Established structural organization of DNA polymerase γ holoenzyme by CryoEM, clearly showing that functional human holoenzyme contains two subunits of the processivity factor and one catalytic subunit, thereby forming a heterotrimer and revealing structural aspects of interaction between subunits. Employed molecular techniques such as enzyme kinetics, footprinting, and photo-crosslinking to characterize binding pocket of Pol G and provided structural insight into role of some mutations in onset of mitochondrial diseases (Yakubovskaya Е., et al. J Biol Chem. (2006) 281(1):374–82; Yakubovskaya E., et al. EMBO J. 26(19): 4283–91).

Technogene Inc., Moscow, Russia, Research Scientist 2001 – 2004

In collaboration with ClonTech Lab (Becton-Dickinson division, CA, USA), developed novel MMLV reverse transcriptase mutant enzyme possessing high processivity, fidelity, and thermostability, and lacking RNase H activity for cDNA libraries. Developed large-scale purification protocol and activity assay.

Build a sensor to detect macromolecules. (Patent # RU2229118) Institute of Bioorganic Chemistry, Moscow, Russia, Postdoctoral Fellow 1998 – 2001

Developed new approach for monitoring topoisomerase reaction using optical dichroism technique to reveal mechanism of topoisomerase inhibitors belonging to camptothecin and ellipticine anticancer drug families.

Established novel activity assays for newly-discovered DNA-hydrolyzing antibodies from lupus erythematosus and rheumatoid arthritis patients based on FRET and linear dichroism techniques. EDUCATION

Institute of Molecular Biology, Moscow, Russia PhD 10/1997 Biochemistry Moscow State University, Moscow, Russia MA 06/1993 Biochemistry Moscow State University, Moscow, Russia BS 06/1991 Chemistry PROFESSIONAL TRAINING

2015 and 2006 Cryo EM Course, NYSBC, New York, NY; 2014 RapiData: A Practical Course in Macromolecular X-Ray Diffraction, Brookhaven Nat. Lab, Upton, NY, USA; 2010 EMBO Practical Course on Single-Molecule Analysis of DNA Protein Interactions, Paris, France; 2009 Analytical Ultracentrifugation Workshop, New York, NY; 2007 EMAN Electron Microscopy Workshop, Houston, TX; 2005 Biacore Workshop, New York, NY

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