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Hire Dr. Zakir T.

United Kingdom

USD 100 /hr

Synthetic biologist experienced in directed evolution, assay development, protein:protein and protein:ligand interaction

Profile Summary

CHEMICAL BIOLOGY • Site-specific protein modification in vitro using a genetic code expansion, puromycin-mediated, native chemical ligation and protein trans-splicing in in vitro translation systems (Wheat Germ, E.coli and L.tarentolae) • Site-specific protein modification of proteins in mammalian cells using genetic code expansion • Enzymatic preparation of UAA-containing aminoacyl-tRNAs in vitro, chemical derivatization and purification • Chemo-enzymatic derivatization of purified recombinant proteins via expressed protein ligation, native chemical ligation, thiol and amine coupling • Basic organic chemical synthesis, characterization and purification of compounds BIOCHEMISTRY AND BIOPHYSICS • Directed evolution studies both in E.coli and in cell-free systems (Ribosome display and similar) • Preparation of cell-free translation mixtures and its components (Ribosomes, translation factors, tRNAs etc) • Kinetic and thermodynamic characterization of biomolecule interactions via Fluorescence Spectroscopy, Fluorescence Anisotropy, Stopped-Flow, Isothermal Titration Calorimetry (ITC), Microscale Thermophoresis (MST), Fluorescence Correlation Spectroscopy (FCS), Fluorescence Cross-Correlation Spectroscopy (FCCS) • Development of enzymatic assays for evaluation of steady-state enzymatic kinetic characteristics GENOME BIOLOGY • Modification of E.coli genome via conventional recombineering (lambda-red) and Cas9 (REXER method) • Nextgen DNA library preparation and sequencing (Illumina, Miseq) CELL BIOLOGY • FACS analysis of transiently transfected mammalian cells • Fixed and live-sell Imaging (FLIM-FRET)

Subject Matter Expertise

• ★ Molecular Biology
• ★ Biotechnology & Bioengineering
• ☆ Biochemistry
• ☆ Biochemical Assays
• ☆ Enzyme Activity Assays
• ☆ Binding Assays
• ☆ Biomarkers
• ☆ PCR
• ☆ Molecular Cloning
• ☆ Next Generation Sequencing (NGS)
• ☆ Synthetic Genomics
• ☆ Genome Sequencing
• ☆ Mutagenesis
• ☆ Recombinant DNA
• ☆ RNA Synthesis
• ☆ Plasmid DNA
• ☆ Cell Biology
• ☆ Cell-Based Assays
• ☆ Cell Signaling Pathways
• ☆ Biophysics
• ☆ Recombinant Protein Expression
• ☆ Nanobiotechnology
• ☆ Biomedical Engineering
• ☆ Biomimetics
• ☆ Biological Systems Engineering
• ☆ Cell Culture
• ☆ Industrial Biotechnology
• ☆ Synthetic Biology
• ☆ Biosensors
• ☆ Chemical Biology
• ☆ Blotting
• ☆ Immunohistochemistry
• ☆ Cytometry
• ☆ Drug Development

Services

• Writing
• Research
• Consulting
• Product Development

Writing Technical Writing

Research Market Research, Feasibility Study, Technology Scouting, Fact Checking, Gap Analysis, Gray Literature Search, Scientific and Technical Research, Systematic Literature Review, Secondary Data Collection

Consulting Business Strategy Consulting, Scientific and Technical Consulting

Product Development Product Evaluation

Work Experience

Project Lead

Constructive Biology Ltd

September 2022 - Present

Career Development Fellow

MRC Laboratory of Molecular Biology

March 2016 - July 2022

Postdoc

Karolinska Institute

February 2015 - February 2016

Postdoc

The University of Queensland

February 2013 - December 2014

Education

Ph.D.

The University of Queensland

February 2008 - February 2013

Master Science (Biology)

Lomonosov Moscow State University

September 2005 - June 2007

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

(2018). Controlling orthogonal ribosome subunit interactions enables evolution of new function . Nature.

(2017). Defective protein prenylation is a diagnostic biomarker of mevalonate kinase deficiency . Journal of Allergy and Clinical Immunology.

(2017). The nature of the Syntaxin4 C-terminus affects Munc18c-supported SNARE assembly . PLOS ONE.

(2017). Combining Sense and Nonsense Codon Reassignment for Site-Selective Protein Modification with Unnatural Amino Acids . ACS Synthetic Biology.

(2015). A highly sensitive prenylation assay reveals in vivo effects of bisphosphonate drug on the Rab prenylome of macrophages outside the skeleton . Small GTPases.

(2015). Semisynthetic tRNA Complement Mediates in Vitro Protein Synthesis . Journal of the American Chemical Society.

(2014). RhoGDI facilitates geranylgeranyltransferase-I-mediated RhoA prenylation . Biochemical and Biophysical Research Communications.

Z. Tnimov, Z. Guo, Y. Gambin, U. T. T. Nguyen, Y.-W. Wu, D. Abankwa, A. Stigter, B. M. Collins, H. Waldmann, R. S. Goody, K. Alexandrov, 2012, 'Quantitative Analysis of Prenylated RhoA Interaction with Its Chaperone, RhoGDI', <i>Journal of Biological Chemistry</i>, vol. 287, no. 32, pp. 26549-26562 .

Ritesh Raju, Andrew M. Piggott, Melissa Conte, Zakir Tnimov, Kirill Alexandrov, Robert J. Capon, 2010, 'Nocardiopsins: New FKBP12-Binding Macrolide Polyketides from an Australian Marine-Derived Actinomycete,Nocardiopsissp.', <i>Chemistry - A European Journal</i>, vol. 16, no. 10, pp. 3194-3200 .

Debapratim Das, Zakir Tnimov, Uyen T. T. Nguyen, Govindaraju Thimmaiah, Harriet Lo, Daniel Abankwa, Yaowen Wu, Roger S. Goody, Herbert Waldmann, Kirill Alexandrov, 2012, 'Flexible and General Synthesis of Functionalized Phosphoisoprenoids for the Study of Prenylation in vivo and in vitro', <i>ChemBioChem</i>, vol. 13, no. 5, pp. 674-683 .