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Morteza Khabiri

Postdoctoral Researcher, Biological Chemistry Department


SPC5606, 1150 W. Medical Center Drive
Ann Arbor, MI 48109-0600

  • Ph.D, Computational Biophysics, University of South Bohemia and ASCR, Czech republic, Nove Hrady, 2011
  • M.Sc., Biophysics, IBB, University of Tehran, Iran, 2007
  • B.Sc., Biology, Tarbiat Moallem University, Tehran, Iran, 2004
Research Interests
  • Regulatory networks play a key role to control the level of expression of various genes in a given genome. The main players in regulatory networks are DNA-binding proteins, also called transcription factors as they modulate the first step in gene expression. The activity of TFs that interact directly with DNA depend on their potent ability to recognize and bind to specific DNA sequence. Among them, the one which provide enough information or has the lowest energy will typically arise as a consensus binding site sequence. I have recently started working on the protein-DNA interactions. I try to provide a clear picture of the full landscape of binding affinities of a given TF for different sequences, or insight into the structure-function interactions that characterize these landscapes with more accuracy using atomistic molecular dynamic simulations.
  • In the interdisciplinary environment of the Peter' Lab I also started to work on mapping of genetic regulatory networks of large nucleotide dataset. In this project I try linking regulatory sites with transcription factors, identifying a transcription factor, finding the genes bound/regulated by a particular TF, and finding regulatory interactions between transcription factors.
  • Of course these new fields did not distract me from Kv potassium channels ;-). I am always fascinated by these amazing membrane proteins, that how they can distinguish the ions in the solutions or regulate the ion passage through the membrane. 
Recent Publications
  • Morteza Khabiri* , Azadeh Nikouee* , Lukasz Cwiklik , Stephan Grissmer , and Rudiger Ettrich. (2011) Charybdotoxin Unbinding from the mKv1.3 Potassium Channel: A Combined Computational and Experimental Study. J. Phys. Chem. B, 2011, 115, 11490–11500        
  • M. Khabiri, M. Roeselova, L. Cwiklik, (2011) Properties of Oxidized Phospholipid Monolayers: an Atomistic Molecular Dynamics Study. J. Chemical Physics Letters 519520 (2012) 9399
  • Azadeh Nikouee*, Morteza Khabiri*, Stephan Grissmer, Rüdiger Ettrich (2012) Charybdotoxin and margatoxin acting on the human voltage-gated potassium channel hKv1.3 and its H399N mutant: An experimental and computational comparison. J. Phys. Chem. B (2012), 116, 5132−5140
  • Morteza Khabiri, Babak Minofar, Jan Březovsky, Jiří Damborský, Rudiger Ettrich (2012) Interaction of organic solvents with protein structures at protein-solvent interface. J. Mol. Model. 19: 4701–4711
  • Veronika Štěpánková*, Morteza Khabiri*, Jan Brezovský, Antonín Pavelka, Babak Minofar, Rudiger Ettrich, Radka Chaloupková, Jiří Damborský (2013) Expansion of Access   Tunnels and Active-Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Cosolvents. Chem.Bio.Chem.(in the section: Very Important Paper (VIP)) Very Important Paper (VIP), 14: 890–897
  • Tana Koudelakova, Radka Chaloupkova, Jan Brezovsky, Zbynek Prokop, Martina Pavlova, Martin Hessler, Morteza Khabiri, Maryia Plevaka, Daryna Kulik, Ivana Kuta Smatanova, Pavlina Rezacova, Rudiger Ettrich, Uwe T Bornscheuer, Jiří Damborský (2013) Engineering Enzyme Stability and Resistance to an Organic Cosolvent by Modification of Residues in the Access Tunnel. Angewandte Chemie (International Edition) 52: 1959 –1963.
  •  Vazdar M, Wernersson E, Khabiri M, Cwiklik L, Jurkiewicz P, Hof M, Mann E, Kolusheva S, Jelinek R, Jungwirth P. (2013) Aggregation of Oligoarginines at Phospholipid Membranes: Molecular Dynamics Simulations, Time-Dependent Fluorescence Shift, and Biomimetic Colorimetric Assays. J. Phys. Chem. B, 117 (39), pp 11530–140
  • D Sinha, K Shamayeva, V Ramasubramani, D Reha, V Bialevich, M Khabiri, A Guzanova, M Weiserova, E Csefalvay, J Carey, R Ettrich (2014) Interdomain communication in the endonuclease/motor subunit of Type I restriction-modification enzyme EcoR124I. Journal of Molecular Modeling, Jul;20(7):2334. doi: 10.1007/s00894-014-2334-1
  • Nikouee A, Khabiri M, Cwiklik L. Scorpion toxins prefer salt solutions. J Mol Model. 2015 ;21(11):287 
Professional History

    2015 to Present 
        Postdoctoral Researcher,  Freddolino Lab, Biological Chemistry Department, University of Michigan
    2014 to 2015
         Postdoctoral Fellow, Dr. Martina Roeselova, Institute of Organic Chemistry and Biochemistry, Academy of sciences of the Czech Republic, Prague

    2012 to 2014 
        Lecturer, Golestan University of Medical Sciences, Gorgan, Iran

    2007 to 2011 
        Graduate Student, University of South Bohemia and Academy of Sciences of the Czech Republic, Nove Hrady

    2004 to 2007:
        Graduate Student, University of Tehran, Iran

Awards and Fellowships

Young Scientist Award at the First International MEFOMP Conference of Medical Physics, Shiraz, Iran, 2011

FEBS Advance Course Fellowship Nove Hrady, Czech Republic, Jun, 2010

International travel grants of the Biophysical Society's 54th Annual Meeting, San Francisco , USA, Feb, 2010

The Novartis International Biotechnology Leadership Camp (BioCamp) award, Basel , Switzerland, Aug, 2009