Itamar Kass


Itamar Kass, Ph.D.
Postdoctoral Research Fellow


Department of Biochemistry and Molecular Biology
Building 77 Clayton Campus
Wellington Road
Monash University,
Victoria 3800

Tel: +61 3 9902 9376
Fax: +61 3 9902 9500
E-mail: Itamar (dot) Kass (at) monash (dot) edu

My Interest

I have a long standing interest in combining experimental and theoretical methods to study the correlation between the 3D structure and dynamics of proteins and their mechanism of action.

During my MSc studies, I investigated how information about ligand binding is transmitted within the protein GroEL. Specifically, I developed and implemented a new algorithm for finding correlated mutations. Using this algorithm, I could identify networks of coupled residues, which were known to be important to allosteric regulation of GroEL.

During my Ph.D. research, I studied the structure and function of membrane proteins. I had improved the utility of FT-IR spectroscopy, and was involved in the first use of 2D-FTIR spectroscopy for the study of membrane proteins. In addition, I was part of the team how investigated a novel mechanism by which the Influenza A virus attains resistance toward amantadine, a blocker of the viral H+ channel M2. In order to understand the molecular basis of this mechanism, I performed MD simulations, and showed an increase in the pore radius of the channel. I also investigated the pH activation of the M2 channel by simulating all possible histidine protonation states in the channel, as these histidines are known to be key residues in the gating process. Analysis of the simulations indicated that only systems with two or more charged histidines are appreciably conductive.

Throughout my postdoctorial studies, with Prof. Alan Mark at UQ, I studied a range of problems, including the molecular mechanism of membrane penetration by pore forming toxins, binding of hydrophobins to air water interfaces and the interaction of pore forming cyclotide with membranes.

Research & Education Experience

Research fellow in the group of A/Prof. Buckle, Department of Biochemistry and Molecular Biology, Monash University, Australia.
Study the correlation between dynamics and function of proteins.

Post Doctoral Fellow in the group of Prof. Alan Mark, Molecular Dynamics Group,
The University of Queensland, Australia.
Study the function and dynamics of proteins at interfaces.

PhD Student,
Department of Biological Chemistry, Institute of Life Sciences,
The Hebrew University of Jerusalem, Jerusalem, Israel.
 Thesis title: ”Structural analysis of membrane proteins complexes with their cognate ligands”
Supervisor: Prof. Isaiah Arkin.

Department of Structural Biology,
Weizmann Institute of Science, Rehovoth, Israel.
 Thesis title: ”Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations”
Supervisor: Prof. Amnon Horovitz.


Molecular Dynamics Workshop, 25-26 September 2012, University of Canterbury, Christchurch, New Zealand (co-organized with A/Prof. Buckle and Mr. Reboul).

Introduction to Computational Biology (With Dr Thomas Huber).

Introduction to Computational Biology (With Dr Thomas Huber)

Awards & Fellowships

Young Investigator Awards at the Lorne Conference on Protein Structure and Function, Australia

University of Queensland Enabling Grant.

Noach Lichtenstein Award, The Hebrew University of Jerusalem, Jerusalem, Israel.

Fellowship of The Sudarsky Center for Computational Biology, The Hebrew University of Jerusalem, Jerusalem, Israel.



  1. Kass, I., Knaupp, A.S., Bottomley, S.B. and Buckle, A.M. (2012). Conformational properties of the disease-causing Z variant of α1 antitrypsin revealed by molecular dynamics simulations. Biophys. J. 102(12):2856-65.
  2. Kass, I., Reboul, C.F. and Buckle, A.M. (2011) Computational methods for studying serpin conformational change and structural plasticity. Methods in enzymology 501: 295-323.
  3. Kwan, A.H., Macindoe, I., Vukasin, P.V., Morris,
V.K., Kass, I., Gupte, R., Mark, A.E., Templeton, M.D., Mackay, J.P. and Sunde, M. (2008) The Cys3-Cys4 Loop of the Hydrophobin EAS Is Not Required for Rodlet Formation and Surface Activity. 
J. Mol. Biol. 382(3):708-20.
  4. Mukherjee, P., Kass, I., Arkin,
I.T. and Zanni, M.T. (2006) Structural disorder of the CD3 ξ transmembrane domain studied with 2D IR spectroscopy and molecular dynamics simulations. J. Phys. Chem. B. 110(48):24740–9.
  5. Arbely, E.,
Granot, Z., Kass, I., Orly, J. and Arkin, I.T. (2006) A Trimerizing GxxxG Motif Is Uniquely Inserted in the Severe Acute Respiratory Syndrome (SARS) Coronavirus Spike Protein Transmembrane Domain. Biochemistry 45(38):11349–56.
  6. Mukherjee, P., Kass, I., Arkin, I.T. and Zanni, M.T. (2006) Picoseconds dynamics of a membrane protein revealed by 2D IR. Proc. Nat. Acad. Sci. 103(10):3528–33.
  7. Kass, I. and Arkin, I.T., (2005) How pH opens a H+ channel: the gating mechanism of Influenza A M2. Structure 13(12):1789–98.
  8. Mukherjee, P.,
Krummel, A.T, Fulmer, E.C., Kass, I., Arkin, I.T. and Zanni, M.T. (2004) Site-specific vibrational dynamics of the CD3zeta membrane peptide using heterodyned two-dimensional infrared photon echo spectroscopy. J. Chem.
Phys. 120(21):10215–24.
  9. Astrahan, P., Kass, I., Cooper, M.A. and Arkin, I.T. (2004) A novel method of resistance for influenza against a channel-blocking antiviral drug. Prot. Struct. Func.
Gen. 55(2):251–7.
  10. Kass, I., Arbely, E. and Arkin, I.T. (2004) Modeling sample disorder in site-specific dichroism studies of uniaxial systems. Biophys. J. 86(4):2502–7.
  11. Arbely, E., Kass, I.* and Arkin, I.T. (2004) Site-specific dichroism analysis utilizing transmission FTIR. Biophys. J. 85(4):2476–83.
  12. Kass, I. and Horovitz, A. (2002) Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Prot. Struct. Func. Gen. 48(4):611–7.

*Joint first author

Book chapters

  1. Kass, I. and Arkin, I.T. (2004) “Studies of viral ion channels.” In Viral membrane proteins: structure, function and drug design, Fischer, W.B. ed. Kluwer, New York.


  1. Conformational properties of the disease-causing Z variant of α1-antitrypsin revealed by molecular dynamics simulations. Invited speaker at the National Institute of Biotechnology Research Seminar Series, Beer-Sheva, Israel, January 2012.
  2. Structural and dynamics studies of the serine protease inhibitor α1-AT. The Australian Molecular Modelling Conference, Melbourne, Australia, October 2010.
  3. (Proteins are) Bridges Over Interfaces – Proteins dynamics at surfaces. Invited speaker at the Victorian eResearch Strategic Initiative, Melbourne, Australia, August 2009.
  4. Computer simulations of the interactions of proteins and membranes – on spontaneous pores formation. Invited speaker at the Lorne Conference on Protein Structure and Function, Lorne, Australia, February 2009.
  5. From Structure to Function of TM Proteins: The story of the Influenza A M2 H+ Channel. World Association of Theoretical and Computational Chemists, Sydney, Australia, September 2008.
  6. The structure and dynamic of class I Hydrophobin EAS at an air water interface. East Coast Protein Meeting, Coffs Harbour, Australia, July 2007.