Prof. Nir Ben-Tal

ביוכימיה וביולוגיה מולקו סגל אקדמי בכיר
Prof. Nir Ben-Tal
Phone: 03-6406709
Fax: 03-6406834
Office: Sherman - Life Sciences, 631

Biography

פרופ' ניר בן-טל הוא חוקר במחלקה לביוכימיה וביולוגיה מולקולרית בפקולטה למדעי החיים ע"ש ג'ורג' ס. וייז.

 

CV

Prof. Nir Ben-Tal completed his bachelor degree in Biology, Chemistry and Physics at the Hebrew University of Jerusalem, Israel, in 1988, and his DSc in Chemistry at the Technion, Israel Institute of Technology, in 1993. Later he did his postdoctoral training in biophysical chemistry at Columbia University, New York. In 1997 he accepted a faculty position at the department of Biochemistry and Molecular Biology, Tel Aviv University, and became full professor in 2007. 

Prof. Ben-Tal is a member of the editorial board of the scientific journals PLoS Computational BiologyeLIFE and J Biol Chem (July 2016 – September 2021), and also serves on the scientific committee of the largest annual computational biology conferences ISMB and ECCB. 

Research Interests

Prof. Ben-Tal’s research focuses mostly in the general area of computational structural biology. This includes both methods development and applications to selected problems. Prof. Ben-Tal’s laboratory has developed the ConSurf methodology and web-server for the detection of interaction regions in proteins based on evolutionary information (http://consurf.tau.ac.il/), jointly with the Mayrose and Pupko laboratories. Prof. Ben-Tal’s laboratory has also developed methods for prediction of structure and motion in membrane proteins and studied selected proteins including human copper transporter 1, the ATP7b copper ATPase, sodium/proton exchangers. He co-authored 132 peer-reviewed publications with 9592 citations (h-index=48, google scholar, October 18, 2015). In 2010 he co-authored the textbook “Introduction to Proteins: Structure, Function and Motion”, jointly with Dr. Amit Kessel.

Recent Publications

Research articles

PhD

2. N. Ben-Tal and N. Moiseyev, C. Leforestier, R. Kosloff. (1991) Positions, lifetimes and partial widths of metastable quasienergy states by solving the time-dependent complex-scaled Schrödinger equation. J. Chem. Phys. 94: 7311-7318.

7. N. Ben-Tal, N. Moseyev, R. Kosloff and C. Cerjan. (1993) Harmonic generation in ionizing systems by the time-dependent complex coordinate Floquet method. J. Phys. B. 26: 1445-1461.

8. N. Ben-Tal, N. Moiseyev and R. Kosloff. (1993) Harmonic generation in ionizing systems by the complex scaled adiabatic-switch method. Phys. Rev. A. 48: 2437-2442. PMID: 9909870.

Postdoc

11. R.D. Coalson, A.M. Walsh, A. Duncan and N. Ben-Tal. (1995) Statistical mechanics of a Coulomb gas with finite size particles: a lattice field theory approach. J. Chem. Phys. 102: 4584-4594.

12. N. Ben-Tal. (1995) Energetics of colloids: do oppositely charged particles necessarily attract each other? A letter in J. Phys. Chem. 99: 9642-9645.

14. N. Ben-Tal, A. Ben-Shaul, A. Nicholls and B. Honig. (1996) Free-energy determinants of a-helix insertion into lipid bilayers. Biophys. J. 70: 1803-1812. PMID: 8785340.

15. A. Ben-Shaul, N. Ben-Tal and B. Honig. (1996) Statistical thermodynamic analysis of peptides and protein insertion into lipid membranes. Biophys. J. 71: 130-138. PMID: 8804596.

16. N. Ben-Tal and B. Honig. (1996) Helix-helix interactions in lipid bilayers. Biophys. J. 71: 3046-3050. PMID: 8968575.

17. N. Ben-Tal, B. Honig, R.M. Peitzsch, G. Denisov and S. McLaughlin. (1996) Binding of small basic peptides to membranes containing acidic lipids: theoretical models and experimental results. Biophys. J. 71: 561-575. PMID: 8842196.

18. N. Ben-Tal, D. Sitkoff, I.A. Topol, A.-S. Yang, S.K. Burt and B. Honig. (1997) The free energy of amide hydrogen bond formation in vacuum, in water and in liquid alkane solutions. J. Phys. Chem. B. 101: 450-457.

Faculty

23. A. Kessel, D.S. Cafiso, and N. Ben-Tal. (2000) Continuum solvent model calculations of alamethicin-membrane interactions: thermodynamic aspects. Biophys. J. 78: 571-583. PMID: 10653772.

25. N. Ben-Tal, B. Honig, C.K. Bagdassarian, and A. Ben-Shaul. (2000) Association entropy in adsorption processes. Biophys. J. 79: 1180-1187. PMID: 10968982.

28. F. Glaser, D. M. Steinberg, I.A. Vakser and N. Ben-Tal. (2001) Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 43: 89-102. PMID: 11276079.

29. A. Armon, D. Graur and N. Ben-Tal. (2001) ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface-mapping of phylogenetic information. J. Mol. Biol. 307: 447-463. PMID: 11243830.

31. A. Kessel, N. Ben-Tal and S. May. (2001) Interactions of cholesterol with lipid bilayers: the preferred configuration and fluctuations. Biophys. J. 81: 643-658. PMID: 11463613.

36. T. Pupko, R.E. Bell, I. Mayrose, F. Glaser and N. Ben-Tal. (2002) Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18 Suppl. 1 S71-S77 (the ISMB issue). PMID: 12169533.

38. S.J. Fleishman and N. Ben-Tal. (2002) A novel scoring function for predicting the conformations of tightly packed pairs of transmembrane a-helices. J. Mol. Biol. 321: 363-378. PMID: 12144792.

39. S.J. Fleishman, J. Schlessinger and N. Ben-Tal. (2002) A putative molecular-activation switch in the transmembrane domain of erbB2. Proc. Natl. Acad. Sci. USA. 99: 15937-15940. PMID: 12461170.

40. F. Glaser, T. Pupko, I. Paz, R.E. Bell, D. Shental-Bechor, E. Martz and N. Ben-Tal. (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163-164. PMID: 12499312.

42. A. Kessel, D. Shental-Bechor, T. Haliloglu and N. Ben-Tal. (2003) Interactions of hydrophobic peptides with lipid bilayers: Monte Carlo simulations with M2d. Biophys. J. 85: 3431-3444. PMID: 14645040.

45. C. Berezin, F. Glaser, J. Rosenberg, I. Paz, T. Pupko, P. Fariselli, R. Casadio and N. Ben-Tal. (2004) ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics 20: 1322-1324. PMID: 14871869.

46. E. Haleva, N. Ben-Tal and H. Diamant. (2004). Increased concentration of polyvalent phospholipids in the adsorption domain of a charged protein. Biophys. J. 86: 2165-2178. PMID: 15041657.

49. S.J. Fleishman, O. Yifrach and N. Ben-Tal. (2004) An evolutionarily conserved network of amino acids mediates gating in voltage-dependent potassium channels. J. Mol. Biol. 340: 307-318. PMID: 15201054.

50. I. Mayrose, D. Graur, N. Ben-Tal and T. Pupko. (2004) Comparison of site-specific rate-inference methods for protein sequences: Empirical Bayesian methods are superior. Mol. Biol. Evol. 21: 1781-1791. PMID: 15201400.

53. Y. Artzy-Randrup, S.J. Fleishman, N. Ben-Tal and L. Stone. (2004) Technical Comment on "Network motifs: simple building blocks of complex networks" and "Superfamilies of evolved and designed networks", Science 305, 1107. PMID: 15326338.

54. S.J. Fleishman, S. Harrington, R.A. Friesner, B. Honig and N. Ben-Tal. (2004) An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data. Biophys. J. 87, 3448-3459. PMID: 15339802.

55. M. Landau, S.J. Fleishman, and N. Ben-Tal. (2004) A putative mechanism for down-regulation of the catalytic activity of the EGF receptor via direct contact between its kinase and C-terminal domains. Structure 12: 2265-2275. PMID: 15576039.

56. D. Shental-Bechor, S. Kirca, N. Ben-Tal and T. Haliloglu. (2005) Monte Carlo studies of folding, dynamic and stability in -helices. Biophys. J. 88:2391-402. PMID: 15653741.

60. G. Nimrod, F. Glaser, D. Steinberg, N. Ben-Tal, and T. Pupko (2005). In silico identification of functional regions in proteins. Bioinformatics. 21 Suppl.:i328-i337. PMID: 15961475.

64. S.J. Fleishman, S.E. Harrington, A. Enosh, D. Halperin, C.G. Tate and N. Ben-Tal. (2006). Quasi-symmetry in the cryo-EM structure of EmrE provides the key to modeling its transmembrane domain. J. Mol. Biol. 364: 54-67. PMID: 17005200. Ranked "must read" in Faculty of 1000 Biology.

68. M. Landau, K. Herz, E. Padan, and N. Ben-Tal. (2007). Model structure of the Na+/H+ exchanger 1 (NHE1): functional and clinical implications. J. Biol. Chem. 282: 37854–37863. PMID: 18031935. Ranked "must read" in Faculty of 1000 Biology.

75. O. Goldenberg, E. Erez, G. Nimrod and N. Ben-Tal (2009). The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. Nucl. Acids Res., doi:10.1093/nar/gkn822. PMID: 18971256.

85. M. Kalman and N. Ben-Tal (2010). Quality assessment of protein model-structures using evolutionary conservation. Bioinformatics 26: 1299–1307 PMID: 20385730.

87.  M. Schushan, Y. Barkan, T. Haliloglu and N. Ben-Tal (2010). Ca-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications. Proc. Natl. Acad. Sci. USA 107: 10908-10913. PMID: 20534491.

93.  D. Meroz, S.W. Yoon, M.F. Ducatez, T.P. Fabrizio, R.J. Webby, T. Hertz, and N. Ben-Tal (2011). Putative amino acid determinants of the emergence of the 2009 influenza A (H1N1) virus in the human population. Proc. Natl. Acad. Sci. USA: 108:13522-13527. PMID: 21808039. (Article was highlighted in the Cover Story department.).

98. J. Dalton, O. Kalid, M. Schushan, N. Ben-Tal*, and J. Villà-Freixa* (2012). New model of CFTR proposes active channel-like conformation. J. Chem. Inf. Model. 52: 1842-1853, PMID: 22747419 (Co-corresponding authors).

99. Y. Gofman, T. Haliloglu and N. Ben-Tal (2012). Monte Carlo simulations of peptide–membrane interactions with the MCPep web server. Nucl. Acids Res. 40: W358-W363.

100. Y. Gofman, S. Shats, B. Attali, T. Haliloglu and N. Ben-Tal (2012). How does KCNE1 regulate the Kv7.1 potassium channel? Model-structure, mutations and dynamics of the Kv7.1-KCNE1 complex. Structure 20:1343-1352.

101. Y. Gofman, T. Haliloglu and N. Ben-Tal (2012). The transmembrane helix tilt may be determined by the balance between precession entropy and lipid perturbation. J. Chem. Theory Comp. DOI: 10.1021/ct300128x.

102. M. Schushan, A. Bhattacharjee, N. Ben-Tal* and S. Lutsenko* (2012). A structural model of the copper ATPase ATP7B to facilitate analysis of Wilson disease-causing mutations and studies of the transport mechanism. Metallomics 4: 669-678. DOI: 10.1039/C2MT20025B (Co-corresponding authors).

106. S. Nepomnyachiy, N. Ben-Tal*, R. Kolodny* (2014). Global view of the protein universe. Proc. Natl. Acad. Sci. USA 111: 1691–11696 (Co-corresponding authors). (Article was highlighted in the TWIP department.).

107. S. Nepomnyachiy, N. Ben-Tal*, R. Kolodny* (2015). CyToStruct: Augmenting the network visualization of Cytoscape with the power of molecular viewers. Structure 23: 941-8. DOI: http://dx.doi.org/10.1016/j.str.2015.02.013 (Co-corresponding authors).

108. A. Narunsky, S. Nepomnyachiy, H. Ashkenazy, R. Kolodny, N. Ben-Tal (2015). ConTemplate suggests possible alternative conformations for a query protein of known structure. Structure 23: 1–9.

Review articles

R4.  S.J. Fleishman, V.M..Unger and N. Ben-Tal (2006). Transmembrane protein structures without x-rays.  Trends in Biochem. Sci. 31: 106-113. PMID: 16406532.
R5.  D. Shental-Bechor, S.J. Fleishman and N. Ben-Tal (2006). Has the code for protein translocation been broken? Trends in Biochem. Sci. 34: 192-196. PMID: 16530414. 
R6.  S.J. Fleishman and N. Ben-Tal (2006). Progress in structure prediction of alpha-helical membrane proteins. Curr. Op. Struct. Biol. 16: 496-504. PMID: 16822664. 
R7.  M. Landau and N. Ben-Tal (2008). Dynamic equilibrium between multiple active and inactive conformations explains regulation and oncogenic mutations in the ErbB receptors. BBA - REVIEWS ON CANCER 1785:12–31. 
 
Chapters in Books
C1.  A. Kessel and N. Ben-Tal (2002). Free energy determinants of peptide association with lipid bilayers. Current Topics in Membranes: Peptide-Lipid Interactions 52: 205-253 (Sydney Simon and Thomas McIntosh, Eds.), Academic Press, San Diego.
 
Books
B1. A. Kessel and N. Ben-Tal. Introduction to proteins: structure, function and motion. CRC press, Taylor and   Francis Group. (2010).
 
Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
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