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Nir Ben-Tal

From EverybodyWiki Bios & Wiki



Nir Ben-Tal
Nir-Square-2118.jpg Nir-Square-2118.jpg
BornSeptember 15, 1961
🏳️ NationalityIsraeli
🎓 Alma materThe Hebrew University of Jerusalem, Technion- Israel Institute of Technology
💼 Occupation
Known forConSurf software and web-site (https://consurf.tau.ac.il/)
🏅 AwardsAlon Foundation Excellence Fellowship, The Wolf Foundation Award of Excellence, The TEVA Foundation Award of Excellence
🌐 Websitehttps://www.bentalab.com

Nir Ben-Tal is an Israeli computational structural biologists, who works in the George S. Wise Faculty of Life Sciences, Tel Aviv University. He holds the Abraham E. Kazan Chair in Bioinformatics, Tel Aviv University. His research interests are in molecular evolution, protein universe, membrane proteins, and drug discovery.

Education

Ben-Tal completed his undergraduate studies in Biology, Chemistry, and Physics at the Hebrew University of Jerusalem in 1988. He earned his D.Sc. in Chemistry at the Technion in 1993, studying quantum dynamics, quantum chaos and high harmonic generation,[1][2][3] [4][5][6][7][8] under the supervision of Nimrod Moiseyev. Between 1993 and 1997 he conducted postdoctoral research in Biophysical Chemistry at Columbia University, studying peptide-membrane interactions in Barry Honig's lab.[9][10][11] [12][13][14][15][16][17]

Career and research

In 1997 Ben-Tal joined the George S. Wise Faculty of Life Sciences, Tel Aviv University, as Senior Lecturer. He became Associate Professor in 2004, and Full Professor in 2007. In collaboration with his colleagues, he has been developing and using computational tools to study protein structure, function, dynamics, and evolution. Presently, his studies are mostly focused on a fundamental question in life sciences, namely, the way in which proteins have emerged and continue to evolve.

Main achievements

ConSurf: Ben-Tal and coworkers have been developing ConSurf (https://consurf.tau.ac.il/), an automated tool that accurately estimates the evolutionary rates of amino acid positions in proteins, color-codes the rates, and maps them on the protein structures.[18][19] [20][21][22][23][24][25][26][27][28]

Protein positions that mediate key functions such as ligand binding and catalysis tend to change particularly slowly during evolution. Thus, ConSurf helps detecting functional positions in proteins.

Membrane proteins: Ben-Tal's early studies in this field aimed to decipher the energetics of the interactions of peptides[10][11][29][30][31][32] [33][34][35][36][37][38] and cholesterol[39] with lipid bilayers, and principles of free diffusion of small drug molecules[40] and hormones[41] across the membrane. His original aim was to use energy guidelines to reveal structure and mechanism of action in membrane proteins.

Eventually, the complexity of the problem has led him to seek alternatives. Thus, Ben-Tal and his student Sarel Fleishman developed a methodology to predict stable conformations of transmembrane helix pairs held together by the packing of small residues within the context of GxxxG-like motifs.[42] They then used the method to predict two stable dimeric conformations of the transmembrane domain of the receptor tyrosine kinase (RTK) erbB2 (also denoted neu or HER2).[43] They associated the predicted conformations with the active and inactive states of the receptor, providing a molecular mechanism of activation. The mechanism has subsequently been supported by ample experimental data, including observation of the predicted conformations. The proposed mechanism still dominates current thinking of activation of ErbB and other RTK receptors.

Later, Fleishman and Ben-Tal developed a computational suite for modeling transmembrane protein structure by combining ConSurf estimates of the evolutionary rates of the amino acids and intermediate resolution structural data, e.g., from cryo-electron microscopy (cryo-EM)/[44] They used the methodology to provide a Cα-trace model of the transmembrane domain of the bacterial multidrug resistance transporter EmrE in complex with its TPP+ substrate. The monomers in this homodimeric model resided in opposite membrane-topologies with respect to each other, in conflict with two X-ray crystal structures that were available at the time.[45][46] The crystal structures (and three other structures from the same lab) were subsequently retracted,[47] and re-interpretation of the same data after error fixing showed a structure that was very similar to Ben-Tal's model.[48] Fleishman and Ben-Tal proposed a novel alternate-access mechanism for substrate translocation in EmrE based on the internal symmetry in the dimer, a proposition that has received support from many subsequent studies including solid-state nuclear magnetic resonance spectroscopy.[49] Ben-Tal and colleagues also used the same approach to study human copper transporter 1 (CTR1).[50]

More recently Ben-Tal and colleagues focus mostly on Cation/Proton Antiporters (CPAs), which play a crucial role in maintaining cells’ pH levels and salt concentrations.[51][52][53][54][55][56][57][58][59] Ben-Tal and coworkers conducted the most extensive evolutionary analysis of CPAs carried so far, encompassing ~6,500 representatives.[57] The analysis identified an eight-amino acids sequence motif, which not only distinguishes the two main groups of CPAs, but also seems to determine both their electrogenicity (i.e., whether they pass one or two proton per each cation) and cation selectivity (Na+ vs. K+). Furthermore, the analysis provided a new way to classify CPAs, and showed that contrary to previous suggestions, the distinction between the two main CPA groups only partially correlates with their electrogenicity. This allowed Ben-Tal and colleagues to identify specificity-determining residues in this family, and based on this, to modify CPAs function and also recover activity in an inactive CPA mutant.

Structures of inward-facing (IF) and outward-facing (OF) conformations of NapA from T. thermophilus (TtNapA) are available, but how they alternate from one to the other is unknown. Two different mechanisms have been suggested: the rocking bundle and the elevator mechanism. Structurally, CPAs comprise a core domain and a dimerization domain, which differ in their mutual interactions between the IF vs OF conformations. In the rocking bundle mechanism, the IF-to-OF conformational transition involves mainly rotation of the core domain, whereas in the elevator mechanism the domain moves vertically. Molecular dynamics simulations and metadynamics analysis of TtNapA, by Ben-Tal and coworkers, provided support to the rocking bundle mechanism.[58] They then turned to another CPA of known structure: E. coli NhaA (EcNhaA), where, starting from the known structure of the IF conformation, they predicted an OF conformation, and validated it using cross-linking experiments.

The outer membrane of Gram-negative bacteria feature β-barrel proteins, many of which form oligomers. Recently, Ben-Tal and colleagues discovered outer membrane proteins with multiple β-barrel domains within the same polypeptide chain.[60]

Protein space and the emergence of proteins on primordial Earth: To trace the evolutionary history of proteins, Ben-Tal and coworkers searched among large representative sets of proteins for segments that are similar in sequence (and often also in structure). They presented the results as a similarity network, using a methodology that they tailor-made for this study,[61] showing that many proteins share smaller segments with each other.[62] The reused segments, which they dubbed themes, appeared in different lengths and manifested very complex patterns.[63] For example, they observed the same amino acid both within a short theme shared by many proteins and within a longer theme shared only by few. Next, they searched for themes that appear in different sequence and structural contexts within proteins, calling these bridging themes.[64][65] They found many bridging themes, with an average length of about 40 residues. Interestingly, only about half of these also share a similar structure; the different environment may have induced a conformational change. Some of the bridging themes bind ligands, which attests to their functional importance. Another testimony to the evolutionary importance of these themes is the fact that some of the most ancient protein folds (e.g. Rossmann, P-loop, and TIM-barrel) were found to share them. The bridging themes may offer hints to the emergence of earliest protein families.

To further understand the evolutionary emergence of protein-ligand binding, Ben-Tal and colleagues studied how proteins recognize the adenine moieties of enzyme cofactors.[66] These cofactors (e.g. ATP, NAD, and FAD) have been present on Earth since the beginning of life. Ben-Tal and coworkers superimposed the structures of around 1,000 proteins based on their bound adenine-containing cofactors, and compared the patterns of hydrogen bonds that mediate adenine binding. The analysis showed that evolution has fully exploited adenine's functional groups. In agreement with previous observations, the team found that on the protein side, these interactions were mediated by linear sequence motifs. However, additional motifs, beyond previously recorded, have been found. They found some evolutionarily distinct proteins that nevertheless shared similar adenine-binding motifs. They also found that adenine recognition often involved specific protein themes, which contained the binding motifs. The analysis offers a possible scenario for the emergence of ligand binding, where primordial peptides with minimal binding activity have gradually evolved into contemporary proteins.

Books

Jointly with Amit Kessel, his former PhD student, Ben-Tal wrote the textbook “Introduction to proteins: Structure, function and dynamics”.[67] Course presentations and recorded lectures to go with the book are openly available.[68]

References

  1. ↑ Ben-Tal, Nir; Moiseyev, Nimrod; Kosloff, Ronnie (1993-09-01). "Harmonic generation in ionizing systems by the complex scaled adiabatic-switch method". Physical Review A. 48 (3): 2437–2442. Bibcode:1993PhRvA..48.2437B. doi:10.1103/physreva.48.2437. ISSN 1050-2947. PMID 9909870.
  2. ↑ Ben‐Tal, Nir; Moiseyev, Nimrod; Leforestier, Claude; Kosloff, Ronnie (1991-06-01). "Positions, lifetimes, and partial widths of metastable quasienergy states by solving the time‐dependent complex‐scaled Schrödinger equation". The Journal of Chemical Physics. 94 (11): 7311–7318. Bibcode:1991JChPh..94.7311B. doi:10.1063/1.460215. ISSN 0021-9606.
  3. ↑ Ben-Tal, N.; Moiseyev, N.; Korsch, H. J. (1992-08-01). "Quantum versus classical dynamics in a periodically driven anharmonic oscillator". Physical Review A. 46 (3): 1669–1672. Bibcode:1992PhRvA..46.1669B. doi:10.1103/PhysRevA.46.1669. PMID 9908291.
  4. ↑ Ben-Tal, N.; Moiseyev, N.; Fishman, S.; Bensch, F.; Korsch, H. J. (1993-03-01). "Weak localization in a chaotic periodically driven anharmonic oscillator". Physical Review E. 47 (3): 1646–1649. Bibcode:1993PhRvE..47.1646B. doi:10.1103/physreve.47.1646. ISSN 1063-651X. PMID 9960189.
  5. ↑ Ben‐Tal, Nir; Moiseyev, Nimrod; Kosloff, Ronnie (1993-06-15). "Creation of discrete quasienergy resonance states in strong electromagnetic fields". The Journal of Chemical Physics. 98 (12): 9610–9617. Bibcode:1993JChPh..98.9610B. doi:10.1063/1.464391. ISSN 0021-9606.
  6. ↑ Ben-Tal, N; Moiseyev, N; Kosloff, R; Cerjan, C (1993-04-28). "Harmonic generation in ionizing systems by the time-dependent complex coordinate Floquet method". Journal of Physics B: Atomic, Molecular and Optical Physics. 26 (8): 1445–1461. Bibcode:1993JPhB...26.1445B. doi:10.1088/0953-4075/26/8/012. ISSN 0953-4075.
  7. ↑ Ben-Tal, Nir; Moiseyev, Nimrod; Kosloff, Ronnie (1993-09-01). "Harmonic generation in ionizing systems by the complex scaled adiabatic-switch method". Physical Review A. 48 (3): 2437–2442. Bibcode:1993PhRvA..48.2437B. doi:10.1103/physreva.48.2437. ISSN 1050-2947. PMID 9909870.
  8. ↑ Ben-Tal, N; Moiseyev, N; Beswick, A (1993-09-28). "The effect of Hamiltonian symmetry on generation of odd and even harmonics". Journal of Physics B: Atomic, Molecular and Optical Physics. 26 (18): 3017–3024. Bibcode:1993JPhB...26.3017B. doi:10.1088/0953-4075/26/18/012. ISSN 0953-4075.
  9. ↑ Ben-Tal, N.; Ben-Shaul, A.; Nicholls, A.; Honig, B. (April 1996). "Free-energy determinants of alpha-helix insertion into lipid bilayers". Biophysical Journal. 70 (4): 1803–1812. Bibcode:1996BpJ....70.1803B. doi:10.1016/s0006-3495(96)79744-8. ISSN 0006-3495. PMC 1225150. PMID 8785340.
  10. ↑ 10.0 10.1 Ben-Shaul, A.; Ben-Tal, N.; Honig, B. (July 1996). "Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes". Biophysical Journal. 71 (1): 130–137. Bibcode:1996BpJ....71..130B. doi:10.1016/s0006-3495(96)79208-1. ISSN 0006-3495. PMC 1233464. PMID 8804596.
  11. ↑ 11.0 11.1 Ben-Tal, N.; Honig, B. (December 1996). "Helix-helix interactions in lipid bilayers". Biophysical Journal. 71 (6): 3046–3050. Bibcode:1996BpJ....71.3046B. doi:10.1016/s0006-3495(96)79498-5. ISSN 0006-3495. PMC 1233793. PMID 8968575.
  12. ↑ Ben-Tal, N.; Honig, B.; Peitzsch, R.M.; Denisov, G.; McLaughlin, S. (August 1996). "Binding of small basic peptides to membranes containing acidic lipids: theoretical models and experimental results". Biophysical Journal. 71 (2): 561–575. Bibcode:1996BpJ....71..561B. doi:10.1016/s0006-3495(96)79280-9. ISSN 0006-3495. PMC 1233514. PMID 8842196.
  13. ↑ Ben-Tal, N.; Honig, B.; Miller, C.; McLaughlin, S. (October 1997). "Electrostatic binding of proteins to membranes. Theoretical predictions and experimental results with charybdotoxin and phospholipid vesicles". Biophysical Journal. 73 (4): 1717–1727. Bibcode:1997BpJ....73.1717B. doi:10.1016/s0006-3495(97)78203-1. ISSN 0006-3495. PMC 1181073. PMID 9336168.
  14. ↑ Murray, Diana; Hermida-Matsumoto, Luz; Buser, Carolyn A.; Tsang, James; Sigal, Catherine T.; Ben-Tal, Nir; Honig, Barry; Resh, Marilyn D.; McLaughlin, Stuart (1998-02-01). "Electrostatics and the Membrane Association of Src: Theory and Experiment". Biochemistry. 37 (8): 2145–2159. doi:10.1021/bi972012b. ISSN 0006-2960. PMID 9485361.
  15. ↑ Murray, Diana; Arbuzova, Anna; Hangyás-Mihályné, Gyöngyi; Gambhir, Alok; Ben-Tal, Nir; Honig, Barry; McLaughlin, Stuart (December 1999). "Electrostatic Properties of Membranes Containing Acidic Lipids and Adsorbed Basic Peptides: Theory and Experiment". Biophysical Journal. 77 (6): 3176–3188. Bibcode:1999BpJ....77.3176M. doi:10.1016/s0006-3495(99)77148-1. ISSN 0006-3495. PMC 1300588. PMID 10585939.
  16. ↑ Murray, Diana; Ben-Tal, Nir; Honig, Barry; McLaughlin, Stuart (August 1997). "Electrostatic interaction of myristoylated proteins with membranes: simple physics, complicated biology". Structure. 5 (8): 985–989. doi:10.1016/s0969-2126(97)00251-7. ISSN 0969-2126. PMID 9309215.
  17. ↑ Ben-Tal, Nir; Honig, Barry; Bagdassarian, Carey K.; Ben-Shaul, Avinoam (September 2000). "Association Entropy in Adsorption Processes". Biophysical Journal. 79 (3): 1180–1187. Bibcode:2000BpJ....79.1180B. doi:10.1016/S0006-3495(00)76372-7. PMC 1301014. PMID 10968982.
  18. ↑ Armon, Aharon; Graur, Dan; Ben-Tal, Nir (March 2001). "ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information". Journal of Molecular Biology. 307 (1): 447–463. doi:10.1006/jmbi.2000.4474. ISSN 0022-2836. PMID 11243830.
  19. ↑ Pupko, T.; Bell, R. E.; Mayrose, I.; Glaser, F.; Ben-Tal, N. (2002-07-01). "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. doi:10.1093/bioinformatics/18.suppl_1.s71. ISSN 1367-4803. PMID 12169533.
  20. ↑ Armon, Aharon; Graur, Dan; Ben-Tal, Nir (March 2001). "ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information". Journal of Molecular Biology. 307 (1): 447–463. doi:10.1006/jmbi.2000.4474. ISSN 0022-2836. PMID 11243830.
  21. ↑ Berezin, C.; Glaser, F.; Rosenberg, J.; Paz, I.; Pupko, T.; Fariselli, P.; Casadio, R.; Ben-Tal, N. (2004-02-10). "ConSeq: the identification of functionally and structurally important residues in protein sequences". Bioinformatics. 20 (8): 1322–1324. doi:10.1093/bioinformatics/bth070. ISSN 1367-4803. PMID 14871869.
  22. ↑ Mayrose, I. (2004-05-21). "Comparison of Site-Specific Rate-Inference Methods for Protein Sequences: Empirical Bayesian Methods Are Superior". Molecular Biology and Evolution. 21 (9): 1781–1791. doi:10.1093/molbev/msh194. ISSN 0737-4038. PMID 15201400.
  23. ↑ Landau, M.; Mayrose, I.; Rosenberg, Y.; Glaser, F.; Martz, E.; Pupko, T.; Ben-Tal, N. (2005-07-01). "ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures". Nucleic Acids Research. 33 (Web Server): W299–W302. doi:10.1093/nar/gki370. ISSN 0305-1048. PMC 1160131. PMID 15980475.
  24. ↑ Goldenberg, Ofir; Erez, Elana; Nimrod, Guy; Ben-Tal, Nir (2008-10-29). "The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures". Nucleic Acids Research. 37 (suppl_1): D323–D327. doi:10.1093/nar/gkn822. ISSN 1362-4962. PMC 2686473. PMID 18971256.
  25. ↑ Ashkenazy, H.; Erez, E.; Martz, E.; Pupko, T.; Ben-Tal, N. (2010-05-16). "ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids". Nucleic Acids Research. 38 (Web Server): W529–W533. doi:10.1093/nar/gkq399. ISSN 0305-1048. PMC 2896094. PMID 20478830.
  26. ↑ Celniker, Gershon; Nimrod, Guy; Ashkenazy, Haim; Glaser, Fabian; Martz, Eric; Mayrose, Itay; Pupko, Tal; Ben-Tal, Nir (April 2013). "ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function". Israel Journal of Chemistry. 53 (3–4): 199–206. doi:10.1002/ijch.201200096. ISSN 0021-2148.
  27. ↑ Ashkenazy, Haim; Abadi, Shiran; Martz, Eric; Chay, Ofer; Mayrose, Itay; Pupko, Tal; Ben-Tal, Nir (2016-05-10). "ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules". Nucleic Acids Research. 44 (W1): W344–W350. doi:10.1093/nar/gkw408. ISSN 0305-1048. PMC 4987940. PMID 27166375.
  28. ↑ Ben Chorin, Adi; Masrati, Gal; Kessel, Amit; Narunsky, Aya; Sprinzak, Josef; Lahav, Shlomtzion; Ashkenazy, Haim; Ben‐Tal, Nir (2019-11-22). "ConSurf‐DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins". Protein Science. 29 (1): 258–267. doi:10.1002/pro.3779. ISSN 0961-8368. PMC 6933843 Check |pmc= value (help). PMID 31702846.
  29. ↑ Kessel, Amit; Cafiso, David S.; Ben-Tal, Nir (February 2000). "Continuum Solvent Model Calculations of Alamethicin-Membrane Interactions: Thermodynamic Aspects". Biophysical Journal. 78 (2): 571–583. Bibcode:2000BpJ....78..571K. doi:10.1016/s0006-3495(00)76617-3. ISSN 0006-3495. PMC 1300662. PMID 10653772.
  30. ↑ Kessel, Amit; Schulten, Klaus; Ben-Tal, Nir (November 2000). "Calculations Suggest a Pathway for the Transverse Diffusion of a Hydrophobic Peptide Across a Lipid Bilayer". Biophysical Journal. 79 (5): 2322–2330. Bibcode:2000BpJ....79.2322K. doi:10.1016/s0006-3495(00)76478-2. ISSN 0006-3495. PMC 1301120. PMID 11053112.
  31. ↑ Bechor, Dalit; Ben-Tal, Nir (February 2001). "Implicit Solvent Model Studies of the Interactions of the Influenza Hemagglutinin Fusion Peptide with Lipid Bilayers". Biophysical Journal. 80 (2): 643–655. Bibcode:2001BpJ....80..643B. doi:10.1016/s0006-3495(01)76045-6. ISSN 0006-3495. PMC 1301264. PMID 11159433.
  32. ↑ Bransburg-Zabary, Sharron; Kessel, Amit; Gutman, Menachem; Ben-Tal, Nir (2002-05-07). "Stability of an Ion Channel in Lipid Bilayers: Implicit Solvent Model Calculations with Gramicidin". Biochemistry. 41 (22): 6946–6954. doi:10.1021/bi0120704. ISSN 0006-2960. PMID 12033927.
  33. ↑ Kessel, Amit; Shental-Bechor, Dalit; Haliloglu, Turkan; Ben-Tal, Nir (December 2003). "Interactions of Hydrophobic Peptides with Lipid Bilayers: Monte Carlo Simulations with M2δ". Biophysical Journal. 85 (6): 3431–3444. Bibcode:2003BpJ....85.3431K. doi:10.1016/s0006-3495(03)74765-1. ISSN 0006-3495. PMC 1303652. PMID 14645040.
  34. ↑ Kessel, Amit; Haliloglu, Turkan; Ben-Tal, Nir (December 2003). "Interactions of the M2δ Segment of the Acetylcholine Receptor with Lipid Bilayers: A Continuum-Solvent Model Study". Biophysical Journal. 85 (6): 3687–3695. Bibcode:2003BpJ....85.3687K. doi:10.1016/s0006-3495(03)74785-7. ISSN 0006-3495. PMC 1303672. PMID 14645060.
  35. ↑ Kessel, Amit; Tieleman, D. Peter; Ben-Tal, Nir (2004-02-01). "Implicit solvent model estimates of the stability of model structures of the alamethicin channel". European Biophysics Journal. 33 (1): 16–28. doi:10.1007/s00249-003-0345-4. ISSN 0175-7571. PMID 13680212. Unknown parameter |s2cid= ignored (help)
  36. ↑ Shental-Bechor, Dalit; Haliloglu, Turkan; Ben-Tal, Nir (September 2007). "Interactions of Cationic-Hydrophobic Peptides with Lipid Bilayers: A Monte Carlo Simulation Method". Biophysical Journal. 93 (6): 1858–1871. Bibcode:2007BpJ....93.1858S. doi:10.1529/biophysj.106.103812. ISSN 0006-3495. PMC 1959530. PMID 17496025.
  37. ↑ Haleva, Emir; Ben-Tal, Nir; Diamant, Haim (April 2004). "Increased Concentration of Polyvalent Phospholipids in the Adsorption Domain of a Charged Protein". Biophysical Journal. 86 (4): 2165–2178. arXiv:physics/0308085. Bibcode:2004BpJ....86.2165H. doi:10.1016/s0006-3495(04)74276-9. ISSN 0006-3495. PMC 1304068. PMID 15041657.
  38. ↑ Kessel, Amit; Ben-Tal, Nir (2002), "Free energy determinants of peptide association with lipid bilayers", Peptide-Lipid Interactions, Current Topics in Membranes, Elsevier, 52, pp. 205–253, doi:10.1016/s1063-5823(02)52010-x, ISBN 9780121533526, retrieved 2022-04-25
  39. ↑ Kessel, Amit; Ben-Tal, Nir; May, Sylvio (August 2001). "Interactions of Cholesterol with Lipid Bilayers: The Preferred Configuration and Fluctuations". Biophysical Journal. 81 (2): 643–658. Bibcode:2001BpJ....81..643K. doi:10.1016/s0006-3495(01)75729-3. ISSN 0006-3495. PMC 1301541. PMID 11463613.
  40. ↑ Kessel, Amit; Musafia, Boaz; Ben-Tal, Nir (June 2001). "Continuum Solvent Model Studies of the Interactions of an Anticonvulsant Drug with a Lipid Bilayer". Biophysical Journal. 80 (6): 2536–2545. Bibcode:2001BpJ....80.2536K. doi:10.1016/s0006-3495(01)76225-x. ISSN 0006-3495. PMC 1301443. PMID 11371432.
  41. ↑ Oren, Idit; Fleishman, Sarel J.; Kessel, Amit; Ben-Tal, Nir (August 2004). "Free Diffusion of Steroid Hormones Across Biomembranes: A Simplex Search with Implicit Solvent Model Calculations". Biophysical Journal. 87 (2): 768–779. Bibcode:2004BpJ....87..768O. doi:10.1529/biophysj.103.035527. ISSN 0006-3495. PMC 1304487. PMID 15298886.
  42. ↑ Fleishman, Sarel J.; Ben-Tal, Nir (August 2002). "A Novel Scoring Function for Predicting the Conformations of Tightly Packed Pairs of Transmembrane α-Helices". Journal of Molecular Biology. 321 (2): 363–378. doi:10.1016/s0022-2836(02)00590-9. ISSN 0022-2836. PMID 12144792.
  43. ↑ Fleishman, Sarel J.; Schlessinger, Joseph; Ben-Tal, Nir (2002-12-02). "A putative molecular-activation switch in the transmembrane domain of erbB2". Proceedings of the National Academy of Sciences. 99 (25): 15937–15940. Bibcode:2002PNAS...9915937F. doi:10.1073/pnas.252640799. ISSN 0027-8424. PMC 138543. PMID 12461170.
  44. ↑ Fleishman, Sarel J.; Harrington, Susan; Friesner, Richard A.; Honig, Barry; Ben-Tal, Nir (November 2004). "An Automatic Method for Predicting Transmembrane Protein Structures Using Cryo-EM and Evolutionary Data". Biophysical Journal. 87 (5): 3448–3459. Bibcode:2004BpJ....87.3448F. doi:10.1529/biophysj.104.046417. ISSN 0006-3495. PMC 1304811. PMID 15339802.
  45. ↑ Ma, Che; Chang, Geoffrey (2004-02-17). "Structure of the multidrug resistance efflux transporter EmrE from Escherichia coli". Proceedings of the National Academy of Sciences. 101 (9): 2852–2857. Bibcode:2004PNAS..101.2852M. doi:10.1073/pnas.0400137101. ISSN 0027-8424. PMC 365709. PMID 14970332.
  46. ↑ Chang, G.; Chen, Y.J. (2007-12-04). "EmrE multidrug transporter in complex with P4P, P21 crystal form". dx.doi.org. doi:10.2210/pdb3b62/pdb. Retrieved 2022-04-25.
  47. ↑ Chang, Geoffrey; Roth, Christopher B.; Reyes, Christopher L.; Pornillos, Owen; Chen, Yen-Ju; Chen, Andy P. (2006-12-22). "Retraction". Science. 314 (5807): 1875. doi:10.1126/science.314.5807.1875b. ISSN 0036-8075. PMID 17185584. Unknown parameter |s2cid= ignored (help)
  48. ↑ Chen, Yen-Ju; Pornillos, Owen; Lieu, Samantha; Ma, Che; Chen, Andy P.; Chang, Geoffrey (2007-11-27). "X-ray structure of EmrE supports dual topology model". Proceedings of the National Academy of Sciences of the United States of America. 104 (48): 18999–19004. Bibcode:2007PNAS..10418999C. doi:10.1073/pnas.0709387104. ISSN 1091-6490. PMC 2141897. PMID 18024586.
  49. ↑ Shcherbakov, Alexander A.; Hisao, Grant; Mandala, Venkata S.; Thomas, Nathan E.; Soltani, Mohammad; Salter, E. A.; Davis, James H.; Henzler-Wildman, Katherine A.; Hong, Mei (2021-01-08). "Structure and dynamics of the drug-bound bacterial transporter EmrE in lipid bilayers". Nature Communications. 12 (1): 172. Bibcode:2021NatCo..12..172S. doi:10.1038/s41467-020-20468-7. ISSN 2041-1723. PMC 7794478 Check |pmc= value (help). PMID 33420032 Check |pmid= value (help).
  50. ↑ Schushan, Maya; Barkan, Yariv; Haliloglu, Turkan; Ben-Tal, Nir (June 2010). "Cα-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications". Proceedings of the National Academy of Sciences. 107 (24): 10908–10913. Bibcode:2010PNAS..10710908S. doi:10.1073/pnas.0914717107. ISSN 0027-8424. PMC 2890728. PMID 20534491.
  51. ↑ Donowitz, Mark (2007-11-15). "Faculty Opinions recommendation of Model structure of the Na+/H+ exchanger 1 (NHE1): functional and clinical implications". Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature. doi:10.3410/f.1094958.549927. Retrieved 2022-04-25.
  52. ↑ Schushan, Maya; Xiang, Minghui; Bogomiakov, Pavel; Padan, Etana; Rao, Rajini; Ben-Tal, Nir (March 2010). "Model-Guided Mutagenesis Drives Functional Studies of Human NHA2, Implicated in Hypertension". Journal of Molecular Biology. 396 (5): 1181–1196. doi:10.1016/j.jmb.2009.12.055. ISSN 0022-2836. PMC 2824056. PMID 20053353.
  53. ↑ Schushan, Maya; Landau, Meytal; Padan, Etana; Ben-Tal, Nir (May 2011). "Two Conflicting NHE1 Model Structures: Compatibility with Experimental Data and Implications for the Transport Mechanism". Journal of Biological Chemistry. 286 (21): le9. doi:10.1074/jbc.l110.159202. ISSN 0021-9258. PMC 3099738. PMID 21602285.
  54. ↑ Schushan, Maya; Rimon, Abraham; Haliloglu, Turkan; Forrest, Lucy R.; Padan, Etana; Ben-Tal, Nir (May 2012). "A Model-Structure of a Periplasm-facing State of the NhaA Antiporter Suggests the Molecular Underpinnings of pH-induced Conformational Changes". Journal of Biological Chemistry. 287 (22): 18249–18261. doi:10.1074/jbc.m111.336446. ISSN 0021-9258. PMC 3365733. PMID 22431724.
  55. ↑ Kondapalli, Kalyan C.; Hack, Anniesha; Schushan, Maya; Landau, Meytal; Ben-Tal, Nir; Rao, Rajini (2013-09-25). "Functional evaluation of autism-associated mutations in NHE9". Nature Communications. 4 (1): 2510. Bibcode:2013NatCo...4.2510K. doi:10.1038/ncomms3510. ISSN 2041-1723. PMC 3815575. PMID 24065030.
  56. ↑ Padan, Etana; Danieli, Tsafi; Keren, Yael; Alkoby, Dudu; Masrati, Gal; Haliloglu, Turkan; Ben-Tal, Nir; Rimon, Abraham (2015-10-13). "NhaA antiporter functions using 10 helices, and an additional 2 contribute to assembly/stability". Proceedings of the National Academy of Sciences of the United States of America. 112 (41): E5575–5582. Bibcode:2015PNAS..112E5575P. doi:10.1073/pnas.1510964112. ISSN 1091-6490. PMC 4611637. PMID 26417087.
  57. ↑ 57.0 57.1 Masrati, Gal; Dwivedi, Manish; Rimon, Abraham; Gluck-Margolin, Yael; Kessel, Amit; Ashkenazy, Haim; Mayrose, Itay; Padan, Etana; Ben-Tal, Nir (2018-10-11). "Broad phylogenetic analysis of cation/proton antiporters reveals transport determinants". Nature Communications. 9 (1): 4205. Bibcode:2018NatCo...9.4205M. doi:10.1038/s41467-018-06770-5. ISSN 2041-1723. PMC 6181914. PMID 30310075.
  58. ↑ 58.0 58.1 Masrati, Gal; Mondal, Ramakanta; Rimon, Abraham; Kessel, Amit; Padan, Etana; Lindahl, Erik; Ben-Ta, Nir (2020). "An angular motion of a conserved four-helix bundle facilitates alternating access transport in the TtNapA and EcNhaA transporters". Proceedings of the National Academy of Sciences. 117 (50): 31850–31860. doi:10.1073/pnas.2002710117. PMC 7749304 Check |pmc= value (help). PMID 33257549 Check |pmid= value (help).
  59. ↑ Papouskova, Klara; Moravcova, Michaela; Masrati, Gal; Ben‐Tal, Nir; Sychrova, Hana; Zimmermannova, Olga (2020-09-20). "C5 conserved region of hydrophilic C‐terminal part of Saccharomyces cerevisiae Nha1 antiporter determines its requirement of Erv14 COPII cargo receptor for plasma‐membrane targeting". Molecular Microbiology. 115 (1): 41–57. doi:10.1111/mmi.14595. ISSN 0950-382X. PMID 32864748 Check |pmid= value (help). Unknown parameter |s2cid= ignored (help)
  60. ↑ Solan, Ron; Pereira, Joana; Lupas, Andrei N.; Kolodny, Rachel; Ben-Tal, Nir (2021-02-17). "Gram-negative outer membrane proteins with multiple β-barrel domains". dx.doi.org. doi:10.1101/2021.02.17.431615. Retrieved 2022-04-25. Unknown parameter |s2cid= ignored (help)
  61. ↑ Nepomnyachiy, Sergey; Ben-Tal, Nir; Kolodny, Rachel (May 2015). "CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers". Structure. 23 (5): 941–948. doi:10.1016/j.str.2015.02.013. ISSN 0969-2126. PMID 25865247.
  62. ↑ Nepomnyachiy, Sergey; Ben-Tal, Nir; Kolodny, Rachel (2014-07-28). "Global view of the protein universe". Proceedings of the National Academy of Sciences. 111 (32): 11691–11696. Bibcode:2014PNAS..11111691N. doi:10.1073/pnas.1403395111. ISSN 0027-8424. PMC 4136566. PMID 25071170.
  63. ↑ Koehl, Patrice (2017-11-14). "Faculty Opinions recommendation of Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths". Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature. doi:10.3410/f.732110432.793538904. Retrieved 2022-04-25.
  64. ↑ Kolodny, Rachel; Nepomnyachiy, Sergey; Tawfik, Dan S.; Ben-Tal, Nir (2020-12-22). "Bridging themes: short protein segments found in different architectures". dx.doi.org. doi:10.1101/2020.12.22.424031. Retrieved 2022-04-25. Unknown parameter |s2cid= ignored (help)
  65. ↑ Longo, Liam M; Jabłońska, Jagoda; Vyas, Pratik; Kanade, Manil; Kolodny, Rachel; Ben-Tal, Nir; Tawfik, Dan S (2020-12-09). "On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment". eLife. 9: e64415. doi:10.7554/eLife.64415. ISSN 2050-084X. PMC 7758060 Check |pmc= value (help). PMID 33295875 Check |pmid= value (help).
  66. ↑ Yamamoto, O. (1980). "Adenine-N-oxide produced from adenine with gamma-rays and its binding to SH protein". Journal of Radiation Research. 21 (3/4): 239–247. Bibcode:1980JRadR..21..239.. doi:10.1269/jrr.21.239. ISSN 0449-3060. PMID 7288703.
  67. ↑ "Introduction to Proteins: Structure, Function, and Motion, Second Edition". Routledge & CRC Press. Retrieved 2022-04-25.
  68. ↑ "Protein Book". Mysite. Retrieved 2022-04-25.


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