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Coauthors
Jeffrey Becker Department of Microbiology, University of Tennessee, USA
2 protocols

Houjian Cai University of Georgia
2 protocols

Melinda Hauser Department of Microbiology, University of Tennessee, USA
2 protocols

Fred Naider
  • Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, USA
Contributions
  • 2 Author merit

Education

Ph.D in Polymer Chemistry, Polytechnic Institute, 1970

Current Position

Professor, Department of Chemistry, College of Staten Island, City University of New York, NY, USA

Publications

  1. Chill, J. H. and Naider, F. (2011). A solution NMR view of protein dynamics in the biological membrane. Curr Opin Struct Biol 21(5): 627-633.
  2. Cohen, L. S., Arshava, B., Neumoin, A., Becker, J. M., Guntert, P., Zerbe, O. and Naider, F. (2011). Comparative NMR analysis of an 80-residue G protein-coupled receptor fragment in two membrane mimetic environments. Biochim Biophys Acta 1808(11): 2674-2684.
  3. Schnur, E., Noah, E., Ayzenshtat, I., Sargsyan, H., Inui, T., Ding, F. X., Arshava, B., Sagi, Y., Kessler, N., Levy, R., Scherf, T., Naider, F. and Anglister, J. (2011). The conformation and orientation of a 27-residue CCR5 peptide in a ternary complex with HIV-1 gp120 and a CD4-mimic peptide. J Mol Biol 410(5): 778-797.
  4. Umanah, G. K., Huang, L. Y., Maccarone, J. M., Naider, F. and Becker, J. M. (2011). Changes in conformation at the cytoplasmic ends of the fifth and sixth transmembrane helices of a yeast G protein-coupled receptor in response to ligand binding. Biochemistry 50(32): 6841-6854.
  5. Mathew, E., Bajaj, A., Connelly, S. M., Sargsyan, H., Ding, F. X., Hajduczok, A. G., Naider, F. and Dumont, M. E. (2011). Differential interactions of fluorescent agonists and antagonists with the yeast G protein coupled receptor Ste2p. J Mol Biol 409(4): 513-528.
  6. Mullen, D. G., Kyro, K., Hauser, M., Gustavsson, M., Veglia, G., Becker, J. M., Naider, F. and Distefano, M. D. (2011). Synthesis of a-factor peptide from Saccharomyces cerevisiae and photoactive analogues via Fmoc solid phase methodology. Bioorg Med Chem 19(1): 490-497.
  7. Umanah, G. K., Huang, L., Ding, F. X., Arshava, B., Farley, A. R., Link, A. J., Naider, F. and Becker, J. M. (2010). Identification of residue-to-residue contact between a peptide ligand and its G protein-coupled receptor using periodate-mediated dihydroxyphenylalanine cross-linking and mass spectrometry. J Biol Chem 285(50): 39425-39436.
  8. Cohen, L. S., Becker, J. M. and Naider, F. (2010). Biosynthesis of peptide fragments of eukaryotic GPCRs in Escherichia coli by directing expression into inclusion bodies. J Pept Sci 16(5): 213-218.
  9. Tantry, S., Ding, F. X., Dumont, M., Becker, J. M. and Naider, F. (2010). Binding of fluorinated phenylalanine alpha-factor analogues to Ste2p: evidence for a cation-pi binding interaction between a peptide ligand and its cognate G protein-coupled receptor. Biochemistry 49(24): 5007-5015.
  10. Moseri, A., Tantry, S., Sagi, Y., Arshava, B., Naider, F. and Anglister, J. (2010). An optimally constrained V3 peptide is a better immunogen than its linear homolog or HIV-1 gp120. Virology 401(2): 293-304.
  11. Kim, H., Lee, B. K., Naider, F. and Becker, J. M. (2009). Identification of specific transmembrane residues and ligand-induced interface changes involved in homo-dimer formation of a yeast G protein-coupled receptor. Biochemistry 48(46): 10976-10987.
  12. Naider, F. and Anglister, J. (2009). Peptides in the treatment of AIDS. Curr Opin Struct Biol 19(4): 473-482.
  13. Mester, B., Manor, R., Mor, A., Arshava, B., Rosen, O., Ding, F. X., Naider, F. and Anglister, J. (2009). HIV-1 peptide vaccine candidates: selecting constrained V3 peptides with highest affinity to antibody 447-52D. Biochemistry 48(33): 7867-7877.
  14. Neumoin, A., Cohen, L. S., Arshava, B., Tantry, S., Becker, J. M., Zerbe, O. and Naider, F. (2009). Structure of a double transmembrane fragment of a G-protein-coupled receptor in micelles. Biophys J 96(8): 3187-3196.
  15. Mor, A., Segal, E., Mester, B., Arshava, B., Rosen, O., Ding, F. X., Russo, J., Dafni, A., Schvartzman, F., Scherf, T., Naider, F. and Anglister, J. (2009). Mimicking the structure of the V3 epitope bound to HIV-1 neutralizing antibodies. Biochemistry 48(15): 3288-3303.
  16. Umanah, G. K., Son, C., Ding, F., Naider, F. and Becker, J. M. (2009). Cross-linking of a DOPA-containing peptide ligand into its G protein-coupled receptor. Biochemistry 48(9): 2033-2044.
  17. Zou, C., Naider, F. and Zerbe, O. (2008). Biosynthesis and NMR-studies of a double transmembrane domain from the Y4 receptor, a human GPCR. J Biomol NMR 42(4): 257-269.
  18. Naider, F. (2007). Synthesis, biosynthesis, and characterization of transmembrane domains of a G protein-coupled receptor. Methods Mol Biol 386: 95-121.
  19. Noah, E., Biron, Z., Naider, F., Arshava, B. and Anglister, J. (2008). The membrane proximal external region of the HIV-1 envelope glycoprotein gp41 contributes to the stabilization of the six-helix bundle formed with a matching N' peptide. Biochemistry 47(26): 6782-6792.
  20. Huang, L. Y., Umanah, G., Hauser, M., Son, C., Arshava, B., Naider, F. and Becker, J. M. (2008). Unnatural amino acid replacement in a yeast G protein-coupled receptor in its native environment. Biochemistry 47(20): 5638-5648.
  21. Neumoin, A., Arshava, B., Becker, J., Zerbe, O. and Naider, F. (2007). NMR studies in dodecylphosphocholine of a fragment containing the seventh transmembrane helix of a G-protein-coupled receptor from Saccharomyces cerevisiae. Biophys J 93(2): 467-482.
  22. Hauser, M., Kauffman, S., Lee, B. K., Naider, F. and Becker, J. M. (2007). The first extracellular loop of the Saccharomyces cerevisiae G protein-coupled receptor Ste2p undergoes a conformational change upon ligand binding. J Biol Chem 282(14): 10387-10397.
  23. Kier, R. and Kinder, B. (1992). Insulinomas: MR imaging with STIR sequences and motion suppression. AJR Am J Roentgenol 158(2): 457-458.
  24. Balambika, R., Inui, T., Sargsyan, H., Arshava, B., Cohen, L. S., Ding, F.X., Becker, J.M. and Naider, F. (2007). Synthesis of a Double Transmembrane Domain Fragment of Ste2p by Native Chemical Ligation. Int J Pept Res Ther 13: 251-263.
  25. Cano-Sanchez, P., Severino, B., Sureshbabu, V. V., Russo, J., Inui, T., Ding, F. X., Arshava, B., Becker, J. and Naider, F. (2006). Effects of N- and C-terminal addition of oligolysines or native loop residues on the biophysical properties of transmembrane domain peptides from a G-protein coupled receptor. J Pept Sci 12(12): 808-822.
  26. Bajaj, A., Connelly, S. M., Gehret, A. U., Naider, F. and Dumont, M. E. (2007). Role of extracellular charged amino acids in the yeast alpha-factor receptor. Biochim Biophys Acta 1773(6): 707-717.
  27. Englander, J., Cohen, L., Arshava, B., Estephan, R., Becker, J. M. and Naider, F. (2006). Selective labeling of a membrane peptide with 15N-amino acids using cells grown in rich medium. Biopolymers 84(5): 508-518.
  28. Gehret, A. U., Bajaj, A., Naider, F. and Dumont, M. E. (2006). Oligomerization of the yeast alpha-factor receptor: implications for dominant negative effects of mutant receptors. J Biol Chem 281(30): 20698-20714.
  29. Lee, Y. H., Naider, F. and Becker, J. M. (2006). Interacting residues in an activated state of a G protein-coupled receptor. J Biol Chem 281(4): 2263-2272.
  30. Biron, Z., Khare, S., Quadt, S. R., Hayek, Y., Naider, F. and Anglister, J. (2005). The 2F5 epitope is helical in the HIV-1 entry inhibitor T-20. Biochemistry 44(41): 13602-13611.
  31. Estephan, R., Englander, J., Arshava, B., Samples, K. L., Becker, J. M. and Naider, F. (2005). Biosynthesis and NMR analysis of a 73-residue domain of a Saccharomyces cerevisiae G protein-coupled receptor. Biochemistry 44(35): 11795-11810.
  32. Naider, F., Khare, S., Arshava, B., Severino, B., Russo, J. and Becker, J. M. (2005). Synthetic peptides as probes for conformational preferences of domains of membrane receptors. Biopolymers 80(2-3): 199-213.
  33. Bajaj, A., Celic, A., Ding, F. X., Naider, F., Becker, J. M. and Dumont, M. E. (2004). A fluorescent alpha-factor analogue exhibits multiple steps on binding to its G protein coupled receptor in yeast. Biochemistry 43(42): 13564-13578.
  34. Son, C. D., Sargsyan, H., Naider, F. and Becker, J. M. (2004). Identification of ligand binding regions of the Saccharomyces cerevisiae alpha-factor pheromone receptor by photoaffinity cross-linking. Biochemistry 43(41): 13193-13203.
  35. Naider, F. and Becker, J. M. (2004). The alpha-factor mating pheromone of Saccharomyces cerevisiae: a model for studying the interaction of peptide hormones and G protein-coupled receptors. Peptides 25(9): 1441-1463.
  36. Naider, F., Ding, F. X., VerBerkmoes, N. C., Arshava, B. and Becker, J. M. (2003). Synthesis and biophysical characterization of a multidomain peptide from a Saccharomyces cerevisiae G protein-coupled receptor. J Biol Chem 278(52): 52537-52545.
  37. Celic, A., Martin, N. P., Son, C. D., Becker, J. M., Naider, F. and Dumont, M. E. (2003). Sequences in the intracellular loops of the yeast pheromone receptor Ste2p required for G protein activation. Biochemistry 42(10): 3004-3017.
  38. Lee, B. K., Lee, Y. H., Hauser, M., Son, C. D., Khare, S., Naider, F. and Becker, J. M. (2002). Tyr266 in the sixth transmembrane domain of the yeast alpha-factor receptor plays key roles in receptor activation and ligand specificity. Biochemistry 41(46): 13681-13689.
  39. Biron, Z., Khare, S., Samson, A. O., Hayek, Y., Naider, F. and Anglister, J. (2002). A monomeric 3(10)-helix is formed in water by a 13-residue peptide representing the neutralizing determinant of HIV-1 on gp41. Biochemistry 41(42): 12687-12696.
  40. Akal-Strader, A., Khare, S., Xu, D., Naider, F. and Becker, J. M. (2002). Residues in the first extracellular loop of a G protein-coupled receptor play a role in signal transduction. J Biol Chem 277(34): 30581-30590.
  41. Henry, L. K., Khare, S., Son, C., Babu, V. V., Naider, F. and Becker, J. M. (2002). Identification of a contact region between the tridecapeptide alpha-factor mating pheromone of Saccharomyces cerevisiae and its G protein-coupled receptor by photoaffinity labeling. Biochemistry 41(19): 6128-6139.
  42. Ding, F. X., Schreiber, D., VerBerkmoes, N. C., Becker, J. M. and Naider, F. (2002). The chain length dependence of helix formation of the second transmembrane domain of a G protein-coupled receptor of Saccharomyces cerevisiae. J Biol Chem 277(17): 14483-14492.
  43. Lee, B. K., Khare, S., Naider, F. and Becker, J. M. (2001). Identification of residues of the Saccharomyces cerevisiae G protein-coupled receptor contributing to alpha-factor pheromone binding. J Biol Chem 276(41): 37950-37961.
  44. Ding, F. X., Lee, B. K., Hauser, M., Davenport, L., Becker, J. M. and Naider, F. (2001). Probing the binding domain of the Saccharomyces cerevisiae alpha-mating factor receptor with rluorescent ligands. Biochemistry 40(4): 1102-1108.
  45. Sommers, C. M., Martin, N. P., Akal-Strader, A., Becker, J. M., Naider, F. and Dumont, M. E. (2000). A limited spectrum of mutations causes constitutive activation of the yeast alpha-factor receptor. Biochemistry 39(23): 6898-6909.
  46. Beckerman, J. L., Naider, F. and Ebbole, D. J. (1997). Inhibition of pathogenicity of the rice blast fungus by Saccharomyces cerevisiae alpha-factor. Science 276(5315): 1116-1119.
  47. Xue, C. B., Eriotou-Bargiota, E., Miller, D., Becker, J. M. and Naider, F. (1989). A covalently constrained congener of the Saccharomyces cerevisiae tridecapeptide mating pheromone is an agonist. J Biol Chem 264(32): 19161-19168.
  48. Goodman, M., Ribeiro, A. A. and Naider, F. (1978). Protected homo-oligopeptide structure: Model for preferred conformation of a linear methionine heptapeptide in chloroform. Proc Natl Acad Sci U S A 75(10): 4647-4651.
  49. Naider, F., Becker, J. M. and Katzir-Katchalski, E. (1974). Utilization of methionine-containing peptides and their derivatives by a methionine-requiring auxotroph of Saccharomyces cerevisiae. J Biol Chem 249(1): 9-20.
  50. Naider, F., Benedetti, E. and Goodman, M. (1971). Conformation of cyclolinopeptide a observed by circular dichroism. Proc Natl Acad Sci U S A 68(6): 1195-1198.
2 Protocols published
Uptake Assay for Radiolabeled Peptides in Yeast
Authors:  Melinda Hauser, Houjian Cai, Fred Naider and Jeffrey M. Becker, date: 11/20/2016, view: 1878, Q&A: 0
We describe an assay for measuring the uptake of radioactive peptides into the yeast Saccharomyces cerevisiae. The methods presented here can be adapted to measure a variety of substrates transported into any bacterial or fungal cell via ...
Halo Assay for Toxic Peptides and Other Compounds in Microorganisms
Authors:  Houjian Cai, Melinda Hauser, Fred Naider and Jeffrey M. Becker, date: 11/20/2016, view: 1946, Q&A: 0
We describe an assay for determination of toxicity in S. cerevisiae involving spotting of a toxic peptide on a lawn of yeast cells. This assay may be generalized to determine toxicity of a variety of compounds by substituting a putative ...