Menu

tRNA Probes

Selected  References

1.    Synthesis of Nε-modified Lys-tRNAs
2.    Synthesis of sulfhydryl-modified Cys-tRNAs
3.    Chemically reactive aa-tRNAs
4.    Photoreactive aa-tRNAs
5.    Fluorescent aa-tRNAs
6.    FRET-detected nascent chain folding
7.    s4U8-modified aa-tRNAs
8.    Reviews/Chapters that include results of modified aa-tRNA studies

9.    SRP, ER microsomes, wheat germ extract, etc.

1.  Synthesis of Nε-modified Lys-tRNAs :

Johnson, A. E. (1973) “Chemically-modified Aminoacyl-tRNA as a Probe of Ribosome Structure: the Synthesis and in vitro Activity of ε-N-Acetyl-Lys-tRNA,” Ph.D. Dissertation, University of Oregon.

Johnson, A.E. (1974) "A Biologically Active Aminoacyl-tRNA Analaogue: Nε-Acetyl-Lys-tRNA," Federation Proceedings 33, 1421.

Johnson, A. E., Woodward, W. R., Herbert, E., and Menninger, J. R. (1976) “Nε-Acetyllysine Transfer Ribonucleic Acid: A Biologically Active Analogue of Aminoacyl Transfer Ribonucleic Acids,” Biochemistry 15, 569-575.

Johnson, A. E., Miller, D. L., and Cantor, C. R. (1978) “Functional Covalent Complex Between Elongation Factor Tu and an Analog of Lysyl-tRNA,” Proceedings of the National Academy of Sciences USA 75, 3075-3079.

Johnson, A. E., and Adkins, H. J. (1984) “Glycerol, Sucrose, and Other Diol-Containing Reagents Are Not Inert Components in In Vitro Incubations Containing Aminoacyl-tRNA,” Analytical Biochemistry 137, 351-359.

Shore, S.K., and Johnson, A.E. (1986) "A Fluorescent Probe Capable of Incorporation into Nascent Polypeptide Chains," Federation Proceedings 45, 1566.

Krieg, U. C., Walter, P., and Johnson, A. E. (1986) “Photocrosslinking of the Signal Sequence of Nascent Preprolactin to the 54-kilodalton Polypeptide of the Signal Recognition Particle,” Proceedings of the National Academy of Sciences USA 83, 8604-8608.

Shore, S.K., and Johnson, A.E. (1988) "Accessibility of aa-tRNA and Nascent Chain During Protein Synthesis," FASEB Journal 2, A1045.

Crowley, K. S., Reinhart, G. D., and Johnson, A. E. (1993) “The Signal Sequence Moves through a Ribosomal Tunnel into a Noncytoplasmic Aqueous Environment at the ER Membrane Early in Translocation,” Cell 73, 1101-1115.


2.  Synthesis of sulfhydryl-modified Cys-tRNAs :

Alder, N. N., Jensen, R. E., and Johnson, A. E. (2008) “Fluorescence Mapping of Mitochondrial TIM23 Complex Reveals a Water-Facing, Substrate-Interacting Helix Surface,” Cell 134, 439-450.  (see Supplemental Material)

Gubbens, J., Kim, S. J., Yang, Z., Johnson, A. E., and Skach, W. R. (2010) "Efficient In Vitro Incorporation of Non-Natural Amino Acids into Protein Using tRNACys-derived Opal, Ochre, and Amber Suppressor tRNAs," RNA 16, 1660-1672.


3.  Chemically reactive aa-tRNAs :

Johnson, A. E., Miller, D. L., and Cantor, C. R. (1978) “Functional Covalent Complex Between Elongation Factor Tu and an Analog of Lysyl-tRNA,” Proceedings of the National Academy of Sciences USA 75, 3075-3079.

Johnson, A. E., and Cantor, C. R. (1980) “Elongation Factor-Dependent Affinity Labeling of Escherichia coli Ribosomes,” Journal of Molecular Biology 138,  273-297.

Johnson, A. E., and Slobin, L. I. (1980) “Affinity Labeling of Eukaryotic Elongation Factors Using Nε-Bromoacetyl-Lys-tRNA,” Nucleic Acids Research 8, 4185-4200.

Guerrier-Takada, C., Johnson, A. E., Miller, D. L., and Cole, P. E. (1981) “Transfer RNA Crosslinked to the Elongation Factor Tu Subunit of Qβ Replicase Does Not Inhibit Qβ RNA Replication,” Journal of Biological Chemistry 256, 5840-5844.

Duffy, L. K., Gerber, L., Johnson, A. E., and Miller, D. L. (1981) “Identification of a Histidine Residue near the Aminoacyl Transfer Ribonucleic Acid Binding Site of Elongation Factor Tu,” Biochemistry 20, 4663-4666.

Kinzy, T. G., Freeman, J. P., Johnson, A. E., and Merrick, W. C. (1992) “A Model for the Aminoacyl-tRNA Binding Site of Eukaryotic Elongation Factor 1α,” Journal of Biological Chemistry 267, 1623-1632.


4.  Photoreactive aa-tRNAs :

Krieg, U. C., Walter, P., and Johnson, A. E. (1986) “Photocrosslinking of the Signal Sequence of Nascent Preprolactin to the 54-kilodalton Polypeptide of the Signal Recognition Particle,” Proceedings of the National Academy of Sciences USA 83, 8604-8608.

Krieg, U. C., Johnson, A. E., and Walter, P. (1989) “Protein Translocation Across the Endoplasmic Reticulum Membrane: Identification by Photocrosslinking of a 39 kDa Integral Membrane Glycoprotein as Part of a Putative Translocation Tunnel,” Journal of Cell Biology 109, 2033-2043.

Thrift, R. N., Andrews, D. W., Walter, P., and Johnson, A. E. (1991) “A Nascent Membrane Protein Is Located Adjacent to ER Membrane Proteins Throughout Its Integration and Translation,” Journal of Cell Biology 112, 809-821.

Do, H., Falcone, D., Lin, J., Andrews, D. W., and Johnson, A. E. (1996) “The Cotranslational Integration of Membrane Proteins into the Phospholipid Bilayer Is a Multistep Process,” Cell 85, 369-378.

Falcone, D., Do, H., Johnson, A. E., and Andrews, D. W. (1999) “Negatively-charged Residues in the IgM Stop-transfer Effector Sequence Regulate Transmembrane Polypeptide Integration,”  Journal of Biological Chemistry 274, 33661-33670.

Vidugiriene, J., Vainauskas, S., Johnson, A. E., and Menon, A. K. (2001) “Endoplasmic Reticulum Proteins Involved in Glycosylphosphatidylinositol Anchor Attachment: Photocrosslinking Studies in a Cell-Free System,” European Journal of Biochemistry 268, 2290-2300.

Nilsson, I., Ohvo-Rekilä, H., Slotte, J. P., Johnson, A. E., and von Heijne, G. (2001) “Inhibition of Protein Translocation across the ER Membrane by Sterols,” Journal of Biological Chemistry 276, 41748-41754.

Nilsson, I., Kelleher, D. J., Miao, Y., Shao, Y., Kreibich, G., Gilmore, R., von Heijne, G., and Johnson, A. E. (2003) “Photocrosslinking of Nascent Chains to the STT3 Subunit of the Oligosaccharyltransferase Complex,” Journal of Cell Biology 161, 715-725.

McCormick, P. J., Miao, Y., Shao, Y., Lin, J., and Johnson, A. E. (2003) “Cotranslational Protein Integration into the ER Membrane Is Mediated by the Binding of Nascent Chains to Translocon Proteins” Molecular Cell 12, 329-341.

Woolhead, C. A., McCormick, P. J., and Johnson A. E. (2004) “Nascent Membrane and Secretory Proteins Differ in FRET-Detected Folding Far Inside the Ribosome and in Their Exposure to Ribosomal Proteins,” Cell 116, 725-736.

Saksena, S., Shao, Y., Braunagel, S., Summers, M. D., and Johnson, A. E. (2004) "Cotranslational Integration and Initial Sorting at the Endoplasmic Reticulum Translocon of Proteins Destined for the Inner Nuclear Membrane," Proceedings of the National Academy of Sciences (USA) 101, 12537-12542.

Zhang, Z., Lapolla, S. M., Annis, M. G., Truscott, M., Roberts, G. J., Miao, Y., Shao, Y., Tan, C., Peng, J., Johnson, A. E., Zhang, X. C., Andrews, D. W., and Lin, J. (2004) “Bcl-2 Homodimerization Involves Two Distinct Binding Surfaces, a Topographic Arrangement that Provides an Effective Mechanism for Bcl-2 to Capture Activated Bax,” Journal of Biological Chemistry 279, 43920-43928.

Saurí, A., Saksena, S., Salgado, J., Johnson, A. E., and Mingarro, I. (2005) "Double-Spanning Plant Viral Movement Protein Integration into the ER Membrane Is SRP-Dependent, Translocon-Mediated, and Concerted" Journal of Biological Chemistry 280, 25907-25912.

Etchells, S. A., Meyer, A. S., Yam, A. Y., Roobol, A., Miao, Y., Shao, Y., Carden, M. J., Skach, W. R., Frydman, J., and Johnson, A. E. (2005) "The Cotranslational Contacts between Ribosome-Bound Nascent Polypeptides and the Subunits of the Hetero-Oligomeric Chaperonin TRiC Probed by Photocrosslinking, " Journal of Biological Chemistry 280, 28118-28126.

Karamyshev, A. L., and Johnson, A. E. (2005) "Selective SecA Association with Signal Sequences in Ribosome-Bound Nascent Chains: A Potential Role for SecA in Ribosome Targeting to the Bacterial Membrane,” Journal of Biological Chemistry 280, 37930-37940.

Sadlish, H., Pitonzo, D., Johnson, A. E., and Skach, W. R. (2005) “Sequential Triage of Transmembrane Segments by Sec61α During Biogenesis of a Native Multispanning Membrane Protein,” Nature Structural & Molecular Biology 12, 870-878.

Karamyshev, A. L., Kelleher, D. J., Gilmore, R., Johnson, A. E., von Heijne, G., and Nilsson, I. (2005) "Mapping the Interaction of the STT3 Subunit of the Oligosaccharyltransferase Complex with Nascent Polypeptide Chains," Journal of Biological Chemistry 280, 40489-40493.

Davis, A. J., Alder, N. N., Jensen, R. E., and Johnson, A. E. (2007) "The Tim9p/10p and Tim8p/13p Complexes Bind to Specific Sites on Tim23p during Mitochondrial Protein Import," Molecular Biology of the Cell 18, 475-486.

Saurí, A., McCormick, P. J., Johnson, A. E., and Mingarro, I. (2007) “Sec61α and TRAM Are Sequentially Adjacent to a Nascent Viral Membrane Protein during Its ER Integration,” Journal of Molecular Biology 366, 366-374.

Daniel, C., Conti, B., Johnson, A. E., and Skach, W. R. (2008) “Control of Translocation through the Sec61 Translocon by Nascent Polypeptide Structure within the Ribosome,” Journal of Biological Chemistry 283, 20864-20873.

Pitonzo, D., Yang, Z., Rusterholtz, K., Johnson, A. E., and Skach, W. R. (2009) “Sequence-Specific Retention and Regulated Integration of a Nascent Membrane Protein by the Endoplasmic Reticulum Sec61 Translocon,” Molecular Biology of the Cell 20, 685-698.

Berndt, U., Oellerer, S., Zhang, Y., Johnson, A. E., and Rospert, S. (2009) “A Signal-Anchor Sequence Stimulates Signal Recognition Particle Binding to Ribosomes from Inside the Exit Tunnel,” Proceedings of the National Academy of Sciences (USA) 106, 1398-1403.

Saurí, A., Tamborero, S., Martínez-Gil, L., Johnson, A. E., and Mingarro, I. (2009) “Viral Membrane Protein Topology Is Dictated by Multiple Determinants in Its Sequence,” Journal of Molecular Biology 387, 113-128.

Martínez-Gil, L., Johnson, A. E., and Mingarro, I. (2010) "Membrane Insertion and Biogenesis of the Turnip Crinkle Virus p9 Movement Protein," Journal of Virology 84, 5520-5527.

Zhang, Z., Zhu, W., Lapolla, S. M., Miao, Y., Shao, Y., Falcone, M., Johnson, A. E., Zhang, X. C., Andrews, D. W., and Lin, J. (2010) "Bax Forms an Oligomer by a Sequential Mechanism Utilizing Separate, Yet Interdependent Surfaces," Journal of Biological Chemistry 285, 17614-17627.

Tamborero, S., Vilar, M., Martínez-Gil, L., Johnson, A. E., and Mingarro, I. (2011) "Membrane Insertion and Topology of the TRanslocating Chain-Associating Membrane (TRAM) Protein," Journal of Molecular Biology 406, 571-582.

Cain, P., Holdermann, I., Sinning, I., Johnson, A. E., and Robinson, C. (2011) "Binding of Chloroplast Signal Recognition Particle to a Thlyakoid Membrane Protein Substrate in Aqueous Solution and Delineation of the cpSRP43-Substrate Interaction Domain," Biochemical Journal 437, 149-155.

Devaraneni, P., Conti, B., Matsumura, Y., Yang, Z., Johnson, A. E., and Skach, W. R. (2011) "Stepwise Insertion and Inversion of a Type II Signal Anchor Occurs in the Ribosome-Sec61 Complex," Cell 146, 134-147.

Lin, P.-J., Jongsma, C. G., Pool, M. R., and Johnson, A. E. (2011) "Polytopic Membrane Protein Folding at L17 in the Ribosome Tunnel Initiates, Cyclical Changes at the Translocon," Journal of Cell Biology 195, 55-70.

Wu, C., Wei, J., Lin, P.-J., Tu, L., Deutsch, C., Johnson, A. E., and Sachs, M. S. (2012) "Arginine Changes the Conformation of the Arginine Attenuator Peptide Relative to the Ribosome Tunnel," Journal of Molecular Biology 418, 518-533.Selected References

Hou, B., Lin, P.-J., and Johnson, A.E. (2012) "Membrane Protein TM Segments Are Retained at the Translocon during Integration Until the Nascent Chain Cues FRET-Detected Release into the Lipid Phase," Molecular Cell 48, 398-408.nski

Gebert, M., Schrempp, S. G., Mehnert, C. S., Heißwolf, A. K., Oeljeklaus, S., Ieva, R., Bohnert, M., von der Malsburg, K., Wiese, S., Kleinschroth, T., Hunte, C., Meyer, H. E., Haferkamp, I., Guiard, B., Warscheid, B., Pfanner, N., and van der Laan, M. (2012) "Mgr2 Promotes Coupling of the Mitochondrial Presequence Translocase to Partner Complexes," Journal of Cell Biology 197, 595-604.

Ieva, R., Schrempp, S. G., Opalinski, L., Wollweber, F., Hoß, P., Heißwolf, A. K., Gebert, M., Zhang, Y., Guiard, B., Rospert, S., Becker, T., Chacinska, A., Pfanner, N., and van der Laan, M. (2014) "Mgr2 Functions as Lateral Gatekeeper for Preprotein Sorting in the Mitochondrial Inner Membrane," Molecular Cell 56, 641-652.

Karamyshev, A. L., Patrick, A. E., Karamysheva, Z. N, Griesemer, D. S., Hudson, H., Tjon-Kon-Sang, S., Nilsson, I., Otto, H, Liu, Q., Rospert, S., von Heijne, G., Johnson, A. E., and Thomas, P. J. (2014) "Inefficient SRP Interaction with a Nascent Chain Triggers a mRNA Quality Control Pathway," Cell 156, 146-157.

Nilsson, I., Lara, P., Hessa, T., Johnson, A. E., von Heijne, G., and Karamyshev, A. L. (2015) "The Code for Directing Proteins for Translocation across the ER Membrane: SRP Co-translationally Recognizes Specific Features of a Signal Sequence," Journal of Molecular Biology 427, 1191-1201.

Mayerhofer, P. U., Bañó-Polo, M., Mingarro, I., and Johnson, A. E. (2016) "Human Peroxin PEX3 Is Co-translationally Integrated into the ER and Exits the ER in Budding Vesicles," Traffic 17, 117-130.


5.  Fluorescent aa-tRNAs :

Crowley, K. S., Reinhart, G. D., and Johnson, A. E. (1993) “The Signal Sequence Moves through a Ribosomal Tunnel into a Noncytoplasmic Aqueous Environment at the ER Membrane Early in Translocation,” Cell 73, 1101-1115.

Crowley, K. S., Liao, S., Worrell, V. E., Reinhart, G. D., and Johnson, A. E. (1994) “Secretory Proteins Move through the Endoplasmic Reticulum Membrane via an Aqueous, Gated Pore,” Cell 78, 461-471.

Hamman, B. D., Chen, J.-C., Johnson, E. E., and Johnson, A. E. (1997) “The Aqueous Pore through the Translocon Has a Diameter of 40-60 Å during Co-translational Protein Translocation at the ER Membrane,” Cell 89, 535-544.

Liao, S., Lin, J., Do, H., and Johnson, A. E. (1997) “Both Lumenal and Cytosolic Gating of the Aqueous ER Translocon Pore Are Regulated from Inside the Ribosome during Membrane Protein Integration,” Cell 90, 31-41.

Hamman, B. D., Hendershot, L. M., and Johnson, A. E. (1998) “BiP Maintains the Permeability Barrier of the ER Membrane by Sealing the Lumenal End of the Translocon Pore Before and Early in Translocation,” Cell 92, 747-758.

Haigh, N. G., and Johnson, A. E. (2002) “A New Role for BiP: Closing the Aqueous Translocon Pore during Protein Integration into the ER Membrane,” Journal of Cell Biology 156, 261-270.

Flanagan, J. J., Chen, J.-C., Miao, Y., Shao, Y., Lin, J., Bock, P. E., and Johnson, A. E. (2003) “SRP Binds to Ribosome-bound Signal Sequences with Fluorescence-detected Subnanomolar Affinity that Does Not Diminish as the Nascent Chain Lengthens,” Journal of Biological Chemistry 278, 18628-18637.

Alder, N. N., Shen, Y., Brodsky, J. L., Hendershot, L. M., and Johnson, A. E. (2005) "The Molecular Mechanisms Underlying BiP-Mediated Gating of the Sec61 Translocon of the Endoplasmic Reticulum," Journal of Cell Biology 168, 389-399.

Woolhead, C. A., Johnson, A. E., and Bernstein, H. D. (2006) “Translation Arrest Requires Two-Way Communication between a Nascent Polypeptide and the Ribosome,” Molecular Cell 22, 587-598.

Alder, N. N., Jensen, R. E., and Johnson, A. E. (2008) “Fluorescence Mapping of Mitochondrial TIM23 Complex Reveals a Water-Facing, Substrate-Interacting Helix Surface,” Cell 134, 439-450.

Gubbens, J., Kim, S. J., Yang, Z., Johnson, A. E., and Skach, W. R. (2010) "Efficient In Vitro Incorporation of Non-Natural Amino Acids into Protein Using tRNACys-derived Opal, Ochre, and Amber Suppressor tRNAs," RNA 16, 1660-1672.

Khushoo, A., Yang, Z., Johnson, A. E., and Skach, W. R. (2011) "Ligand-Driven Vectorial Folding of Ribosome-Bound Human CFTR NBD1," Molecular Cell 41, 682-692.

Devaraneni, P., Conti, B., Matsumura, Y., Yang, Z., Johnson, A. E., and Skach, W. R. (2011) "Stepwise Insertion and Inversion of a Type II Signal Anchor Occurs in the Ribosome-Sec61 Complex," Cell 146, 134-147.

Lin, P.-J., Jongsma, C. G., Liao, S., and Johnson, A. E. (2011) "Transmembrane Segments of Nascent Polytopic Membrane Proteins Control Cytosol/ER Targeting during Membrane Integration," Journal of Cell Biology 195, 41-54.

Lin, P.-J., Jongsma, C. G., Pool, M. R., and Johnson, A. E. (2011) "Polytopic Membrane Protein Folding at L17 in the Ribosome Tunnel Initiates, Cyclical Changes at the Translocon," Journal of Cell Biology 195, 55-70.

Wu, C., Wei, J., Lin, P.-J., Tu, L., Deutsch, C., Johnson, A. E., and Sachs, M. S. (2012) "Arginine Changes the Conformation of the Arginine Attenuator Peptide Relative to the Ribosome Tunnel," Journal of Molecular Biology 418, 518-533.

Hou, B., Lin, P.-J., and Johnson, A.E. (2012) "Membrane Protein TM Segments Are Retained at the Translocon during Integration Until the Nascent Chain Cues FRET-Detected Release into the Lipid Phase," Molecular Cell 48, 398-408.

Malhotra, K., Sathappa, M., Landin, J. S., Johnson, A. E., and Alder, N. N. (2013) "Structural Changes in the Mitochondrial Tim23 Channel Are Coupled to the Protonmotive Force," Nature Structural and Molecular Biology 20, 965-972.

Mayerhofer, P. U., Bañó-Polo, M., Mingarro, I., and Johnson, A. E. (2016) "Human Peroxin PEX3 Is Co-translationally Integrated into the ER and Exits the ER in Budding Vesicles," Traffic 17, 117-130.

 

6.  FRET-detected nascent chain folding :

Woolhead, C. A., McCormick, P. J., and Johnson A. E. (2004) “Nascent Membrane and Secretory Proteins Differ in FRET-Detected Folding Far Inside the Ribosome and in Their Exposure to Ribosomal Proteins,” Cell 116, 725-736.

Woolhead, C. A., Johnson, A. E., and Bernstein, H. D. (2006) “Translation Arrest Requires Two-Way Communication between a Nascent Polypeptide and the Ribosome,” Molecular Cell 22, 587-598.

Khushoo, A., Yang, Z., Johnson, A. E., and Skach, W. R. (2011) "Ligand-Driven Vectorial Folding of Ribosome-Bound Human CFTR NBD1," Molecular Cell 41, 682-692.

Lin, P.-J., Jongsma, C. G., Pool, M. R., and Johnson, A. E. (2011) "Polytopic Membrane Protein Folding at L17 in the Ribosome Tunnel Initiates, Cyclical Changes at the Translocon," Journal of Cell Biology 195, 55-70.

Hou, B., Lin, P.-J., and Johnson, A.E. (2012) "Membrane Protein TM Segments Are Retained at the Translocon during Integration Until the Nascent Chain Cues FRET-Detected Release into the Lipid Phase," Molecular Cell 48, 398-408.

Robinson, P. J., Findlay, J. E., and Woolhead, C. A. (2012) "Compaction of a Prokaryotic Signal-Anchor Transmembrane Domain Begins within the Ribosome Tunnel and Is Stabilized by SRP during Targeting," Journal of Molecular Biology 423, 600-612.

 

7.  s4U8-modified aa-tRNAs :

Johnson, A. E., Adkins, H. J., Matthews, E. A., and Cantor, C. R. (1982) “The Distance Moved by Transfer RNA During Translocation from the A Site to the P Site on the Ribosome,” Journal of Molecular Biology 156, 113-140.

Adkins, H. J., Miller, D. L., and Johnson, A. E. (1983) “Changes in Aminoacyl Transfer Ribonucleic Acid Conformation Upon Association with Elongation Factor Tu•Guanosine 5’-Triphosphate. Fluorescence Studies of Ternary Complex Conformation and Topology,” Biochemistry 22, 1208-1217.

Abrahamson, J. K., Laue, T. M., Miller, D. L., and Johnson, A. E. (1985) “Direct Determination of the Association Constant Between Elongation Factor Tu•GTP and Aminoacyl-tRNA Using Fluorescence,” Biochemistry 24, 692-700.

Hazlett, T. L., Johnson, A. E., and Jameson, D. M. (1989) “Time-Resolved Fluorescence Studies on the Ternary Complex Formed Between Bacterial Elongation Factor Tu, Guanosine 5’-Triphosphate, and Phenylalanyl-tRNAPhe,” Biochemistry 28, 4109-4117.

Dell, V. A., Miller, D. L., and Johnson, A. E. (1990) “The Effects of Nucleotide- and Aurodox-Induced Changes in Elongation Factor Tu Conformation Upon Its Interactions with Aminoacyl Transfer RNA. A Fluorescence Study,” Biochemistry 29, 1757-1763.

Janiak, F., Dell, V. A., Abrahamson, J. K., Watson, B. S., Miller, D. L., and Johnson, A. E. (1990) “Fluorescence Characterization of the Interaction of Various Transfer RNA Species With Elongation Factor Tu•GTP: Evidence for a New Functional Role for Elongation Factor Tu in Protein Biosynthesis,” Biochemistry 29, 4268-4277.

Watson, B. S., Hazlett, T. L., Eccleston, J. F., Davis, C., Jameson, D. M., and Johnson, A. E. (1995) “Macromolecular Arrangement in the Aminoacyl-tRNA•Elongation Factor Tu•GTP Ternary Complex. A Fluorescence Energy Transfer Study,” Biochemistry 34, 7904-7912.

 

8. Reviews/Chapters that discuss studies using modified aa-tRNA studies :

Johnson, A. E., and Cantor, C. R. (1977) “Affinity Labeling of Multicomponent Systems,” Methods in Enzymology 46, 180-194.

Johnson, A. E. (1979) “Analogues of Lysyl-tRNA as Probes of Ribosome and Elongation Factor Tu Structure and Function,” in Transfer RNA: Structure, Properties, and Recognition (Schimmel, P., Söll, D., and Abelson, J., eds.), pp. 487-499, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

Johnson, A. E., Janiak, F., Dell, V. A., and Abrahamson, J. K. (1986) “The Aminoacyl-tRNA•Elongation Factor Tu•GTP Ternary Complex and its Role in Aminoacyl-tRNA Selection at the Ribosome,” in Structure, Function, and Genetics of Ribosomes (Hardesty, B., and Kramer, G., eds.), pp. 541-555, Springer-Verlag, New York.

Johnson, A. E., Crowley, K. S., Shore, S. K., and Reinhart, G. D. (1993) “Protein Synthesis and Secretion as Seen by the Nascent Chain,” in The Translational Apparatus (Nierhaus, K. H., Subramanian, A. R., Erdmann, V. A., Francheschi, F., and Wittman-Liebold, B., eds.), pp. 359-370, Plenum, New York, NY.

Johnson, A. E. (1993) “Protein Translocation Across the ER Membrane: a Fluorescent Light at the End of the Tunnel,” Trends in Biochemical Sciences 18, 456-458.

Johnson, A. E., Liao, S., Lin, J., Hamman, B. D., Do, H., Cowie, A., and Andrews, D. W. (1995) “The Environment of Nascent Secretory and Membrane Proteins at the ER Membrane during Translocation and Integration,” in Protein Kinesis: The Dynamics of Protein Trafficking and Stability, Cold Spring Harbor Symposia on Quantitative Biology 60, 71-82.

Johnson, A. E. (1997) “Protein Translocation at the ER Membrane: a Complex Process Becomes More So,” Trends in Cell Biology 7, 90-95.

Johnson, A. E., and van Waes, M. A. (1999) “The Translocon: a Dynamic Gateway at the ER Membrane,” Annual Review of Cell and Developmental Biology 15, 799-842.

Johnson, A. E., Chen, J.-C., Flanagan, J. J., Miao, Y., Shao, Y., Lin, J., and Bock, P. E. (2001) “Structure, Function, and Regulation of Free and Membrane-bound Ribosomes: The View from their Substrates and Products,” in The Ribosome, Cold Spring Harbor Symposia on Quantitative Biology 66, 531-541.

Johnson, A. E. (2003) “Maintaining the Permeability Barrier during Protein Trafficking at the Endoplasmic  Reticulum Membrane,” Biochemical Society Transactions 31, 1227-1231.

Alder, N. N., and Johnson, A. E. (2004) "Cotranslational Membrane Protein Biogenesis at the Endoplasmic Reticulum," Journal of Biological Chemistry 279, 22787-22790.

Johnson, A. E. (2004) “Functional Ramifications of FRET–Detected Nascent Chain Folding Far Inside the Membrane–Bound Ribosome,” Biochemical Society Transactions 32, 668-672.

Johnson, A. E. (2005) "The Co-translational Folding and Interactions of Nascent Protein Chains: A New Approach Using Fluorescence Resonance Energy Transfer," FEBS Letters 579, 916-920.  Nobel Symposium special issue.

Johnson, A. E. (2005) “Fluorescence Approaches for Determining Protein Conformations, Interactions and Mechanisms at Membranes,” Traffic 6, 1078-1092.

Johnson, A. E. (2009) "The Structural and Functional Coupling of Two Molecular Machines, the Ribosome and the Translocon," Journal of Cell Biology 185, 765-767.

 

9.  Studies that have used SRP, ER microsomes, wheat germ extract, or other tRNA Probes product:

Wycisk, A. I., Lin, J., Loch, S., Hobohm, K., Funke, J., Wieneke, R., Koch, J., Skach, W. R., Mayerhofer, P. U., and Tampé, R. (2011) "Epstein-Barr Viral BNLF2a Protein Hijacks the Tail-anchored Protein Insertion Machinery to Block Antigen Processing by the Transport Complex TAP*,"  Journal of Biological Chemistry 286, 41402-41412.