Proteomics (protein mass spectrometry), virion structure, molecular structure, systems biology, nucleic acid-protein interactions and their molecular dynamics, catalytic mechanisms
Laboratory of Viral Diseases, NIAID, NIH, USA
Animal Virus Research Institute, Pirbright, UK
My lab currently has a major and a minor interest:
The major interest is, currently, the quantitative analysis of complex systems at the protein level via mass spectrometry. This includes virus molecular structure, the effects of infection processes on all proteins of the infected cell, and mechanisms of oncogenesis.
My minor interest (currently) is the molecular dynamics of nucleic acid polymerization using, as a model, the simplest known translocating nucleic acid polymerase and the only known polymerase that can translocate independently on single-stranded nucleic acid (a non-rigid polymer).
Mirzakhanyan, Y and Gershon, P. D. 2017. Multi-subunit DNA-dependent RNA polymerases from Vaccinia and other nucleocytoplasmic large DNA viruses: Impressions from the age of structure. MMBR Jul 12; 81(3). pii: e00010-17. doi: 10.1128/MMBR.00010-17. Print 2017 Sep.
Ngo, T., Mirzakhanyan, Y. and Gershon, P.D. 2016. Protein primary structure of the Vaccinia virion at increased resolution. J. Virol. 90(21) 9905-9919.
Flather, D., Cathcart, A., Cruz, C., Baggs, Ngo, T., Gershon, P.D., Semler, B.L. 2016. Generation of recombinant polioviruses harboring RNA affinity tags in the 5' and 3' noncoding regions of genomic RNAs. Viruses 8(2).
Kristeene A. Knopp, Tuan Ngo, Paul D. Gershon, Michael J. Buchmeier. 2015. Single Nucleoprotein Residue Modulates Arenavirus Replication Complex Formation. mBio vol. 6 no. 3e00524-15.
Marinotti, O., Ngo, T., Kojin B.B., Chou, S-P., Nguyen, B., Juhn, J., Carballar-Lejarazú, R., Marinotti, P.N., Jiang, X., Walter, M.F., Tu, Z., Gershon, P.D.,and James, A.A. 2014. Integrated proteomic and transcriptomic analysis of the Aedes aegypti eggshell. BMC Development 14:15.
Matson, J.P., Chou, W., Ngo, T. and Gershon, P.D. 2014. Static and dynamic protein phosphorylation in the Vaccinia virion. Virology 452-453, 310-323. doi: 10.1016/j.virol.2014.01.012. “Paper of the Month” (Virology highlights: http://www.virologyhighlights.com/?p=297).
Gershon, P.D. 2014. Cleaved and missed sites for trypsin, lys-C, and lys-N can be predicted with high confidence on the basis of sequence context. Journal of Proteome Research 13(2), 702-709.
Li, C., Li, H., Zhou, S., Poulos, T. and Gershon, P.D. 2013. Conformational remodeling of vaccinia virus poly(A) polymerase in the presence of its processivity factor: Processive elongation of poly(A) tails. Acta Crystallographica Section D: Biological Crystallography, Volume 69(Part 4), 617-624.
Virgen-Slane R, Rozovics JM, Fitzgerald KD, Ngo T, Chou W, van der Heden van Noort GJ, Filippov DV, Gershon PD, Semler BL. 2012. An RNA virus hijacks an incognito function of a DNA repair enzyme. Proc Natl Acad Sci U S A. 2012, 109(36):14634-9
Newman, A.C., Nakatsu, M.N., Chou, W., Gershon, P.D., Hughes, C.C. 2011. The requirement for fibroblasts in angiogenesis: Fibroblast-derived matrix proteins are essential for endothelial cell lumen formation. Mol Biol Cell. Aug 24. [Epub ahead of print]. PMID: 21865599
Chou, W. Ngo, T. and Gershon, P.D. 2012. An overview of the vaccinia virus “Infectome”: A survey of the proteins of the poxvirus-infected cell. Journal of Virology, 86(3), 1487-1499.
Gershon, P.D. 2010. Two tools for applying chromatographic retention data to the mass-based identification of peptides by mass during HD-exchange experiments by nanoLC-MALDI. Rapid Communications in Mass Spectrometry 24(23), 3373-3379.
Amenya DA, Chou W, Li J, Yan G, Gershon PD, James AA, Marinotti O. 2010. Proteomics reveals novel components of the Anopheles gambiae eggshell. J Insect Physiol. 56(10), 1414-1419.
Li, C-Z., Koter, M., Ye, X., Zhou, S-F., Chou, W., Luo, R. and Gershon, P.D. 2010. Widespread but Small-Scale Changes in the Structural and Dynamic Properties of Vaccinia Virus Poly(A) Polymerase upon Association with Its Processivity Factor in Solution. Biochemistry, 49(29), 6247-6262.
Souki, S.K., Gershon, P.D., Sandri-Goldin, R.M. 2009. Arginine methylation of the ICP27 RGG box regulates ICP27 export and is required for efficient herpes simplex virus 1 replication. Journal of Virology 83(11), 5309-5320.
Li, C-Z., Li, H., Zhou, S-F., Sun, E., Yoshizawa, J., Poulos, T.L., Gershon, P.D. 2009. Polymerase translocation with respect to single-stranded nucleic acid: Looping or wrapping of primer around a poly(A) polymerase. STRUCTURE 17, 1-10.
Nikamanon, P., Pun, E., Chou, W., Koter, M. and Gershon, P.D. 2008. "TOF2H": A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis BMC Bioinformatics 9, 387.
Kuznetsov Y, Gershon P.D., McPherson A. 2008. Atomic force microscopy investigation of vaccinia virus structure. J. Virol. 82(15), 7551-7566.
Yoshizawa, J., Li, C. and Gershon, P.D. 2007. Saltatory forward movement of a Poly(A) polymerase during poly(A) tail addition. J. Biol. Chem. 282 (26), 19144-19151.
Moure, C.M., Bowman, B.M., Gershon, P.D. and Quiocho, F.A. 2006. Crystal Structures of the Vaccinia Virus Polyadenylate Polymerase Heterodimer: Insights into ATP Selectivity and Processivity. Molecular Cell 22(3), 339-349.
Li, C., and Gershon, P.D. 2006. pKa of the mRNA cap-specific 2’-O-methyltransferase catalytic lysine by HSQC-NMR detection of a two-carbon probe. Biochemistry 45(3), 907-917.
Li, C., Xia, Y., Gao, L. and Gershon, P.D. 2004. Mechanism of RNA 2'-O-methylation: Evidence that the catalytic lysine acts to steer rather than deprotonate the target nucleophile. Biochemistry 43(19), 5680-5687.
Johnson, L., Liu, S. and Gershon, P.D. 2004. Molecular flexibility and discontinuous translocation of a non-templated polymerase. Journal of Molecular Biology 337(4), 843-885.
Malkin, A.J. McPherson, A. and Gershon, P.D. 2003. Structure of intracellular mature vaccinia virus visualized by in situ atomic force microscopy. J. Virol. 77(11), 6332-40.
Oguro, A., Johnson, L. and Gershon, P.D. 2002. Path of an RNA Ligand around the Surface of the Vaccinia VP39 Subunit of Its Cognate VP39-VP55 Protein Heterodimer. Chemistry & Biology 9(6), 679-690.
Peng, Z-H., Sharma, V., Singleton, S. and Gershon, P.D. 2002. Synthesis and application of a chain-terminating dinucleotide mRNA cap analog. Org. Lett., 4(2), 161-164.
Gershon. P.D. 2000. (A)-tail of two polymerase structures (News & Views). Nature Structural Biology, 7(10), 819-821.
Quiocho, F.A., Hu, G. and Gershon, P.D. 2000. Structural basis for mRNA cap recognition by proteins. Current Opinion in Structural Biology. 10(1), 78-86.
Hu, G., Gershon, P.D., Hodel, A.E. and Quiocho, F.A. 1999. mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic sidechains. Proc. Natl. Acad. Sci. 96(13), 7149-7154.
Hodel, A. E., Quiocho, F. A. and Gershon, P. D. 1999. VP39 – an mRNA cap-specific 2'-O-methyltransferase. In: Structure and function of AdoMet-dependent methyltransferases. X. Cheng, R. M. Blumenthal, Eds. World Scientific Publishing Co./Imperial College Press.
Lockless, S., Cheng, H.-T., Hodel, A.E., Quiocho, F.A. and Gershon, P.D. 1998. Recognition of capped RNA substrates by VP39, the vaccinia virus-encoded mRNA cap-specific 2’-O-methyltransferase. Biochemistry 37(23), 8564-8574.
Hodel, A. E., Gershon, P. D., and Quiocho, F. A. 1998. Structural basis for sequence non-specific recognition of 5' capped mRNA by a cap-modifying enzyme. Molecular Cell 1(3), 443-447.
Shi, X., Bernhardt, T.G., Wang, S-M. and Gershon, P.D. 1997. The surface region of the bifunctional vaccinia RNA modifying protein VP39 that interfaces with poly(A) polymerase is remote from the RNA binding cleft used for its mRNA 5’ cap methylation function. J. Biol. Chem. 272(37), 23292-23302
Hodel, A.E., Gershon, P.D., Shi, X., Wang, S-M. and Quiocho, F.A. 1997. Specific protein recognition of an mRNA cap through its alkylated base. Nature Structural Biology 4(5), 350-354.
Deng, L. and Gershon, P.D. 1997. Interplay of two uridylate-specific RNA binding sites in the translocation of poly(A) polymerase from vaccinia virus. EMBO J. 16(5), 1103-1113.
Hodel, A.E., Gershon, P.D., Shi, X. and Quiocho, F.A. 1996. The 1.85 Å structure of vaccinia protein VP39: A bifunctional enzyme that participates in the modification of both mRNA ends. Cell 85, 247-256.
Gershon, P. D. and Khilko, S. N. 1995. Stable chelating linkage for reversible immobilization of oligohistidine tagged proteins in the BIAcore Surface Plasmon Resonance detector. J. Immunol. Methods 183, 65-76.
Gershon, P. D., Ahn, B-Y, Garfield, M. and Moss, B. 1991. Poly(A) polymerase and a dissociable polyadenylation stimulatory factor encoded by vaccinia virus. Cell 66, 1269-1278.
“Poliovirus Gene Function and Regulation"
“The pox virion molecular interactome”
Structural Biology and Molecular Biophysics
Center for Virus Research