Publications:

Selected publications:

Krasheninnikov I.A., Komar A.A. and Adzhubei I.A. (1988) Role of the rare codon clusters in the determination of the boundaries of polypeptide chain regions with identical secondary structure in the process of cotranslational protein folding. Doklady Akademii Nauk SSSR, 303, 995-999.

Krasheninnikov I.A., Komar A.A. and Adzhubei I.A. (1989) The role of the genetic code redundance in determination of the mode of cotranslational protein folding. Biokhimiya SSSR, 54, 187-200.

Krasheninnikov I.A., Komar A.A. and Adzhubei I.A. (1989) Usage of codons in mRNA and coding of protein domain structure. Doklady Akademii Nauk SSSR, 305, 1006-1012.

Krasheninnikov I.A., Komar A.A. and Adzhubei I.A. (1991) Nonuniform size distribution of nascent globin peptides, evidence for pause localization sites, and a cotranslational protein-folding model. J. Prot. Chem., 10, 445-454.

Komar A.A., Kommer A., Krasheninnikov I.A. and Spirin A.S. (1993) Cotranslational heme binding to nascent globin chains. FEBS Letters, 326, 261-263.

Komar A.A. and Jaenicke R. (1995) Kinetics of translation of gamma-B crystallin and its circularly permutated variant in an in vitro cell-free system: possible relations to codon distribution and protein folding. FEBS Letters, 376, 195-198.

Komar A.A., Kommer A., Krasheninnikov I.A. and Spirin A.S. (1997) Cotranslational folding of globin. J. Biol. Chem., 272, 10646-10651.

Komar A.A., Lesnik T., Cullin C., Guillemet E., Ehrlich R. and Reiss C. (1997) Differential resistance to proteinase K digestion of the yeast prion-like (Ure2p) protein synthesized in vitro in wheat germ extract and rabbit reticulocyte lysate cell-free translation systems, FEBS Letters, 415, 6-10.

Komar A.A., Guillemet E., Reiss C. and Cullin C. (1998) Enhanced expression of the yeast Ure2 protein in Escherichia coli: the effect of synonymous codon substitutions at a selected place in the gene. Biol. Chem., 379, 1295-1300.

Fernandez-Bellot E., Guillemet E., Baudin-Baillieu A., Gaumer S., Komar A.A. and Cullin C. (1999) Characterization of the interacting domains of Ure2p - a prion-like protein of yeast. Biochem. J., 338,  403-407.

Thual C., Komar A.A., Bousset L., Fernandez-Bellot E., Cullin C. and Melki R (1999) Structural characterization of Saccharomyces cerevisiae prion-like protein Ure2. J. Biol. Chem., 274, 13666-13614.

Komar A.A., Melki R. and Cullin C. (1999) The [URE3] yeast prion, from genetics to biochemistry. Biochemistry (Moscow), 64, 75-83.

Komar A.A., Lesnik T. and Reiss C. (1999) Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation. FEBS Letters, 462, 387-391.

Thual C., Bousset L., Komar A.A., Walter S., Buchner J., Cullin C. and Melki R. (2001) Stability, folding, dimerization and assembly properties of the yeast prion Ure2p. Biochemistry, 40, 1764-1773.

Zoll W.L., Horton L.E., Komar A.A., Hensold JO. and Merrick W. C. (2002) Characterization of mammalian eIF2A and identification of the yeast homolog J. Biol. Chem., 277, 37079-37087.

Rogers G.W. Jr., Komar A.A. and Merrick W.C. (2002) eIF4A: The Godfather of the DEAD-box Helicases.  In Progress in Nucleic Acid Research and Molecular Biology. (K. Moldave, ed.) Academic Press, San Diego, p. 307-331.

Yang H-S., Jansen A.P., Komar A.A., Zheng X., Merrick W.C., Costes S., Lockett, S.J., Sonenberg N. and Colburn N.H. (2003) The transformation suppressor Pdcd4 is a novel eIF4A binding protein that inhibits translation. Mol. Cell. Biol., 23, 26-37.

Kao H.Y., Han C.C., Komar A.A. and Evans RM. (2003) Co-repressor release, but not ligand binding, is a pre-requisite for transcription activation by human RAR-alpha ligand binding domains. J. Biol. Chem., 278, 7366-7373.

Komar A.A., Lesnik T., Cullin C., Merrick W.C., Trachsel H. and Altmann M. (2003) Internal initiation drives the synthesis of Ure2 protein lacking the prion domain and affects [URE3] propagation in yeast cells. EMBO J., 22, 1199-1209.

Yaman I., Fernandez J., Liu H., Caprara M., Komar A.A., Koromilas A., Zhou L., Snider M., Scheuner D., Kaufman R.J. and Hatzoglou M. (2003) The zipper model of translational control: a small upstream ORF is the switch that controls structural remodeling of an mRNA leader. Cell, 113, 519-531.

Merrick W.C. and Komar A.A. (2004) Eukaryotic protein biosynthesis: The elongation cycle. In Encyclopedia of Biological Chemistry (Lennarz W.J. and Lane M. D., eds), Academic Press/Elsevier Science, Elsevier, Oxford, Vol. 4, 224-230.

Fernandez J., Yaman I., Huang C., Liu H., Lopez A.B., Komar A.A., Caprara M., Merrick W.C. Snider M., Kaufman R.J., Lamers W.H. and Hatzoglou M. (2005) Ribosome stalling regulates IRES-mediated translation in eukaryotes, a parallel to prokaryotic attenuation. Mol. Cell. 17, 405-416.

Komar A.A., Gross S., Barth-Baus D., Strachan R., Hensold J.O., Kinzy T. and Merrick W.C. (2005) Novel characteristics of the biological properties of the yeast Saccharomyces cerevisae initiation factor eIF2A J. Biol. Chem. 280, 15601-15611.

Komar A.A. and Hatzoglou M. (2005) Internal Ribosome Entry Sites in cellular mRNAs: Mystery of their existence. J. Biol. Chem. 280, 23425-23428.

Komar A.A. (2007) SNPs, Silent But Not Invisible, Science, 315, 466-467.

Kapasi P., Chaudhuri S, Vyas K., Baus D., Komar A.A., Fox P.L. Merrick W.C. and Mazumder B. (2007) L13a Blocks 48S Assembly: Role of a General Initiation Factor in mRNA-specific translational Control. Mol. Cell, 25, 113-126.

Silva A.M., Wang D., Komar A.A., Castihlo B.A. and Williams B.R.G. (2007) Acetyl salicylic acid and its metabolite sodium salicylate trigger protein synthesis inhibition in a PKR-like endoplasmic reticulum kinase-dependent manner. J. Biol. Chem., 282, 10164-10171.

Komar A.A. (2007) Silent SNPs; impact on gene function and phenotype, Pharmacogenomics, 8, 1075-1080.

Galkin O., Bentley A.A., Gupta S., Toth B-A., Mazumder B., Kinzy T.G. Merrick W.C., Hatzoglou M., Pestova T.V., Hellen C.U.T. and Komar, A.A. (2007) Possible roles of the negatively charged N-terminal extension of Saccharomyces cerevisiae ribosomal protein S5 revealed by characterization of a yeast strain containing human ribosomal protein S5. RNA, 13, 2116-2128.

Chaudhuri S., Vyas K., Kapasi P., Komar A.A., Dinman J.D., Barik S. and Mazumder B. (2007) Human ribosomal protein L13a is Dispensable for Canonical Ribosome Function but Indispensable for Efficient rRNA Methylation. RNA, 13, 2224-2237.

Merkulov S., Zhang W.M, Komar A.A., Schmaier A.H., Barnes E., Zhou Y., Lu X., Luo G and McCrae K.R. (2008) Deletion of Murine Kininogen Gene 1 (mKng1) Causes Loss of Plasma Kininogen and Delays Thrombosis. Blood, 111, 1274-1281.

Zeenko V., Wang C., Majumdar M., Komar A.A., Snider M.D., Merrick W.C., Kaufman R.J. and Hatzoglou M. (2008) An efficient mammalian cell-free translation system from cells-resistant to translational inhibition due to eIF2 phosphorylation. RNA, 14, 593-602.

Laine S., Thouard A, Komar A.A. and Rossignol J.M. (2008) Tandem rare argininine codons AGA_AGA induce +1 and -1  ribosome frameshifting during the overexpression of a viral protein in Escherichia coli. Gene, 412, 95-101.

Reineke LC, Komar AA, Caprara MG, Merrick WC (2008) A small stem loop element directs internal initiation of the URE2 IRES in Saccharmyces cerevisiae. J. Biol. Chem. 283, 19011-19025.

Komar AA (2008) Protein Translation Rates and Protein Misfolding: Is there any link? In Protein Misfolding: New Research (O'Doherty C.B. and Byrne, A.C. eds), Nova Science Publishers, Inc. NY, pp, 61-80.

Pisareva VP, Pisarev AV, Komar AA, Hellen CUT, Pestova TV (2008) Efficient translation initiation on mammalian mRNAs with structured 5'-UTRs requires DExH-box protein DHX29. Cell, 135, 1237-1250.

Vyas K, Chaudhuri S, Leaman DW, Komar AA, Musiyenko A, Barik S, Mazumder B. (2009) Genome-wide polysome profiling reveals an inflammation-responsive post-transcriptional operon in IFN-gamma-activated monocytes. Mol. Cell. Biol. 29, 458-470.

Komar AA (2009) A pause for thought along the co-translational folding pathway. Trends Biochem. Sci. 34, 16-24.

Guo C, Gasparian AV, Zhuang Z, Bosykh DA, Komar AA, Gudkov AV and Gurova KV. (2009) 9-Aminoacridine-based anticancer drugs target the PI3K/AKT/mTOR, NF-kappaB and p53 pathways Oncogene 28, 1151-1161.

Majumder M, Yaman I, Gaccioli F, Wang C, Zeenko V, Caprara MG, Venema R, Komar AA, Snider MD and Hatzoglou M. (2009) The hnRNA-binding proteins hnRNP L and PTB are required for efficient translation of the Cat-1 arginine/lysine transporter mRNA during amino acid starvation. Mol. Cell. Biol. 29, 2899-2912.

Lumsden T, Bentley AA, Beutler W, Ghosh A, Galkin O, and Komar AA (2010) Yeast strains with N-terminally truncated ribosomal protein S5; implications for the evolution, structure and function of the Rps5/Rps7 proteins. Nucleic Acids Res. 38, 1261-1272.

Skabkin M.A., Skabkina O.V., Dhote V., Komar A.A., Hellen C.U. and Pestova TV. (2010) Activities of Ligatin and MCT-1/DENR in eukaryotic translation initiation and ribosomal recycling. Genes Dev. 24, 1787-1801.

Gasparian A.V., Neznanov N., Jha. S., Galkin O., Moran J.J., Gudkov A.V., Gurova K.V., and Komar A.A. (2010) Inhibition of EMCV and poliovirus replication by quinacrine: implications for the design and discovery of novel anti-viral drugs. J. Virol. 18, 9390-9397.

Komar, A.A. and Hatzoglou, M. (2011) Cellular IRES-mediated translation: the war of ITAFs in pathophysiological states. Cell Cycle, 10, 229-240.

Jha, S. and Komar, A.A. (2011) Birth, life and death of nascent polypeptide chains, Biotechnol. J., 6, 623-640.

Krokowski, D, Gaccioli, F., Majumder, M., Mullins, M.R., Yuan, C.L. Papadopoulou, B., Merrick, W.C., Komar, A.A., Taylor, D.J. and Hatzoglou, M. (2011) Characterization of hibernating ribosomes in mammalian cells. Cell Cycle, 10, 2691-2702.

Gasparian, A.V., Burkhart, C.A., Purmal, A.A., Brodsky, L., Pal, M., Saranadasa, M., Bosykh, D.A., Commane, M., Guryanova, O.A., Pal, S., Safina, A., Sviridov, S., Koman, I.E., Veith, J., Komar, A.A., Gudkov, A.V. and Gurova, K.V. (2011) Curaxins: Anticancer Compounds That Simultaneously Suppress NF-{kappa}B and Activate p53 by Targeting FACT. Science Transl Med, 3, 95ra74.

Basu, A., Das, P., Chaudhuri, S., Bevilacqua, E., Andrews, J., Barik, S., Hatzoglou, M., Komar, A.A. and Mazumder B. (2011) Requirement of rRNA methylation for 80S ribosome assembly on a cohort of cellular Internal Ribosome Entry Sites. Mol. Cell Biol. 31, 4482-4499.

Majumder, M., Huang, C., Snider, M.D., Komar, A.A., Tanaka, J, Kaufman, R.J., Krokowski, D. and Hatzoglou, M. (2012) A novel feedback loop regulates the response to endoplasmic reticulum stress via the cooperation of cytoplasmic splicing and mRNA translation, Mol. Cell Biol. 31, 992-1003.

Komar, A.A. Mazumder, B, and Merrick, WC. (2012) A New Framework for Understanding IRES-mediated translation. Gene 502, 75-86.

Bentley, A.A. Merkulov, S.M., Peng, Y., Rozmarynowycz, R., Qi, X., Pusztai-Carey, M., Merrick, W.C., Yee, V., McCrae, K.R., and Komar, A.A. (2012) Chimeric glutathione S-transferases containing inserts of kininogen peptides ¿ potential novel protein therapeutics. J. Biol. Chem. 287, 22142-22150.

Hamasaki-Katagiri, N., Salari, R., Simhadri, V.L., Tseng, S.C., Needlman, E., Edwards, N.C., Sauna, Z.E. Grigoryan, V., Komar, A.A., Przytycka, T.M. and Kimchi-Sarfaty, C. (2012) Analysis of F9 point mutations and their correlation to severity of hemophilia B disease. Hemophilia B, 1-8.

Jha, S. and Komar, A.A. (2012) Using SecM arrest sequence as a tool to isolate ribosome bound polypeptides. J. Vis Exp. 64, 4027.

Edwards, N.C., Perry, A., Blaisdell, A., Kopelman, D.B. Fathke, R. Plum, W., Newell, J., Allen, C.E., Geetha S., Shapiro, A., Okunji, C., Kosti, I., Shomron, N., Grigoryan, V., Sauna, Z.E., Mandel-Gutfreund, Y., Komar, A.A. and Kimchi-Sarfaty, C. (2012). Characterization of coding synonymous and non-synonymous polymorphisms in ADAMTS13 using ex vivo and in silico approaches. PloS One. 7, e38864.

Jha, S. and Komar, A.A. (2012) Isolation of ribosome bound nascent polypeptides in vitro to identify translational pause sites along mRNA. J. Vis Exp. 65, 4026.

Hershko, K., Simhadri, V., Blaisdell, A., Hunt, R.C., Newell, J., Tseng, S.C., Hershko, A.Y., Choi, J.W., Sauna, Z.E., Wu, A., Bram, R.J., Komar, A.A., Kimchi-Sarfaty C. (2012) Cyclosporin A impairs the secretion and activity of ADAMTS13. J Biol Chem. 287, 44361-44371.

Komar, A.A., Taylor, D.J. and Merrick W.C. (2013) Eukaryotic Protein Biosynthesis: The Elongation Cycle. In: Lennarz W.J. and Lane M.D. (eds.) The Encyclopedia of Biological Chemistry, vol. 2, pp. 249-255. Waltham, MA: Academic Press.

Shaltouki, A., Harford T., Komar, A.A. and Weyman, C.M. (2013) IRES-mediated translation of the pro-apoptotic Bcl2 family member PUMA, Translation, 1, e24391.

Das, P., Basu, A., Biswas, A., Poddar, P., Andrews, J., Barik, S., Komar, A.A. and Mazumder, B. (2013) Insights into the mechanism of ribosomal incorporation of mammalian L13a protein during ribosome biogenesis. Mol. Cell Biol,33, 2829-2842.

Komar, A.A. (2013) "Naked" FACT is unstable. Cell Cycle. 12,(15).

Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK; NISC Comparative Sequencing Program, Chen G, Elnitski LL, Davies MA, Gershenwald JE, Carter H, Karchin R, Robinson W, Robinson S, Rosenberg SA, Collins FS, Parmigiani G, Komar AA, Kimchi-Sarfaty C, Hayward NK, Margulies EH, Samuels Y. (2013) Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci U S A, 110, 13481-13486.

Hamasaki-Katagiri N, Salari R, Wu A, Qi Y, Schiller T, Filiberto AC, Schisterman EF, Komar AA, Przytycka TM, Kimchi-Sarfaty C. (2013) A gene-specific method for predicting hemophilia-causing point mutations. J Mol Biol., 425, 4023-4033.

Simhadri VL, Hamasaki-Katagiri N, Tseng SC, Bentley AA, Zichel R, Hershko AY, Komar AA, Kimchi-Sarfaty C. (2014) Factor IX oligomerization underlies reduced activity upon disruption of physiological conditions. Haemophilia, 20, e157-163.

Ghosh A, Jindal S, Bentley AA, Hinnebusch AG, Komar AA. (2014) Rps5-Rps16 communication is essential for efficient translation initiation in yeast S. cerevisiae. Nucleic Acids Res., 42, 8537-8555.

Ghosh A, Komar, A.A. (2014) Eukaryote-specific extensions in ribosomal proteins of the small subunit: structure and function. Translation. 3, 1, e999576.

Komar AA, Hatzoglou M. (2015) Exploring Internal Ribosome Entry Sites as Therapeutic Targets. Front Oncol. 5, 233.

Holtkamp W, Kokic G, Jäger M, Mittelstaet J, Komar AA, Rodnina MV. (2015) Cotranslational protein folding on the ribosome monitored in real time. Science, 350, 1104-1107.

Buhr F, Jha S, Thommen M, Mittelstaet J, Kutz F, Schwalbe H, Rodnina MV, Komar AA. (2016) Synonymous codons direct cotranslational folding toward different protein conformations. Mol Cell, 61, 341-351.

Komar AA. (2016) The art of gene redesign and recombinant protein production: approaches and perspectives. Top. Med. Chem. (in press).