Publications:

Selected publications:

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

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

Krasheninnikov IA, Komar AA, Adzhubei IA (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 AA, Kommer A, Krasheninnikov IA, Spirin AS (1993) Cotranslational heme binding to nascent globin chains. FEBS Letters, 326, 261-263.

Komar AA, 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 AA, Kommer A, Krasheninnikov IA, Spirin AS (1997) Cotranslational folding of globin. J. Biol. Chem., 272, 10646-10651.

Komar AA, Lesnik T, Cullin C, Guillemet E, Ehrlich R, 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 AA, Guillemet E, Reiss C, 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 AA, Cullin C. (1999) Characterization of the interacting domains of Ure2p - a prion-like protein of yeast. Biochem. J., 338,  403-407.

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

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

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

Zoll WL, Horton LE, Komar AA, Hensold JO, Merrick WC (2002) Characterization of mammalian eIF2A and identification of the yeast homolog J. Biol. Chem., 277, 37079-37087.

Rogers GWJr, Komar AA, Merrick WC (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 AP, Komar AA, Zheng X, Merrick WC, Costes S, Lockett SJ, Sonenberg N, Colburn NH. (2003) The transformation suppressor Pdcd4 is a novel eIF4A binding protein that inhibits translation. Mol. Cell. Biol., 23, 26-37.

Kao HY, Han CC, Komar AA, 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 AA, Lesnik T, Cullin C, Merrick WC, Trachsel H, 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 AA, Koromilas A, Zhou L, Snider M, Scheuner D, Kaufman RJ, 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 WC, Komar AA (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 AB, Komar AA, Caprara M, Merrick WC, Snider M, Kaufman RJ, Lamers WH, Hatzoglou M. (2005) Ribosome stalling regulates IRES-mediated translation in eukaryotes, a parallel to prokaryotic attenuation. Mol. Cell. 17, 405-416.

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

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

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

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

Silva AM, Wang D, Komar AA, Castihlo BA, Williams BRG (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 AA (2007) Silent SNPs; impact on gene function and phenotype, Pharmacogenomics, 8, 1075-1080.

Galkin O, Bentley AA, Gupta S, Toth B-A, Mazumder B, Kinzy TG, Merrick WC, Hatzoglou M, Pestova TV, Hellen CUT, Komar AA (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 AA, Dinman JD, Barik S, 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 WM, Komar AA, Schmaier AH, Barnes E, Zhou Y, Lu X, Luo G, McCrae KR (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 AA, Snider MD, Merrick WC, Kaufman RJ, 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 AA, Rossignol JM (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 MA, Skabkina OV, Dhote V, Komar AA, Hellen CU, Pestova TV (2010) Activities of Ligatin and MCT-1/DENR in eukaryotic translation initiation and ribosomal recycling. Genes Dev. 24, 1787-1801.

Gasparian AV, Neznanov N, Jha S, Galkin O, Moran JJ, Gudkov AV, Gurova KV, Komar AA (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 AA, Hatzoglou M (2011) Cellular IRES-mediated translation: the war of ITAFs in pathophysiological states. Cell Cycle, 10, 229-240.

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

Krokowski D, Gaccioli F, Majumder M, Mullins MR, Yuan CL, Papadopoulou B, Merrick WC, Komar AA, Taylor DJ, Hatzoglou M (2011) Characterization of hibernating ribosomes in mammalian cells. Cell Cycle, 10, 2691-2702.

Gasparian AV, Burkhart CA, Purmal AA, Brodsky L, Pal M, Saranadasa M, Bosykh DA, Commane M, Guryanova OA, Pal S, Safina A, Sviridov S, Koman IE, Veith J, Komar AA, Gudkov AV, Gurova KV (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 AA, 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 MD, Komar AA, Tanaka J, Kaufman RJ, Krokowski D, 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 AA, Mazumder B, Merrick WC (2012) A New Framework for Understanding IRES-mediated translation. Gene 502, 75-86.

Bentley AA, Merkulov SM, Peng Y, Rozmarynowycz R, Qi X, Pusztai-Carey M, Merrick WC, Yee V, McCrae KR, Komar AA (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 VL, Tseng SC, Needlman E, Edwards NC, Sauna ZE, Grigoryan V, Komar AA, Przytycka TM, Kimchi-Sarfaty C (2012) Analysis of F9 point mutations and their correlation to severity of hemophilia B disease. Hemophilia B, 1-8.

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

Edwards NC, Perry A, Blaisdell A, Kopelman DB, Fathke R, Plum W, Newell J, Allen CE, Geetha S, Shapiro A, Okunji C, Kosti I, Shomron N, Grigoryan V, Sauna ZE, Mandel-Gutfreund Y, Komar AA, 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, Komar AA (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 RC, Newell J, Tseng SC, Hershko AY, Choi JW, Sauna ZE, Wu A, Bram RJ, Komar AA, Kimchi-Sarfaty C (2012) Cyclosporin A impairs the secretion and activity of ADAMTS13. J Biol Chem. 287, 44361-44371.

Komar AA, Taylor DJ, Merrick WC (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.

Shaltouk A, Harford T, Komar AA, Weyman CM (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 AA, Mazumder B (2013) Insights into the mechanism of ribosomal incorporation of mammalian L13a protein during ribosome biogenesis. Mol. Cell Biol,33, 2829-2842.

Komar AA (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 AA (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. 2, 1-17.

Komar AA (2016) The yin and yang of codon usage. Hum Mol Genet., Oct 1;25(R2):R77-R85

Singh J, Sikand K, Conrad H, Will CL, Komar AA, Shukla GC (2016) U6atac snRNA stem-loop interacts with U12 p65 RNA binding protein and is functionally interchangeable with the U12 apical stem-loop III. Sci Rep., 6:31393.

Komar AA (2016) The "periodic table" of the genetic code: a new way to look at the code and the decoding process. Translation (Austin), 4(2):e1234431.

Golovko A, Kojukhov A., Guan B-J, Morpurgo B, Merrick WC, Mazumder B, Hatzoglou M, Komar AA (2016) The eIF2A knockout mouse. Cell Cycle, 15(22):3115-3120.

Simhadri VL, Katagiri NH, Lin BC, Hunt R, Jha S, Tseng SC, Wu A,  Bentley AA, Zichel R, Lu Q, Zhu L, Freedberg DI, Monroe DM, Sauna ZE, Peters R, Komar AA, Kimchi-Sarfaty C (2017) Single synonymous mutation in Factor IX alters protein properties and underlies hemophilia B. J Med Genet, (5):338-345.

Nobuko K, Lin B, Simon J, Hunt R, Schiller T, Russek-Cohen E, Komar AA, Bar H, Kimchi-Sarfaty C (2017) The importance of mRNA structure in determining the pathogenicity of synonymous and non-synonymous mutations in Haemophilia, Haemophilia, 23(1):e8-e17.

Guan B-J, van Hoef V, Jobava R, Elroy-Stein O, Valasek LS, Cargnello M, Gao X-H, Krokowski D, Merrick WC, Kimball SR, Komar AA, Koromilas AE, Wynshaw-Boris A, Topisirovic I, Larsson O, Hatzoglou M (2017) A Unique ISR Program Determines Cellular Responses to Chronic Stress. Mol Cell, 68(5):885-900.

Basu A, Wells N, Tolbert BS, Komar AA, Mazumder B (2017) Conserved structures formed by heterogeneous RNA sequences drive silencing of an inflammation responsive post transcriptional operon. Nucleic Acids Res., 45(22):12987-13003.

Komar AA (2017) Unraveling co-translational protein folding: concepts and methods. Methods, S1046-2023(17)30273-30276.

Arndt, N., Ross-Kaschitza D, Kojukhov A, Komar AA, Altmann M (2018) Properties of the ternary complex formed by yeast 1 eIF4E, p20 and mRNA. Sci Rep., 8(1):6707.

Zinoviev A, Goyal A, Jindal S, LaCava J, Komar AA, Rodnina MV, Hellen CUT, Pestova TV (2018) Functions of unconventional mammalian translational GTPases GTPBP1 and GTPBP2. Genes Dev., 32(17-18):1226-1241.

Yehia L, Jindal S, Komar AA, Eng C (2018) COPII-Independent Role of Cancer-Associated Mutant SEC23B in the Ribosome Biogenesis Pathway. Hum Mol Genet., 27(18):3154-3164.

Jindal S, Ghosh A, Singh N, Komar AA (2019) Role of uS9/yS16 C-terminal tail in translation initiation and elongation in yeast Saccharomyces cerevisiae. Nucleic Acids Res., 47(2):806-823.

Alexaki A, Kames J, Holcomb DD, Athey J, Santana-Quintero LV, Lam PVN, Hamasaki-Katagiri N, Osipova E, Simonyan V, Bar H, Komar AA, Kimchi-Sarfaty C. (2019) Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design. J Mol Biol., 431(13):2434-2441.

Singh N, Jindal S, Ghosh A, Komar AA. (2019) Communication between RACK1/Asc1 and uS3 (Rps3) is essential for RACK1/Asc1 function in yeast Saccharomyces cerevisiae. Gene, 706:69-76.

Katneni UK, Liss A, Holcomb D, Katagiri NH, Hunt R, Bar H, Ismail A, Komar AA, Kimchi-Sarfaty C. (2019) Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants. Mol Genet Genomic Med. 7(8):e840.

Kour R, Komar AA, Mazumder B. (2019) Mutually exclusive amino acid residues of L13a are responsible for its ribosomal incorporation and translational silencing leading to resolution of inflammation. RNA, 25(10):1377-1392.

Alexaki A, Hettiarachchi GK, Athey JC, Katneni UK, Simhadri V, Hamasaki-Katagiri N, Nanavaty P, Lin B, Takeda K, Freedberg D, Monroe D, McGill JR, Peters R, Kames JM, Holcomb DD, Hunt RC, Sauna ZE, Gelinas A, Janjic N, DiCuccio M, Bar H, Komar AA, Kimchi-Sarfaty C. (2019) Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies. Sci Rep. 9(1):15449.

Komar AA. (2019) Synonymous Codon Usage ¿ a Guide for Co-translational Protein Folding in the Cell. Mol. Biol., 53(6):883-898.

Alexaki A, Hettiarachchi GK, Athey JC, Katneni UK, Simhadri V, Hamasaki-Katagiri N, Nanavaty P, Lin B, Takeda K, Freedberg D, Monroe D, McGill JR, Peters R, Kames JM, Holcomb DD, Hunt RC, Sauna ZE, Gelinas A, Janjic N, DiCuccio M, Bar H, Komar AA, Kimchi-Sarfaty C. (2020) Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX. F1000Res, 9, 174.

Komar AA., Merrick WC. (2020) A retrospective on eIF2A ¿ and not the alpha subunit of eIF2. Int J Mol Sci. 21(6):2054.

Mazumder S., Swank V., Komar AA, Johnson J.M Tuohy VK (2020) Monoclonal Antibody against Extracellular Domain of Anti-Müllerian Hormone Receptor II for Immunotargeting of Epithelial Ovarian Carcinoma. Oncotarget, 11(20):1894-1910.

Kames J, Holcomb DD, Kimchi O, DiCuccio M, Hamasaki-Katagiri N, Wang T, Komar AA, Alexaki A, Kimchi-Sarfaty C (2020) Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design. bioRxiv, Mar 31:2020.03.30.016832.