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Dmitri N. Ermolenko, Ph.D.


Showing all 43 journal articles & 0 books available

Journal Articles

Lai WC, Zhu M, Belinite M, Ballard G, Mathews DH, Ermolenko DN. "Intrinsically unstructured sequences in the mRNA 3' UTR reduce the ability of poly(A) tail to enhance translation." Journal of molecular biology.. 2022 Nov 8; :167877. Epub 2022 Nov 08.

Bao C, Zhu M, Nykonchuk I, Wakabayashi H, Mathews DH, Ermolenko DN. "Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation." Nature communications.. 2022 Feb 21; 13(1):988. Epub 2022 Feb 21.

Bao C, Ermolenko DN. "Ribosome as a Translocase and Helicase." Biochemistry. Biokhimii?a?.. 2021 Aug; 86(8):992-1002.

Ermolenko DN, Mathews DH. "Making ends meet: New functions of mRNA secondary structure." Wiley interdisciplinary reviews. RNA.. 2020 Jun 29; :e1611. Epub 2020 Jun 29.

Wakabayashi H, Warnasooriya C, Ermolenko DN. "Extending the Spacing between the Shine-Dalgarno Sequence and P-Site Codon Reduces the Rate of mRNA Translocation." Journal of molecular biology.. 2020 Jun 13; Epub 2020 Jun 13.

Warnasooriya C, Feeney CF, Laird KM, Ermolenko DN, Kielkopf CL. "A splice site-sensing conformational switch in U2AF2 is modulated by U2AF1 and its recurrent myelodysplasia-associated mutation." Nucleic acids research.. 2020 Jun 4; 48(10):5695-5709.

Bao C, Loerch S, Ling C, Korostelev AA, Grigorieff N, Ermolenko DN. "mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding." eLife.. 2020 May 19; 9Epub 2020 May 19.

Ermolenko DN, Whitford PC. "Experimental and computational techniques for studying structural dynamics and function of RNA." Methods : a companion to Methods in enzymology.. 2019 Jun 1; 162-163:1-2. Epub 2019 Jun 20.

Lai WC, Kayedkhordeh M, Cornell EV, Farah E, Bellaousov S, Rietmeijer R, Salsi E, Mathews DH, Ermolenko DN. "mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances." Nature communications.. 2018 Oct 18; 9(1):4328. Epub 2018 Oct 18.

Warnasooriya C, Ling C, Belashov IA, Salim M, Wedekind JE, Ermolenko DN. "Observation of preQ-II riboswitch dynamics using single-molecule FRET." RNA biology.. 2018 Oct 17; :1-7. Epub 2018 Oct 17.

Lai CW, Ermolenko DN. "Ensemble and single-molecule FRET studies of protein synthesis." Methods : a companion to Methods in enzymology.. 2018 Mar 15; 137:37-48. Epub 2017 Dec 13.

Ling C, Ermolenko DN. "Caught on Camera: Intermediates of Ribosome Recycling." Structure.. 2016 Dec 6; 24(12):2035-2036.

Ling C, Ermolenko DN. "Structural insights into ribosome translocation." Wiley interdisciplinary reviews. RNA.. 2016 Sep; 7(5):620-36. Epub 2016 Apr 27.

Salsi E, Farah E, Ermolenko DN. "EF-G Activation by Phosphate Analogs." Journal of molecular biology.. 2016 May 22; 428(10 Pt B):2248-58. Epub 2016 Apr 08.

Agrawal AA, Salsi E, Chatrikhi R, Henderson S, Jenkins JL, Green MR, Ermolenko DN, Kielkopf CL. "An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal." Nature communications.. 2016 Mar 8; 7:10950. Epub 2016 Mar 08.

Ling C, Ermolenko DN. "Initiation factor 2 stabilizes the ribosome in a semirotated conformation." Proceedings of the National Academy of Sciences of the United States of America.. 2015 Dec 29; 112(52):15874-9. Epub 2015 Dec 14.

Ling C, Ermolenko DN. "Ribosome subunit joining frozen in time." Structure.. 2015 Jun 2; 23(6):977-8.

Salsi E, Farah E, Netter Z, Dann J, Ermolenko DN. "Movement of elongation factor G between compact and extended conformations." Journal of molecular biology.. 2015 Jan 30; 427(2):454-67. Epub 2014 Nov 15.

Salsi E, Farah E, Dann J, Ermolenko DN. "Following movement of domain IV of elongation factor G during ribosomal translocation." Proceedings of the National Academy of Sciences of the United States of America.. 2014 Oct 21; 111(42):15060-5. Epub 2014 Oct 06.

Kurosaki T, Li W, Hoque M, Popp MW, Ermolenko DN, Tian B, Maquat LE. "A post-translational regulatory switch on UPF1 controls targeted mRNA degradation." Genes & development.. 2014 Sep 1; 28(17):1900-16.

Brilot AF, Korostelev AA, Ermolenko DN, Grigorieff N. "Structure of the ribosome with elongation factor G trapped in the pretranslocation state." Proceedings of the National Academy of Sciences of the United States of America.. 2013 Dec 24; 110(52):20994-9. Epub 2013 Dec 09.

Azpurua J, Ke Z, Chen IX, Zhang Q, Ermolenko DN, Zhang ZD, Gorbunova V, Seluanov A. "Naked mole-rat has increased translational fidelity compared with the mouse, as well as a unique 28S ribosomal RNA cleavage." Proceedings of the National Academy of Sciences of the United States of America.. 2013 Oct 22; 110(43):17350-5. Epub 2013 Sep 30.

Svidritskiy E, Ling C, Ermolenko DN, Korostelev AA. "Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome." Proceedings of the National Academy of Sciences of the United States of America.. 2013 Jul 23; 110(30):12283-8. Epub 2013 Jul 03.

Ermolenko DN, Cornish PV, Ha T, Noller HF. "Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation." RNA.. 2013 Feb; 19(2):158-66. Epub 2012 Dec 17.

Rudenko MI, Holmes MR, Ermolenko DN, Lunt EJ, Gerhardt S, Noller HF, Deamer DW, Hawkins A, Schmidt H. "Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip." Biosensors & bioelectronics.. 2011 Nov 15; 29(1):34-9. Epub 2011 Aug 05.

Ermolenko DN, Noller HF. "mRNA translocation occurs during the second step of ribosomal intersubunit rotation." Nature structural & molecular biology.. 2011 Apr; 18(4):457-62. Epub 2011 Mar 13.

Cornish PV, Ermolenko DN, Staple DW, Hoang L, Hickerson RP, Noller HF, Ha T. "Following movement of the L1 stalk between three functional states in single ribosomes." Proceedings of the National Academy of Sciences of the United States of America.. 2009 Feb 24; 106(8):2571-6. Epub 2009 Feb 03.

Korostelev A, Ermolenko DN, Noller HF. "Structural dynamics of the ribosome." Current opinion in chemical biology.. 2008 Dec; 12(6):674-83. Epub 2008 Oct 09.

Cornish PV, Ermolenko DN, Noller HF, Ha T. "Spontaneous intersubunit rotation in single ribosomes." Molecular cell.. 2008 Jun 6; 30(5):578-88.

Spiegel PC, Ermolenko DN, Noller HF. "Elongation factor G stabilizes the hybrid-state conformation of the 70S ribosome." RNA.. 2007 Sep; 13(9):1473-82. Epub 2007 Jul 13.

Ermolenko DN, Majumdar ZK, Hickerson RP, Spiegel PC, Clegg RM, Noller HF. "Observation of intersubunit movement of the ribosome in solution using FRET." Journal of molecular biology.. 2007 Jul 13; 370(3):530-40. Epub 2007 Apr 20.

Ermolenko DN, Spiegel PC, Majumdar ZK, Hickerson RP, Clegg RM, Noller HF. "The antibiotic viomycin traps the ribosome in an intermediate state of translocation." Nature structural & molecular biology.. 2007 Jun; 14(6):493-7. Epub 2007 May 21.

Ermolenko DN, Dangi B, Gvritishvili A, Gronenborn AM, Makhatadze GI. "Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences." Biophysical chemistry.. 2007 Mar; 126(1-3):25-35. Epub 2006 Apr 05.

Ermolenko DN, Zherdev AV, Dzantiev BB. "Horseradish peroxidase renaturation is less efficient at lower protein concentrations." Protein and peptide letters.. 2005 Oct; 12(7):639-43.

Ermolenko DN, Zherdev AV, Dzantiev BB. "Antibodies as specific chaperones." Biochemistry. Biokhimii?a?.. 2004 Nov; 69(11):1233-8.

Ermolenko DN, Richardson JM, Makhatadze GI. "Noncharged amino acid residues at the solvent-exposed positions in the middle and at the C terminus of the alpha-helix have the same helical propensity." Protein science : a publication of the Protein Society.. 2003 Jun; 12(6):1169-76.

Makhatadze GI, Loladze VV, Ermolenko DN, Chen X, Thomas ST. "Contribution of surface salt bridges to protein stability: guidelines for protein engineering." Journal of molecular biology.. 2003 Apr 11; 327(5):1135-48.

Bezsudnova EIu, Zherdev AV, Ermolenko DN, Iakovleva IV, Sviridov VV, Popov VO, Dzantiev BB. "[Peroxidase refolding in the presence of specific antibodies]." Prikladnaia biokhimiia i mikrobiologiia. 2003 39(5):509-17.

Ermolenko DN, Makhatadze GI. "Bacterial cold-shock proteins." Cellular and molecular life sciences : CMLS.. 2002 Nov; 59(11):1902-13.

Ermolenko DN, Thomas ST, Aurora R, Gronenborn AM, Makhatadze GI. "Hydrophobic interactions at the Ccap position of the C-capping motif of alpha-helices." Journal of molecular biology.. 2002 Sep 6; 322(1):123-35.

Loladze VV, Ermolenko DN, Makhatadze GI. "Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior." Journal of molecular biology.. 2002 Jul 5; 320(2):343-57.

Ermolenko DN, Zherdev AV, Dzantiev BB, Popov VO. "Antiperoxidase antibodies enhance refolding of horseradish peroxidase." Biochemical and biophysical research communications.. 2002 Mar 8; 291(4):959-65.

Loladze VV, Ermolenko DN, Makhatadze GI. "Heat capacity changes upon burial of polar and nonpolar groups in proteins." Protein science : a publication of the Protein Society.. 2001 Jul; 10(7):1343-52.