Recent Publications

• 1. De Zoysa T
  2. Hauke AC
  3. Iyer NR
  4. Marcus E
  5. Ostrowski SM
  6. Stegemann F
  7. Ermolenko DN
  8. Fay JC
  9. Phizicky EM
  A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay.; PLoS genetics; Vol 20(1), pp. e1011146. 2024 Jan 31.
• 1. Das A
  2. Bao C
  3. Ermolenko DN
  Comparing FRET Pairs that Report on Intersubunit Rotation in Bacterial Ribosomes.; Journal of molecular biology; Vol 435(15), pp. 168185. 2023 Jun 20.
• 1. Das A
  2. Bao C
  3. Ermolenko DN
  Comparing FRET pairs that report on intersubunit rotation in bacterial ribosomes.; bioRxiv : the preprint server for biology. 2023 May 09.
• 1. Das A
  2. Adiletta N
  3. Ermolenko DN
  Interplay between Inter-Subunit Rotation of the Ribosome and Binding of Translational GTPases.; International journal of molecular sciences; Vol 24(8). 2023 Apr 07.
• 1. Bao C
  2. Zhu M
  3. Nykonchuk I
  4. Wakabayashi H
  5. Mathews DH
  6. Ermolenko DN
  Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation.; Nature communications; Vol 13(1). 2022 Feb 21.
• 1. Lai WC
  2. Zhu M
  3. Belinite M
  4. Ballard G
  5. Mathews DH
  6. 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 Jan 08.
• 1. Bao C
  2. Ermolenko DN
  Ribosome as a Translocase and Helicase.; Biochemistry. Biokhimiia; Vol 86(8). 2021 Aug.
• 1. Ermolenko DN
  2. Mathews DH
  Making ends meet: New functions of mRNA secondary structure.; Wiley interdisciplinary reviews. RNA. 2020 Jun 29.
• 1. Wakabayashi H
  2. Warnasooriya C
  3. 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.
• 1. Warnasooriya C
  2. Feeney CF
  3. Laird KM
  4. Ermolenko DN
  5. Kielkopf CL
  A splice site-sensing conformational switch in U2AF2 is modulated by U2AF1 and its recurrent myelodysplasia-associated mutation.; Nucleic acids research; Vol 48(10). 2020 Jun 04.
• 1. Bao C
  2. Loerch S
  3. Ling C
  4. Korostelev AA
  5. Grigorieff N
  6. Ermolenko DN
  mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding.; eLife; Vol 9. 2020 May 19.
• 1. Ermolenko DN
  2. Whitford PC
  Experimental and computational techniques for studying structural dynamics and function of RNA.; Methods (San Diego, Calif.); Vol 162-163. 2019 Jun 01.
• 1. Lai WC
  2. Kayedkhordeh M
  3. Cornell EV
  4. Farah E
  5. Bellaousov S
  6. Rietmeijer R
  7. Salsi E
  8. Mathews DH
  9. Ermolenko DN
  mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances.; Nature communications; Vol 9(1). 2018 Oct 18.
• 1. Warnasooriya C
  2. Ling C
  3. Belashov IA
  4. Salim M
  5. Wedekind JE
  6. Ermolenko DN
  Observation of preQ1-II riboswitch dynamics using single-molecule FRET.; RNA biology. 2018 Oct 17.
• 1. Lai CW
  2. Ermolenko DN
  Ensemble and single-molecule FRET studies of protein synthesis.; Methods (San Diego, Calif.). 2017 Dec 13.
• 1. Ling C
  2. Ermolenko DN
  Caught on Camera: Intermediates of Ribosome Recycling.; Structure (London, England : 1993); Vol 24(12). 2016 Dec 06.
• 1. Salsi E
  2. Farah E
  3. Ermolenko DN
  EF-G Activation by Phosphate Analogs.; Journal of molecular biology; Vol 428(10 Pt B). 2016 May 22.
• 1. Ling C
  2. Ermolenko DN
  Structural insights into ribosome translocation.; Wiley interdisciplinary reviews. RNA. 2016 Apr 27.
• 1. Agrawal AA
  2. Salsi E
  3. Chatrikhi R
  4. Henderson S
  5. Jenkins JL
  6. Green MR
  7. Ermolenko DN
  8. Kielkopf CL
  An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal.; Nature communications; Vol 7. 2016.
• 1. Ling C
  2. 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; Vol 112(52). 2015 Dec 29.
• 1. Ling C
  2. Ermolenko DN
  Ribosome subunit joining frozen in time.; Structure (London, England : 1993); Vol 23(6). 2015 Jun 2.
• 1. Salsi E
  2. Farah E
  3. Netter Z
  4. Dann J
  5. Ermolenko DN
  Movement of elongation factor G between compact and extended conformations.; Journal of molecular biology; Vol 427(2). 2015 Jan 30.
• 1. Salsi E
  2. Farah E
  3. Dann J
  4. 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; Vol 111(42). 2014 Oct 21.
• 1. Kurosaki T
  2. Li W
  3. Hoque M
  4. Popp MW
  5. Ermolenko DN
  6. Tian B
  7. Maquat LE
  A post-translational regulatory switch on UPF1 controls targeted mRNA degradation.; Genes & development; Vol 28(17). 2014 Sep 1.
• 1. Brilot AF
  2. Korostelev AA
  3. Ermolenko DN
  4. 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; Vol 110(52). 2013 Dec 24.
• 1. Azpurua J
  2. Ke Z
  3. Chen IX
  4. Zhang Q
  5. Ermolenko DN
  6. Zhang ZD
  7. Gorbunova V
  8. 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; Vol 110(43). 2013 Oct 22.
• 1. Svidritskiy E
  2. Ling C
  3. Ermolenko DN
  4. 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; Vol 110(30). 2013 Jul 23.
• 1. Ermolenko DN
  2. Cornish PV
  3. Ha T
  4. Noller HF
  Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation.; RNA (New York, N.Y.); Vol 19(2). 2013 Feb.
• 1. Rudenko MI
  2. Holmes MR
  3. Ermolenko DN
  4. Lunt EJ
  5. Gerhardt S
  6. Noller HF
  7. Deamer DW
  8. Hawkins A
  9. Schmidt H
  Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip.; Biosensors & bioelectronics; Vol 29(1). 2011 Nov 15.
• 1. Ermolenko DN
  2. Noller HF
  mRNA translocation occurs during the second step of ribosomal intersubunit rotation.; Nature structural & molecular biology; Vol 18(4). 2011 Apr.
• 1. Cornish PV
  2. Ermolenko DN
  3. Staple DW
  4. Hoang L
  5. Hickerson RP
  6. Noller HF
  7. 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; Vol 106(8). 2009 Feb 24.
• 1. Korostelev A
  2. Ermolenko DN
  3. Noller HF
  Structural dynamics of the ribosome.; Current opinion in chemical biology; Vol 12(6). 2008 Dec.
• 1. Cornish PV
  2. Ermolenko DN
  3. Noller HF
  4. Ha T
  Spontaneous intersubunit rotation in single ribosomes.; Molecular cell; Vol 30(5). 2008 Jun 6.
• 1. Spiegel PC
  2. Ermolenko DN
  3. Noller HF
  Elongation factor G stabilizes the hybrid-state conformation of the 70S ribosome.; RNA (New York, N.Y.); Vol 13(9). 2007 Sep.
• 1. Ermolenko DN
  2. Majumdar ZK
  3. Hickerson RP
  4. Spiegel PC
  5. Clegg RM
  6. Noller HF
  Observation of intersubunit movement of the ribosome in solution using FRET.; Journal of molecular biology; Vol 370(3). 2007 Jul 13.
• 1. Ermolenko DN
  2. Spiegel PC
  3. Majumdar ZK
  4. Hickerson RP
  5. Clegg RM
  6. Noller HF
  The antibiotic viomycin traps the ribosome in an intermediate state of translocation.; Nature structural & molecular biology; Vol 14(6). 2007 Jun.
• 1. Ermolenko DN
  2. Dangi B
  3. Gvritishvili A
  4. Gronenborn AM
  5. Makhatadze GI
  Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences.; Biophysical chemistry; Vol 126(1-3). 2007 Mar.
• 1. Ermolenko DN
  2. Zherdev AV
  3. Dzantiev BB
  Horseradish peroxidase renaturation is less efficient at lower protein concentrations.; Protein and peptide letters; Vol 12(7). 2005 Oct.
• 1. Ermolenko DN
  2. Zherdev AV
  3. Dzantiev BB
  Antibodies as specific chaperones.; Biochemistry. Biokhimii︠a︡; Vol 69(11). 2004 Nov.
• 1. Bezsudnova EIu
  2. Zherdev AV
  3. Ermolenko DN
  4. Iakovleva IV
  5. Sviridov VV
  6. Popov VO
  7. Dzantiev BB
  [Peroxidase refolding in the presence of specific antibodies].; Prikladnaia biokhimiia i mikrobiologiia; Vol 39(5). 2003 Sep.
• 1. Ermolenko DN
  2. Richardson JM
  3. 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; Vol 12(6). 2003 Jun.
• 1. Makhatadze GI
  2. Loladze VV
  3. Ermolenko DN
  4. Chen X
  5. Thomas ST
  Contribution of surface salt bridges to protein stability: guidelines for protein engineering.; Journal of molecular biology; Vol 327(5). 2003 Apr 11.
• 1. Ermolenko DN
  2. Makhatadze GI
  Bacterial cold-shock proteins.; Cellular and molecular life sciences : CMLS; Vol 59(11). 2002 Nov.
• 1. Ermolenko DN
  2. Thomas ST
  3. Aurora R
  4. Gronenborn AM
  5. Makhatadze GI
  Hydrophobic interactions at the Ccap position of the C-capping motif of alpha-helices.; Journal of molecular biology; Vol 322(1). 2002 Sep 6.
• 1. Loladze VV
  2. Ermolenko DN
  3. Makhatadze GI
  Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior.; Journal of molecular biology; Vol 320(2). 2002 Jul 5.
• 1. Ermolenko DN
  2. Zherdev AV
  3. Dzantiev BB
  4. Popov VO
  Antiperoxidase antibodies enhance refolding of horseradish peroxidase.; Biochemical and biophysical research communications; Vol 291(4). 2002 Mar 8.
• 1. Loladze VV
  2. Ermolenko DN
  3. Makhatadze GI
  Heat capacity changes upon burial of polar and nonpolar groups in proteins.; Protein science : a publication of the Protein Society; Vol 10(7). 2001 Jul.