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Dmitri N. Ermolenko, Ph.D.

Dmitri N. Ermolenko, Ph.D.

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About Me

Faculty Appointments

Professor - Department of Biochemistry and Biophysics (SMD)

Research

We are interested in the mechanisms of the ribosome function. The ribosome is a central component of cell metabolism, translating genetic code and synthesizing proteins in all living organism. The ribosome is an extremely complex and highly dynamic machine. Our research is focused on the mechanics o...
We are interested in the mechanisms of the ribosome function. The ribosome is a central component of cell metabolism, translating genetic code and synthesizing proteins in all living organism. The ribosome is an extremely complex and highly dynamic machine. Our research is focused on the mechanics of ribosome movement along mRNA during protein synthesis. Movement of ribosomes along mRNA is essential attribute of protein synthesis in all organisms and often used to regulate protein expression.

Publications

Journal Articles

40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion.

Wakabayashi H, Zhu M, Grayhack EJ, Mathews DH, Ermolenko DN

bioRxiv : the preprint server for biology.. 2025 January 4 Epub 01/04/2025.

A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay.

De Zoysa T, Hauke AC, Iyer NR, Marcus E, Ostrowski SM, Stegemann F, Ermolenko DN, Fay JC, Phizicky EM

PLoS genetics.. 2024 January 20 (1):e1011146. Epub 01/31/2024.

Comparing FRET Pairs that Report on Intersubunit Rotation in Bacterial Ribosomes.

Das A, Bao C, Ermolenko DN

Journal of molecular biology.. 2023 August 1435 (15):168185. Epub 06/20/2023.

Comparing FRET pairs that report on intersubunit rotation in bacterial ribosomes.

Das A, Bao C, Ermolenko DN

bioRxiv : the preprint server for biology.. 2023 May 9 Epub 05/09/2023.

Interplay between Inter-Subunit Rotation of the Ribosome and Binding of Translational GTPases.

Das A, Adiletta N, Ermolenko DN

International journal of molecular sciences.. 2023 April 724 (8)Epub 04/07/2023.

Intrinsically Unstructured Sequences in the mRNA 3' UTR Reduce the Ability of Poly(A) Tail to Enhance Translation.

Lai WC, Zhu M, Belinite M, Ballard G, Mathews DH, Ermolenko DN

Journal of molecular biology.. 2022 December 30434 (24):167877. Epub 11/08/2022.

Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation.

Bao C, Zhu M, Nykonchuk I, Wakabayashi H, Mathews DH, Ermolenko DN

Nature communications.. 2022 February 2113 (1):988. Epub 02/21/2022.

Ribosome as a Translocase and Helicase.

Bao C, Ermolenko DN

Biochemistry. Biokhimii?a?.. 2021 August 86 (8):992-1002. Epub 1900 01 01.

Making ends meet: New functions of mRNA secondary structure.

Ermolenko DN, Mathews DH

Wiley interdisciplinary reviews. RNA.. 2021 March 12 (2):e1611. Epub 06/29/2020.

Extending the Spacing between the Shine-Dalgarno Sequence and P-Site Codon Reduces the Rate of mRNA Translocation.

Wakabayashi H, Warnasooriya C, Ermolenko DN

Journal of molecular biology.. 2020 July 24432 (16):4612-4622. Epub 06/13/2020.

A splice site-sensing conformational switch in U2AF2 is modulated by U2AF1 and its recurrent myelodysplasia-associated mutation.

Warnasooriya C, Feeney CF, Laird KM, Ermolenko DN, Kielkopf CL

Nucleic acids research.. 2020 June 448 (10):5695-5709. Epub 1900 01 01.

mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding.

Bao C, Loerch S, Ling C, Korostelev AA, Grigorieff N, Ermolenko DN

eLife.. 2020 May 199 Epub 05/19/2020.

Observation of preQ-II riboswitch dynamics using single-molecule FRET.

Warnasooriya C, Ling C, Belashov IA, Salim M, Wedekind JE, Ermolenko DN

RNA biology.. 2019 September 16 (9):1086-1092. Epub 10/30/2018.

Experimental and computational techniques for studying structural dynamics and function of RNA.

Ermolenko DN, Whitford PC

Methods : a companion to Methods in enzymology.. 2019 June 1162-163 :1-2. Epub 06/20/2019.

mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances.

Lai WC, Kayedkhordeh M, Cornell EV, Farah E, Bellaousov S, Rietmeijer R, Salsi E, Mathews DH, Ermolenko DN

Nature communications.. 2018 October 189 (1):4328. Epub 10/18/2018.

Ensemble and single-molecule FRET studies of protein synthesis.

Lai CW, Ermolenko DN

Methods : a companion to Methods in enzymology.. 2018 March 15137 :37-48. Epub 12/13/2017.

Caught on Camera: Intermediates of Ribosome Recycling.

Ling C, Ermolenko DN

Structure.. 2016 December 624 (12):2035-2036. Epub 1900 01 01.

Structural insights into ribosome translocation.

Ling C, Ermolenko DN

Wiley interdisciplinary reviews. RNA.. 2016 September 7 (5):620-36. Epub 04/27/2016.

EF-G Activation by Phosphate Analogs.

Salsi E, Farah E, Ermolenko DN

Journal of molecular biology.. 2016 May 22428 (10 Pt B):2248-58. Epub 04/08/2016.

An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal.

Agrawal AA, Salsi E, Chatrikhi R, Henderson S, Jenkins JL, Green MR, Ermolenko DN, Kielkopf CL

Nature communications.. 2016 March 87 :10950. Epub 03/08/2016.

Initiation factor 2 stabilizes the ribosome in a semirotated conformation.

Ling C, Ermolenko DN

Proceedings of the National Academy of Sciences of the United States of America.. 2015 December 29112 (52):15874-9. Epub 12/14/2015.

Ribosome subunit joining frozen in time.

Ling C, Ermolenko DN

Structure.. 2015 June 223 (6):977-8. Epub 1900 01 01.

Movement of elongation factor G between compact and extended conformations.

Salsi E, Farah E, Netter Z, Dann J, Ermolenko DN

Journal of molecular biology.. 2015 January 30427 (2):454-67. Epub 11/15/2014.

Following movement of domain IV of elongation factor G during ribosomal translocation.

Salsi E, Farah E, Dann J, Ermolenko DN

Proceedings of the National Academy of Sciences of the United States of America.. 2014 October 21111 (42):15060-5. Epub 10/06/2014.

A post-translational regulatory switch on UPF1 controls targeted mRNA degradation.

Kurosaki T, Li W, Hoque M, Popp MW, Ermolenko DN, Tian B, Maquat LE

Genes & development.. 2014 September 128 (17):1900-16. Epub 1900 01 01.

Structure of the ribosome with elongation factor G trapped in the pretranslocation state.

Brilot AF, Korostelev AA, Ermolenko DN, Grigorieff N

Proceedings of the National Academy of Sciences of the United States of America.. 2013 December 24110 (52):20994-9. Epub 12/09/2013.

Naked mole-rat has increased translational fidelity compared with the mouse, as well as a unique 28S ribosomal RNA cleavage.

Azpurua J, Ke Z, Chen IX, Zhang Q, Ermolenko DN, Zhang ZD, Gorbunova V, Seluanov A

Proceedings of the National Academy of Sciences of the United States of America.. 2013 October 22110 (43):17350-5. Epub 09/30/2013.

Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome.

Svidritskiy E, Ling C, Ermolenko DN, Korostelev AA

Proceedings of the National Academy of Sciences of the United States of America.. 2013 July 23110 (30):12283-8. Epub 07/03/2013.

Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation.

Ermolenko DN, Cornish PV, Ha T, Noller HF

RNA.. 2013 February 19 (2):158-66. Epub 12/17/2012.

Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip.

Rudenko MI, Holmes MR, Ermolenko DN, Lunt EJ, Gerhardt S, Noller HF, Deamer DW, Hawkins A, Schmidt H

Biosensors & bioelectronics.. 2011 November 1529 (1):34-9. Epub 08/05/2011.

mRNA translocation occurs during the second step of ribosomal intersubunit rotation.

Ermolenko DN, Noller HF

Nature structural & molecular biology.. 2011 April 18 (4):457-62. Epub 03/13/2011.

Following movement of the L1 stalk between three functional states in single ribosomes.

Cornish PV, Ermolenko DN, Staple DW, Hoang L, Hickerson RP, Noller HF, Ha T

Proceedings of the National Academy of Sciences of the United States of America.. 2009 February 24106 (8):2571-6. Epub 02/03/2009.

Structural dynamics of the ribosome.

Korostelev A, Ermolenko DN, Noller HF

Current opinion in chemical biology.. 2008 December 12 (6):674-83. Epub 10/09/2008.

Spontaneous intersubunit rotation in single ribosomes.

Cornish PV, Ermolenko DN, Noller HF, Ha T

Molecular cell.. 2008 June 630 (5):578-88. Epub 1900 01 01.

Elongation factor G stabilizes the hybrid-state conformation of the 70S ribosome.

Spiegel PC, Ermolenko DN, Noller HF

RNA.. 2007 September 13 (9):1473-82. Epub 07/13/2007.

Observation of intersubunit movement of the ribosome in solution using FRET.

Ermolenko DN, Majumdar ZK, Hickerson RP, Spiegel PC, Clegg RM, Noller HF

Journal of molecular biology.. 2007 July 13370 (3):530-40. Epub 04/20/2007.

The antibiotic viomycin traps the ribosome in an intermediate state of translocation.

Ermolenko DN, Spiegel PC, Majumdar ZK, Hickerson RP, Clegg RM, Noller HF

Nature structural & molecular biology.. 2007 June 14 (6):493-7. Epub 05/21/2007.

Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences.

Ermolenko DN, Dangi B, Gvritishvili A, Gronenborn AM, Makhatadze GI

Biophysical chemistry.. 2007 March 126 (1-3):25-35. Epub 04/05/2006.

Horseradish peroxidase renaturation is less efficient at lower protein concentrations.

Ermolenko DN, Zherdev AV, Dzantiev BB

Protein and peptide letters.. 2005 October 12 (7):639-43. Epub 1900 01 01.

Antibodies as specific chaperones.

Ermolenko DN, Zherdev AV, Dzantiev BB

Biochemistry. Biokhimii?a?.. 2004 November 69 (11):1233-8. Epub 1900 01 01.

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.

Ermolenko DN, Richardson JM, Makhatadze GI

Protein science : a publication of the Protein Society.. 2003 June 12 (6):1169-76. Epub 1900 01 01.

Contribution of surface salt bridges to protein stability: guidelines for protein engineering.

Makhatadze GI, Loladze VV, Ermolenko DN, Chen X, Thomas ST

Journal of molecular biology.. 2003 April 11327 (5):1135-48. Epub 1900 01 01.

[Peroxidase refolding in the presence of specific antibodies].

Bezsudnova EIu, Zherdev AV, Ermolenko DN, Iakovleva IV, Sviridov VV, Popov VO, Dzantiev BB

Prikladnaia biokhimiia i mikrobiologiia. 2003 39 (5):509-17. Epub 1900 01 01.

Bacterial cold-shock proteins.

Ermolenko DN, Makhatadze GI

Cellular and molecular life sciences : CMLS.. 2002 November 59 (11):1902-13. Epub 1900 01 01.

Hydrophobic interactions at the Ccap position of the C-capping motif of alpha-helices.

Ermolenko DN, Thomas ST, Aurora R, Gronenborn AM, Makhatadze GI

Journal of molecular biology.. 2002 September 6322 (1):123-35. Epub 1900 01 01.

Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior.

Loladze VV, Ermolenko DN, Makhatadze GI

Journal of molecular biology.. 2002 July 5320 (2):343-57. Epub 1900 01 01.

Antiperoxidase antibodies enhance refolding of horseradish peroxidase.

Ermolenko DN, Zherdev AV, Dzantiev BB, Popov VO

Biochemical and biophysical research communications.. 2002 March 8291 (4):959-65. Epub 1900 01 01.

Heat capacity changes upon burial of polar and nonpolar groups in proteins.

Loladze VV, Ermolenko DN, Makhatadze GI

Protein science : a publication of the Protein Society.. 2001 July 10 (7):1343-52. Epub 1900 01 01.