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Dmitri Ermolenko

TitleAssistant Professor
InstitutionSchool of Medicine and Dentistry
DepartmentBiochemistry and Biophysics
AddressUniversity of Rochester Medical Center
School of Medicine and Dentistry
601 Elmwood Ave, Box 712
Rochester NY 14642
Other Positions
TitleAssistant Professor
InstitutionUniversity of Rochester, River Campus
DepartmentBiology RC

 
 Overview
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.

 
 Selected Publications
List All   |   Timeline
  1. Brilot AF, Korostelev AA, Ermolenko DN, Grigorieff N. Structure of the ribosome with elongation factor G trapped in the pretranslocation state. Proc Natl Acad Sci U S A. 2013 Dec 24; 110(52):20994-9.
    View in: PubMed
  2. 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. Proc Natl Acad Sci U S A. 2013 Oct 22; 110(43):17350-5.
    View in: PubMed
  3. Svidritskiy E, Ling C, Ermolenko DN, Korostelev AA. Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome. Proc Natl Acad Sci U S A. 2013 Jul 23; 110(30):12283-8.
    View in: PubMed
  4. 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.
    View in: PubMed
  5. 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. Biosens Bioelectron. 2011 Nov 15; 29(1):34-9.
    View in: PubMed
  6. Ermolenko DN, Noller HF. mRNA translocation occurs during the second step of ribosomal intersubunit rotation. Nat Struct Mol Biol. 2011 Apr; 18(4):457-62.
    View in: PubMed
  7. 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. Proc Natl Acad Sci U S A. 2009 Feb 24; 106(8):2571-6.
    View in: PubMed
  8. Korostelev A, Ermolenko DN, Noller HF. Structural dynamics of the ribosome. Curr Opin Chem Biol. 2008 Dec; 12(6):674-83.
    View in: PubMed
  9. Cornish PV, Ermolenko DN, Noller HF, Ha T. Spontaneous intersubunit rotation in single ribosomes. Mol Cell. 2008 Jun 6; 30(5):578-88.
    View in: PubMed
  10. 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.
    View in: PubMed
  11. Ermolenko DN, Spiegel PC, Majumdar ZK, Hickerson RP, Clegg RM, Noller HF. The antibiotic viomycin traps the ribosome in an intermediate state of translocation. Nat Struct Mol Biol. 2007 Jun; 14(6):493-7.
    View in: PubMed
  12. Ermolenko DN, Majumdar ZK, Hickerson RP, Spiegel PC, Clegg RM, Noller HF. Observation of intersubunit movement of the ribosome in solution using FRET. J Mol Biol. 2007 Jul 13; 370(3):530-40.
    View in: PubMed
  13. Ermolenko DN, Dangi B, Gvritishvili A, Gronenborn AM, Makhatadze GI. Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences. Biophys Chem. 2007 Mar; 126(1-3):25-35.
    View in: PubMed
  14. Ermolenko DN, Zherdev AV, Dzantiev BB. Horseradish peroxidase renaturation is less efficient at lower protein concentrations. Protein Pept Lett. 2005 Oct; 12(7):639-43.
    View in: PubMed
  15. Ermolenko DN, Zherdev AV, Dzantiev BB. Antibodies as specific chaperones. Biochemistry (Mosc). 2004 Nov; 69(11):1233-8.
    View in: PubMed
  16. Bezsudnova EIu, Zherdev AV, Ermolenko DN, Iakovleva IV, Sviridov VV, Popov VO, Dzantiev BB. [Peroxidase refolding in the presence of specific antibodies]. Prikl Biokhim Mikrobiol. 2003 Sep-Oct; 39(5):509-17.
    View in: PubMed
  17. 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 Sci. 2003 Jun; 12(6):1169-76.
    View in: PubMed
  18. Makhatadze GI, Loladze VV, Ermolenko DN, Chen X, Thomas ST. Contribution of surface salt bridges to protein stability: guidelines for protein engineering. J Mol Biol. 2003 Apr 11; 327(5):1135-48.
    View in: PubMed
  19. Ermolenko DN, Makhatadze GI. Bacterial cold-shock proteins. Cell Mol Life Sci. 2002 Nov; 59(11):1902-13.
    View in: PubMed
  20. Ermolenko DN, Thomas ST, Aurora R, Gronenborn AM, Makhatadze GI. Hydrophobic interactions at the Ccap position of the C-capping motif of alpha-helices. J Mol Biol. 2002 Sep 6; 322(1):123-35.
    View in: PubMed
  21. Loladze VV, Ermolenko DN, Makhatadze GI. Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior. J Mol Biol. 2002 Jul 5; 320(2):343-57.
    View in: PubMed
  22. Ermolenko DN, Zherdev AV, Dzantiev BB, Popov VO. Antiperoxidase antibodies enhance refolding of horseradish peroxidase. Biochem Biophys Res Commun. 2002 Mar 8; 291(4):959-65.
    View in: PubMed
  23. Loladze VV, Ermolenko DN, Makhatadze GI. Heat capacity changes upon burial of polar and nonpolar groups in proteins. Protein Sci. 2001 Jul; 10(7):1343-52.
    View in: PubMed

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