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Items: 35

1.

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.

Nat Commun. 2018 Oct 18;9(1):4328. doi: 10.1038/s41467-018-06792-z.

2.

Observation of preQ1-II riboswitch dynamics using single-molecule FRET.

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

RNA Biol. 2018 Oct 17:1-7. doi: 10.1080/15476286.2018.1536591. [Epub ahead of print]

PMID:
30328747
3.

Ensemble and single-molecule FRET studies of protein synthesis.

Lai WC, Ermolenko DN.

Methods. 2018 Mar 15;137:37-48. doi: 10.1016/j.ymeth.2017.12.007. Epub 2017 Dec 13.

4.

Caught on Camera: Intermediates of Ribosome Recycling.

Ling C, Ermolenko DN.

Structure. 2016 Dec 6;24(12):2035-2036. doi: 10.1016/j.str.2016.11.009.

5.

Structural insights into ribosome translocation.

Ling C, Ermolenko DN.

Wiley Interdiscip Rev RNA. 2016 Sep;7(5):620-36. doi: 10.1002/wrna.1354. Epub 2016 Apr 27. Review.

6.

EF-G Activation by Phosphate Analogs.

Salsi E, Farah E, Ermolenko DN.

J Mol Biol. 2016 May 22;428(10 Pt B):2248-58. doi: 10.1016/j.jmb.2016.03.032. Epub 2016 Apr 8.

7.

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.

Nat Commun. 2016 Mar 8;7:10950. doi: 10.1038/ncomms10950.

8.

Initiation factor 2 stabilizes the ribosome in a semirotated conformation.

Ling C, Ermolenko DN.

Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15874-9. doi: 10.1073/pnas.1520337112. Epub 2015 Dec 14.

9.

Ribosome subunit joining frozen in time.

Ling C, Ermolenko DN.

Structure. 2015 Jun 2;23(6):977-8. doi: 10.1016/j.str.2015.05.007.

10.

Movement of elongation factor G between compact and extended conformations.

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

J Mol Biol. 2015 Jan 30;427(2):454-67. doi: 10.1016/j.jmb.2014.11.010. Epub 2014 Nov 15.

11.

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

Salsi E, Farah E, Dann J, Ermolenko DN.

Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15060-5. doi: 10.1073/pnas.1410873111. Epub 2014 Oct 6.

12.

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 Dev. 2014 Sep 1;28(17):1900-16. doi: 10.1101/gad.245506.114.

13.

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

Brilot AF, Korostelev AA, Ermolenko DN, Grigorieff N.

Proc Natl Acad Sci U S A. 2013 Dec 24;110(52):20994-9. doi: 10.1073/pnas.1311423110. Epub 2013 Dec 9.

14.

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.

Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):17350-5. doi: 10.1073/pnas.1313473110. Epub 2013 Sep 30.

15.

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

Svidritskiy E, Ling C, Ermolenko DN, Korostelev AA.

Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12283-8. doi: 10.1073/pnas.1304922110. Epub 2013 Jul 3.

16.

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 Feb;19(2):158-66. doi: 10.1261/rna.035964.112. Epub 2012 Dec 17.

17.

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.

Biosens Bioelectron. 2011 Nov 15;29(1):34-9. doi: 10.1016/j.bios.2011.07.047. Epub 2011 Aug 5.

PMID:
21855314
18.

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

Ermolenko DN, Noller HF.

Nat Struct Mol Biol. 2011 Apr;18(4):457-62. doi: 10.1038/nsmb.2011. Epub 2011 Mar 13.

19.

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.

Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2571-6. doi: 10.1073/pnas.0813180106. Epub 2009 Feb 3. Erratum in: Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5448.

20.

Structural dynamics of the ribosome.

Korostelev A, Ermolenko DN, Noller HF.

Curr Opin Chem Biol. 2008 Dec;12(6):674-83. doi: 10.1016/j.cbpa.2008.08.037. Epub 2008 Oct 9. Review.

21.

Spontaneous intersubunit rotation in single ribosomes.

Cornish PV, Ermolenko DN, Noller HF, Ha T.

Mol Cell. 2008 Jun 6;30(5):578-88. doi: 10.1016/j.molcel.2008.05.004.

22.

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

Spiegel PC, Ermolenko DN, Noller HF.

RNA. 2007 Sep;13(9):1473-82. Epub 2007 Jul 13.

23.

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

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

Nat Struct Mol Biol. 2007 Jun;14(6):493-7. Epub 2007 May 21.

PMID:
17515906
24.

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

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

J Mol Biol. 2007 Jul 13;370(3):530-40. Epub 2007 Apr 20.

PMID:
17512008
25.

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

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

Biophys Chem. 2007 Mar;126(1-3):25-35. Epub 2006 Apr 5.

PMID:
16713063
26.

Horseradish peroxidase renaturation is less efficient at lower protein concentrations.

Ermolenko DN, Zherdev AV, Dzantiev BB.

Protein Pept Lett. 2005 Oct;12(7):639-43.

PMID:
16522186
27.

Antibodies as specific chaperones.

Ermolenko DN, Zherdev AV, Dzantiev BB.

Biochemistry (Mosc). 2004 Nov;69(11):1233-8. Review.

28.

[Peroxidase refolding in the presence of specific antibodies].

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

Prikl Biokhim Mikrobiol. 2003 Sep-Oct;39(5):509-17. Russian.

PMID:
14593862
30.

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

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

J Mol Biol. 2003 Apr 11;327(5):1135-48.

PMID:
12662936
31.

Bacterial cold-shock proteins.

Ermolenko DN, Makhatadze GI.

Cell Mol Life Sci. 2002 Nov;59(11):1902-13. Review.

PMID:
12530521
32.

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

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

J Mol Biol. 2002 Sep 6;322(1):123-35.

PMID:
12215419
33.

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

Loladze VV, Ermolenko DN, Makhatadze GI.

J Mol Biol. 2002 Jul 5;320(2):343-57.

PMID:
12079391
34.

Antiperoxidase antibodies enhance refolding of horseradish peroxidase.

Ermolenko DN, Zherdev AV, Dzantiev BB, Popov VO.

Biochem Biophys Res Commun. 2002 Mar 8;291(4):959-65.

PMID:
11866459
35.

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

Loladze VV, Ermolenko DN, Makhatadze GI.

Protein Sci. 2001 Jul;10(7):1343-52.

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