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Items: 50

1.

Mechanochemistry in Translation.

Leininger SE, Narayan K, Deutsch C, O'Brien EP.

Biochemistry. 2019 Jun 11. doi: 10.1021/acs.biochem.9b00260. [Epub ahead of print]

PMID:
31134795
2.

A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data.

Sharma AK, Sormanni P, Ahmed N, Ciryam P, Friedrich UA, Kramer G, O'Brien EP.

PLoS Comput Biol. 2019 May 23;15(5):e1007070. doi: 10.1371/journal.pcbi.1007070. eCollection 2019 May.

3.

Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming.

Ahmed N, Sormanni P, Ciryam P, Vendruscolo M, Dobson CM, O'Brien EP.

Sci Rep. 2019 Apr 18;9(1):6256. doi: 10.1038/s41598-019-42348-x.

4.

Domain topology, stability, and translation speed determine mechanical force generation on the ribosome.

Leininger SE, Trovato F, Nissley DA, O'Brien EP.

Proc Natl Acad Sci U S A. 2019 Mar 19;116(12):5523-5532. doi: 10.1073/pnas.1813003116. Epub 2019 Mar 1.

PMID:
30824598
5.

Structural Origins of FRET-Observed Nascent Chain Compaction on the Ribosome.

Nissley DA, O'Brien EP.

J Phys Chem B. 2018 Nov 1;122(43):9927-9937. doi: 10.1021/acs.jpcb.8b07726. Epub 2018 Oct 18.

PMID:
30265800
6.

Kinetic and structural comparison of a protein's cotranslational folding and refolding pathways.

Samelson AJ, Bolin E, Costello SM, Sharma AK, O'Brien EP, Marqusee S.

Sci Adv. 2018 May 30;4(5):eaas9098. doi: 10.1126/sciadv.aas9098. eCollection 2018 May.

7.

Erythromycin leads to differential protein expression through differences in electrostatic and dispersion interactions with nascent proteins.

Nguyen HL, Pham DL, O'Brien EP, Li MS.

Sci Rep. 2018 Apr 24;8(1):6460. doi: 10.1038/s41598-018-24344-9.

8.

Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis.

Fritch B, Kosolapov A, Hudson P, Nissley DA, Woodcock HL, Deutsch C, O'Brien EP.

J Am Chem Soc. 2018 Apr 18;140(15):5077-5087. doi: 10.1021/jacs.7b11044. Epub 2018 Apr 6.

9.

Determinants of translation speed are randomly distributed across transcripts resulting in a universal scaling of protein synthesis times.

Sharma AK, Ahmed N, O'Brien EP.

Phys Rev E. 2018 Feb;97(2-1):022409. doi: 10.1103/PhysRevE.97.022409.

PMID:
29548178
10.

Non-equilibrium coupling of protein structure and function to translation-elongation kinetics.

Sharma AK, O'Brien EP.

Curr Opin Struct Biol. 2018 Apr;49:94-103. doi: 10.1016/j.sbi.2018.01.005. Epub 2018 Feb 3. Review.

PMID:
29414517
11.

Profiling Ssb-Nascent Chain Interactions Reveals Principles of Hsp70-Assisted Folding.

Döring K, Ahmed N, Riemer T, Suresh HG, Vainshtein Y, Habich M, Riemer J, Mayer MP, O'Brien EP, Kramer G, Bukau B.

Cell. 2017 Jul 13;170(2):298-311.e20. doi: 10.1016/j.cell.2017.06.038.

12.

Increasing Protein Production Rates Can Decrease the Rate at Which Functional Protein Is Produced and Their Steady-State Levels.

Sharma AK, O'Brien EP.

J Phys Chem B. 2017 Jul 20;121(28):6775-6784. doi: 10.1021/acs.jpcb.7b01700. Epub 2017 Jul 7.

PMID:
28650169
13.

Fast Protein Translation Can Promote Co- and Posttranslational Folding of Misfolding-Prone Proteins.

Trovato F, O'Brien EP.

Biophys J. 2017 May 9;112(9):1807-1819. doi: 10.1016/j.bpj.2017.04.006.

14.

Altered Co-Translational Processing Plays a Role in Huntington's Pathogenesis-A Hypothesis.

Nissley DA, O'Brien EP.

Front Mol Neurosci. 2016 Jul 6;9:54. doi: 10.3389/fnmol.2016.00054. eCollection 2016.

15.

Insights into Cotranslational Nascent Protein Behavior from Computer Simulations.

Trovato F, O'Brien EP.

Annu Rev Biophys. 2016 Jul 5;45:345-69. doi: 10.1146/annurev-biophys-070915-094153. Epub 2016 May 23. Review.

PMID:
27297399
16.

Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding.

Nissley DA, Sharma AK, Ahmed N, Friedrich UA, Kramer G, Bukau B, O'Brien EP.

Nat Commun. 2016 Feb 18;7:10341. doi: 10.1038/ncomms10341.

17.

Physical Origins of Codon Positions That Strongly Influence Cotranslational Folding: A Framework for Controlling Nascent-Protein Folding.

Sharma AK, Bukau B, O'Brien EP.

J Am Chem Soc. 2016 Feb 3;138(4):1180-95. doi: 10.1021/jacs.5b08145. Epub 2016 Jan 21.

PMID:
26716464
18.

Cotranslational Protein Folding inside the Ribosome Exit Tunnel.

Nilsson OB, Hedman R, Marino J, Wickles S, Bischoff L, Johansson M, Müller-Lucks A, Trovato F, Puglisi JD, O'Brien EP, Beckmann R, von Heijne G.

Cell Rep. 2015 Sep 8;12(10):1533-40. doi: 10.1016/j.celrep.2015.07.065. Epub 2015 Aug 28.

19.

Modeling the effect of codon translation rates on co-translational protein folding mechanisms of arbitrary complexity.

Caniparoli L, O'Brien EP.

J Chem Phys. 2015 Apr 14;142(14):145102. doi: 10.1063/1.4916914.

20.

Timing is everything: unifying codon translation rates and nascent proteome behavior.

Nissley DA, O'Brien EP.

J Am Chem Soc. 2014 Dec 31;136(52):17892-8. doi: 10.1021/ja510082j. Epub 2014 Dec 19. Review.

PMID:
25486504
21.

Understanding the influence of codon translation rates on cotranslational protein folding.

O'Brien EP, Ciryam P, Vendruscolo M, Dobson CM.

Acc Chem Res. 2014 May 20;47(5):1536-44. doi: 10.1021/ar5000117. Epub 2014 May 1. Review.

PMID:
24784899
22.
23.

Protein folding: from theory to practice.

Thirumalai D, Liu Z, O'Brien EP, Reddy G.

Curr Opin Struct Biol. 2013 Feb;23(1):22-9. doi: 10.1016/j.sbi.2012.11.010. Epub 2012 Dec 21. Review.

PMID:
23266001
24.

In vivo translation rates can substantially delay the cotranslational folding of the Escherichia coli cytosolic proteome.

Ciryam P, Morimoto RI, Vendruscolo M, Dobson CM, O'Brien EP.

Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):E132-40. doi: 10.1073/pnas.1213624110. Epub 2012 Dec 19.

25.

Trigger factor slows co-translational folding through kinetic trapping while sterically protecting the nascent chain from aberrant cytosolic interactions.

O'Brien EP, Christodoulou J, Vendruscolo M, Dobson CM.

J Am Chem Soc. 2012 Jul 4;134(26):10920-32. doi: 10.1021/ja302305u. Epub 2012 Jun 22.

PMID:
22680285
26.

Prediction of variable translation rate effects on cotranslational protein folding.

O'Brien EP, Vendruscolo M, Dobson CM.

Nat Commun. 2012 May 29;3:868. doi: 10.1038/ncomms1850. Erratum in: Nat Commun. 2013;4:1519.

PMID:
22643895
27.

Effects of pH on proteins: predictions for ensemble and single-molecule pulling experiments.

O'Brien EP, Brooks BR, Thirumalai D.

J Am Chem Soc. 2012 Jan 18;134(2):979-87. doi: 10.1021/ja206557y. Epub 2011 Dec 27.

28.

Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide.

O'Brien EP, Straub JE, Brooks BR, Thirumalai D.

J Phys Chem Lett. 2011 May 19;2(10):1171-1177.

29.

Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins.

Liu Z, Reddy G, O'Brien EP, Thirumalai D.

Proc Natl Acad Sci U S A. 2011 May 10;108(19):7787-92. doi: 10.1073/pnas.1019500108. Epub 2011 Apr 21.

30.

Design, fabrication, and implementation of thermally driven outdoor testing devices for building joint sealants.

White CC, Tan KT, O'Brien EP, Hunston DL, Chin JW, Williams RS.

Rev Sci Instrum. 2011 Feb;82(2):025112. doi: 10.1063/1.3543817.

PMID:
21361638
31.

New scenarios of protein folding can occur on the ribosome.

O'Brien EP, Christodoulou J, Vendruscolo M, Dobson CM.

J Am Chem Soc. 2011 Jan 26;133(3):513-26. doi: 10.1021/ja107863z. Epub 2011 Jan 4.

PMID:
21204555
32.

Transient tertiary structure formation within the ribosome exit port.

O'Brien EP, Hsu ST, Christodoulou J, Vendruscolo M, Dobson CM.

J Am Chem Soc. 2010 Dec 1;132(47):16928-37. doi: 10.1021/ja106530y. Epub 2010 Nov 9.

PMID:
21062068
33.

Theoretical perspectives on protein folding.

Thirumalai D, O'Brien EP, Morrison G, Hyeon C.

Annu Rev Biophys. 2010;39:159-83. doi: 10.1146/annurev-biophys-051309-103835. Review.

PMID:
20192765
34.

Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils.

O'Brien EP, Okamoto Y, Straub JE, Brooks BR, Thirumalai D.

J Phys Chem B. 2009 Oct 29;113(43):14421-30. doi: 10.1021/jp9050098.

35.

How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins?

O'Brien EP, Morrison G, Brooks BR, Thirumalai D.

J Chem Phys. 2009 Mar 28;130(12):124903. doi: 10.1063/1.3082151.

36.

Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins.

O'Brien EP, Brooks BR, Thirumalai D.

Biochemistry. 2009 May 5;48(17):3743-54. doi: 10.1021/bi8021119.

37.

Factors governing helix formation in peptides confined to carbon nanotubes.

O'Brien EP, Stan G, Thirumalai D, Brooks BR.

Nano Lett. 2008 Nov;8(11):3702-8. doi: 10.1021/nl8019328. Epub 2008 Sep 26.

38.

Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model.

O'Brien EP, Ziv G, Haran G, Brooks BR, Thirumalai D.

Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13403-8. doi: 10.1073/pnas.0802113105. Epub 2008 Aug 29.

39.

Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism.

O'Brien EP, Dima RI, Brooks B, Thirumalai D.

J Am Chem Soc. 2007 Jun 13;129(23):7346-53. Epub 2007 May 16.

PMID:
17503819
40.

Effect of finite size on cooperativity and rates of protein folding.

Kouza M, Li MS, O'brien EP Jr, Hu CK, Thirumalai D.

J Phys Chem A. 2006 Jan 19;110(2):671-6.

PMID:
16405339
42.

Hermansky-Pudlak syndrome type 7 (HPS-7) results from mutant dysbindin, a member of the biogenesis of lysosome-related organelles complex 1 (BLOC-1).

Li W, Zhang Q, Oiso N, Novak EK, Gautam R, O'Brien EP, Tinsley CL, Blake DJ, Spritz RA, Copeland NG, Jenkins NA, Amato D, Roe BA, Starcevic M, Dell'Angelica EC, Elliott RW, Mishra V, Kingsmore SF, Paylor RE, Swank RT.

Nat Genet. 2003 Sep;35(1):84-9. Epub 2003 Aug 17.

43.

Ru2 and Ru encode mouse orthologs of the genes mutated in human Hermansky-Pudlak syndrome types 5 and 6.

Zhang Q, Zhao B, Li W, Oiso N, Novak EK, Rusiniak ME, Gautam R, Chintala S, O'Brien EP, Zhang Y, Roe BA, Elliott RW, Eicher EM, Liang P, Kratz C, Legius E, Spritz RA, O'Sullivan TN, Copeland NG, Jenkins NA, Swank RT.

Nat Genet. 2003 Feb;33(2):145-53. Epub 2003 Jan 27.

PMID:
12548288
44.

Analysis of the degradation of oligonucleotide strands during the freezing/thawing processes using MALDI-MS.

Davis DL, O'Brien EP, Bentzley CM.

Anal Chem. 2000 Oct 15;72(20):5092-6.

PMID:
11055733
45.

An integrated genetic map of the pearl locus of mouse chromosome 13.

Seymour AB, Yanak BL, O'Brien EP, Rusiniak ME, Novak EK, Pinto LH, Swank RT, Gorin MB.

Genome Res. 1996 Jun;6(6):538-44.

46.

The gene encoding the thrombin receptor (Cf2r) maps to mouse chromosome 13.

Poirier C, O'Brien EP, Bueno Brunialti AL, Chambard J, Swank RT, Guénet J.

Mamm Genome. 1996 Apr;7(4):322. No abstract available.

PMID:
8661713
47.

High-resolution genetic mapping of the gunmetal gene which regulates platelet production.

O'Brien EP, Zhen L, Jiang SY, Novak EK, Swank RT.

Mamm Genome. 1996 Mar;7(3):206-8. No abstract available.

PMID:
8833241
48.

Molecular markers near the mouse brachymorphic (bm) gene, which affects connective tissues and bleeding time.

Rusiniak ME, O'Brien EP, Novak EK, Barone SM, McGarry MP, Reddington M, Swank RT.

Mamm Genome. 1996 Feb;7(2):98-102.

PMID:
8835524
49.

Molecular markers near two mouse chromosome 13 genes, muted and pearl, which cause platelet storage pool deficiency (SPD).

O'Brien EP, Novak EK, Zhen L, Manly KF, Stephenson D, Swank RT.

Mamm Genome. 1995 Jan;6(1):19-24.

PMID:
7719021
50.

Molecular map of chromosome 19 including three genes affecting bleeding time: ep, ru, and bm.

O'Brien EP, Novak EK, Keller SA, Poirier C, Guénet JL, Swank RT.

Mamm Genome. 1994 Jun;5(6):356-60.

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