O'Brien Lab

Publications

32) A. K. Sharma and E. P. O’Brien. “Antagonism between the kinetics of translation and protein folding result in complex behavior
in the rate of functional nascent protein production” Under Review.

31) K. Döring, N. Ahmed, T. Riemer, H.G. Suresh, Y. Vainshtein, M. Habich, J. Riemer, M. P. Mayer, E. P. O’Brien, G. Kramer and B. Bukau.
“Profiling of Ssb interactions with nascent proteins reveals principles of Hsp70 assisted co-translational folding”. Cell, 2017 (In
Press).

30) F. Trovato and E. P. O’Brien. “Fast protein translation can promote co- and posttranslational folding of misfolding-prone proteins”
Biophys. J., 2017. 112, 1807-1819. Read More.

29) D. A. Nissley and E. P. O’Brien. “Altered co-translational processing plays a role in Huntington’s pathogenesis — A hypothesis” Front.
Mol. Neurosci., 2016. 9:54. Read More.

28) F. Trovato and E. P. O’Brien. “Insights into co-translational nascent protein behavior from computer simulations” Annu. Rev. Biophys.,
2016. 45, 345-371. Read More.

27) D. A. Nissley, A. K. Sharma, N. Ahmed, U. Friedrich, G. Kramer, B. Bukau and E. P. O’Brien. “Accurate prediction of cellular co-
translational folding indicates proteins can switch from post- to co-translational folding” Nat. Commun., 2016. 7, 10341.
Read More.

26) A. K. Sharma, B. Bukau, E. P. O’Brien. “Physical origins of codon positions that strongly influence cotranslational folding: A
framework for controlling nascent-protein folding” J. Am. Chem. Soc., 2016. 138(4), 1180-1195. Read More.

25) O. B. Nilsson, R. Hedman, J. Marino, S. Wickles, L. Bischoff, M. Johansson, A. Muller-Lucks, F. Trovato, J. D. Puglisi, E. P. O’Brien, R.
Beckmann and G. von Heijne. “Co-translational protein folding inside the ribosome exit tunnel” Cell Rep., 2015. 12, 1533-1540
Read More.

24) L. Caniparolli and E. P. O’Brien. “Modeling the effect of codon translation rates on co-translational protein folding mechanisms of
arbitrary complexity” J. Chem. Phys., 2015. 142, 145102. [PDF]

23) D. A. Nissley and E. P. O’Brien. “Timing is everything: Unifying codon translation rates and nascent proteome
behavior” J. Am. Chem. Soc., 2014. 136, 17892–17898. [PDF]

22) E. P. O’Brien, P. Ciryam, M. Vendruscolo and C. M. Dobson. “Understanding the influence of codon translation rates
on cotranslational protein folding” Acc. Chem. Res., 2014. 47, 1536-1544. [PDF]
* Corresponding author

21) E. P. O’Brien*, M. Vendruscolo and C. M. Dobson. “Kinetic modeling indicates that fast translating codons can coordinate
cotranslational folding by helping avoid misfolded intermediates” Nat. Commun., 2014. 5, 2988. [PDF]
[PDF SI]
* Corresponding author

20) P. Ciryam, R. I. Morimoto, M. Vendruscolo, C. M. Dobson and E. P. O’Brien*. “In vivo translation rates can substantially delay
the cotranslational folding of the E. coli cytosolic proteome” Proc. Natl. Acad. Sci. U.S.A., 2013. 110, E132-E140 [PDF]
* Corresponding author

- Highlighted in the journal Biopolymers 99(4):v.
- Highlighted on the NSF’s SEE Innovation website.

19) D. Thirumalai, Z. Liu, E. P. O’Brien and G. Reddy. “Protein folding: From theory to practice” Curr. Opin. Struc. Biol., 2013. 23, 22-29.

18) E. P. O’Brien, J. Christodoulou, M. Vendruscolo and C. M. Dobson. “Trigger factor slows co-translational folding through kinetic
trapping while sterically protecting the nascent chain from aberrant cytosolic interactions” J. Am. Chem. Soc., 2012. 134, 10920-
10932. [PDF] [PDF SI]
- Highlighted in JACS Spotlights 134:12321.

17) E. P. O’Brien, M. Vendruscolo and C. M. Dobson. “Prediction of variable translation rate effects on co-translational folding” Nat.
Commun.,
2012. 3, 868. [PDF] [PDF SI]
- Highlighted on the NSF’s SEE Innovation website.

16) E. P. O’Brien, B. R. Brooks and D. Thirumalai. “Effects of pH on proteins: Predictions for ensemble and single molecule pulling
experiments” J. Am. Chem. Soc., 2012. 134, 979-987.

15) E. P. O’Brien, J. Christodoulou, M. Vendruscolo and C. M. Dobson. “New scenarios of protein folding can occur on the ribosome” J. Am.
Chem. Soc.
, 2011. 133, 513-526. [PDF]
- Recommended on the Faculty of 1000 website.

14) Z. Liu, G. Reddy, E. P. O’Brien and D. Thirumalai. “Denaturant dependent folding of globular proteins: Collapse kinetics and
chevron plots” Proc. Natl. Acad. Sci. U.S.A., 2011. 108, 7787-7792.

13) E. P. O’Brien, J. E. Straub, B. R. Brooks and D. Thirumalai. “Influence of nanoparticle size and shape on oligomer formation of an
amyloidogenic peptide” J. Phys. Chem. Letters, 2011. 10, 1171-1177.

12) E. P. O’Brien, S. T. D. Hsu, J. Christodoulou, M. Vendruscolo and C. M. Dobson. “Transient tertiary structure formation within the
ribosome exit port” J. Am. Chem. Soc., 2010. 132, 16928-16937. [PDF]

11) D. Thirumalai, E. P. O’Brien, G. Morrison and C. H. Hyeon. “Theoretical perspectives on protein folding” Annu. Rev. Biophys., 2010. 39,
159-183.

10) E. P. O’Brien, Y. Okamoto, J. E. Straub, B. R. Brooks and D. Thirumalai. “Thermodynamic perspective on the dock-lock growth
mechanism of amyloid fibrils” J. Phys. Chem. B, 2009. 113, 14421-14430.

9) E. P. O’Brien, B. R. Brooks and D. Thirumalai. “Molecular origin of constant m-values, denatured state collapse, and residue-dependent
transition midpoints in globular proteins” Biochem., 2009. 48, 3743–3754.

8) E. P. O’Brien, G. Morrison, B. R. Brooks and D. Thirumalai. “How accurate are polymer models in the analysis of Forster resonance
energy transfer experiments on proteins?” J. Chem. Phys., 2009. 130, 124903.

7) E. P. O’Brien, G. Stan, D. Thirumalai and B. R. Brooks. “Factors governing helix formation in peptides confined to carbon nanotubes”
Nano Letters, 2008. 8, 3702–3708.

6) E. P. O’Brien, G. Ziv, G. Haran, B. R. Brooks and D. Thirumalai. “Effects of denaturants and osmolytes on proteins are accurately
predicted by the molecular transfer model” Proc. Natl. Acad. Sci. U.S.A., 2008. 105, 13403–13408.

5) E. P. O’Brien, R. I. Dima, B. R. Brooks and D. Thirumalai. “Interactions between hydrophobic and ionic solutes in aqueous guanidinium
chloride and urea solutions: Lessons for protein denaturation mechanism” J. Am. Chem. Soc., 2007. 129, 7346–7353.

4) K. Maksim, L. Mai Suan, E. P. O’Brien, H. Chin-Kun and D. Thirumalai. “Effect of finite size on cooperativity and rates of protein
folding” J. Phys. Chem. A, 2006. 110, 671–676.

3) E. P. O’Brien and G. Moyna. “Use of 13C chemical shift surfaces in the study of carbohydrate conformation. Application to cyclodextrins
in the solid state and in solution” Carbohydr. Res., 2004. 339, 87–96.

2) C. W. Swalina, E. P. O’Brien and G. Moyna. “Study of the temperature dependent conformational averaging of 1H NMR resonances in
vinylcyclopropane through the use of ab initio methodology and Boltzmann statistics” Magn. Reson. Chem., 2002. 40, 195–201.

1)  D. Davis, E. P. O’Brien and C. Bentzley. “Analysis of the degradation of DNA strands during the freezing/thawing process using MALDI-
MS”Analy. Chem., 2000. 72, 5092–5096.