Researcher Profile

Researcher Profile

Edward P. O'Brien, Jr., PhD

Edward P. O'Brien, Jr., PhD

Assistant Professor, Chemistry
Scientific Program:Mechanisms of Carcinogenesis
Disease Teams:
Institute for CyberScience (ICS) - Co-hire
epo2@psu.edu

Research Interests

  • Proteins
  • Ribosomes
  • Protein Folding
  • Kinetics
  • Codon
  • Messenger RNA
  • Peptides
  • Molecular Models
  • Amino Acids
  • Proteome
  • Temperature
  • Static Electricity

Recent Publications

2021

Shao, D, Ahmed, N, Soni, N & O’Brien, EP 2021, 'RiboA: a web application to identify ribosome A-site locations in ribosome profiling data', BMC bioinformatics, vol. 22, no. 1, 156. https://doi.org/10.1186/s12859-021-04068-w

2020

Nguyen, HL, Lan, PD, Thai, NQ, Nissley, DA, O'Brien, EP & Li, MS 2020, 'Does SARS-CoV-2 bind to human ACE2 more strongly than does SARS-CoV?', Journal of Physical Chemistry B, vol. 124, no. 34, pp. 7336-7347. https://doi.org/10.1021/acs.jpcb.0c04511
Nissley, DA, Vu, QV, Trovato, F, Ahmed, N, Jiang, Y, Li, MS & O'Brien, EP 2020, 'Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling', Journal of the American Chemical Society, vol. 142, no. 13, pp. 6103-6110. https://doi.org/10.1021/jacs.9b12264
Leininger, SE, Deutsch, C & O’Brien, EP 2020, 'Forcing the ribosome to change its message', Journal of Biological Chemistry, vol. 295, no. 20, pp. 6809-6810. https://doi.org/10.1074/jbc.H120.013747
Wolfe, DK, Persichetti, JR, Sharma, AK, Hudson, PS, Woodcock, HL & O'brien, EP 2020, 'Hierarchical Markov State Model Building to Describe Molecular Processes', Journal of Chemical Theory and Computation, vol. 16, no. 3, pp. 1816-1826. https://doi.org/10.1021/acs.jctc.9b00955
Ahmed, N, Friedrich, UA, Sormanni, P, Ciryam, P, Altman, NS, Bukau, B, Kramer, G & O'Brien, EP 2020, 'Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates: Amino acid pairs module translation-elongation rates', Journal of Molecular Biology, vol. 432, no. 24, 166696. https://doi.org/10.1016/j.jmb.2020.10.030

2019

Sharma, AK, Sormanni, P, Ahmed, N, Ciryam, P, Friedrich, UA, Kramer, G & O'Brien, EP 2019, 'A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data', PLoS computational biology, vol. 15, no. 5, e1007070. https://doi.org/10.1371/journal.pcbi.1007070
Leininger, SE, Trovato, F, Nissley, DA & O’Brien, EP 2019, 'Domain topology, stability, and translation speed determine mechanical force generation on the ribosome', Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 12, pp. 5523-5532. https://doi.org/10.1073/pnas.1813003116
Ahmed, N, Sormanni, P, Ciryam, P, Vendruscolo, M, Dobson, CM & O’Brien, EP 2019, 'Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming', Scientific reports, vol. 9, no. 1, 6256. https://doi.org/10.1038/s41598-019-42348-x
Leininger, SE, Narayan, K, Deutsch, C & O'Brien, EP 2019, 'Mechanochemistry in Translation', Biochemistry, vol. 58, no. 47, pp. 4657-4666. https://doi.org/10.1021/acs.biochem.9b00260

2018

Sharma, AK, Ahmed, N & O'Brien, EP 2018, 'Determinants of translation speed are randomly distributed across transcripts resulting in a universal scaling of protein synthesis times', Physical Review E, vol. 97, no. 2, 022409. https://doi.org/10.1103/PhysRevE.97.022409
Nguyen, HL, Pham, DL, O'Brien, EP & Li, MS 2018, 'Erythromycin leads to differential protein expression through differences in electrostatic and dispersion interactions with nascent proteins', Scientific reports, vol. 8, no. 1, 6460. https://doi.org/10.1038/s41598-018-24344-9
Samelson, AJ, Bolin, E, Costello, SM, Sharma, AK, O’Brien, EP & Marqusee, S 2018, 'Kinetic and structural comparison of a protein’s cotranslational folding and refolding pathways', Science Advances, vol. 4, no. 5, eaas9098. https://doi.org/10.1126/sciadv.aas9098
Sharma, AK & O'Brien, EP 2018, 'Non-equilibrium coupling of protein structure and function to translation–elongation kinetics', Current Opinion in Structural Biology, vol. 49, pp. 94-103. https://doi.org/10.1016/j.sbi.2018.01.005
Fritch, B, Kosolapov, A, Hudson, P, Nissley, DA, Woodcock, HL, Deutsch, C & O'Brien, EP 2018, 'Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis', Journal of the American Chemical Society, vol. 140, no. 15, pp. 5077-5087. https://doi.org/10.1021/jacs.7b11044
Nissley, DA & O'Brien, EP 2018, 'Structural Origins of FRET-Observed Nascent Chain Compaction on the Ribosome', Journal of Physical Chemistry B, vol. 122, no. 43, pp. 9927-9937. https://doi.org/10.1021/acs.jpcb.8b07726

2017

Trovato, F & O'Brien, EP 2017, 'Fast Protein Translation Can Promote Co- and Posttranslational Folding of Misfolding-Prone Proteins', Biophysical journal, vol. 112, no. 9, pp. 1807-1819. https://doi.org/10.1016/j.bpj.2017.04.006
Sharma, AK & O'Brien, EP 2017, 'Increasing Protein Production Rates Can Decrease the Rate at Which Functional Protein is Produced and Their Steady-State Levels', Journal of Physical Chemistry B, vol. 121, no. 28, pp. 6775-6784. https://doi.org/10.1021/acs.jpcb.7b01700
Döring, K, Ahmed, N, Riemer, T, Suresh, HG, Vainshtein, Y, Habich, M, Riemer, J, Mayer, MP, O'Brien, EP, Kramer, G & Bukau, B 2017, 'Profiling Ssb-Nascent Chain Interactions Reveals Principles of Hsp70-Assisted Folding', Cell, vol. 170, no. 2, pp. 298-311.e20. https://doi.org/10.1016/j.cell.2017.06.038

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