Edward O’Brien

Associate Professor of Chemistry

Edward O’Brien

Research Summary

Developing and applying Physical Bioinformatic techniques to measure rates of translation transcriptome-wide and their molecular origins as relates to fundamental biology and disease.

Huck Graduate Students

Huck Affiliations

Publication Tags

Proteins Protein Folding Ribosomes Kinetics Messenger Rna Tunnels Molecules Peptides Membranes Amino Acids Codon Coulomb Interactions Experiments Folding Recycling Enzymes Peptidyl Transferases Thermodynamics Molecular Models Free Energy Temperature Protein Domains Integer Programming Entropy Translating

Most Recent Papers

RiboA

Danying Shao, Nabeel Ahmed, Nishant Soni, Edward P. O’Brien, 2021, BMC Bioinformatics

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

Nabeel Ahmed, Ulrike A. Friedrich, Pietro Sormanni, Prajwal Ciryam, Naomi S. Altman, Bernd Bukau, Günter Kramer, Edward P. O'Brien, 2020, Journal of Molecular Biology

Does SARS-CoV-2 bind to human ACE2 more strongly than does SARS-CoV?

Hoang Linh Nguyen, Pham Dang Lan, Nguyen Quoc Thai, Daniel A. Nissley, Edward P. O'Brien, Mai Suan Li, 2020, Journal of Physical Chemistry B on p. 7336-7347

Forcing the ribosome to change its message

Sarah E. Leininger, Carol Deutsch, Edward P. O’Brien, 2020, Journal of Biological Chemistry on p. 6809-6810

Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling

Daniel A. Nissley, Quyen V. Vu, Fabio Trovato, Nabeel Ahmed, Yang Jiang, Mai Suan Li, Edward P. O'Brien, 2020, Journal of the American Chemical Society on p. 6103-6110

Hierarchical Markov State Model Building to Describe Molecular Processes

David K. Wolfe, Joseph R. Persichetti, Ajeet K. Sharma, Phillip S. Hudson, H. Lee Woodcock, Edward P. O'brien, 2020, Journal of Chemical Theory and Computation on p. 1816-1826

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

Nabeel Ahmed, Pietro Sormanni, Prajwal Ciryam, Michele Vendruscolo, Christopher M. Dobson, Edward P. O’Brien, 2019, Scientific Reports

Mechanochemistry in Translation

Sarah E. Leininger, Karthik Narayan, Carol Deutsch, Edward P. O'Brien, 2019, Biochemistry on p. 4657-4666

Domain Topology, Stability, and Translation Speed Determine Co-Translational Folding Force Generation

S. Leininger, D. Nissley, F. Trovato, E. O'Brien, 2019, Proc. Natl. Acad. Sci. U.S.A. on p. 5523-5532

A Chemical Kinetic Basis for Measuring Initiation and Elongation Rates from Ribosome Profiling Data

A. Sharma, N. Ahmed, P. Sormani, P. Ciryam, E. O'Brien, 2019, PLoS Comp. Bio.

Most-Cited Papers

Cotranslational Protein Folding inside the Ribosome Exit Tunnel

Ola B. Nilsson, Rickard Hedman, Jacopo Marino, Stephan Wickles, Lukas Bischoff, Magnus Johansson, Annika Müller-Lucks, Fabio Trovato, Joseph D. Puglisi, Edward P. O'Brien, Roland Beckmann, Gunnar von Heijne, 2015, Cell Reports on p. 1533-1540

New scenarios of protein folding can occur on the ribosome

Edward P. O'Brien, John Christodoulou, Michele Vendruscolo, Christopher M. Dobson, 2011, Journal of the American Chemical Society on p. 513-526

Prediction of variable translation rate effects on cotranslational protein folding

Edward P. O'Brien, Michele Vendruscolo, Christopher M. Dobson, 2012, Nature Communications

Understanding the influence of codon translation rates on cotranslational protein folding

Edward P. O'Brien, Prajwal Ciryam, Michele Vendruscolo, Christopher M. Dobson, 2014, Accounts of Chemical Research on p. 1536-1544

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

Kristina Döring, Nabeel Ahmed, Trine Riemer, Harsha Garadi Suresh, Yevhen Vainshtein, Markus Habich, Jan Riemer, Matthias P. Mayer, Edward P. O'Brien, Günter Kramer, Bernd Bukau, 2017, Cell on p. 298-311.e20

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

Zhenxing Liu, Govardhan Reddy, Edward P. O'Brien, D. Thirumalai, 2011, Proceedings of the National Academy of Sciences of the United States of America on p. 7787-7792

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

Edward P. O'Brien, John Christodoulou, Michele Vendruscolo, Christopher M. Dobson, 2012, Journal of the American Chemical Society on p. 10920-10932

Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates

Edward P. O'brien, Michele Vendruscolo, Christopher M. Dobson, 2014, Nature Communications

Protein folding

D. Thirumalai, Zhenxing Liu, Edward P. O'Brien, Govardhan Reddy, 2013, Current Opinion in Structural Biology on p. 22-29

Effects of pH on proteins

Edward P. O'Brien, Bernard R. Brooks, D. Thirumalai, 2012, Journal of the American Chemical Society on p. 979-987