Edward O’Brien

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 Protein Messenger Rna Kinetics Ribosomes Enzymes Codon Simulation Proteome Mutation Genes Molecular Dynamics Folding Antibodies Biochemistry Genome Proteostasis Application Molecules Mechanics Molecule Quality Control Integer Programming Viruses

Most Recent Publications

Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and less functional

Daniel A. Nissley, Yang Jiang, Fabio Trovato, Ian Sitarik, Karthik B. Narayan, Philip To, Yingzi Xia, Stephen D. Fried, Edward P. O’Brien, 2022, Nature Communications

A pan-CRISPR analysis of mammalian cell specificity identifies ultra-compact sgRNA subsets for genome-scale experiments

Boyang Zhao, Yiyun Rao, Scott Leighow, Edward P. O’Brien, Luke Gilbert, Justin R. Pritchard, 2022, Nature Communications

Modeling Ensembles of Enzyme Reaction Pathways with Hi-MSM Reveals the Importance of Accounting for Pathway Diversity

Joseph R. Persichetti, Yang Jiang, Phillip S. Hudson, Edward P. O'Brien, 2022, Journal of Physical Chemistry B on p. 9748-9758

Pulse labeling reveals the tail end of protein folding by proteome profiling

Mang Zhu, Erich R. Kuechler, Ryan W.K. Wong, Gaetano Calabrese, Ian M. Sitarik, Viraj Rana, Nikolay Stoynov, Edward P. O'Brien, Jörg Gsponer, Thibault Mayor, 2022, Cell Reports

Cocktail of REGN Antibodies Binds More Strongly to SARS-CoV-2 Than Its Components, but the Omicron Variant Reduces Its Neutralizing Ability

Hung Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O'Brien, Mai Suan Li, 2022, Journal of Physical Chemistry B on p. 2812-2823

Erratum: Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force (Biochemistry (2021) 60:43 (3223−3235) DOI:10.1021/acs.biochem.1c00507)

Sarah E. Leininger, Judith Rodriguez, Quyen V. Vu, Yang Jiang, Mai Suan Li, Carol Deutsch, Edward P. O’Brien, 2022, Biochemistry on p. 125

How synonymous mutations alter enzyme structure and function over long timescales

Yang Jiang, Syam Sundar Neti, Ian Sitarik, Priya Pradhan, Philip To, Yingzi Xia, Stephen D. Fried, Squire J. Booker, Edward P. O’Brien, 2022, Nature Chemistry

Combinations of slow-translating codon clusters can increase mRNA half-life in Saccharomyces cerevisiae

Ajeet K. Sharma, Johannes Venezian, Ayala Shiber, Günter Kramer, Bernd Bukau, Edward P. O’Brien, 2021, Proceedings of the National Academy of Sciences of the United States of America

RiboA: a web application to identify ribosome A-site locations in ribosome profiling data

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

Genomic and experimental evidence that ALK<sup>ATI</sup> does not predict single agent sensitivity to ALK inhibitors

Haider Inam, Ivan Sokirniy, Yiyun Rao, Anushka Shah, Farnaz Naeemikia, Edward O'Brien, Cheng Dong, David M. McCandlish, Justin R. Pritchard, 2021, iScience

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

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

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

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

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: From theory to practice

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

Timing is everything: Unifying Codon translation rates and nascent proteome behavior

Daniel A. Nissley, Edward P. Obrien, 2014, Journal of the American Chemical Society on p. 17892-17898

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

Daniel A. Nissley, Ajeet K. Sharma, Nabeel Ahmed, Ulrike A. Friedrich, Günter Kramer, Bernd Bukau, Edward P. O'Brien, 2016, Nature Communications

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

Ajeet K. Sharma, Edward P. O'Brien, 2018, Current Opinion in Structural Biology on p. 94-103

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

Avi J. Samelson, Eric Bolin, Shawn M. Costello, Ajeet K. Sharma, Edward P. O’Brien, Susan Marqusee, 2018, Science advances