Edward P. O’Brien, Ph.D. Assistant Professor Department of Chemistry 402 Chemistry Bldg. Pennsylvania State University Phone: 814-867-5100 University Park, PA. 16802 Email: [email protected] Education 1/2009 – 12/2013 Postdoctoral Fellow, University of Cambridge Advisor, Prof. Christopher Dobson Co-advisor, Prof. Michele Vendruscolo 11/2013 Training, “Advanced Sequencing Technologies and Applications Course” Cold Spring Harbor Laboratory 9/2002 – 10/2008 Ph.D., Chemical Physics University of Maryland College Park Advisor, Prof. Dave Thirumalai Co-advisor, PI Bernard Brooks (National Institutes of Health) Thesis: Protein folding and amyloid formation in various environments 9/1998 – 5/2002 B.S., Biochemistry, minors in Mathematics and Physics University of the Sciences in Philadelphia Graduated with honors (Magna Cum Laude) Research Experience 1/2014 – present Assistant Professor, Department of Chemistry, Pennsylvania State University, University Park. 1/2009 – 12/2013 NSF and EPSRC Postdoctoral Research Fellow, Department of Chemistry, University of Cambridge. Advisor, Prof. Christopher Dobson; Co-advisor, Prof. Michele Vendruscolo. 9/2002 – 10/2008 NIH Graduate Research Fellow in Biophysics, University of Maryland College Park. Advisor, Dave Thirumalai; Co-advisor, Bernard Brooks (NIH). 6/2007 – 8/2007 NSF EAPSI Graduate Research Fellow, Department of Physics, Nagoya University, Japan. Advisor, Yuko Okamoto. 5/2002 – 9/2002 Schering-Plough Summer Research Fellow, University of the Sciences in Philadelphia. Advisor, Guillermo Moyna. 5/2001 – 9/2001 Summer Researcher, The Scripps Research Institute. Advisor, Gary Suizdak. Grants 7/2018 – 6/2021 National Science Foundation Advances in Biological Informatics “ABI INNOVATION: Physical Bioinformatics Tools for Measuring Translation Rates from Next-Generation Sequencing Data”. PI Ed O’Brien. 3 years, totalling $760,000. 8/2017 – 7/2022 National Institutes of Health (NIGMS) R35 MIRA Research Grant “Modeling the influence of translation-elongation kinetics on protein structure and function”. 5 years, totaling $1,900,000. 8/2016 – 7/2019 National Science Foundation - Deutsche Forschungsgemeinschaft CAREER Supplement. PI Ed O’Brien. 3 years, totalling $21,000. Page 1 of 7 6/2016 – 5/2021 National Science Foundation CAREER Grant “CAREER: The origins of codon translation rates and their consequences for nascent protein behavior”. PI Ed O’Brien. 5 years, totalling $900,000. 5/2015 – 5/2018 Human Frontier’s Science Program Research Grant “Quantifying and predicting the influence of translation kinetics on nascent proteome behavior”. PI Ed O’Brien; Co-PI, Bernd Bukau. 3 years, totalling $750,000 ($375k for PI). 5/2013 Biotechnology and Biology Sciences Research Council (UK) David Phillips Fellowship “A systems approach to understanding and manipulating In vivo nascent protein behavior at the molecular and cellular levels”. 5 years, totalling $1,700,000. Declined fellowship to start position at Penn State. 5/2013 The Royal Society (UK) University Research Fellowship “Model-based prediction of nascent protein behaviour in cells”. 5 years, totaling $1,000,000. Declined fellowship to start position at Penn State. 1/2012 – 1/2015 Engineering and Physical Sciences Research Council (UK) Research co- investigator on a grant that I wrote entitled “Tools for Understanding and Controlling the Non-Equilibrium Self-Assembly of Multi-Component Macromolecular Systems”. 3 years, totaling $473,000. 1/2009 – 1/2012 National Science Foundation Postdoctoral Research Fellowship in Bioinformatics. 3 years, totalling $187,000. 9/2002 – 10/2008 National Institutes of Health GPP Graduate Research Fellowship in Biophysics. 6/2007 – 8/2007 National Science Foundation East Asia and Pacific Summer Institutes Fellowship. Honors and Awards 8/2018 American Chemical Society OpenEye Outstanding Junior Faculty Award 5/2017 Priestly Undergraduate Teaching Award (2016) – A student-nominated teaching award given by Penn State University for excellence in undergraduate chemistry instruction. $5,000 cash prize. 6/2008 Best Poster Award, Gordon Research Conference on Biopolymers, “Osmolyte and denaturant effects on proteins are accurately predicted with the Molecular Transfer Model”. 3/2008 Best Poster Award, National Institutes of Health NHLBI Fellows Retreat, “Thermodynamic basis for the Dock-Lock mechanism of amyloid formation”. 5/2002 Lewis A. Reber Award for Excellence in Research, University of the Sciences in Philadelphia. 2001 Scherling-Plough sponsored Summer Research Fellowship. 1999, 2000 Merck sponsored Summer Research Fellowships. Professional Service Outside of Penn State: 10/2018 Conference co-organizer “Computational Biophysics at the Molecular and Mesoscales”, 5 days long, Quy Nhon, Vietnam. 4/2018 NSF Grant Review panel in Molecular and Cellular Biology. 3 days long, Arlington VA. 4/2017 Grant reviewer for the Netherlands Organization for Scientific Research, Natuurkunde Projectruimte program. Ad-hoc reviewer. 1/2018 Grant reviewer for the European Research Council, Advanced Grants research program. Ad hoc reviewer. 1/2018 Session Chair at the Gordon Research Seminar on Protein Folding Dynamics, Galveston, TX. 1/2018 Panelist on Round-table discussion of Careers in Research at the Gordon Research Seminar on Protein Folding Dynamics, Galveston, TX. Page 2 of 7 12/2017 Session Chair at the “New Approaches for Investigating Nascent Peptide Folding” Conference, Cambridge, UK. 11/2017 Grant reviewer for the Netherlands Organization for Scientific Research, Vidi program. Ad-hoc reviewer. 9/2017 Grant reviewer for the Canada Foundation for Innovation. Ad-hoc reviewer and panelist. 6/2016 Upward Bound Math and Science Program. 6-week program in which four high- school students from underserved communities carried out research in the O’Brien Lab. Penn State University. 2/2016 NSF EAPSI Grant Review panel in Mathematical and Physical Sciences. 2 days long, Teleconference, Arlington, VA. 2/2016 Elected Program Chair, 60th Biophysical Society National Meeting, Biopolymers In Vivo Sub subgroup. Los Angeles, CA. 2/2015 NSF EAPSI Grant Review panel in Mathematical and Physical Sciences. 2 days long, NSF Headquarters, Arlington, VA. 4/2015 Poster Judge. Penn State Undergraduate Research Exhibition. University Park, PA. 1/2015 NSF EAPSI Grant Review panel in Mathematical and Physical Sciences. 2 days long, NSF Headquarters, Arlington, VA. 8/2014 Organizer of the CECAM conference “Modeling Cellular Life: From single molecules to cellular function.” 4 day conference held in Lausanne, Switzerland. 2/2014 Session Chair on RNA dynamics at the Biophysical Society National Meeting, San Francisco, CA. 1/2014 NSF EAPSI Grant Review panel in Mathematical and Physical Sciences. 2 days long, NSF Headquarters, Arlington, VA. 12/2012 Co-organizer for the 23rd Annual Molecular Chaperone Club Meeting, University of Cambridge, UK. 5/2012 Organizer of the 3-day CECAM workshop on “Ribosome-associated protein folding: Translation, auxiliary factors, and translocation,” Lausanne, Switzerland. 1/2012 Discussion leader at the Gordon Research Seminar in Protein Folding, Ventura, CA. Within Penn State: 2017 - Present Faculty Awards Committee 2017 - Present Research Funding Committee 2017 - Present Teaching Awards Committee 2014 - 2017 Graduate Student Admissions Committee 2014 - 2017 Departmental Seminar Committee Teaching Experience Spring 2018 Lecturer, CHEM 110: “Introductory Chemistry” Penn State Fall 2017 Lecturer, CHEM 540: “Biophysical Chemistry” Penn State Spring 2017 Lecturer, CHEM 110: “Introductory Chemistry” Penn State Fall 2016 Lecturer, CHEM 540: “Biophysical Chemistry” Penn State Spring 2016 Lecturer, CHEM 110: “Introductory Chemistry” Penn State Fall 2015 Lecturer, CHEM 540: “Biophysical Chemistry” Penn State Fall 2014 Lecturer, CHEM 540: “Biophysical Chemistry” Penn State Fall 2012 Lecturer, “Computer simulation methods in chemistry and physics,” University of Cambridge. Taught six lectures on molecular dynamics methods. Fall 2009 Teaching assistant in the Theoretical Chemistry Lab, University of Cambridge. Covered topics including Huckel theory, isomerization, and magnetic phase transitions. Page 3 of 7 Journal Reviewer Activity (past 3 years) Nature Communications Proceedings of the National Academy of Sciences Journal of the American Chemical Society Journal of Chemical Physics Journal of Physical Chemistry B Nucleic Acids Research FEBS Letters Biochemistry eLife Professional Society Affiliations American Chemical Society Biophysical Society Patents Patent application US 20170016008 A1 – “Design of mRNA sequences to control co-translational folding of proteins.” Submitted in 2016. Publications Submitted (* indicates corresponding author) 41. D. Nissley and E. P. O’Brien*. “Interpreting co-translational folding FRET measurements at the molecular level” Submitted. 40. S. Leininger, D. Nissley, F. Trovato and E. P. O’Brien*. “Domain topology, stability, and translation speed determine co-translational folding force generation.” Submitted. 39. A. K. Sharma, N. Ahmed, P. Sormani, P. Ciryam and E. P. O’Brien*. “A chemical kinetic basis for measuring initiation and elongation rates from ribosome profiling data.” Submitted. 38. N. Ahmed, P. Sormani, P. Ciryam, M. Vendruscolo, C.M. Dobson and E. P. O’Brien*. “Identifying the ribosome’s A- and P-site locations on ribosome-protected mRNA fragments using Linear Programming.” Submitted. Publications (* indicates corresponding author) At Penn State: 37. B. Fritch, A. Kosolapov, P. Hudson, L. Woodcock,