Peter L. Freddolino, Ph.D.
Postdoctoral Research Scientist Department of Systems Biology, Columbia University
Contact 406 Russ Berrie Pavilion Voice: +1 (609) 439-1811 Information Columbia University Fax: +1 (212) 851-5149 1150 St. Nicholas Avenue Email: [email protected] New York, NY 10032 Website: http://tavazoielab.c2b2.columbia.edu/petefred
Education University of Illinois at Urbana-Champaign, Urbana, Illinois, 2004-2009 Ph.D., Biophysics and Computational Biology GPA: 4.0 Advisor: Klaus Schulten Thesis title: “Application of all-atom and coarse-grained molecular dynamics to long timescale structural transitions of proteins” Completed additional option in Computational Science and Engineering (see http://cse.illinois.edu/programs)
California Institute of Technology, Pasadena, California, 2000-2004 B.S. with Honors, Biology GPA: 4.0
Research Postdoctoral Research Scientist with Dr. Saeed Tavazoie, Columbia University Experience (2011-present) and Princeton University (2009-2011) • Development of methods for genome-scale profiling of DNA binding protein locations under physiological conditions • Identification of mechanisms for rapid microbial adaptation to stressful conditions • Investigation of the fitness landscape effects of perturbation of Rho-dependent termi- nation in E. coli • Identification of anticipatory behavior evolutionarily hard-wired into bacterial genetic regulatory networks
Graduate Research Fellow with Dr. Klaus Schulten, University of Illinois at Urbana-Champaign, 2004-2009 • Molecular dynamics and QM/MM investigation of light-induced receptor activation in LOV domains • Investigation of satellite tobacco mosaic virus assembly and disassembly through molec- ular dynamics simulations and single molecule fluorescence microscopy (with Prof. T. Ha, University of Illinois) • Development of coarse-grained models for large polymeric biological assemblies • Modeling of switching in the bacterial flagellum using multiscale simulations and com- bined crystallographic and cryo-EM data • Coarse-grained simulation of high density lipoprotein particle assembly mechanisms • Molecular dynamics analysis of ligand binding and ligand-induced structural changes in the NR3A NMDA receptor
Freddolino – Curriculum vitae – Page 1 of 8 • Investigation of the protein folding processes for the villin headpiece and WW domain using molecular dynamics simulations
Undergraduate Research Assistant with Dr. William A. Goddard III, California Institute of Technology, 2001-2004 • Development of methods for structure prediction of GPCRs • Structural prediction and virtual ligand screening for the β adrenergic receptor family
Honors and NIH Pathway to Independence Award (K99, 2013–2015; pending R00, 2015–2018, with Awards option for earlier conversion to R00) Beckman Fellowship, University of Illinois at Urbana-Champaign, 2008-2009
National Science Foundation Graduate Research Fellowship, 2004-2009
Distinguished Fellowship, University of Illinois at Urbana-Champaign, 2004-2007
Sigma Xi Award for Undergraduate Research, California Institute of Technology, 2004 (awarded to one graduating senior each year)
President’s Scholarship, California Institute of Technology, 2000-2004
Journal H-index: 21 (ISI Web of Science), 22 (Google Scholar) Articles See my Google Scholar page for full text links and citation information
33. P. Freddolino, H. Goodarzi, and S. Tavazoie. Revealing the genetic basis of natural bacterial phenotypic divergence. J. Bacteriol., in press, 2013.
32. A. Hottes, P. Freddolino, A. Khare, Z. Donnell, J. Liu, and S. Tavazoie. Bacterial Adaptation Through Loss of Function. PLoS Genetics, 9(7): e1003617, 2013.
31. P. Freddolino, K. Gardner, and K. Schulten. Signaling mechanisms of LOV do- mains: New insights from molecular dynamics studies. Photochem. Photobiol. Sci., 12:1158–1170, 2013.
30. P. Freddolino and S. Tavazoie. The Dawn of Virtual Cell Biology. Cell 150:248–250, 2012.
29. P. Freddolino and S. Tavazoie. Beyond Homeostasis: A Predictive-Dynamic Frame- work for Understanding Cellular Behavior. Ann. Rev. Cell. Dev. Biol., 28:363-384, 2012.
28. P. Freddolino, H. Goodarzi, and S. Tavazoie. Fitness Landscape Transformation through a Single Amino Acid Change in the Rho Terminator. PLoS Genetics 8(5):e1002744, 2012.
27. Y. Liu, J. Str¨umpfer, P. Freddolino, M. Gruebele, and K. Schulten. Structural Char- acterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations. J. Phys. Chem. Lett. 3:1117–1123, 2012.
26. P. Freddolino, S. Amini, and S. Tavazoie. Newly Identified Genetic Variations in Common Escherichia coli MG1655 Stock Cultures. J. Bacteriol., 194:303–306, 2012.
25. E. Schreiner, L. Trabuco, P. Freddolino, and K. Schulten. Stereochemical errors and
Freddolino – Curriculum vitae – Page 2 of 8 their implications for molecular dynamics simulations. BMC Bioinformatics, 12:190, 2011.
24. S.-H. Song, P. Freddolino, A. Nash, E. Carroll, K. Schulten, K. Gardner, and D. Larsen. Modulating LOV Domain Photodynamics with a Residue Alteration out- side the Chromophore Binding Site. Biochemistry, 50:2411–2423, 2011.
23. P. Freddolino, C. Harrison, Y. Liu, and K. Schulten. Challenges in protein folding simulations: Force field, timescale, sampling, and analysis. Nature Physics, 6:751–758, 2010.
22. D. Cerutti, P. Freddolino, R. Duke, and D. Case. Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models J. Phys. Chem. B, 114:12811–12824, 2010.
21. A. Rajan, P. Freddolino and K. Schulten. Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding. PLoS One, 5:e9890, 2010.
20. P. Freddolino and K. Schulten. Common structural transitions in explicit-solvent simulations of villin headpiece folding. Biophysical Journal, 97:2338-2347, 2009.
19. P. Freddolino, S. Park, B. Roux, and K. Schulten. Force field bias in protein folding simulations. Biophysical Journal, 96:3772–378, 2009.
18. D. S. Cerutti, R. Duke, P. Freddolino, H. Fan, and T. Lybrand. A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics. J. Chem. Theor. Comput., 4:1669-1680, 2008.
17. Y. Yao, C. B. Harrison, P. Freddolino, K. Schulten, and M. L. Mayer. Molecular mechanisms of ligand recognition by NR3 subtype glutamate receptors. EMBO Jour- nal, 27:2158-2170, 2008.
16. P. Freddolino, F. Liu, M. Gruebele, and K. Schulten. Ten-microsecond MD simula- tion of a fast-folding WW domain. Biophysical Journal, 94:L75-L77, 2008.
15. J. Stone, J. Phillips, P. Freddolino, D. Hardy, L. Trabuco, and K. Schulten. Accel- erating molecular modeling applications with graphics processors. J. Comp. Chem., 28:2618-2640, 2007.
14. A. Shih, P. Freddolino, S. Sligar, and K. Schulten. Disassembly of nanodiscs with cholate. Nano Letters, 7:1692-1696, 2007.
13. A. Shih, A. Arkhipov, P. Freddolino, S. Sligar, and K. Schulten. Assembly of lipids and proteins into lipoprotein particles. J. Phys. Chem. B, 111:11095-11104, 2007.
12. A. Shih, P. Freddolino, A. Arkhipov, and K. Schulten. Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. J. Struct. Biol., 157:579-592, 2007.
11. A. Arkhipov, P. Freddolino, and K. Schulten. Stability and dynamics of virus cap- sids described by coarse-grained modeling. Structure, 14:1767-1777, 2006.
10. P. Freddolino, M. Dittrich, and K. Schulten. Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. Biophysical Journal, 91:3630-3639, 2006.
9. P. Spijker, N. Vaidehi, P. Freddolino, P. Hilbers, and W. Goddard III. Dynamic behavior of fully solvated beta2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist. PNAS 103:4882-4887, 2006.
Freddolino – Curriculum vitae – Page 3 of 8 8. A. Arkhipov, P. Freddolino, K. Imada, K. Namba, and K. Schulten. Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Biophysical Journal, 91:4589-4597, 2006.
7. P. Freddolino, A. Arkhipov, S. Larson, A. McPherson, and K. Schulten. Molecu- lar dynamics simulations of the complete satellite tobacco mosaic virus. Structure, 14:437-449, 2006.
6. D. Lu, A. Aksimentiev, A. Shih, E. Cruz-Chu, P. Freddolino, A. Arkhipov, and K. Schulten. The role of molecular modeling in bionanotechnology. Physical Biology, 3:S40-S53, 2006.
5. A. Shih, A. Arkhipov, P. Freddolino, and K. Schulten. Coarse grained protein-lipid model with application to lipoprotein particles. J. Phys. Chem. B, 110:3674-3684, 2006.
4. M. Dittrich, P. Freddolino, and K. Schulten. When light falls in LOV: A quantum mechanical/molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamy- domonas reinhardtii. J. Phys. Chem. B, 109:13006-13013, 2005.
3. P. Freddolino, M. Kalani, N. Vaidehi, W. Floriano, S. Hall, R. Trabanino, V. Kam, and W. Goddard III. Predicted 3D structure for the human β2 adrenergic receptor and its binding site for agonists and antagonists. PNAS 101:2736-2741, 2004.
2. M. Kalani, N. Vaidehi, S. Hall, R. Trabanino, P. Freddolino, M. Kalani, W. Flo- riano, V. Kam, and W. Goddard III. The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antag- onists. PNAS 101:3815-2820, 2004.
1. N. Vaidehi, W. Floriano, R. Trabanino, S. Hall, P. Freddolino, E. Choi, G. Za- manakos, and W. Goddard III. Prediction of structure and function of G protein- coupled receptors. PNAS 99:12622-12627, 2002.
Book Chapters 2. A. Shih, P. Freddolino, A. Arkhipov, S. Sligar, and K. Schulten. Molecular model- ing of the structural properties and formation of high-density lipoprotein particles. In Scott Feller, editor, Current Topics in Membranes: Computational Modeling of Mem- brane Bilayers, chapter 11, pp. 313–342. Elsevier, 2008.
1. P. Freddolino, A. Arkhipov, A. Shih, Y. Yin, Z. Chen, and K. Schulten. Appli- cation of residue-based and shape-based coarse graining to biomolecular simulations. In Gregory A. Voth, editor, Coarse-Graining of Condensed Phase and Biomolecular Systems, chapter 20, pp. 299–315. Chapman and Hall/CRC Press, Taylor and Francis Group, 2008.
Invited Talks 8. Paths of information flow in LOV domains. Gordon Research Conference on Photo- sensory Receptors and Signal Transduction, Barga, Italy, April 6-11, 2014.
7. Coping with the unknown: A guide for bacteria and bacteriologists. Center for the Physics of Living Cells Seminar, University of Illinois at Urbana-Champaign, Novem- ber 16th, 2012.
6. Fitness landscape transformation through a single amino acid change in the Rho ter- minator. Columbia University Microbial Data Club, January 17th, 2012.
Freddolino – Curriculum vitae – Page 4 of 8 5. Unraveling unknown mechanisms of action for antibiotics and toxic peptides. Prince- ton University/Rutgers High Throughput Sequencing Workgroup, August 8th, 2011.
4. Reconfiguration of the E. coli fitness landscape due to perturbation of a global regu- lator. Princeton University Molecular Biology Department Annual Retreat, October 8th, 2010.
3. Coarse-grained Molecular Dynamics: Approaches, potential, and limitations. Semi- nar, T. Martinez Laboratory, August 12th, 2007.
2. All-atom Molecular Dynamics Study of a Complete Virus. Theoretical and Com- putational Biophysics Group Seminar, Beckman Institute, University of Illinois at Urbana-Champaign, April 10th, 2006.
1. Structure and Function Predictions for Beta Adrenergic Receptors, Material Simula- tion Center Annual Meeting, Caltech, April 1st, 2004.
Poster 6. P. Freddolino and S. Tavazoie. Genome-wide measurement of bacterial transcrip- Presentations tional regulatory states. Biophysical Society Annual Meeting 2013, Philadelphia, PA.
5. P. Freddolino, H. Goodarzi, and S. Tavazoie. Global transformation of the E. coli fitness landscape by a point mutation in the transcriptional terminator Rho. Cold Spring Harbor Laboratory meeting on Systems Biology: Global Regulation of Gene Expression, 2012, Laurel Hollow, NY.
4. P. Freddolino, F. Liu, S. Park, M. Gruebele, and K. Schulten. Microsecond Explicit Solvent Molecular Dynamics Simulations of Protein Folding. Biophysical Society An- nual Meeting 2009, Boston, MA.
3. P. Freddolino, C. Harrison, M. Mayer, and K. Schulten. Agonist binding and al- lostery in the NR3A subunit of NMDA receptors. Gordon Research Conference on Biomolecular Interactions and Methods 2008, Ventura, CA.
2. P. Freddolino, A. Arkhipov, and K. Schulten. Coarse-grained molecular dynamics simulations of rotation-induced structural transitions in the bacterial flagellum. Bio- physical Society Annual Meeting 2007, Baltimore, MD.
1. P. Freddolino, A. Arkhipov, and K. Schulten. Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus. Biophysical Society Annual Meeting 2006, Salt Lake City, UT.
Teaching Completed the McGraw Center Teaching Transcript Program, Princeton University, Fall 2009-Summer 2012 (see http://www.princeton.edu/mcgraw/gs/transcript/)
Lecturer for WWS/MOL320 (Human Genetics, Reproduction, and Public Policy), Woodrow Wilson School for Public and International Affairs, Princeton University, Spring 2011. • Led two weekly discussion sections for students to debate interpretations and policy implications of class material • Graded midterm and final exams
Freddolino – Curriculum vitae – Page 5 of 8 Instructor for Princeton Summer Undergraduate Research Program in Molecular Biology, Princeton University, Summer 2010 (Program designed to provide research opportunities to undergraduate students from under-represented backgrounds or from colleges with few research opportunities). • Led two weekly sections for students to present and discuss their research
Teaching Assistant for MCB250 (Molecular Genetics). University of Illinois, Fall 2006. • Led two weekly recitation sections for groups of 20 students • Graded class-wide homework assignments
Teaching Assistant for Bi1 (Drugs and the Brain). Caltech, Spring 2003 & Spring 2004. • Co-taught two weekly recitation sections for groups of 15 students • Wrote and graded problem sets
Professional Member, Biophysical Society, 2005-present associations Service Acted as a peer reviewer for the Journal of the American Chemical Society, Journal of Physical Chemistry, Biophysical Journal, Open Biology, PLoS One, and the Journal of Structural Biology
Co-author of Case Study on Lipid Bilayers for the NIH Resource for Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu/Training/CaseStudies)
Software GLINT: Computational framework for post-processing genome-wide fitness profiling ex- Development periments using transposon libraries (https://tavazoielab.c2b2.columbia.edu/GLINT/) AutoPSF: VMD (www.ks.uiuc.edu/Research/vmd) plugin for automating structure prepa- ration for molecular dynamics.
NAMDEnergy: VMD plugin for calculating interaction energies in MD trajectory post- processing.
Molefacture: VMD plugin for small molecule building and editing.
cionize: GPU-accelerated tool for calculating Coulomb potentials and placing ions.
Implementation of additional water models and a fluctuating charge model in NAMD (www.ks.uiuc.edu/Research/namd)
Multiple file I/O plugins for VMD
Contributed to MembStruk, a suite of tools for ab initio prediction of GPCR structure, and HierDock, a hierarchical protocol for docking small molecule ligands to GPCR models using DOCK 4.0 as a docking engine.
Funding Personal funding through competitive grants and fellowships:
NIH K99/R00 Pathway to Independence Award (1K99GM097033, 2013–2015; pending R00, 2015–2018, with option for earlier conversion to R00)
Beckman Fellowship, University of Illinois at Urbana-Champaign, 2008-2009
Freddolino – Curriculum vitae – Page 6 of 8 National Science Foundation Graduate Research Fellowship, 2004-2009
Contributed sections to successful grant proposals for NIH and NSF:
Physics Frontier Center: Center for the Physics of Living Cells (NSF PHY0822613).
NIH Resource for Macromolecular Modeling (NIH P41-RR05969 Renewal 2007).
Supercomputing time from 2004-2009 (LRAC MCA93S028).
NSF Grant for Photobiology Research (NSF MCB02-34938).
Freddolino – Curriculum vitae – Page 7 of 8 References Dr. Saeed Tavazoie Professor of Biochemistry and Molecular Biophysics Columbia University 1130 St. Nicholas Ave 8th floor, Room 810B Mail Code: 200 New York NY 10032 Phone: (212) 851-5166 Fax: (212) 851-5149 Email: [email protected]
Dr. Klaus Schulten Swanlund Professor of Physics University of Illinois at Urbana-Champaign 3147 Beckman Institute 405 N. Mathews Urbana, IL 61801 Phone: (217) 244-1604 Fax: (217) 244-6078 Email (administrative): [email protected] (Nancy Mallon, secretary) Email (personal): [email protected]
Dr. Martin Gruebele William H. and Janet G. Lycan Professor of Chemistry University of Illinois at Urbana-Champaign A214 Chemical and Life Sciences Lab 600 S. Mathews Urbana, IL 61801 Phone: (217) 333-1624 Fax: (217) 244-3186 Email (administrative): [email protected] (Theresa Struss, Secretary) Email (personal): [email protected]
Dr. Kevin Gardner W.W. Caruth, Jr. Scholar in Biomedical Research and Virginia Lazenby O’Hara Chair in Biochemistry UT Southwestern Medical Center North Campus, Room ND8.300 5323 Harry Hines Blvd. Dallas, TX 75390 Phone: (214) 645-6365 Fax: (214) 645-6353 Email (administrative): [email protected] (Jo Appleton, Secretary) Email (personal): [email protected]
Freddolino – Curriculum vitae – Page 8 of 8