Biophysics

I have an academic background in Biology, Engineering, and Physics having conducted research during my BS at Cornell University, Department of Chemical Engineering with Matthew DeLisa, PhD at the University of Minnesota, Department of Biomedical Engineering with Jonathan Sachs, and Post-Doctoral work at Brandeis University, Department of Physics with Michael Hagan.

My interests were primarily in using simulations to understand self-assembly of biological molecules and I've published papers on protein structure, lipids and membrane proteins, and viral particles.

Here's a fun video from a project simulating the assembly of a viral shell (blue) around the viral genome (red). See the paper published at eLife for more.

Publications

• Perlmutter JD, Hagan MF, Mohajerani F. Many-molecule encapsulation by an icosahedral shell. eLife 5:e14078 (2016)
• Perlmutter JD, Hagan MF. The role of packaging sites in efficient and specific virus assembly. J. Mol. Biol. 427(15):2451–2467 (2015)
• Perlmutter JD, Hagan MF. Mechanisms of virus assembly. Annu. Rev. Phys. Chem. 66:217-39 (2015)
• Perlmutter JD, Perkett M, Hagan MF. Pathways for virus assembly around nucleic acids. J. Mol. Biol. 426(18):3148-3165 (2014)
• Tehei M, Perlmutter JD, Giusti F, Sachs JN, Zaccai G, Popot J-L. Thermal fluctuations in amhpipol A8-35 particles. A neutron scattering and molecular dynamics study. J. Membr. Biol. 247(9-10):897-908 (2014)
• Perlmutter JD, Popot J-L, Sachs JN. Molecular dynamics simulations of a membrane protein/amphipol complex. J. Membr. Biol. 247(9-10):883-895 (2014)
• Perlmutter JD, Qiao C, Hagan MF. Viral genome structures are optimal for capsid assembly. eLife 2:e00632 (2013)
• Valley CC, Cembran A, Perlmutter JD, Lewis AK, Labello NP, Gao J, Sachs JN. The Methionine-aromatic motif plays a unique role in stabilizing protein structure. J. Biol. Chem. 287(42):34979-34991 (2012)
• Valley CC, Lewis AK, Mudaliar DJ, Perlmutter JD, Braun AR, Karim CB, Thomas DD, Brody JR, Sachs JN. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces Death Receptor 5 networks that are highly organized. J. Biol. Chem. 287(25):21265-21278 (2012)
• Valley CC, Perlmutter JD, Braun AR, Sachs JN. NaCl Interactions with Phosphatidylcholine Bilayers Do Not Alter Membrane Structure but Induce Long-Range Ordering of Ions and Water. J. Membr. Biol. 244(1):35 (2011)
• Perlmutter JD, Drasler WJ, Xie W, Gao J, Popot J-L, Sachs JN. All-Atom and Coarse-Grained Molecular Dynamics Simulations of a Membrane Protein Stabilizing Polymer. Langmuir 27(17):10523-10537 (2011)
• Perlmutter JD, Sachs JN. Inter-Leaflet Interaction and Asymmetry in Phase Separated Lipid Bilayers: Molecular Dynamics Simulations. J. Am. Chem. Soc. 133(17):6563–6577 (2011)
• Perlmutter JD, Sachs JN. Inhibiting Lateral Domain Formation in Lipid Bilayers: Simulations of Alternative Steroid Headgroup Chemistries. J. Am. Chem. Soc. 131(45):16362-16363 (2009)
• Perlmutter JD, Sachs JN. Experimental verification of lipid bilayer structure through multi-scale modeling. Biochim. Biophys. Acta, Biomembr. 1788(10):2284-2290 (2009)
• Perlmutter JD, Braun AR, Sachs JN. Curvature dynamics of α-synuclein familial Parkinson's disease mutants: Molecular simulations of the micelle- and bilayer-bound forms. J. Biol. Chem. 284(11):7177-7189 (2009)
• Kucerka N, Perlmutter JD, Katsaras J, Sachs JN. The effect of cholesterol on short- and long-chain monounsaturated lipid bilayers as determined by molecular dynamics simulations and X-ray scattering. Biophys J 95(6):2792-2805 (2008)
• Perez-Rodriguez R, Fisher AC, Perlmutter JD, Hicks MG, Chanal A, Santini CL, Wu LF, Palmer T, DeLisa MP. An essential role for the DnaK molecular chaperone in stabilizing over-expressed substrate proteins of the bacterial twin-arginine translocation pathway. J. Mol. Biol. 367(3):715-730 (2007)