Publications

2024

• Nathan Kochen, N., Seaney, D., Vasandani, V., Murry, M., Braun, A. R., and Sachs, J. N. (2024). Post-translational modification sites are present in hydrophilic cavities of alpha-synuclein, tau, FUS, and TDP-43 fibrils: A molecular dynamics study. Proteins: Structure, Function, Bioinformatics Neuro, 92-7; p854-864.

2023

• Braun, A.R., Nathan Kochen, N., Yeun, S.L., Liao, E.E., Cornea, R.L., Thomas, D.D., and Sachs, J. N. (2023). Advancements in a FRET biosensor for live-cell fluorescence-lifetime high-throughput screening of alpha-synuclein. ASN Neuro, July 10. 
• Liao, E.E., Yang, M., Nathan Kochen, N., Vunnam, N., Braun, A.R., Ferguson, D.M., and Sachs, J.N. (2023) Proteasomal Stimulation by MK886 and Its Derivatives Can Rescue Tau-Induced Neurite Pathology. Molecular Neurobiology. July 10. 
• Nagamani,V., Young, M.C., Liao, E.E., Lo, C.H. ,Huber, E., Been, M. O. ,Thomas, D.D.  and Sachs, J.N. (2023). Nimesulide, a COX-2 inhibitor, Sensitizes Pancreatic Cancer Cells to TRAIL-induced Apoptosis by Promoting DR5 Clustering. Cancer Biol Ther. Dec 31;24(1):2176692. 
• Nagamani, V., Been, M. O., Huber, E., Paulson, C. N., Szymonski, S.,  Hackel, B.J. and Sachs, J.N. (2023). Discovery of a Non-competitive TNFR1 Antagonist Affibody with Picomolar Monovalent Potency that Does not Affect TNFR2 Function. Mol Pharm. Mar 10. 
• Pandey A.K., Buchholz C.R., Kochen, N. N., Pomerantz, W.C.K., Braun, A.R., Sachs, JN.(2023) pH affects Can Dominate Chemical Shift Perturbations in ¹H,¹⁵N-HSQC NMR Spectroscopy for Studies of Small Molecule/α-Synuclein Interactions. ACS Chem Neurosci. Feb 15;14(4):800-808. 
• Nagamani, V., Yang, M,  Lo, C.H., Paulson, C.N., Fiers, W.D., Huber, E., Been, M. O., Ferguson, D. M. and Sachs, J. N. (2023). Zafirlukast is a promising scaffold for selectively inhibiting TNFR1 through alteration in receptor conformational states. ACS Bio & Med Chem Au, 3(3), 270–282. 

2022

• Kochen, N. N., Vasandani, V., Seaney, D., Pandey, A. K., Walters, M. A., Braun, A. R., & Sachs, J. N. (2022). Threonine Cavities Are Targetable Motifs That Control Alpha-Synuclein Fibril Growth. ACS Chemical Neuroscience. 2022 Sep 7;13(17):2646-2657. 
• Vunnam, N., Hansen, S., Been, M. O., Lo, C. H., Pandey, A. K., Paulsen, C. N.,  and Wood, D. K. (2022). Fluorescence Lifetime Measurement of Prefibrillar Sickle Hemoglobin Oligomers as a Platform for Drug Discovery in Sickle Cell Disease. Biomacromolecules. Sep 12;23(9):3822-3830. 
• Ratnapriya S, Braun AR, Cervera Benet H, Carlson D, Ding S, Paulson CN, Mishra N, Sachs JN, Aldrich CC, Finzi A, Herschhorn, A. (2022) Broad Tricyclic Ring Inhibitors Block SARS-CoV-2 Spike Function Required for Viral Entry. ACS Infect Dis. Oct 14;8(10):2045-2058.

2021

• Lo, Chih Hung et al. “Fluorescence-Based TNFR1 Biosensor for Monitoring Receptor Structural and Conformational Dynamics and Discovery of Small Molecule Modulators.” Methods in molecular biology (Clifton, N.J.) vol. 2248 (2021): 121-137.
• Braun, A. R., Liao, E. E., Horvath, M., Kalra, P., Acosta, K., Young, M. C., Kochen, N., Lo, C. H., Brown, R., Evans, M. D., Pomerantz, W. C. K., Rhoades, E., Luk, K., Cornea, R. L., Thomas, D. D., and Sachs, J. N. (2021). Potent inhibitors of toxic alpha-synuclein identified via cellular time-resolved FRET biosensors. npj Parkinson's Disease, Vol. 7, 52. 

2020

• Lo, C. H., and Sachs, J.N. The role of wild-type tau in Alzheimer's disease and related tauopathies. Journal of life sciences (Westlake Village, Calif.) vol. 2,4 (2020): 1-17.
• Vunnam, N., Szymonski, S., Hirsova, P., Gores, G. J., Sachs, J. N and Hackel, B. J. (2020). Noncompetitive Allosteric Antagonism of Death Receptor 5 by a Synthetic Affibody Ligand. Biochemistry, 59, 40, 3856–3868.
• Lo, C. H., Huber, E. C., Sachs, J. N. (2020). Conformational states of TNFR1 as a molecular switch for receptor function. Protein Science, 1-15.
• Lo, C. H., Pandey, N. K., Lim, C. K. W., Ding, Z. Tao, M., Thomas, D. D., Langen, R., and Sachs, J. N. (2020). Discovery of Small Molecule Inhibitors of Huntingtin Exon 1 Aggregation by FRET-Based High-Throughput Screening in Living Cells. ACS Chem. Neuroscience. 2020, 11, 15, 2286–2295. 
• West, A., Zoni, V., Teague Jr., W. E., Leonard, A. N., Vanni, S., Gawrisch, K., Tristram-Nagle, S., Sachs, J. N., Klauda, J. B. (2020). How Do Ethanolamine Plasmalogens Contribute to Order and Structure of Neurological Membranes? J. Phys. Chem. B 2020, 124, 5, 828-839.

2019

• Lo, C. H., Lim, C. K. W., Ding, Z., Wickramasinghe, S. P., Braun, A. R., Ashe, K. H., Rhoades, E., Thomas, D. D., Sachs, J. N. (2019). Targeting the ensemble of heterogeneous tau oligomers in cells: A novel small molecule screening platform for tauopathies. Alzheimer's and Dementia, 15(11), 1489-1502.
• Lo, C. H., Schaaf, T. M., Grant, B. D., Lim, C. K. W., Bawaskar, P., Aldrich, C. C., Thomas, D. D., Sachs, J. N. (2019). Noncompetitive inhibitors of TNFR1 probe conformational activation states. Science signaling, 12(592), 5637. 

2017

• Vunnam, N., Lo, C.H., Grant, B.D., Thomas, D.D., Sachs, J.N. Soluble Extracellular Domain of Death Receptor 5 Inhibits TRAIL-Induced Apoptosis by Disrupting Receptor–Receptor Interactions. J. Mol. Biol., September 2017.
• Valley, C.C., Lewis, A.K., Sachs, J.N. Piecing it together: Unraveling the elusive structure-function relationship in single-pass membrane receptors. BBA-Biomembranes, September 2017. 
• Vunnam, N., Campbell-Bezat, C.K., Lewis, A.K., Sachs, J.N. Death Receptor 5 Activation is Energetically Coupled to Opening of the Transmembrane Domain Dimer. Biophys. J., July 2017. 
• Romo, T.D., Lewis, A.K., Braun, A.R., Grossfield, A., Sachs, J.N. Minimal Nucleation State of α-Synuclein Is Stabilized by Dynamic Threonine–Water Networks. ACS Chem. Neurosci., July 2017.
• Lo, C.H., Vunnam, N., Lewis, A.K., Chiu, T.L., Brummel, B.E., Schaaf, T.M., Grant, B.D., Bawaskar, P., Thomas, D.D., Sachs, J.N. An Innovative High-Throughput Screening Approach for Discovery of Small Molecules That Inhibit TNF Receptors., SLAS Discovery, May 2017. 
• Braun, A.R., Lacy, M.M., Ducas, V.C., Rhoades, E., Sachs, J.N. α-Synuclein’s Uniquely Long Amphipathic Helix Enhances its Membrane Binding and Remodeling Capacity. J. Membrane Biol., April 2017. 
• Brummel, B.E., Braun, A.R., Sachs, J.N. Polyunsaturated chains in asymmetric lipids disorder raft mixtures and preferentially associate with α-Synuclein. BBA-Biomembranes, April 2017. 
• Hennig, R., West, A., Debus, M., Saur, M., Markl, J., Sachs, J.N., Schneider, D. The IM30/Vipp1 C-terminus associates with the lipid bilayer and modulates membrane fusion. BBA-Bioenergetics, February 2017. 

2016

• Lewis, A.K., Valley, C.C., Peery, S.L., Brummel, B.E., Braun, A.R., Karim, C.B., Sachs, J.N. Death Receptor 5 Networks Require Membrane Cholesterol for Proper Structure and Function. J. Mol. Biol., December 2016.
• Lewis, A.K., Dunleavy, K.M., Senkow, T.L., Her, C., Horn, B.T., Jersett, M.A., Mahling, R., McCarthy, M.R., Perell, G.T., Valley, C.C., Karim, C.B., Gao, J., Pomerantz, W.C.K., Thomas, D.D., Cembran, A., Hinderliter, A., Sachs, J.N. Oxidation increases the strength of the methionine-aromatic interaction. Nature Chemical Biology, August 2016. 
• Romeo, C., Weber, M.C., Zarei, M., DeCicco, D., Chand, S.N., Lobo, A.D., Winter, J.M., Sawicki, J.A., Sachs, J.N., Meisner-Kober, N., Yeo, C.J., Vadigepalli, R., Tykocinski, M.L., Brody, J.R. HuR Contributes to TRAIL Resistance by Restricting Death Receptor 4 Expression in Pancreatic Cancer Cells. Mol. Cancer Res., July 2016. 
• West, A., Brummel, B.E., Braun, A.R., Rhoades, E., Sachs, J.N. Membrane remodeling and mechanics: Experiments and simulations of α-Synuclein. BBA-Biomembranes, March 2016. 

2015

• Braun, A.R., Sachs, J.N. Alpha-synuclein reduces membrane surface tension and increases undulations in molecular dynamics simulations of small unilamellar vesicles. Biophys. J. Letters, April 2015.
• Shi, Z., Sachs, J.N., Rhoades E., and Baumgart, T. Biophysics of alpha-Synuclein induced membrane remodeling. Phys. Chem. Chem. Phys., Feb 2015. 

2014

• Perlmutter, J.D., Popot, J.-L., and Sachs, J.N.Molecular Dynamics Simulations of a Membrane Protein/Amphipol Complex. J. Membr. Bio., June 2014. 
• Tehei, M., Perlmutter, J.D., Giusti, F., Sachs, J.N., Zaccai, G., and Popot. J.-L. Thermal Fluctuations in Amphipol A8-35 Particles: A Neutron Scattering and Molecular Dynamics Study. J. Membr. Bio., Sep 2014.
• Braun, A.R. and Sachs, J.N. Determining structural and mechanical properties from molecular dynamics simulations of lipid vesicles. JCTC. Aug 2014.
• Braun, A.R., Lacy, M.M., Ducas, D.C., Rhoades, E., and Sachs, J.N. alpha-Synuclein induced membrane remodeling is driven by binding affinity, partition depth, and inter-leaflet order asymmetry. J. Am. Chem. Soc., June 2014, 136 (28), pp 9962–9972. 
• Lewis, A.K., James, Z.M., McCaffrey, J.E., Braun, A.R., Karim, C.B., Thomas, D.D., and Sachs, J.N. Open and Closed Conformations of the Isolated Transmembrane Domain of Death Receptor 5 Support of a New Model of Activation. Biophys J. Volume 106, Issue 6, 18 March 2014, Pages L21–L24.

2013

• Braun, A.R., Sachs, J.N., and Nagle, J.F. Comparing Simulations of Lipid Bilayers to Scattering Data: The GROMOS 43A1-S3 Force Field. J Phys Chem B, 2013 May 2;117(17):5065-5072.

2012

• Valley, C.C., Cembran, A., Perlmutter, J.D., Lewis, A.K., Labello, N.P., Gao, J. and Sachs, J.N. The Methionine-aromatic motif plays a unique role in stabilizing protein structure. J Biol Chem. 2012 Oct 12;287(42):34979-91 
• Lewis, A.K., Valley, C.C. and Sachs, J.N. TNFR1 Signaling is Associated with Backbone Conformational Changes of Receptor Dimers Consistent with Overactivation in the R92Q TRAPS Mutant. Biochemistry 2012 Jul 16;51(33):6545-6555 
• Valley, C.C., Lewis, A.K., Mudaliar, D.J., Perlmutter, J.D., Braun, A.R., Karim, C.B., Thomas, D.D, Brody, J.R. and Sachs, J.N. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces Death Receptor 5 networks that are highly organized. J Biol Chem. 2012 Jun 15;287(25):21265-78. Epub 2012 Apr 10. 
• Braun, A.R., Sevcsik, E., Chin, P., Rhoades, E., Tristram-Nagle, S., and Sachs, J.N. α-Synuclein induces both positive mean curvature and negative Gaussian curvature in membranes. J Am Chem Soc. 2012 Feb 8; 134(5):2613-20.

2000-2011

• Valley, C.C., Perlmutter, J.D., Braun, A.R., and Sachs, J.N. NaCl interactions with phosphatidylcholine bilayers do not alter membrane structure, but induce long-range ordering of ions and water. J Membrane Biology. 2011 Nov; 244(1):35-42. 
• Braun, A.R., Sachs, J.N. Extracting experimental measurables from molecular dynamics simulations of membranes. Annual Reports in Computational Chemistry, ARCC Vol 7, Chapter 6. 
• Popot, J.L., ..., Sachs, J.N., ... et al. Amphipols From A to Z. Annual Review of Biophysics Volume: 40 Pages: 379-408. 
• Perlmutter, J.D., Drasler W.J., Xie W., Gao J., Popot J.L., and Sachs J.N. All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer. Langmuir. 2011 Sep 6;27(17):10523-37. Epub 2011 Aug 15.
• Perlmutter, J.D., Sachs, J.N. Inter-Leaflet Interaction and Asymmetry in Phase Separated Lipid Bilayers: Molecular Dynamics Simulations. J Am Chem Soc. 2011 May 4;133(17):6563-77.
• Braun, A.R., Brandt, E., Edholm, O., Nagle, J.F., and Sachs, J.N. Determination of Electron Density Profiles and Area from Simulations of Undulating Membranes. Biophys J. 2011 May 4;100(9):2112-20.
• Brandt, E., Braun, A.R., Sachs, J.N., Nagle, J.F., and Edholm, O. Interpretation of Fluctuation Spectra in Lipid Bilayer Simulations. Biophys J. 2011 May 4;100(9):2104-11.
• Denning E.J., Crozier P.S., Sachs J.N., and Woolf, T.B. From the gating charge response to pore domain movement: initial motions of Kv1.2 dynamics under physiological voltage changes. Mol Membr Biol. 2009 Dec;26(8):397-421.
• Perlmutter, JD., Sachs, JN. Inhibiting Lateral Domain Formation in Lipid Bilayers: Simulations of Alternative Steroid Headgroup Chemistries. J. Am. Chem. Soc. 2009 131:16362–16363. 
• Perlmutter, JD., Sachs, JN. Experimental verification of lipid bilayer structure through multi-scale modeling. Biochim. Biophys. Acta, Biomembr. 2009 1788:2284-2990. 
• Perlmutter, JD., Braun, AR, and Sachs, JN. Curvature Dynamics of alpha-Synuclein Familial Parkinson’s Disease Mutants: Molecular Simulations of the Micelle-and Bilayer-Bound Forms. J. Biol. Chem. 2009 284: 7177-7189. 
• Kucerka, N., Perlmutter J., Pan J., Tristram-Nagle S., Katsaras J. and 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. 2008. 95:2792-2805. 
• Kucerka, N., Nagle JF., Sachs, JN.., Feller S.E., Pencer J., Jackson A., and Katsaras J. Lipid area refinement based on a simultaneous analysis of neutron and x-ray scattering data and all-atom molecular dynamics simulations. Biophys. J. 2008. 95:2356-2367. 
• Kucerka, K., Pencer, J., Sachs, JN., Nagle, JF. and Katsaras J. Curvature effect on the structure of phospholipid bilayers. Langmuir. 23 (3): 1292-1299 JAN 30 2007. 
• Sachs, JN., Engelman, DM. Introduction to the Membrane Protein Reviews: The Interplay of Structure, Dynamics, and Environment in Membrane Protein Function. Annu Rev Biochem. 2006. 
• Chin C, Sachs JN and Engelman DM. Transmembrane homodimerization of receptor-like protein tyrosine phosphatases. FEBS Lett. 579(17), 3855-8 2005. 
• Nanda H, Sachs JN, Petrache HI, Woolf TB. Environmental effects on glycophorin A folding and structure examined through molecular simulations. J. Chem. Theory and Comp. (3): 375-388 2005. 
• Sachs JN, Shen H, and Saltzman WM. Polymers for gene therapy in cancer: New approaches for specificity of expression. Gene Therapy 12 (12): 954-955 2005. 
• Sachs JN, Crozier PS and Woolf TB. Atomistic simulations of biologically realistic transmembrane potential gradients. J. Chem. Phys. 121 (22): 10847-10851 2004. 
• Sachs JN, Petrache HI, and Woolf TB. Changes in phosphatidylcholine headgroup tilt and water order induced by monovalent salt: molecular dynamics simulations. Biophys. J. 86; 3772-3782 2004. 
• Sachs JN, Woolf, TB. Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers: Molecular dynamics simulations. J. Amer. Chem. Soc. 125 (29): 8742-8743 2003.
• Sachs JN, Petrache HI, and Woolf TB. Interpretation of small angle X-ray measurements guided by molecular dynamics simulations of lipid bilayers. Chem. Phys. Lip. 126: 211-223 2003.
• Sachs JN, Petrache HI, Zuckerman DM, and Woolf, TB. Molecular dynamics simulations of ionic concentration gradients across model bilayers. J. Chem. Phys. 118 (4): 1957-1969 2003. 
• Petrache HI, Zuckerman DM, Sachs JN, Killian JA, Koeppe RE II and Woolf, TB. Hydrophobic matching mechanism investigated by molecular dynamics simulations. Langmuir 18 (4): 1340-1351 2002. 
• Grossfield, A., Sachs, J., and Woolf, TB. Dipole lattice membrane model for protein calculations. Proteins 41:211-223 2000.