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Contact information Lawrence Livermore National Laboratory |
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Education
Deputy Group Leader, LLNL (2017-present)
Post-doctoral researcher, LLNL (2009-2012)
Ph.D., Biochemistry, University of Oxford (2008)
Masters Biochemistry, University of Oxford (2005)
Research
I am interested in the modeling and biomolecular simulation of cellular membranes and membrane proteins, with recent focus on critical neuroreceptors, such as the GABAA receptor and glutamate receptors. Additionally, I have been working on small molecule permeability studies, to investigate the energetic barriers associated with crossing a lipid bilayer, with a view to developing screening methods to accurately predict blood-brain barrier permeability in drug design.
I was a Post-Doctoral researcher at LLNL from 2009-2012. In 2012, I was converted to a Staff Scientist, and in 2017 was appointed Deputy Group Leader in the Biochemical and Biophysical Systems group.
My 2017 paper, ‘Computational Lipidomics of the Neuronal Plasma Membrane’ was chosen as one of the 8 ‘articles of the year’ for the Biophysical Journal.
I received my combined Undergraduate/Masters degree in Biochemistry (MBiochem) from the University of Oxford in 2005, and PhD in Biochemistry from the University of Oxford in 2008. My thesis was titled ‘Simulation Studies of the Influenza A M2 Channel Protein’.
Publications
Carpenter, T.S., López, C.A., Neale, C., Montour, C., Ingólfsson, H.I., Di Natale, F., Lightstone, F.C. and Gnanakaran, S., Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field. Journal of chemical theory and computation, 2018. 14(11), pp.6050-6062.
Witkin, J.M., Shenvi, R.A., Li, X., Gleason, S.D., Weiss, J., Morrow, D., Catow, J.T., Wakulchik, M., Ohtawa, M., Lu, H.H. and Martinez, M.D., Schkeryantz, J.M., Carpenter, T.S., Lightstone, F.C., Cerne, R. Pharmacological characterization of the neurotrophic sesquiterpene jiadifenolide reveals a non-convulsant signature and potential for progression in neurodegenerative disease studies. Biochemical Pharmacology, 2018. 155, pp.61-70.
Gilmore, S.F., Carpenter, T.S., Ingólfsson, H.I., Peters, S.K., Henderson, P.T., Blanchette, C.D. and Fischer, N.O., Lipid composition dictates serum stability of reconstituted high-density lipoproteins: implications for in vivo applications. Nanoscale, 2018. 10(16), pp.7420-7430.
Yung, M.C., Bourguet, F.A., Carpenter, T.S. and Coleman, M.A., Re-directing bacterial microcompartment systems to enhance recombinant expression of lysis protein E from bacteriophage ϕX174 in Escherichia coli. Microbial cell factories, 2017. 16(1), p.71.
Ingólfsson, H.I.*, Carpenter, T.S.*, Bhatia, H., Bremer, P.T., Marrink, S.J. and Lightstone, F.C. Computational lipidomics of the neuronal plasma membrane. Biophys J, 2017. 113(10), pp.2271-2280.
Malfatti, M.A., Enright, H.A., Nicholas, A.B., Kuhn, E.A., Hok, S., McNerney, M.W., Lao, V., Nguyen, T.H., Lightstone, F.C., Carpenter, T.S., Bennion, B.J., and Valdez, C.A. The biodistribution and pharmacokinetics of the oxime acetylcholinesterase reactivator RS194B in guinea pigs. Chemico-biological interactions, 2017. 277, pp.159-167.
Bennion, B.J., Be, N.A., McNerney, M.W., Lao, V., Carlson, E.M., Valdez, C.A., Malfatti, M.A., Enright, H.A., Nguyen, T.H., Lightstone, F.C. and Carpenter, T.S. Predicting a drug’s membrane permeability: a computational model validated with in vitro permeability assay data. J Phys Chem B, 2017. 121(20), pp.5228-5237.
Carpenter T.S., Parkin J., and Khalid S. The Free Energy of Small Solute Permeation through the Escherichia coli Outer Membrane Has a Distinctly Asymmetric Profile. J. Phys Chem Lett, 2016. 7(17): p. 3446-3451
Witzke S., Petersen M., Carpenter T.S.§, Khalid S§. Molecular dynamics simulations reveal the conformational flexibility of Lipid II and its loose association with the defensin plectasin in the Staphylococcus aureus membrane. Biochemistry, 2016. 55(23): p. 3303-3314
Carpenter T.S., Lightstone F.C. An Electrostatic Funnel in the GABA-Binding Pathway. PLOS Comput Biol, 2016. 12(4): p. e1004831.
Carpenter, T.S., Kirshner, D.A., Lau, E.Y., Wong, S.E., Nilmeier, J.P. and Lightstone, F.C., A method to predict blood-brain barrier permeability of drug-like compounds using molecular dynamics simulations. Biophysical journal, 2014. 107(3), pp.630-641.
Zhao C., Hwang S.H., Buchholz B.A., Carpenter T.S., Lightstone F.C., Yang J., Hammock B.D., Casida J.E. GABAA receptor target of tetramethylenedisulfotetramine. Proc Natl Acad Sci USA, 2014. 111(23): p. 8607-8612.
Carpenter T.S., Lau E.Y., Lightstone F.C. Identification of a Possible Secondary Picrotoxin-Binding Site on the GABAA Receptor. Chem Res Toxicol, 2013. 26(10): p. 1444-54
Carson B., Harmon B., Kozina C., Maar D., Carpenter T.S., Branda C., Negrete O.A. Identification of critical amino acids within the nucleoprotein of Tacaribe virus important for anti-interferon activity. J Biol Chem, 2013. 288(12): p. 8702-11.
Carpenter T.S., Lau E.Y., Lightstone F.C. A role for loop F in modulating GABA binding affinity in the GABA(A) receptor. J Mol Biol, 2012. 422(2): p. 310-23.
Rouse, S.L., Carpenter T., Sansom M.S.P. Coarse-grained Molecular Dynamics Simulations of Membrane Proteins. In Molecular Simulations and Biomembranes: From Biophysics to Function. 2010
Cover image. The Biochemist Magazine. Biochemical Society. 2009. 31(5).
Rouse, S.L.*, Carpenter T.*, Stansfeld, P.J., Sansom M.S.P. Simulations of the BM2 proton channel transmembrane domain from influenza virus B. Biochemistry, 2009. 48(42): p. 9949-51.
Klingelhoefer J.*, Carpenter T.*, Sansom M.S.P. Peptide Nanopores and Lipid Bilayers: Interactions by Coarse-Grained Molecular Dynamics Simulations. Biophys J, 2009. 96(9): p. 3519-28.
Carpenter T., Bond P.J., Khalid S., Sansom M.S.P. Self-Assembly of a Simple Membrane Protein: Coarse Grain Molecular Dynamics Simulations of the Influenza M2 Channel. Biophys J, 2008. 95(8): p. 3790-801.
Khalid S., Bond P.J., Carpenter T., Sansom M.S.P. OmpA: Gating and dynamics via molecular dynamics simulations. Biochim Biophys Acta, 2008. 1778(9): p. 1871-80.
Carpenter T., Khalid S., Sansom M.S.P. A multidomain outer membrane protein from Pasteurella multocida: modelling and simulation studies of PmOmpA. Biochim Biophys Acta. 2007 Nov; 1768(11):2831-40.