Peer-reviewed Research Papers

Electrochemical Ion Gradients and the Sodium-Calcium Exchange Stoichiometry. 
Axelsen, P.H., and J. H. B. Bridge. 
Journal of General Physiology 85:471-475, 1985.

A Constraint on the Stoichiometry of the Sodium-Calcium Exchange in Rabbit Myocardium. 
Axelsen, P. H., and J. B. Bassingthwaighte. 
Basic Research in Cardiology 83:314-316, 1988.

Electronic Transitions in Molecules in Static External Fields. I.  Indole and Tryptophan-59 in Ribonuclease-T1.
Ilich, P., Axelsen, P. H., and F. G. Prendergast.
Biophysical Chemistry 29:341-349, 1988.

Molecular Dynamics of Tryptophan in Ribonuclease-T1: I. Simulation Strategies and Fluorescence Anisotropy Decay.
Axelsen, P. H., Haydock, C., and F. G. Prendergast.
Biophysical Journal 54:249-258, 1988.

Molecular Dynamics of Tryptophan in Ribonuclease-T1: II. Correlations with Fluorescence.
Axelsen, P. H., and F. G. Prendergast.
Biophysical Journal 56:43-66, 1989.

Experimentally Verifying Molecular Dynamics Simulations Through Fluorescence Anisotropy Measurements (accelerated publication).
Axelsen, P.H., Gratton, E., and F.G. Prendergast.
Biochemistry 30:1173-1179, 1991.

Resolution of Fluorescence Intensity Decays of the Two Tryptophan Residues in Glutamine-binding Protein of E. coli Using Single Tryptophan Mutants.
Axelsen, P.H., Bajzer, Z., Prendergast, F.G., Cottam, P., and C. Ho.
Biophysical Journal 60:650-659, 1991.

Fluorescence Analysis of Calmodulin Mutants Containing Tryptophan: Conformational Changes Induced by Calmodulin-Binding Peptides from Myosin Light Chain Kinase. Chabbert, M., Lukas, T.J., Watterson, M, Axelsen, P.H., and F.G. Prendergast.
Biochemistry 30:7615-7630, 1991.

Buried Water in Homologous Serine Proteases. 
Sreenivasan, U, and P.H. Axelsen.
Biochemistry 31:12785-12791, 1992.

An electrostatic mechanism for substrate guidance down the aromatic gorge of acetylcholinesterase.
Ripoll, D.R., Faerman, C.H., Axelsen, P.H., Silman, I. and J.L. Sussman.
Proceedings of the National Academy of Sciences USA 90:5128-5132, 1993.

Quaternary ligand binding to aromatic residues in the active-site gorge of acetylcholinesterase.
Harel, M., Schalk, I., Ehret-Sabatier, L., Bouet, F., Goeldner, M., Hirth, C., Axelsen, P., Silman, I. and J.L. Sussman.
Proceedings of the National Academy of Sciences USA 90:9031-9035, 1993.

Structure and Dynamics of the Active Site Gorge of Acetylcholinesterase: Synergistic Use of Molecular Dynamics Simulation and X-ray Crystallography.
Axelsen, P., Harel, M., Silman, I. and J.L. Sussman.
Protein Science 3:188-197, 1994.

Open "Back Door" in a Molecular Dynamics Simulation of Acetylcholinesterase.
Gilson, M.K., Straatsma, T.P., McCammon, J.A., Ripoll, D.R., Faerman, C.H., Axelsen, P.H., Silman, I., and J.L. Sussman. 
Science 263:1276-1278, 1994.

Acetylcholine Recognition by an Aromatic Host: The Role of an All-hydrogen Topology
in Simulations of the Cation-pi Interaction.  P.H. Axelsen. 
Israel Journal of Chemistry 32:159-163, 1994.

Use of Internal Reflectance Infrared Spectroscopy for the in-situ Study of Supported Lipid Monolayers. 
P.H. Axelsen, W.D. Braddock, H.L. Brockman, C.M. Jones, R.A. Dluhy, B.S. Kaufman, and F.J. Puga II. 
Applied Spectroscopy 49:526-531, 1995.

The Infrared Dichroism of Transmembrane Helical Polypeptides. 
P.H. Axelsen, B.S. Kaufman, R.N. McElhaney, and R.N.A.H. Lewis.
Biophysical Journal 69:2770-2781, 1995.

The Determination of Molecular Order in Supported Lipid Membranes by Internal Reflection FTIR Spectroscopy. 
Citra, M.J., and P.H. Axelsen
Biophysical Journal 71:1796-1805, 1996.

Simultaneous Recognition of a Carboxylate-containing Ligand and an Intramolecular
Surrogate Ligand in the Crystal Structure of an Asymmetric Vancomycin Dimer.
Loll, P.J., Bevivino, A.E., Korty, B.D., and P.H. Axelsen
Journal of the American Chemical Society 119:1516-1522, 1997.

Simulated Dipeptide Recognition by Vancomycin. 
Li, D., Sreenivasan, U., Juranic, N., Macura, S., Puga II, F.J., Frohnert, P.M., and P.H. Axelsen
Journal of Molecular Recognition 10:73-87, 1997.

A Proposed Common Pharmacophore in Paclitaxel and Epothilone
Winkler, J.D., and P.H. Axelsen
Bioorganic and Medicinal Chemistry Letters 6:2963-2966, 1997.

Orientational Order Determination by Internal Reflection Infrared Spectroscopy
Axelsen, P.H., and M.J. Citra (new data and analyses presented within an invited review)
Progress in Biophysics and Molecular Biology 66:227-253,1997.

The Concentration-dependent Membrane Activity of Cecropin A
Silvestro, L., Gupta, K., Weiser, J.N., and P.H. Axelsen
Biochemistry 36:11452-11460, 1997.

Morphological Changes and Fusogenic Activity of the Influenza Virus Hemagglutinin
Shangguan, T., Siegel, D.P., Lear, J.D., Axelsen, P.H., Alford, D., and J. Bentz
Biophysical Journal 74:54-62, 1998.

A Ligand-mediated Dimerization Mode for Vancomycin
Loll, P.J., Miller, R., Weeks, C.M., and P.H. Axelsen
Chemistry and Biology 5:293-298, 1998.

Folding of beta-sheet Membrane Proteins: A Hydrophobic Hexapeptide Model
Wimley, W.C., Hristova, K., Ladokhin, A.S., Silvestro, L., Axelsen, P.H., and S.H. White
Journal of Molecular Biology 277:1091-1110, 1998.

A Rational Strategy for Enhancing the Affinity of Vancomycin Towards Depsipeptide Ligands.  Axelsen, P.H., and D. Li. 
Bioorganic and Medicinal Chemistry 6:877-881, 1998.

Interactions of Substrate and Product with Cytochrome P450: P4502B4 versus P450CAM.
Narasimhulu, S., Havran, L.M., Axelsen, P.H., and J.D. Winkler.
Archives of Biochemistry and Biophysics 353:228-238, 1998.

Improved Convergence in Dual-topology Free Energy Calculations Through the Use of Harmonic Restraints.
Axelsen, P.H., and D. Li. 
Journal of Computational Chemistry 19:1278-1283, 1998

Infrared Spectroscopy of Supported Lipid Monolayer, Bilayer, and Multibilayer Membranes.  Silvestro, L., and P.H. Axelsen.
Chemistry and Physics of Lipids 96:69-80, 1998.

Design and Synthesis of Constrained Epothilone Analogues: The Efficient Synthesis of Eleven-Membered Rings by Olefin Metathesis. 
Winkler, J.D., Holland, J.M., Kasparec, J., and P.H. Axelsen
Tetrahedron 55:8199-8214, 1999.

FTIR Linked Analysis of Conformational Changes in Annexin V Upon Membrane Binding.
Silvestro, L., and P. H. Axelsen. 
Biochemistry 38:113-121, 1999.

The Structure of Human Lipoprotein A-I: Evidence for the "Belt" Model.
Koppaka, V., Silvestro, L., Engler, J., Brouillette, C.G., and P. H. Axelsen.
Journal of Biological Chemistry, 274:14541-14544, 1999.

Vancomycin Binding to Low Affinity Ligands: Delineating a Minimum Set of Interactions Necessary for High Affinity Binding. 
Loll, P.J., Kaplan, J., Selinsky, B.S., and P. H. Axelsen.
Journal of Medicinal Chemistry 42:4714-4719, 1999.

Antibacterial and Antimembrane Activities of Cecropin A in E. coli
Silvestro, L., Weiser, J.N., and P. H. Axelsen
Antimicrobial Agents and Chemotherapy 44:602-607, 2000.

Prothrombinase Acceleration by Oxidatively Damaged Phospholipids
Weinstein, E.A., Li, H., Lawson, J.A., Rokach, J., FitzGerald G.A., and Axelsen, P.H.
Journal of Biological Chemistry 275:22925-22930, 2000.

Accelerated Accumulation of Amyloid b Proteins on Oxidatively Damaged Lipid Membranes
Koppaka, V., and P.H. Axelsen
Biochemistry 39:10011-10016, 2000.

Membrane-Induced Folding of Cecropin A Silvestro, L., and P.H. Axelsen
Biophysical Journal 79:1465-1477, 2000.

Design and Synthesis of Novel Foldamers Based on an Anthracene Diels-Alder Adduct.
Winkler, J.D., Piatnitski, E.L., Mehlmann, J., Kasparec, J., and P. H. Axelsen.
Angewandte Chemie 40 (4): 743-745 2001.

Toward a Rational Design of Peptide Inhibitors of Ribonucleotide Reductase: Structure-Function and Modeling Studies. 
Pender, B.A., Wu, X., Axelsen, P.H., and B. S. Cooperman.
Journal of Medicinal Chemistry 44 (1): 36-46 JAN 4 2001.

The Role of Sugar Residues in Molecular Recognition by Vancomycin
Kaplan, J., Korty, B.D., Axelsen, P.H., and P.J. Loll.
Journal of Medicinal Chemistry 44:1837-1840, 2001.

Evanescent Electric Field Amplitudes in Internal Reflection Infrared Spectroscopy
Koppaka, V., and P.H. Axelsen
17:6309-6316, 2001.

The Role of Configurational Entropy in Biochemical Cooperativity.
Sutjano Jusuf, Patrick J. Loll, and Paul H. Axelsen
Journal of the American Chemical Society 124:3490-3491, 2002.

Transcriptional Profile of the E. coli Response to the Antimicrobial Insect Peptide Cecropin A
Hong, R.W., Shchepetov, M., Weiser, J.N. and P. H. Axelsen
Antimicrobial Agents and Chemotherapy 47:1-6, 2003.

Configurational Entropy and Cooperativity Between Ligand Binding and Dimerization in Glycopeptide Antibiotics. 
Jusuf, S., Loll, P.J., and P. H. Axelsen
Journal of the American Chemical Society 125:3988-3994, 2003.

Early synergy between A beta 42 and oxidatively damaged membranes in promoting amyloid fibril formation by Ab 40. 
Koppaka, V., Paul, C., Murray, I.V.J., and P. H. Axelsen.
Journal of Biological Chemistry 278:36277-36284, 2003

Role of alpha-synuclein carboxy-terminus on fibril formation in vitro. 
Murray, I.V.J., Giasson, B.I.,. Quinn, S.M., Koppaka, V., Axelsen, P.H., Ischiropoulos, H., Trojanowski, J.Q., and Lee, V. M.-Y.
Biochemistry 42:8530-8540, 2003.

Vibrational Coupling, Isotopic Editing, and b Sheet Structure in a Membrane Bound Polypeptide. 
Paul, C. Wang, J., Wimley, W.C., Hochstrasser, R.M., Axelsen, P.H.   
Journal of the American Chemical Society
126:5843-5850, 2004.

Synchronized conformational fluctuations and binding site desolvation during molecular recognition. 
Jusuf, S., Axelsen, P.H.
Biochemistry 43:15446-15452, 2004.

The E46K Mutation in Alpha-Synuclein Increases Amyloid Fibril Formation.
Greenbaum,E.A., Graves,C.L., Mishizen-Eberz,A.J., Lupoli,M.A., Lynch,D.R., Englander,S.W., Axelsen,P.H. & Giasson,B.I. 
Journal of Biological Chemistry 280:7800-7807, 2005.

b Sheet Structure in Amyloid b Fibrils and Vibrational Dipolar Coupling. 
C. Paul and P. Axelsen. 
Journal of the American Chemical Society 127:5754, 2005.

Structural Analysis of Lipoprotein E Particles
Lumelle A. Schneeweis, Vishwanath Koppaka, S. Lund-Katz, M. C. Phillips, and P. H. Axelsen
Biochemistry 44:12525-12534, 2005.

Promotion Of Oxidative Lipid Membrane Damage By Amyloid b Proteins.
I.V.J. Murray, M. E. Sindoni, and P. H. Axelsen
Biochemistry 44:12606-12613, 2005.

Properties and Structures of the Influenza and HIV Fusion Peptides on Lipid Membranes: Implications for a Role in Fusion. 
M.E. Haque, V. Koppaka, P. H. Axelsen, and B.R. Lentz.
Biophysical Journal 89:3183-3194, 2005.

Conformational and Quantitative Characterization of Oritavancin-Peptidoglycan Complexes in Whole Cells of Staphylococcus aureus by in vivo 13 C and 15 N Labeling. Lynette Cegelski, Dirk Steuber, Anil K. Mehta, Daniel W. Kulp, Paul H. Axelsen, and Jacob Schaefer
Journal of Molecular Biology 357:1253-1262, 2006.

Two-dimensional infrared spectroscopy displays signatures of structural ordering in peptide aggregates. 
Casey H. Londergan, Jianping Wang, Paul H. Axelsen, and Robin M. Hochstrasser
Biophysical Journal 90:4672-4685, 2006.

Mass Spectrometric Analysis Demonstrates that BODIPY 581/591 C11 Overestimates and Inhibits Oxidative Lipid Damage. 
MacDonald, M.L., Murray, I.V.J., and Axelsen, P.H. 
Free Radical Biology and Medicine 42:1392-1397, 2007.

The Structure Of Apolipoprotein A-II In Discoidal High Density Lipoproteins. 
R.A.G.D. Silva, L.A. Schneeweis, S.C.Krishnan, X. Zhang, P.H. Axelsen, and W.S. Davidson. 
Journal of Biological Chemistry 282:9713-9721, 2007.

Membrane Mediated Amyloidogenesis and the Promotion of Oxidative Lipid Damage by Amyloid b Proteins. 
Murray, I.V.J., Liu, L., Komatsu, H., Uryu, K., Xiao, G., Lawson, J.A., and Axelsen, P.H.
Journal of Biological Chemistry
282:9335-9345, 2007.

Promotion of Amyloid b Protein Misfolding and Fibrillogenesis by a Lipid Oxidation Product. 
Liu, L., Komatsu, H., Murray, I.V.J., and Axelsen, P.H.
Journal of Molecular Biology 377:1236-1250, 2008.

Two dimensional infrared spectra of isotopically diluted amyloid fibrils from Ab40. 
Kim, Y.S., Liu, L., Axelsen, P.H., and Hochstrasser, R.M.
Proceedings of the National Academy of Sciences USA 105:7720-7725, 2008. 

Vancomycin forms supramolecular complexes in a ligand-mediated fashion.
Loll, P.J., Derhovanessian, A., Kaplan, J., Yang, L., and Axelsen, P.H.
Journal of Molecular Biology 385:200-211, 2009.

2D IR Evidence for Mobile Water Molecules in beta-Amyloid Fibrils.
Kim, Y.S., Liu, L., Axelsen, P.H., and Hochstrasser, R.M.
Proceedings of the National Academy of Sciences USA 106:17751-17763, 2009

Quantitative Analysis of Phospholipids Containing Arachidonate and Docosahexaenoate Chains in Microdissected Regions of Mouse Brain.
Axelsen, P.H., and Murphy, R.M.
Journal of Lipid Research 51:660-671, 2010.

Intrinsic linear heterogeneity of amyloid beta protein fibrils revealed by higher resolution mass-per-length determinations.
Komatsu, H., Feingold-Link, E., Sharp, K.A., Rastogi, T., and Axelsen, P.H.
Journal of Biological Chemistry 285:41843-41851, 2010.

Hemagglutinin Fusion Peptide Mutants in Model Membranes: Structural Properties, Membrane Physical Properties, and PEG-Mediated Fusion.
M.E. Haque, H. Chakraborty, T. Koklic, H. Komatsu, P. H. Axelsen, and B.R. Lentz.
Biophysical Journal 101:1095-1104, 2011

Frequency Distribution of the Amide-I Vibration Sorted by Residues in Amyloid Fibrils Revealed by 2D-IR Measurements and Simulations.
Falvo, C., Zhuang, W., Kim, Y.S., Axelsen, P.H. Hochstrasser, R.M., and Mukamel, S.
Journal of Physical Chemistry B 116:3322-3330, 2012

The Crowded Environment of a Reverse Micelle Induces the Formation of Beta-strand Seed Structures for Nucleating Amyloid Fibril Formation.
Yeung, P. S.-W., and Axelsen, P.H.
Journal of the American Chemical Society 134:6061-6063, 2012


The Structural Biology of Ligand Recognition by Vancomycin. 
Loll, P.J., and Axelsen, P.H.
Annual Reviews of Biophysics and Bioengineering 29:265-289, 2000.

The Structure of Lipoprotein A-I. Axelsen, P.H., and Koppaka, V.
Trends in Cardiovascular Science 9:192-195, 2000.

Investigations of Membrane Mediated Amyloidogenesis with Internal Reflection Infrared Spectroscopy. 
Komatsu, H., Liu L., Murray, I.V.J., and Axelsen, P.H. 
BBA – Biomembranes 1768:1913-1922, 2007

Mass Spectrometric Analysis of Long Chain Lipids
Murphy, R.C. and Axelsen, P.H.
Mass Spectrometry Reviews 30:579-599, 2011.

Oxidative Stress and Cell Membranes in the Pathogenesis of Alzheimer's Disease
Axelsen, P.H., Komatsu, H., and I.V.J. Murray
Physiology 26:54-69, 2011.

Copper and Oxidative Stress in the Pathogenesis of Alzheimer's Disease
Eskici, G. and Axelsen, P.H.
Biochemistry 51:6289-6311, 2012.

Infrared Spectroscopy of Proteins in Reverse Micelles
Yeung, P. S.-W., Eskici, G. and Axelsen, P.H.
BBA – Biomembranes (in press)

Peer-reviewed Clinical Papers

Coexistence of Primary Biliary Cirrhosis and a Systemic Lupus-like Syndrome
Hall, S., Axelsen, P. H., Bunch, T., and D. Larsen.
Annals of Internal Medicine 100:388-389, 1984.

Hepatitis A and B Infections Among Expatriates in Papua New Guinea: A Missed Opportunity for Immunization.
Poland, G.A., Axelsen, P.H., and M. Felz.
Journal of Travel Medicine 4:209-213, 1996.

Non peer-reviewed Research Publications

Three-dimensional Structures of Acetylcholinesterase and of its Complexes with Anticholinesterase Agents.
Silman, I., Harel, M., Axelsen, P., Raves, M., and J.L. Sussman.
Biochemical Society Transactions 22:745-749, 1994.

Editorial Commentaries

A Chaotic Pore Model of Polypeptide Antibiotic Action.
Biophysical Journal 94:1549-1550, 2008.


Essentials of Antimicrobial Pharmacology : A Guide to Fundamentals for Practice
P. H. Axelsen.  © 2000, Humana Press

Book Chapters

Analysis and Interpretation of Tryptophan Fluorescence Intensity Decays in Proteins. 
Prendergast, F.G., Bajzer, Z., Axelsen, P.H., and C. Haydock. In
Proteins: Structure, Function, and Design. pp 208-219 (ESCOM/Leiden, 1991)
Renugopalakrishnan, V., Carey, P.R., Smith, I.C.P., Huang, S.G., and S. Storer, eds.

The Role of Oxidatively Stressed Lipids in Amyloid Formation and Toxicity, Komatsu, H., and Axelsen, P.H.  in
Protein Misfolding Diseases: Basis of Protein Misfolding, Pathophysiology, Current, and Emerging Therapies
(Wiley, in press), Ramirez-Alvarado, M., Kelly, J.W., and Dobson, C.M., eds.

Book Reviews

Zoonoses: Biology, Clinical Practice, and Public Health Control.
Journal of the American Medical Association 281:669-670, 1999.

Infectious Diseases Epidemiology: Theory and Practice.
Journal of the American Medical Association 286:355-356, 2001.

Vaccine A.
Journal of the American Medical Association 293:2664, 2005.