42. Resonance Raman Analysis of the Tryptophan Cation Radical. H. S. Shafaat and J. E. Kim. J. Phys. Chem. Lett. 2014, 5, 3009-3014.

41. Interaction of heat shock protein 70 with membranes depends on the lipid environment. G. Armijo, J. Okerblom, D. M. Cauvi, V. Lopez, D. E. Schlamadinger, J. E., Kim, N. Arispe, and A. De Maio. Cell Stress and Chaperones 2014, in press.

40. Structures and Dynamics of Proteins Probed by UV Resonance Raman Spectroscopy. B. S. Leigh, D. E. Schlamadinger, and J. E. Kim. Biophysical Methods for Biotherapeutics: Discovery and Development Applications, ed. Tapan Das John Wiley and Sons, Inc. 2014, 243-268.

39. Probing Membrane Protein Structure and Dynamics by Fluorescence. G. Kang, I. López-Peña, S. Bhakta, and J. E. Kim. Encylopedia of Analytical Chemistry 2013, DOI: 10.1002/9780470027318.a9353.

38. Spectroscopic and computational study of melittin, cecropin A, and the hybrid peptide CM15. D. E. Schlamadinger, D. E. Wang, J. A. McCammon, and J. E. Kim. J. Phys. Chem. B 2012, 116, 10600-10608.

37. UV resonance Raman study of TrpZip2 and related peptides: π-π interactions of tryptophan. D. E. Schlamadinger, B. S. Leigh, and J. E. Kim. J. Raman Spectrosc. 2012, 43, 1459-1464.

36. Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers. Y. Wang, D. E. Schlamadinger, J. E. Kim, and J. A. McCammon. BBA-Biomembranes 2012, 1818, 1402-1409.

35. Förster resonance energy transfer as a probe of membrane protein folding. G. Kang, I. López-Peña, V. Oklejas, C. S. Gary, W. Cao, and J. E. Kim. BBA-Biomembranes 2012, 1818, 154-161.

34. Hydrogen bonding of tryptophan radicals revealed by EPR at 700 GHz. S. Stoll, H. S. S. Shafaat, J. Krzystek, A. Ozarowski, M. J. Tauber, J. E. Kim, and R. D. Britt. J. Am. Chem. Soc. 2011, 133, 18098-18101.

33. Using charge to control the functional properties of self-assembled nanopores in membranes. M. X. Macrae, D. E. Schlamadinger, J. E. Kim, M. Mayer, and J. Yang. Small 2011, 7, 2016-220.

32. Thermodynamics of membrane protein folding measured by fluorescence spectroscopy. D. E. Schlamadinger and J. E. Kim. JOVE 2011, published online. VIDEO

31. Tryptophan-lipid interactions in membrane protein folding probed by UV resonance Raman and fluorescence spectroscopy. K. M. Sanchez, G. Kang, B. Wu, and J. E. Kim. Biophys. J. 2011, 100, 2121-2130.

30. UV resonance Raman study of cation-π interactions in an indole crown ether. D. E. Schlamadinger, M. M. Daschbach, G. W. Gokel, and J. E. Kim. J. Raman Spectrosc. 2011, 42, 633-638.

29. Spectroscopic comparison of photogenerated tryptophan radicals in azurin: Effects of local environment and structure. H. S. Shafaat, B. S. Leigh, M. J. Tauber, and J. E. Kim. J. Am. Chem. Soc. 2010, 132(26), 9030-9039.

28. Quenching of Tryptophan Fluorescence in Unfolded Cytochrome c: A Biophysics Experiment for Physical Chemistry Students. D. E. Schlamadinger, D. I. Kats, and J. E. Kim. J. Chem. Ed. 2010, 87(9), 961-964.

27. Staphylococcus epidermidis antimicrobial phenol soluble modulins cooperate with host antimicrobial peptides to kill Group A Streptococcus. A. L. Cogen, K. Yamasaki, J. Muto, K. M. Sanchez, L. Alexander, J. Tanios, Y. Lai, J. E. Kim, V. Nizet, R. L. Gallo. PLoS ONE 2010, 5(1), e8557.

26. PRIMER: Optical techniques to probe protein dynamics. J. E. Kim. Nat. Chem. Biol. 2009, 11.

25. Fluorescence and UV resonance Raman study of peptide-vesicle interactions of human cathelicidin LL-37 and its F6W and F17W mutants. J. E. Gable, D. E. Schlamadinger, A. L. Cogen, R. L. Gallo, and J. E. Kim. Biochemistry 2009, 48, 11264-11272.

24. Hydrogen-bonding and solvent polarity markers in the UV resonance Raman spectrum of tryptophan: Application to membrane proteins. D. E. Schlamadinger, J. E. Gable, and J. E. Kim. J. Phys. Chem. B 2009, 113,14769-14778.

23. Toxins and antimicrobial peptides: Interactions with membranes. D. E. Schlamadinger, J. E. Gable, and J. E. Kim. Proc. of SPIE 2009, 7397, 73970J-1-73970J-13.

22. Selective antimicrobial action is provided by phenol-soluble modulins derived from Staphylococcus epidermidis, a normal resident of the skin A. L. Cogen, K. Yamasaki, K. M. Sanchez, R. A. Dorschner, Y. Lai, D. T. MacLeod, J. W. Torpey, M. Otto, V. Nizet, J. E. Kim, and R. L. Gallo J. Invest. Dermatol. 2009,130, 192-200.

21. Resonance Raman studies of the (His)(Cys)3 2Fe-2S cluster of mitoNEET: Comparison to the (Cys)4 mutant and implications of the pH effects on the labile metal center. T. F. Tirrell, M. L. Paddock, A. R. Conlan, E. J. Smoll, Jr., R. Nechushtai, P. A. Jennings, and J. E. Kim. Biochemistry 2009, 128, 4747-4752.

20. Ultraviolet resonance Raman spectroscopy of a β-sheet peptide: A model for membrane protein folding. H. S. Shafaat, K. M. Sanchez, T. J. Neary, and J. E. Kim. J. Raman Spectrosc. 2009, 40, 1060-1064.

19. Resonance Raman characterization of a stable tryptophan radical in an azurin mutant. H. S. Shafaat, B. S. Leigh, M. J. Tauber. and J. E. Kim. J. Phys. Chem. B 2009, 113, 382-388.

18. Effects of tryptophan microenvironment, soluble domain, and vesicle size on the thermodynamics of membrane protein folding: Lessons from the transmembrane protein OmpA. K. M. Sanchez, J. E. Gable, D. E. Schlamadinger, and J. E. Kim. Biochemistry 2008, 47, 12844-12852.

17. Ultraviolet Resonance Raman Spectroscopy of Folded and Unfolded States of an Integral Membrane Protein. K. M. Sanchez, T. J. Neary, and J. E. Kim. J. Phys. Chem. B 2008, 112, 9507-9511.

16. Förster Resonance Energy Transfer and Conformational Stability of Proteins. K. M. Sanchez, D. E. Schlamadinger, J. E. Gable, and J. E. Kim. J. Chem. Ed. 2008, 85, 1253-1256.

15. Thermodynamics of Peptide Insertion and Aggregation in a Lipid Bilayer. A. Babakhani, A. A. Gorfe, J. E. Kim, and J. A. McCammon. J. Phys. Chem B 2008, 112, 10528-10534.

14. Peptide Insertion, Positioning, and Stabilization in a Membrane: Insight from an All-Atom Molecular Dynamics Simulation. A. Babakhani, A. A. Gorfe, J. Gullingsrud, J. E. Kim, and J. A. McCammon. Biopolymers 2007, 85, 490-497.


------------------------------------------------- Papers prior to UCSD -------------------------------------------------


13. Protein Folding, Misfolding, and Disease. J. C. Lee, J. E. Kim, E. V. Pletneva, J. Faraone-Mennella, H. B. Gray, and J. R. Winkler. Met. Ions Life Sci. I. 9-60 (2006).

12. Probing Folded and Unfolded States of Outer Membrane Protein A with Steady-State and Time-Resolved Tryptophan Fluorescence. J. E. Kim, G. Arjara, J. H. Richards, H. B. Gray, and J. R. Winkler.
J. Phys. Chem. B 2006, 110, 17656-17662.

11. Zinc-porphyrin Solvation in Folded and Unfolded States of Zn-cytochrome C. J. E. Kim, M. A. Pribisko, H. B. Gray, and J. R. Winkler. Inorg. Chem. 2004, 43, 7953-7960.

10. Picosecond Dynamics of G-Protein Coupled Receptor Activation in Rhodopsin from Time-Resolved UV Resonance Raman Spectroscopy. J. E. Kim, D. Pan, and R. A. Mathies. Biochemistry 2003, 42, 5169-5175.

9. Analysis of the Mode-Specific Excited-State Energy Distribution and Wavelength-Dependent Photoreaction Quantum Yield in Rhodopsin. J. E. Kim, M. J. Tauber, and R. A. Mathies. Biophysical Journal 2003, 84, 2492–2501.

8. Vibrational Relaxation in ß-Carotene Probed by Picosecond Stokes and Anti-Stokes Resonance Raman Spectroscopy. D. W. McCamant, J. E. Kim, and R. A. Mathies. J. Phys. Chem. A 2002, 106, 6030-6038.

7. Anti-Stokes Raman Study of Vibrational Cooling Dynamics in the Primary Photochemistry of Rhodopsin.
J. E. Kim and R. A. Mathies. J. Phys. Chem. A 2002, 106, 8508-8515.

6. Time-Resolved Resonance Raman Analysis of Chromophore Structural Changes in the Formation and Decay of Rhodopsin’s BSI Intermediate. D. Pan, Z. Ganim, J. E. Kim, M. A. Verhoeven, J. Lugtenburg, and R. A. Mathies. J. Am. Chem. Soc. 2002, 124, 4857-4864.

5. Wavelength Dependent Cis-Trans Isomerization in Vision. J. E. Kim, M. J. Tauber, and R. A. Mathies. Biochemistry 2001, 40, 13774-13778.

4. Resonance Raman Structural Evidence that the Cis-to-Trans Isomerization in Rhodopsin Occurs in Femtoseconds. J. E. Kim, D. W. McCamant, L. Zhu, and R. A. Mathies. J. Phys. Chem. B 2001, 105, 1240-1249.

3. Picosecond Time-Resolved Raman System for Studying Photochemical Reaction Dynamics: Application to the Primary Events in Vision. L. Zhu, J. E. Kim and R. A. Mathies. J. Raman Spectrosc. 1999, 30, 777–783.

2. HCl Vapour Pressures and Reaction Probabilities for ClONO2 + HCl on Liquid H2SO4-HNO3-HCl-H2O Solutions. M. J. Elrod, R. E. Koch, J. E. Kim and M. J. Molina. Faraday Discuss. 1995, 100, 269-278.

1. Physical Chemistry of the H2SO4/HNO3/H2O Systems: Implications for Polar Stratospheric Clouds. M. J. Molina, R.Zhang, P. J. Woolridge, J. R. McMahon, J. E. Kim, H. Y. Chang, and K. D. Beyer. Science 1993, 261, 1418-1423.