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Judy Kim
Biophysical chemistry: Spectroscopic studies of membrane protein folding and dynamics |
| Contact Information |
| Office: UHA 3040B |
| Phone: (858) 534-8080 |
| Fax: (858) 534-7042 |
| Email: judyk@ucsd.edu |
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| View group members
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| Education and Appointments |
| 2001 |
Ph.D., University of California at Berkeley
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| 1994 |
M.S., Massachusetts Institute of Technology
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| 1993 |
B.S., Massachusetts Institute of Technology
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| Awards and Academic Honors |
| 2003-2005 |
N.I.H. Postdoctoral Fellow, California Institute of Technology |
| 2002 |
Postdoctoral fellow, University of California at Berkeley, |
| Research Interests |
Integral membrane proteins comprise ~30% of all cell proteins, and play essential roles in cellular functions as gates, pumps, receptors, energy transducers, and enzymes. Despite recent progress towards understanding the structure and function of membrane proteins, a more complex and fundamental question persists: What are the molecular mechanisms for the folding, insertion, and assembly of integral membrane proteins that give rise to functional structures?
A broad range of spectroscopic and kinetics studies in our laboratory are aimed towards unveiling the mechanisms of folding, misfolding, and aggregation of ubiquitous bacterial membrane proteins. We aim to elucidate the structural evolution of beta-barrel membrane pores (PDB file 2OMF shown) and alpha-helical membrane proteins as well as changes in their immediate environment during a folding reaction, with special emphasis on: (1) site-specific intra- and intermolecular distances; (2) development of secondary, tertiary, and hydrogen bonding structures; and (3) changes in solvation. An additional critical component is to probe the triggers that induce protein misfolding and aggregation. Tools available in our lab include steady-state and time-resolved resonance emission spectroscopy, correlation spectroscopy, and molecular cell biology and peptide synthesis techniques.
A molecular understanding of membrane protein folding in vitro may provide clues to the complex folding process in vivo and hence, shed light on important topics in health and medicine. Specifically, our studies may elucidate pathogenic pathways of bacterial toxins as well as deepen our understanding of numerous membrane protein misfolding diseases, such as cystic fibrosis and diabetes. Our group's efforts in the study of biomolecules in cell membranes will not only contribute to progress in fundamental research, but will exemplify the exciting progress that can be made by working at the intersection of chemistry, physics, and biology.
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Interdisciplinary Specialties: |
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Physical/Analytical Chemistry
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Biophysics
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| Selected Publications |
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Shafaat HS,
Leigh BS,
Tauber MJ,
Kim JE,
"Resonance Raman characterization of a stable tryptophan radical in an azurin mutant." J Phys Chem B 1(382-8):
, 2009. [Go to PubMed]
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Gable JE,
Schlamadinger DE,
Cogen AL,
Gallo RL,
Kim JE,
"Fluorescence and UV resonance Raman study of peptide-vesicle interactions of human cathelicidin LL-37 and its F6W and F17W mutants." Biochemistry 47(11264-72):
, 2009. [Go to PubMed]
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Schlamadinger DE,
Gable JE,
Kim JE,
"Hydrogen bonding and solvent polarity markers in the uv resonance raman spectrum of tryptophan: application to membrane proteins." J Phys Chem B 44(14769-78):
, 2009. [Go to PubMed]
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Tirrell TF,
Paddock ML,
Conlan AR,
Smoll EJ Jr,
Nechushtai R,
Jennings PA,
Kim JE,
"Resonance Raman studies of the (His)(Cys)3 2Fe-2S cluster of MitoNEET: comparison to the (Cys)4 mutant and implications of the effects of pH on the labile metal center." Biochemistry 22(4747-52):
, 2009. [Go to PubMed]
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Babakhani A,
Gorfe AA,
Kim JE,
McCammon JA,
"Thermodynamics of peptide insertion and aggregation in a lipid bilayer." J Phys Chem B 34(10528-34):
, 2008. [Go to PubMed]
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Sanchez KM,
Gable JE,
Schlamadinger DE,
Kim JE,
"Effects of tryptophan microenvironment, soluble domain, and vesicle size on the thermodynamics of membrane protein folding: lessons from the transmembrane protein OmpA." Biochemistry 48(12844-52):
, 2008. [Go to PubMed]
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Sanchez KM,
Neary TJ,
Kim JE,
"Ultraviolet resonance Raman spectroscopy of folded and unfolded states of an integral membrane protein." J Phys Chem B 31(9507-11):
, 2008. [Go to PubMed]
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