Protein Conformation and Dynamics

The Laboratory of Protein Conformation and Dynamics integrates complementary biophysical and biochemical techniques to understand the molecular mechanisms of amyloid formation.

Jennifer Lee

Research Interests

Research Interests

Dr. Lee’s laboratory integrates a variety of biophysical and biochemical techniques to understand the molecular mechanisms of amyloid formation. Aggregation of proteins into amyloid structures is a hallmark of human diseases such as Alzheimer’s, Parkinson’s, and Hungtington’s. Interestingly, amyloid fibrils can also serve essential biological roles in organisms ranging from bacteria to humans. Moreover, many polypeptides with widely varying amino acid sequences and folded states can form amyloid in vitro, implying common formation pathways.

Dr. Lee focuses her research efforts on studying changes in protein conformation and dynamics important for the mechanisms by which amyloid structures assemble under normal and pathological conditions. A central question under investigation is: what are the distinguishing features between functional and pathological amyloids? For example, do functional amyloids aggregate such that specific pathogenic conformations are avoided? Or is the formation and degradation of amyloids regulated more efficiently in healthy cells? 

To begin to understand these differences, Dr. Lee is currently investigating the mechanisms of amyloid formation for two human proteins: α-synuclein, which is localized to nerve terminals and associated with Parkinson’s disease, and Pmel17, which serves as structural scaffolding for melanin deposition in skin and eyes.

To determine the critical features guiding amyloid formation, Dr. Lee is characterizing how individual amino acid residues affect protein-protein interaction during the amyloid assembly process. A broad approach is taken to gain insights at the residue- to ultrastructural-level. Steady-state and time-resolved fluorescence and anisotropy measurements are utilized to probe local conformational changes. Protein secondary structure is determined using circular dichroism spectroscopy, and transmission electron microscopy is used to visualize filament morphology. Complementary methods, such as dynamic light scattering and atomic force microscopy, are also used. Dr. Lee is also particularly interested in the effect of metal ions and the influence of different cellular membrane compartments on protein misfolding and aggregation. Emerging methods such as neutron reflectometry are also employed to investigate protein-lipid interactions. More recently, she has studied the interaction between α-synuclein and glucocerebrosidase, the enzyme deficient in Gaucher disease, to explain why mutations in GBA, the gene encoding glucocerebrosidase, is a risk factor for Parkinsonism.

Ultimately, Dr. Lee wants to understand the mechanisms of amyloid aggregation and function at a detailed level in the context of the multiple cellular compartments with which they interact. She would like to not only describe the self-assembly process and its critical features, but also determine points of intervention in which amyloid assembly is linked to pathology.

Graphical Abstracts

Tryptophan probes of TDP-43 C-terminal domain amyloid formation
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Image 1

Shuster, S.O. & Lee, J.C. (2021) Tryptophan probes of TDP-43 C-terminal domain amyloid formation, J. Phys. Chem. B., 125, 3781-3789. DOI: 10.1021/acs.jpcb.1c00767

Membrane interactions of α-synuclein probed by neutrons and photons
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Image 2

Kaur U. & Lee, J.C. (2021) Membrane interactions of α-synuclein probed by neutrons and photons, Acc. Chem. Res. 54, 302-310. DOI: 10.1021/acs.accounts.0c00453

Raman spectral imaging of 13C2H15N-labeled α-synuclein amyloid fibrils in cells
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Image 3

Watson, M.D., Flynn, J.D., Lee, J.C. (2021) Raman spectral imaging of 13C2H15N-labeled α-synuclein amyloid fibrils in cells, Biophys. Chem. 269, 106528. DOI: 10.1016/j.bpc.2020.106528

Terminal alkynes as Raman probes of α-synuclein in solution and in cells
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Image 4

Flynn, J.D., Gimmen, M., Dean, D.N., Lacy, S.M., Lee, J.C. (2020) Terminal alkynes as Raman probes of α-synuclein in solution and in cells, ChemBioChem, 21, 1582-1586. DOI: 10.1002/cbic.202000026

N-terminal acetylation affects α-synuclein fibril polymorphism
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Image 5

Watson, M.D. & Lee, J.C. (2019) N-terminal acetylation affects α-synuclein fibril polymorphism, Biochemistry, 58, 3630-3633. DOI: 10.1021/acs.biochem.9b00629

J. Mol. Biol cover
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Image 6

Ni, X., McGlinchey, R.P., Jiang, J., Lee, J.C. (2019) Structural insights into α-synuclein fibril polymorphism: Effects of Parkinson’s disease-related C-terminal truncations, J. Mol. Biol. 431, 3913-3919. DOI: 10.1016/j.jmb.2019.07.001

Segmental 13C-labeling and Raman microspectroscopy of α-synuclein amyloid formation
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Image 7

Flynn, J.D., Jiang, Z., Lee, J.C. (2018) Segmental 13C-labeling and Raman microspectroscopy of α-synuclein amyloid formation, Angew. Chem. Int. Ed. Engl. 57, 17069-17072. DOI: 10.1002/anie.201809865

Raman fingerprints of amyloid structures
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Image 8

Flynn, J.D. & Lee, J.C. (2018) Raman fingerprints of amyloid structures, Chem. Commun. 54, 6983-6986. DOI: 10.1039/c8cc03217c

Stimulation of α-synuclein amyloid formation by phosphatidyglycerol micellar tubules,
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Image 9

Jiang, Z., Flynn, J.D., Teague, W.E., Gawrisch, K., Lee, J.C. (2018) Stimulation of α-synuclein amyloid formation by phosphatidyglycerol micellar tubules, Biochim. Biophys. Acta Biomembr.1860, 1840-1847. DOI:10.1016/j.bbamem.2018.02.025

J. Biol. Chem. Cover
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Image 10

Flynn, J.D., McGlinchey, R.P., Walker III, R.L., Lee, J.C. (2018) Structural features of α-synuclein amyloid fibrils revealed by Raman spectroscopy, J. Biol. Chem. 293, 767-776. DOI:10.1074/jbc.M117.812388

Journal Cover - Biochemistry
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Image 11

McGlinchey, R.P., Dominah, G., Lee, J.C. (2017) Taking a bite out of amyloid: Mechanistic insights into α-synuclein degradation by cathepsin L, Biochemistry, 56, 3881-3884. DOI: 10.1021/acs.biochem.7b00360

 

 

Segmental deuteration of α-synuclein for neutron reflectometry on tethered bilayers
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Image 12

Jiang, Z., Heinrich, F., McGlinchey, R.P., Gruschus, J.M., Lee, J.C. (2017) Segmental deuteration of α-synuclein for neutron reflectometry on tethered bilayers, J. Phys. Chem. Lett. 8, 29-34. DOI: 10.1021/acs.jpclett.6b02304

Apolipoprotein C-III nanodiscs studied by site-specific tryptophan fluorescence
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Image 13

Brisbois, C.A. & Lee, J.C. (2016) Apolipoprotein C-III nanodiscs studied by site-specific tryptophan fluorescence, Biochemistry, 55, 4939-4948. DOI: 10.1021/acs.biochem.6b00599

Single particle-tracking of human lipoproteins
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Image 14

de Messieres M., Ng A., Duarte, C.J., Remaley, A.T., Lee, J.C. (2016) Single particle-tracking of human lipoproteins, Anal. Chem. 88, 596-599. DOI: 10.1021/acs.analchem.5b03749

Tryptophan probes reveal residue-specific phospholipid interactions of apolipoprotein C-III
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Image 15

Pfefferkorn, C.M., Walker III, R.L., He, Y., Lee, J.C. (2015) Tryptophan probes reveal residue-specific phospholipid interactions of apolipoprotein C-III, Biochim. Biophys. Acta Biomembr.,1848, 2821-2828. DOI: 10.1016/j.bbamem.2015.08.018

Molecular details of α-synuclein membrane association probed by neutrons and photons
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Image 16

Jiang, Z., Hess, S.K., Heinrich, F., Lee, J.C. (2015) Molecular details of α-synuclein membrane association probed by neutrons and photons, J. Phys. Chem. B 119, 4812-4823. DOI: 10.1021/jp512499r

Structural features of membrane-bound glucocerebrosidase and α-synuclein probed by neutron reflectometry and fluorescence spectroscopy
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Image 17

Yap, T.L., Jiang, Z., Heinrich, F., Gruschus, J.M., Pfefferkorn, C.M., Barros M., Curtis, J.E., Sidransky, E., Lee, J.C. (2015) Structural features of membrane-bound glucocerebrosidase and α-synuclein probed by neutron reflectometry and fluorescence spectroscopy, J. Biol. Chem. 290, 744-754. DOI: 10.1074/jbc.M114.610584

Lysophospholipid-containing membranes modulate the fibril formation of the repeat domain of a human functional amyloid
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Image 18

Jiang, Z. & Lee, J.C. (2014) Lysophospholipid-containing membranes modulate the fibril formation of the repeat domain of a human functional amyloid, Pmel17, J. Mol. Biol. 426, 4074-4086. DOI: 10.1016/j.jmb.2014.10.009

Journal Cover - Chem Bio Chem
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Image 19

McGlinchey, R.P., Jiang, Z., Lee, J.C. (2014) Molecular origin of the pH dependent fibril formation of a functional amyloid, ChemBioChem, 15, 1569-1572. DOI: 10.1002/cbic.201402074

Membrane remodeling by α-synuclein and effects on amyloid formation
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Image 20

Jiang, Z., de Messieres, M., Lee, J.C. (2013) Membrane remodeling by α-synuclein and effects on amyloid formation, J. Am. Chem. Soc. 135, 15970-15973. DOI: 10.1021/ja405993r

Saposin C protects glucocerebrosidase against α-synuclein inhibition
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Image 21

Yap, T.L., Gruschus, J.M., Velayati, A., Sidransky, E., Lee, J.C. (2013) Saposin C protects glucocerebrosidase against α-synuclein inhibition, Biochemistry 52, 7161-7163. DOI: 10.1021/bi401191v

NMR structure of calmodulin complexed to an N-terminally acetylated α-synuclein peptide
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Image 22

Gruschus, J.M., Yap, T.L., Pistolesi, S., Maltsev, A.S., Lee, J.C. (2013) NMR structure of calmodulin complexed to an N-terminally acetylated α-synuclein peptide, Biochemistry 52, 3436-3445.

Probing fibril dissolution of the repeat domain of a functional amyloid, Pmel17, on the microscopic and residue level
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Image 23

McGlinchey, R.P., Gruschus, J.M., Nagy, A., Lee, J.C. (2011) Probing fibril dissolution of the repeat domain of a functional amyloid, Pmel17, on the microscopic and residue level, Biochemistry 50, 10567-10569. DOI: 10.1021/bi201578h

Residue-specific fluorescent probes of α-synuclein: Detection of early events at the N- and C-termini during fibril assembly
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Image 24

Yap, T.L., Pfefferkorn, C.M., Lee, J.C. (2011) Residue-specific fluorescent probes of α-synuclein: Detection of early events at the N- and C-termini during fibril assembly, Biochemistry 50, 1963-1965. DOI: 10.1021/bi2000824

 

Evidence for copper-dioxygen reactivity during α-synuclein fibril formation
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Image 25

Lucas, H.R., DeBeer, S., Hong, M.-S., Lee, J.C. (2010) Evidence for copper-dioxygen reactivity during α-synuclein fibril formation, J. Am. Chem. Soc. 132, 6636-6637.DOI: 10.1021/ja101756m

Tryptophan probes at the α-synuclein and membrane interface
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Image 26

Pfefferkorn, C.M. & Lee, J.C. (2010) Tryptophan probes at the α-synuclein and membrane interface, J. Phys. Chem. B. 114, 4615-4622. DOI: 10.1021/jp908092e

Energy transfer probes of GluR2 ligand binding core
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Image 27

Petrik, A.F., Strub, M.-P., Lee, J.C. (2010) Energy transfer probes of GluR2 ligand binding core, Biochemistry 49, 2051-2057. DOI: 10.1021/bi9020007

Identification of the minimal copper(II)-binding α-synuclein sequence
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Image 28

Jackson, M.S. & Lee, J.C. (2009) Identification of the minimal copper(II)-binding α-synuclein sequence, Inorg. Chem. 48, 9303-9307. DOI: 10.1021/ic901157w

Meet the Team

Jennifer Lee

Jennifer Lee, Ph.D.

Senior Investigator

Jennifer C. Lee graduated with a B.S. in chemistry and a B.A. in economics from the University of California, Berkeley, in 1997, and earned her Ph.D. in chemistry from the California Institute of Technology in 2002. Following a one-year postdoctoral stint at the University of Southern California, she became a Beckman Senior Research Fellow at the Beckman Institute Laser Resource Center at the California Institute of Technology where she investigated the structures and dynamics of an intrinsically disordered and amyloid forming protein using time-resolved spectroscopic measurements. In 2006, Dr. Lee joined the NHLBI as a tenure-track Investigtor. She was awarded an NIH Graduate Partnerships Program Outstanding Mentor Award in 2009. Dr. Lee is a member of the American Chemical Society and the Protein Society.

Contact the lab

Jared Shadish

Jared Shadish, Ph.D.

Postdoctoral Fellow
team photo

Join Our Lab

Current Vacancy

Protein Conformation and Dynamics Postdoctoral Fellow Position

Alumni

Genevieve A. Verville

Postbaccalaureate Fellow
2020 - 2021

Sydney O. Shuster

Postbaccalaureate Fellow
2019 - 2021
Sydney O. Shuster is currently a Ph.D. Student at Chemistry Department, Yale University.

Dexter N. Dean, Ph.D.

Postdoctoral IRTA
2018 - 2021
Dexter N. Dean, Ph.D. is currently a Instructional Laboratory Instrumentation Manager at College of Sciences, Georgia Institute of Technology.

Upneet Kaur

Postbaccalaureate Fellow
2019 - 2020
Upneet Kaur is currently a M.D./Ph.D. Student at University of California, San Francisco.

Jessica D. Flynn, Ph.D.

Postdoctoral IRTA Fellow
2015 - 2020
Jessica D. Flynn, Ph.D. is currently a Staff Fellow at U.S. Food and Drug Administration.

Shannon M. Lacy

Postbaccalaureate Fellow
2016 - 2018
Shannon M. Lacy is currently a Ph.D. Student at Cellular and Molecular Biology Program, University of Michigan.

Emma I. O'Leary

Postbaccalaureate Fellow
2016 - 2018
Emma I. O'Leary is currently a M.D./Ph.D. Student at University of Pittsburgh.

Zhiping Jiang, Ph.D.

Visiting Fellow and Research Fellow
2011 - 2017
Zhiping Jiang, Ph.D. is currently a Senior Scientist at Pfizer.

Gifty Dominah

Postbaccalaureate Fellow
2015 - 2016
Gifty Dominah is currently a MD Student at George Washington University.

Chase A. Brisbois

Postbaccalaureate Fellow
2014 - 2016
Chase A. Brisbois is currently a Ph.D. Student at Department of Materials Science and Engineering, Northwestern University.

Michel de Messieres, Ph.D.

Postdoctoral IRTA Fellow
2012 - 2015
Michel de Messieres, Ph.D. is currently a Associate Research Scientist at Tech-X Corp..

Sara K. Hess

Postbaccalaureate Fellow
2013 - 2015
Sara K. Hess is currently a Ph.D. Student at Department of Chemistry, University of Chicago.

Stephanie A. Hill

Ox-Cam Graduate Student
2009 - 2013
Stephanie A. Hill is currently a Visiting Assistant Professor of Biology at Rose-Hulman Institute of Technology.

Thai Leong Yap, Ph.D.

Visiting Fellow
2008 - 2013
Thai Leong Yap, Ph.D. is currently a Research Scientist at Institute of Bioengineering and Nanotechnology, Singapore.

Candace M. Pfefferkorn

GPP-Maryland Chemical Physics Graduate Student
2007 - 2012
Candace M. Pfefferkorn is currently a Project Manager at U.S. Nuclear Regulatory Commission.

Robert L. Walker III

Postbaccalaureate Fellow
2010 - 2011
Robert L. Walker III is currently a M.D. Student at Howard University.

Heather R. Lucas, Ph.D.

Postdoctoral Fellow
2008 - 2011
Heather R. Lucas, Ph.D. is currently a Assistant Professor of Chemistry at Virginia Commonwealth University.

Amy F. Petrik, Ph.D.

Postdoctoral Fellow
2007 - 2009
Amy F. Petrik, Ph.D. is currently a Technology Development Associate at Technology Transfer and Intellectual Property Office, NIAID, NIH.

Mark S. Jackson

Postbaccalaureate Fellow
2008 - 2009
Mark S. Jackson is currently a Research Assistant at University of Wisconsin.