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Single
Molecule Biophysics – Probing Folding, Misfolding, and Assembly in Proteins,
Amyloids and Cellular Machines.
Welcome to the Deniz Laboratory
We develop and use
single-molecule fluorescence methods to address key issues in protein, nucleic
acid and cellular dynamics and function. Single molecule detection methods have
recently emerged as powerful tools for investigating the structural
distributions and dynamics of complex systems. These novel methods provide
unprecedented abilities to directly probe static and dynamic heterogeneity in
biological and cellular systems, under both equilibrium and non-equilibrium
conditions. For example, directly observing multiple steps and pathways in
protein folding and misfolding, visualizing and understanding the steps
involved in the assembly of complex structures such as the ribosome, and directly
observing and testing mechanisms of RNAi in live cells are some of the
important capabilities of single-molecule methods that we are developing and
applying in our research.
We also synergistically use ensemble fluorescence and other methods to complement our single-molecule studies. Our research tools range from molecular/cell biology and protein chemistry, to optical instrumentation development, imaging, spectroscopy and computer modeling/data analysis.
Our current research is focused on the following areas:
Mechanisms of Protein folding, Misfolding and Aggregation
Assembly of Complex Biological Machines
Pathways and Mechanisms of RNAi
Development and optimization of single-molecule
fluorescence methods
Representative
publications.
Gambin,
Y., Schug, A., Lemke, E.A., Lavinder, J.J., Ferreon, A.C.M., Magliery, T.J.,
Onuchic, J.N., Deniz, A.A.
“Direct single-molecule observation of a protein living in two
opposed native structures” Proc. Natl. Acad. Sci.
U.S.A., 2009, 106: 10153.
Also see TSRI
Press Release.
Ferreon,
A.C.M., Gambin, Y., Lemke, E.L., Deniz A.A. “Interplay of α-synuclein binding
and conformational switching probed by single-molecule fluorescence” Proc. Natl. Acad. Sci. U.S.A., 2009, 106: 5645 (pdf).
Also see TSRI Press
Release.
Vandelinder, V., Ferreon, A.C.M.,
Gambin, Y., Deniz, A.A. and Groisman, A.
“High-Resolution Temperature−Concentration Diagram of α-Synuclein
Conformation Obtained from a Single Förster
Resonance Energy Transfer Image in a Microfluidic Device” Analytical Chem., 2009, ASAP, Online.
Brustad,
E.M., Lemke, E.A., Schultz, P.G., Deniz, A.A. “A General and Efficient Method
for the Site-Specific Dual-Labeling of Proteins for Single Molecule
Fluorescence Resonance Energy Transfer” Journal of the American Chemical Society, 2008, 130:17664.
Our recent broad review of single
molecule biophysics – includes history, fluorescence and force methods,
and applications ranging from folding biophysics to cellular studies.
Deniz,
A.A., Mukhopadhyay, S., Lemke, E.L. “Single-molecule biophysics: at the
interface of biology, physics and chemistry” J.
Royal Soc. Interface,
2008, 5(18):15-45.
A concise review of an interesting
subfield of Single Molecule Biophysics.
Mukhopadhyay,
S., Deniz, A.A. “Fluorescence from diffusing single molecules
illuminates biomolecular structure and dynamics ” Journal of Fluorescence, 2007,
17(6):775-783.
Ferreon,
A.C.M., Deniz, A.A. “a-Synuclein
Multi-State Folding Thermodynamics: Implications for Protein Misfolding and
Aggregation”. Biochemistry,
2007, 46:
Mukhopadhyay,
S., Krishnan, R., Lemke, E.L., Lindquist, S., Deniz, A.A. “A natively unfolded yeast prion
monomer adopts an ensemble of compact and fluctuating structures”.
Proc. Natl. Acad. Sci. USA, 2007,
104: 2649
(pdf).
Also
see TSRI Press Release.
Berezhna, S.Y., Supekova, L., Supek,
F., Schultz, P.G., Deniz, A.A. “siRNA in human cells selectively
localizes to target RNA sites”
Proc.
Natl. Acad. Sci., USA, 2006, 103: 7682-7687
(pdf).
Zhu,
P., Clamme, J-P., Deniz, A.A. "Fluorescence quenching by TEMPO: a sub-30
Å single molecule ruler" Biophysical Journal, 2005, 89:L37-L39.
Clamme,
J-P, Deniz, AA “Three-color single-molecule fluorescence resonance
energy transfer” ChemPhysChem, published
online Dec. 13, 2004.
Pljevaljcic,
G., Millar, D.P., Deniz, A.A. “Freely-diffusing single hairpin ribozymes
provide insights into the role of secondary structure and partially folded
states in RNA folding” Biophysical Journal 2004, 87:457.
Deniz,
A.A., Laurence, T., Beligere, G.S., Dahan, M., Martin, A.B., Chemla, D.S., Dawson,
P.E., Schultz, P.G., Weiss, S. "Single molecule protein folding: Diffusion
Fluorescence energy transfer studies of the denaturation of Chymotrysin
Inhibitor 2." Proc. Natl. Acad. Sci., USA 2000, 97:5179.
Deniz, A.A., Dahan, M., Grunwell, J.R., Ha, T.J.,
Faulhaber, A.E., Chemla, D.S., Weiss, S., Schultz, P.G. "Single-pair FRET
on freely diffusing molecules: Observation of Förster distance dependence
and subpopulations" Proc. Natl. Acad. Sci., USA 1999, 96:3670.
Last modified June 30, 2009. Please e-mail
comments/corrections to Deniz Lab Webpage
Administrator.