Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Science 4 December 1998:
Vol. 282. no. 5395, pp. 1877 - 1882
DOI: 10.1126/science.282.5395.1877
Prev | Table of Contents | Next

Reports

Single-Molecule Enzymatic Dynamics

H. Peter Lu, Luying Xun, X. Sunney Xie *

Enzymatic turnovers of single cholesterol oxidase molecules were observed in real time by monitoring the emission from the enzyme's fluorescent active site, flavin adenine dinucleotide (FAD). Statistical analyses of single-molecule trajectories revealed a significant and slow fluctuation in the rate of cholesterol oxidation by FAD. The static disorder and dynamic disorder of reaction rates, which are essentially indistinguishable in ensemble-averaged experiments, were determined separately by the real-time single-molecule approach. A molecular memory phenomenon, in which an enzymatic turnover was not independent of its previous turnovers because of a slow fluctuation of protein conformation, was evidenced by spontaneous spectral fluctuation of FAD.

H. P. Lu and X. S. Xie, Pacific Northwest National Laboratory, William R. Wiley Environmental Molecular Sciences Laboratory, Richland, WA 99352, USA. L. Xun, Washington State University, Department of Microbiology, Pullman, WA 99164, USA.
*   To whom correspondence should be addressed. E-mail: xsxie{at}pnl.gov

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Stabilization of the E* Form Turns Thrombin into an Anticoagulant.
A. Bah, C. J. Carrell, Z. Chen, P. S. Gandhi, and E. Di Cera (2009)
J. Biol. Chem. 284, 20034-20040
   Abstract »    Full Text »    PDF »
Single-molecule biophysics: at the interface of biology, physics and chemistry.
A. A Deniz, S. Mukhopadhyay, and E. A Lemke (2008)
J R Soc Interface 5, 15-45
   Abstract »    Full Text »    PDF »
Multiple-state reactions between the epidermal growth factor receptor and Grb2 as observed by using single-molecule analysis.
M. Morimatsu, H. Takagi, K. G. Ota, R. Iwamoto, T. Yanagida, and Y. Sako (2007)
PNAS 104, 18013-18018
   Abstract »    Full Text »    PDF »
Stochastic inhibitor release and binding from single-enzyme molecules.
H. H. Gorris, D. M. Rissin, and D. R. Walt (2007)
PNAS 104, 17680-17685
   Abstract »    Full Text »    PDF »
Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability.
D. N. Fuller, D. M. Raymer, V. I. Kottadiel, V. B. Rao, and D. E. Smith (2007)
PNAS 104, 16868-16873
   Abstract »    Full Text »    PDF »
An interpretation of fluctuations in enzyme catalysis rate, spectral diffusion, and radiative component of lifetimes in terms of electric field fluctuations.
M. K. Prakash and R. A. Marcus (2007)
PNAS 104, 15982-15987
   Abstract »    Full Text »    PDF »
Instrumentation and metrology for single RNA counting in biological complexes or nanoparticles by a single-molecule dual-view system.
H. Zhang, D. Shu, F. Huang, and P. Guo (2007)
RNA 13, 1793-1802
   Abstract »    Full Text »    PDF »
Single-molecule Chemistry and Biology Special Feature: Fueling protein DNA interactions inside porous nanocontainers.
I. Cisse, B. Okumus, C. Joo, and T. Ha (2007)
PNAS 104, 12646-12650
   Abstract »    Full Text »    PDF »
Single-molecule Chemistry and Biology Special Feature: Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase.
G. Luo, M. Wang, W. H. Konigsberg, and X. S. Xie (2007)
PNAS 104, 12610-12615
   Abstract »    Full Text »    PDF »
From the Cover: Single-molecule Chemistry And Biology Special Feature: Single-molecule fluorescence spectroscopy in (bio)catalysis.
M. B. J. Roeffaers, G. De Cremer, H. Uji-i, B. Muls, B. F. Sels, P. A. Jacobs, F. C. De Schryver, D. E. De Vos, and J. Hofkens (2007)
PNAS 104, 12603-12609
   Abstract »    Full Text »    PDF »
Rotational Catalysis of Escherichia coli ATP Synthase F1 Sector: STOCHASTIC FLUCTUATION AND A KEY DOMAIN OF THE beta SUBUNIT.
M. Nakanishi-Matsui, S. Kashiwagi, T. Ubukata, A. Iwamoto-Kihara, Y. Wada, and M. Futai (2007)
J. Biol. Chem. 282, 20698-20704
   Abstract »    Full Text »    PDF »
Utilizing the information content in two-state trajectories.
O. Flomenbom and R. J. Silbey (2006)
PNAS 103, 10907-10910
   Abstract »    Full Text »    PDF »
Real-time Enzyme Dynamics Illustrated with Fluorescence Spectroscopy of p-Hydroxybenzoate Hydroxylase.
A. H. Westphal, A. Matorin, M. A. Hink, J. W. Borst, W. J. H. van Berkel, and A. J. W. G. Visser (2006)
J. Biol. Chem. 281, 11074-11081
   Abstract »    Full Text »    PDF »
Single-molecule kinetics reveals signatures of half-sites reactivity in dihydroorotate dehydrogenase A catalysis.
J. Shi, J. Dertouzos, A. Gafni, D. Steel, and B. A. Palfey (2006)
PNAS 103, 5775-5780
   Abstract »    Full Text »    PDF »
Pre-Unfolding Resonant Oscillations of Single Green Fluorescent Protein Molecules.
G. Baldini, F. Cannone, and G. Chirico (2005)
Science 309, 1096-1100
   Abstract »    Full Text »    PDF »
COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures.
J. Vertrees, P. Barritt, S. Whitten, and V. J. Hilser (2005)
Bioinformatics 21, 3318-3319
   Abstract »    Full Text »    PDF »
Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins.
S. T. Whitten, B. Garcia-Moreno E., and V. J. Hilser (2005)
PNAS 102, 4282-4287
   Abstract »    Full Text »    PDF »
Activation of pausing F1 motor by external force.
Y. Hirono-Hara, K. Ishizuka, K. Kinosita Jr., M. Yoshida, and H. Noji (2005)
PNAS 102, 4288-4293
   Abstract »    Full Text »    PDF »
Stretched exponential decay and correlations in the catalytic activity of fluctuating single lipase molecules.
O. Flomenbom, K. Velonia, D. Loos, S. Masuo, M. Cotlet, Y. Engelborghs, J. Hofkens, A. E. Rowan, R. J. M. Nolte, M. Van der Auweraer, et al. (2005)
PNAS 102, 2368-2372
   Abstract »    Full Text »    PDF »
Single-Molecule Fluorescence Spectroscopy: New Probes of Protein Function and Dynamics.
C. K. Johnson, K. D. Osborn, M. W. Allen, and B. D. Slaughter (2005)
Physiology 20, 10-14
   Abstract »    Full Text »    PDF »
Probing conformational dynamics in single donor-acceptor synthetic molecules by means of photoinduced reversible electron transfer.
M. Cotlet, S. Masuo, G. Luo, J. Hofkens, M. Van der Auweraer, J. Verhoeven, K. Mullen, X. S. Xie, and F. De Schryver (2004)
PNAS 101, 14343-14348
   Abstract »    Full Text »    PDF »
Simultaneous atomic force microscope and fluorescence measurements of protein unfolding using a calibrated evanescent wave.
A. Sarkar, R. B. Robertson, and J. M. Fernandez (2004)
PNAS 101, 12882-12886
   Abstract »    Full Text »    PDF »
Single-molecule enzymology of RNA: Essential functional groups impact catalysis from a distance.
D. Rueda, G. Bokinsky, M. M. Rhodes, M. J. Rust, X. Zhuang, and N. G. Walter (2004)
PNAS 101, 10066-10071
   Abstract »    Full Text »    PDF »
The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques.
M. Schlierf, H. Li, and J. M. Fernandez (2004)
PNAS 101, 7299-7304
   Abstract »    Full Text »    PDF »
Single-molecule and transient kinetics investigation of the interaction of dihydrofolate reductase with NADPH and dihydrofolate.
Z. Zhang, P. T. R. Rajagopalan, T. Selzer, S. J. Benkovic, and G. G. Hammes (2004)
PNAS 101, 2764-2769
   Abstract »    Full Text »    PDF »
Diversity in the Rates of Transcript Elongation by Single RNA Polymerase Molecules.
S. F. Tolic-Norrelykke, A. M. Engh, R. Landick, and J. Gelles (2004)
J. Biol. Chem. 279, 3292-3299
   Abstract »    Full Text »    PDF »
Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme.
Z. Xie, N. Srividya, T. R. Sosnick, T. Pan, and N. F. Scherer (2004)
PNAS 101, 534-539
   Abstract »    Full Text »    PDF »
Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer.
H. Yang, G. Luo, P. Karnchanaphanurach, T.-M. Louie, I. Rech, S. Cova, L. Xun, and X. S. Xie (2003)
Science 302, 262-266
   Abstract »    Full Text »    PDF »
Single metallic nanoparticle imaging for protein detection in cells.
L. Cognet, C. Tardin, D. Boyer, D. Choquet, P. Tamarat, and B. Lounis (2003)
PNAS 100, 11350-11355
   Abstract »    Full Text »    PDF »
Single-Molecule Kinetics of {lambda} Exonuclease Reveal Base Dependence and Dynamic Disorder.
A. M. van Oijen, P. C. Blainey, D. J. Crampton, C. C. Richardson, T. Ellenberger, and X. S. Xie (2003)
Science 301, 1235-1238
   Abstract »    Full Text »    PDF »
The structural basis for giant enhancement enabling single-molecule Raman scattering.
Z. Wang, S. Pan, T. D. Krauss, H. Du, and L. J. Rothberg (2003)
PNAS 100, 8638-8643
   Abstract »    Full Text »    PDF »
Multiparameter single-molecule fluorescence spectroscopy reveals heterogeneity of HIV-1 reverse transcriptase:primer/template complexes.
P. J. Rothwell, S. Berger, O. Kensch, S. Felekyan, M. Antonik, B. M. Wohrl, T. Restle, R. S. Goody, and C. A. M. Seidel (2003)
PNAS 100, 1655-1660
   Abstract »    Full Text »    PDF »
Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations.
M. J. Levene, J. Korlach, S. W. Turner, M. Foquet, H. G. Craighead, and W. W. Webb (2003)
Science 299, 682-686
   Abstract »    Full Text »    PDF »
Vibrationally Resolved Fluorescence Excited with Submolecular Precision.
X. H. Qiu, G. V. Nazin, and W. Ho (2003)
Science 299, 542-546
   Abstract »    Full Text »    PDF »
Conformational-relaxation models of single-enzyme kinetics.
H.-P. Lerch, A. S. Mikhailov, and B. Hess (2002)
PNAS 99, 15410-15415
   Abstract »    Full Text »    PDF »
Correlating Structural Dynamics and Function in Single Ribozyme Molecules.
X. Zhuang, H. Kim, M. J. B. Pereira, H. P. Babcock, N. G. Walter, and S. Chu (2002)
Science 296, 1473-1476
   Abstract »    Full Text »    PDF »
Two-photon excitation microscopy of tryptophan-containing proteins.
M. Lippitz, W. Erker, H. Decker, K. E. van Holde, and T. Basche (2002)
PNAS 99, 2772-2777
   Abstract »    Full Text »    PDF »
Network of coupled promoting motions in enzyme catalysis.
P. K. Agarwal, S. R. Billeter, P. T. R. Rajagopalan, S. J. Benkovic, and S. Hammes-Schiffer (2002)
PNAS
   Abstract »    Full Text »    PDF »
Real-Time Single-Molecule Imaging of the Infection Pathway of an Adeno-Associated Virus.
G. Seisenberger, M. U. Ried, T. Endre{beta}, H. Buning, M. Hallek, and C. Brauchle (2001)
Science 294, 1929-1932
   Abstract »    Full Text »    PDF »
Single molecules.
Th. Basche, S. Nie, and J. M. Fernandez (2001)
PNAS 98, 10527-10528
   Full Text »    PDF »
Balanced branching in transcription termination.
K. J. Harrington, R. B. Laughlin, and S. Liang (2001)
PNAS
   Abstract »    Full Text »
Photoactivated Fluorescence from Individual Silver Nanoclusters.
L. A. Peyser, A. E. Vinson, A. P. Bartko, and R. M. Dickson (2001)
Science 291, 103-106
   Abstract »    Full Text »
Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy.
D. S. Talaga, W. L. Lau, H. Roder, J. Tang, Y. Jia, W. F. DeGrado, and R. M. Hochstrasser (2000)
PNAS 97, 13021-13026
   Abstract »    Full Text »    PDF »
Memory landscapes of single-enzyme molecules.
L. Edman and R. Rigler (2000)
PNAS
   Abstract »    Full Text »
A Single-Molecule Study of RNA Catalysis and Folding.
X. Zhuang, L. E. Bartley, H. P. Babcock, R. Russell, T. Ha, D. Herschlag, and S. Chu (2000)
Science 288, 2048-2051
   Abstract »    Full Text »
Single-Molecule Study of Transcriptional Pausing and Arrest by E. coli RNA Polymerase.
R. J. Davenport, G. J. Wuite, R. Landick, and C. Bustamante (2000)
Science 287, 2497-2500
   Abstract »    Full Text »
From residue matching patterns to protein folding topographies: General model and bovine pancreatic trypsin inhibitor.
A. Fernandez, K. Kostov, and R. S. Berry (1999)
PNAS 96, 12991-12996
   Abstract »    Full Text »    PDF »
Single molecule physics and chemistry.
C. Bai, C. Wang, X. S. Xie, and P. G. Wolynes (1999)
PNAS 96, 11075-11076
   Abstract »    Full Text »    PDF »
The dynamics of structural deformations of immobilized single light-harvesting complexes.
M. A. Bopp, A. Sytnik, T. D. Howard, R. J. Cogdell, and R. M. Hochstrasser (1999)
PNAS 96, 11271-11276
   Abstract »    Full Text »    PDF »
Ligand-induced conformational changes observed in single RNA molecules.
T. Ha, X. Zhuang, H. D. Kim, J. W. Orr, J. R. Williamson, and S. Chu (1999)
PNAS 96, 9077-9082
   Abstract »    Full Text »    PDF »
Single-molecule Enzymology.
X. S. Xie and H. P. Lu (1999)
J. Biol. Chem. 274, 15967-15970
   Full Text »    PDF »
Single-pair fluorescence resonance energy transfer on freely diffusing molecules: Observation of Forster distance dependence and subpopulations.
A. A. Deniz, M. Dahan, J. R. Grunwell, T. Ha, A. E. Faulhaber, D. S. Chemla, S. Weiss, and P. G. Schultz (1999)
PNAS 96, 3670-3675
   Abstract »    Full Text »    PDF »
Illuminating Single Molecules in Condensed Matter.
W. E. Moerner and M. Orrit (1999)
Science 283, 1670-1676
   Abstract »    Full Text »
Fluorescence Spectroscopy of Single Biomolecules.
S. Weiss (1999)
Science 283, 1676-1683
   Abstract »    Full Text »
Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism.
T. Ha, A. Y. Ting, J. Liang, W. B. Caldwell, A. A. Deniz, D. S. Chemla, P. G. Schultz, and S. Weiss (1999)
PNAS 96, 893-898
   Abstract »    Full Text »    PDF »
Network of coupled promoting motions in enzyme catalysis.
P. K. Agarwal, S. R. Billeter, P. T. R. Rajagopalan, S. J. Benkovic, and S. Hammes-Schiffer (2002)
PNAS 99, 2794-2799
   Abstract »    Full Text »    PDF »
Memory landscapes of single-enzyme molecules.
L. Edman and R. Rigler (2000)
PNAS 97, 8266-8271
   Abstract »    Full Text »    PDF »
Balanced branching in transcription termination.
K. J. Harrington, R. B. Laughlin, and S. Liang (2001)
PNAS 98, 5019-5024
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)