2D Regional Correlation Analysis of Single-Molecule Time Trajectories

Wang, Xuefei; Lu, H. Peter

doi:10.1021/jp804453j

Cited by 15 publications

(43 citation statements)

References 82 publications

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“…35, 36 In a single-molecule FRET measurement of protein conformational dynamics, the measured D-A fluorescence intensity trajectories should show the anti-correlated D-A intensity fluctuations associated with the D-A distance fluctuations. On the other hand, local-environment thermal fluctuations typically give correlated or non-correlated D-A florescence intensity fluctuations.…”

Section: Resultsmentioning

confidence: 99%

“…Specifically, measurement noise, fluctuations beyond the measurement time resolution, and the thermal fluctuations of the local environment often intermittently dominate segments of a trajectory to show correlated or non-correlated fluctuations. 35, 36 Practically, an overall calculation of time-correlation function may not reveal the intermittently-appearing anti-correlated FRET fluctuation, or even show correlated thermal fluctuations. 38 Our 2D regional correlation analysis method is capable of identifying the FRET D-A anti-correlated fluorescence intensity fluctuations at any segments of an experimental fluctuation time trajectory, which is not possible for a conventional correlation analysis to average over across the whole time trajectory.…”

Section: Resultsmentioning

confidence: 99%

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Probing Single-Molecule Enzyme Active-Site Conformational State Intermittent Coherence

Mukherjee

et al. 2011

J. Am. Chem. Soc.

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115

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The relationship between protein conformational dynamics and enzymatic reactions has been a fundamental focus in modern enzymology. Using single-molecule Fluorescence Resonance Energy Transfer (FRET) with a combined statistical data analysis approach, we have identified the intermittently appearing coherence of the enzymatic conformational state from the recorded single molecule intensity-time trajectories of enzyme 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) in catalytic reaction. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing, presenting as an extreme dynamic behavior intrinsically related to the time bunching effect that we have reported previously. The coherence frequency, identified by statistical results of the correlation function analysis from single-molecule FRET trajectories, increases with the increasing substrate concentrations. The intermittent coherence in conformational state changes at the enzymatic reaction active site is likely to be common and exist in other conformation regulated enzymatic reactions. Our results of HPPK interaction with substrate support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Probing Single-Molecule Enzyme Active-Site Conformational State Intermittent Coherence

Mukherjee

et al. 2011

J. Am. Chem. Soc.

Self Cite

115

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“…This is consistent with the previously reported slow fluctuation of the SMSERS. 65,69 We also carried out a 2D regional cross-correlation analysis 80 between ν 4 and ν 3 ( Figure 3D), and we observed that, with ν 4 fluctuating between two redox states, ν 3 shows correlation or anticorrelation with ν 4 . Previously, ensemble-averaged SERS measurements of hemin indicated complex correlation between ν 4 and ν 3.…”

Section: Article ' Results and Discussionmentioning

confidence: 92%

Probing Ground-State Single-Electron Self-Exchange across a Molecule−Metal Interface

Wang

Sevinç

et al. 2011

J. Am. Chem. Soc.

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We have probed single-molecule redox reaction dynamics of hemin (chloride) adsorbed on Ag nanoparticle surfaces by single-molecule surface-enhanced Raman spectroscopy (SMSERS) combined with spectroelectrochemistry. Redox reaction at the molecule/Ag interface is identified and probed by the prominent fluctuations of the Raman frequency of a specific vibrational mode, ν(4), which is a typical marker of the redox state of the iron center in a hemin molecule. On the basis of the autocorrelation and cross-correlation analysis of the single-molecule Raman spectral trajectories and the control measurements of single-molecule spectroelectochemistry and electrochemical STM, we suggest that the single-molecule redox reaction dynamics at the hemin-Ag interface is primarily driven by thermal fluctuations. The spontaneous fluctuation dynamics of the single-molecule redox reaction is measured under no external electric potential across the molecule-metal interfaces, which provides a novel and unique approach to characterize the interfacial electron transfer at the molecule-metal interfaces. Our demonstrated approaches are powerful for obtaining molecular coupling and dynamics involved in interfacial electron transfer processes. The new information obtained is critical for a further understanding, design, and manipulation of the charge transfer processes at the molecule-metal interface or metal-molecule-metal junctions, which are fundamental elements in single-molecule electronics, catalysis, and solar energy conversion.

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“…Cross-correlation can also be used to scan through larger data sets to detect, for example, temporal fluctuations of the correlation. [36] Herein, we measured the time-dependent fluctuations of fluorescence polarization degree (modulation depth) and polarization axis of single chains of two different polymers: poly[2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylene vinylene] (MEH-PPV) and a polythiophene derivative, poly[3-(2,5-dioctylphenyl)thiophene] (PDOPT). Several factors, for example bleaching and blinking, work together in the observed fluctuations of fluorescence polarization, which interfere with each other and make it difficult to understand the fundamental physics behind the fluctuations.…”

Section: Introductionmentioning

confidence: 99%

Correlation Analysis of Fluorescence Intensity and Fluorescence Anisotropy Fluctuations in Single‐Molecule Spectroscopy of Conjugated Polymers

2010

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Single-molecule spectroscopy techniques are used to investigate time fluctuations of the fluorescence properties of two different types of conjugated polymer, a polythiophene derivative (PDOPT) and a phenylene vinylene derivative (MEH-PPV), at 100 and 293 K. Linear correlation coefficients between fluorescence intensity and polarization are used to characterize fluctuations. We are able to distinguish between different blinking and bleaching effects on the polarization. Furthermore, the polarization data reveal clear differences in the topology of these two polymers, which is related to the ordered conformation of the MEH-PPV. Plots of correlation coefficients appear to be very different for the two polymers and are also very sensitive to temperature. These observations prove that correlation analysis is a useful tool to understand fluorescence fluctuations in multi-chromophoric systems.

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2D Regional Correlation Analysis of Single-Molecule Time Trajectories

Cited by 15 publications

References 82 publications

Probing Single-Molecule Enzyme Active-Site Conformational State Intermittent Coherence

Probing Single-Molecule Enzyme Active-Site Conformational State Intermittent Coherence

Probing Ground-State Single-Electron Self-Exchange across a Molecule−Metal Interface

Correlation Analysis of Fluorescence Intensity and Fluorescence Anisotropy Fluctuations in Single‐Molecule Spectroscopy of Conjugated Polymers

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