Jump to main content
Jump to site search
PLANNED MAINTENANCE Close the message box

Scheduled maintenance upgrade on Thursday 4th of May 2017 from 8.00am to 9.00am (BST).

During this time our websites will be offline temporarily. If you have any questions please use the feedback button on this page. We apologise for any inconvenience this might cause and thank you for your patience.


Issue 15, 2011
Previous Article Next Article

Revealing time bunching effect in single-molecule enzyme conformational dynamics

Author affiliations

Abstract

In this perspective, we focus our discussion on how the single-molecule spectroscopy and statistical analysis are able to reveal enzyme hidden properties, taking the study of T4 lysozyme as an example. Protein conformational fluctuations and dynamics play a crucial role in biomolecular functions, such as in enzymatic reactions. Single-molecule spectroscopy is a powerful approach to analyze protein conformational dynamics under physiological conditions, providing dynamic perspectives on a molecular-level understanding of protein structure–function mechanisms. Using single-molecule fluorescence spectroscopy, we have probed T4 lysozyme conformational motions under the hydrolysis reaction of a polysaccharide of E. coli B cell walls by monitoring the fluorescence resonant energy transfer (FRET) between a donor–acceptor probe pair tethered to T4 lysozyme domains involving open–close hinge-bending motions. Based on the single-molecule spectroscopic results, molecular dynamics simulation, a random walk model analysis, and a novel 2D statistical correlation analysis, we have revealed a time bunching effect in protein conformational motion dynamics that is critical to enzymatic functions. Bunching effect implies that conformational motion times tend to bunch in a finite and narrow time window. We show that convoluted multiple Poisson rate processes give rise to the bunching effect in the enzymatic reaction dynamics. Evidently, the bunching effect is likely common in protein conformational dynamics involving in conformation-gated protein functions. In this perspective, we will also discuss a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anti-correlated fluctuations under a non-correlated noise background. Using this new method, we are able to map out any defined segments along the fluctuation trajectories and determine whether they are correlated, anti-correlated, or non-correlated; after which, a cross correlation analysis can be applied for each specific segment to obtain a detailed fluctuation dynamics analysis.

Graphical abstract: Revealing time bunching effect in single-molecule enzyme conformational dynamics

Back to tab navigation
Please wait while Download options loads

Publication details

The article was received on 12 Dec 2010, accepted on 23 Jan 2011 and first published on 15 Mar 2011


Article type: Perspective
DOI: 10.1039/C0CP02860F
Citation: Phys. Chem. Chem. Phys., 2011,13, 6734-6749
  •   Request permissions

    Revealing time bunching effect in single-molecule enzyme conformational dynamics

    H. P. Lu, Phys. Chem. Chem. Phys., 2011, 13, 6734
    DOI: 10.1039/C0CP02860F

Search articles by author