Literature DB >> 34461104

Fast and robust two-dimensional inverse Laplace transformation of single-molecule fluorescence lifetime data.

Saurabh Talele1, John T King2.   

Abstract

Fluorescence spectroscopy at the single-molecule scale has been indispensable for studying conformational dynamics and rare states of biological macromolecules. Single-molecule two-dimensional (2D) fluorescence lifetime correlation spectroscopy is an emerging technique that holds promise for the study of protein and nucleic acid dynamics, as the technique is 1) capable of resolving conformational dynamics using a single chromophore, 2) resolves forward and reverse transitions independently, and 3) has a dynamic window ranging from microseconds to seconds. However, the calculation of a 2D fluorescence relaxation spectrum requires an inverse Laplace transform (ILT), which is an ill-conditioned inversion that must be estimated numerically through a regularized minimization. Current methods for performing ILTs of fluorescence relaxation can be computationally inefficient, sensitive to noise corruption, and difficult to implement. Here, we adopt an approach developed for NMR spectroscopy (T1-T2 relaxometry) to perform one-dimensional (1D) and 2D-ILTs on single-molecule fluorescence spectroscopy data using singular-valued decomposition and Tikhonov regularization. This approach provides fast, robust, and easy to implement Laplace inversions of single-molecule fluorescence data. We compare this approach to the widely used maximal entropy method.
Copyright © 2021 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2021        PMID: 34461104      PMCID: PMC8553602          DOI: 10.1016/j.bpj.2021.08.031

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   3.699


  28 in total

1.  Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy.

Authors:  Benjamin Schuler; Everett A Lipman; William A Eaton
Journal:  Nature       Date:  2002-10-17       Impact factor: 49.962

2.  Protein conformational dynamics probed by single-molecule electron transfer.

Authors:  Haw Yang; Guobin Luo; Pallop Karnchanaphanurach; Tai-Man Louie; Ivan Rech; Sergio Cova; Luying Xun; X Sunney Xie
Journal:  Science       Date:  2003-10-10       Impact factor: 47.728

3.  Ultrafast dynamics of protein collapse from single-molecule photon statistics.

Authors:  Daniel Nettels; Irina V Gopich; Armin Hoffmann; Benjamin Schuler
Journal:  Proc Natl Acad Sci U S A       Date:  2007-02-14       Impact factor: 11.205

4.  Analyzing the distribution of decay constants in pulse-fluorimetry using the maximum entropy method.

Authors:  A K Livesey; J C Brochon
Journal:  Biophys J       Date:  1987-11       Impact factor: 4.033

5.  Single-molecule spectroscopy reveals photosynthetic LH2 complexes switch between emissive states.

Authors:  Gabriela S Schlau-Cohen; Quan Wang; June Southall; Richard J Cogdell; W E Moerner
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-17       Impact factor: 11.205

6.  Two-dimensional fluorescence lifetime correlation spectroscopy. 1. Principle.

Authors:  Kunihiko Ishii; Tahei Tahara
Journal:  J Phys Chem B       Date:  2013-09-12       Impact factor: 2.991

7.  Kinetics of conformational fluctuations in DNA hairpin-loops.

Authors:  G Bonnet; O Krichevsky; A Libchaber
Journal:  Proc Natl Acad Sci U S A       Date:  1998-07-21       Impact factor: 11.205

8.  Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor.

Authors:  T Ha; T Enderle; D F Ogletree; D S Chemla; P R Selvin; S Weiss
Journal:  Proc Natl Acad Sci U S A       Date:  1996-06-25       Impact factor: 11.205

9.  Microsecond and millisecond dynamics in the photosynthetic protein LHCSR1 observed by single-molecule correlation spectroscopy.

Authors:  Toru Kondo; Jesse B Gordon; Alberta Pinnola; Luca Dall'Osto; Roberto Bassi; Gabriela S Schlau-Cohen
Journal:  Proc Natl Acad Sci U S A       Date:  2019-05-17       Impact factor: 11.205

10.  An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases.

Authors:  Kathryn H Gunn; John F Marko; Alfonso Mondragón
Journal:  Nat Struct Mol Biol       Date:  2017-04-17       Impact factor: 15.369

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