Ensemble and Single-Molecule Detected Time-Resolved FRET Methods in Studies of Protein Conformations and Dynamics

Abstract P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.

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Increasing the time resolution of single-molecule experiments with Bayesian inference

10.1101/099648 ◽

2017 ◽

Author(s):

Colin D. Kinz-Thompson ◽

Ruben L. Gonzalez

Keyword(s):

Bayesian Inference ◽

Single Molecule ◽

Time Resolution ◽

Rate Constants ◽

Computational Approach ◽

Biomolecular Systems ◽

Time Resolved ◽

The Given ◽

Kinetics Of ◽

Resolution Data

AbstractMany time-resolved, single-molecule biophysics experiments seek to characterize the kinetics of biomolecular systems exhibiting dynamics that challenge the time resolution of the given technique. Here we present a general, computational approach to this problem that employs Bayesian inference to learn the underlying dynamics of such systems, even when they are much faster than the time resolution of the experimental technique being used. By accurately and precisely inferring rate constants, our Bayesian Inference for the Analysis of Sub-temporal-resolution Data (BIASD) approach effectively enables the experimenter to super-resolve the poorly resolved dynamics that are present in their data.

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Hierarchical coupling between ATP hydrolysis and Hsp90’s client binding site

10.1101/2020.02.15.950725 ◽

2020 ◽

Author(s):

Steffen Wolf ◽

Benedikt Sohmen ◽

Björn Hellenkamp ◽

Johann Thurn ◽

Gerhard Stock ◽

...

Keyword(s):

Binding Site ◽

Single Molecule ◽

Information Transfer ◽

Atp Hydrolysis ◽

Structural Information ◽

Substrate Binding ◽

Signal Propagation ◽

Nonequilibrium Molecular Dynamics ◽

Time Resolved ◽

Substrate Binding Site

I.ABSTRACTSeveral indicators for a signal propagation from a binding site to a distant functional site have been found in the Hsp90 dimer. Here we determined a time-resolved pathway from ATP hydrolysis to changes in a distant folding substrate binding site. This was possible by combining single-molecule fluorescence-based methods with extensive atomistic nonequilibrium molecular dynamics simulations. We find that hydrolysis of one ATP effects a structural asymmetry in the full Hsp90 dimer that leads to the collapse of a central folding substrate binding site. Arg380 is the major mediator in transferring structural information from the nucleotide to the substrate binding site. This allosteric process occurs via hierarchical dynamics that involve timescales from picoto milliseconds and length scales from Ångstroms to several nanometers. We presume that similar hierarchical mechanisms are fundamental for information transfer through many other proteins.

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The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds

10.1101/2020.11.09.374991 ◽

2020 ◽

Author(s):

Jiaxing Chen ◽

Sofia Zaer ◽

Paz Drori ◽

Joanna Zamel ◽

Khalil Joron ◽

...

Keyword(s):

Single Molecule ◽

Resonance Energy Transfer ◽

Resonance Energy ◽

Intrinsically Disordered Protein ◽

Structural Heterogeneity ◽

Conformational Space ◽

Conformational Ensemble ◽

Time Resolved ◽

Intrinsically Disordered ◽

Transient Nature

AbstractThe intrinsically disordered protein, α-synuclein, implicated in synaptic vesicle homeostasis and neurotransmitter release, is also associated with several neurodegenerative diseases. The different roles of α-synuclein are characterized by distinct structural states (membrane-bound, dimer, tetramer, oligomer, and fibril), which are originated from its various monomeric conformations. The pathological states, determined by the ensemble of α-synuclein monomer conformations and dynamic pathways of interconversion between dominant states, remain elusive due to their transient nature. Here, we use inter-dye distance distributions from bulk time-resolved Förster resonance energy transfer as restraints in discrete molecular dynamics simulations to map the conformational space of the α-synuclein monomer. We further confirm the generated conformational ensemble in orthogonal experiments utilizing far-UV circular dichroism and cross-linking mass spectrometry. Single-molecule protein-induced fluorescence enhancement measurements show that within this conformational ensemble, some of the conformations of α-synuclein are surprisingly stable, exhibiting conformational transitions slower than milliseconds. Our comprehensive analysis of the conformational ensemble reveals essential structural properties and potential conformations that promote its various functions in membrane interaction or oligomer and fibril formation.

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Time-Resolved Single Molecule Spectroscopy of Conjugated Polymer Nanoparticles

Femtochemistry VII ◽

10.1016/b978-044452821-6/50041-1 ◽

2006 ◽

pp. 284-294

Author(s):

Young Jong Lee ◽

Rodrigo E. Palacios ◽

Paul F. Barbara

Keyword(s):

Single Molecule ◽

Conjugated Polymer ◽

Polymer Nanoparticles ◽

Single Molecule Spectroscopy ◽

Time Resolved ◽

Conjugated Polymer Nanoparticles

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Electron Transfer in a Naphthalene Diimide System Studied by Single-Molecule Delayed Fluorescence

Australian Journal of Chemistry ◽

10.1071/ch19555 ◽

2020 ◽

Vol 73 (8) ◽

pp. 699

Author(s):

Rosalind P. Cox ◽

Saman Sandanayake ◽

Steven J. Langford ◽

Toby D. M. Bell

Keyword(s):

Electron Transfer ◽

Single Molecule ◽

Delayed Fluorescence ◽

Pmma Film ◽

Time Resolved ◽

Single Molecule Level ◽

Film Interpretation ◽

Fluorescence Measurements ◽

Naphthalene Diimide ◽

Prompt And Delayed Fluorescence

Electron transfer (ET) is a key chemical reaction in nature and has been extensively studied in bulk systems, but remains challenging to investigate at the single-molecule level. A previously reported naphthalene diimide (NDI)-based system (Higginbotham et al., Chem. Commun. 2013, 49, 5061–5063) displays delayed fluorescence with good quantum yield (~0.5) and long-lived (nanoseconds) prompt and delayed fluorescence lifetimes, providing an opportunity to interrogate the underlying ET processes in single molecules. Time-resolved single-molecule fluorescence measurements enabled forward and reverse ET rate constants to be calculated for 45 individual molecules embedded in poly(methylmethacrylate) (PMMA) film. Interpretation of the results within the framework of Marcus–Hush theory for ET demonstrates that variation in both the electronic coupling and the driving force for ET is occurring from molecule to molecule within the PMMA film and over time for individual molecules.

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