scholarly journals Conformational and dynamical plasticity in substrate-binding proteins underlies selective transport in ABC importers

2019 ◽  
Author(s):  
Marijn de Boer ◽  
Giorgos Gouridis ◽  
Ruslan Vietrov ◽  
Stephanie L. Begg ◽  
Gea K. Schuurman-Wolters ◽  
...  
Keyword(s):  
Single Molecule ◽  
Binding Proteins ◽  
Substrate Binding ◽  
Conformational Dynamics ◽  
Complex Interplay ◽  
Substrate Transport ◽  
Selective Transport ◽  
Closed Conformation ◽  
Single Molecule Fret ◽  
The Impact

ABSTRACTSubstrate-binding proteins (SBPs) are associated with ATP-binding cassette importers and switch from an open-to a closed-conformation upon substrate binding providing specificity for transport. We investigated the effect of substrates on the conformational dynamics of six SBPs and the impact on transport. Using single-molecule FRET, we reveal an unrecognized diversity of plasticity in SBPs. We show that a unique closed SBP conformation does not exist for transported substrates. Instead, SBPs sample a range of conformations that activate transport. Certain non-transported ligands leave the structure largely unaltered or trigger a conformation distinct from that of transported substrates. Intriguingly, in some cases similar SBP conformations are formed by both transported and non-transported ligands. In this case, the inability for transport arises from slow opening of the SBP or the selectivity provided by the translocator. Our results reveal the complex interplay between ligand-SBP interactions, SBP conformational dynamics and substrate transport.

scholarly journals Conformational and dynamic plasticity in substrate-binding proteins underlies selective transport in ABC importers

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Marijn de Boer ◽  
Giorgos Gouridis ◽  
Ruslan Vietrov ◽  
Stephanie L Begg ◽  
Gea K Schuurman-Wolters ◽  
...  
Keyword(s):  
Single Molecule ◽  
Binding Proteins ◽  
Substrate Binding ◽  
Conformational Dynamics ◽  
Complex Interplay ◽  
Selective Transport ◽  
Closed Conformation ◽  
Single Molecule Fret ◽  
The Impact ◽  
Dynamic Plasticity

Substrate-binding proteins (SBPs) are associated with ATP-binding cassette importers and switch from an open to a closed conformation upon substrate binding, providing specificity for transport. We investigated the effect of substrates on the conformational dynamics of six SBPs and the impact on transport. Using single-molecule FRET, we reveal an unrecognized diversity of plasticity in SBPs. We show that a unique closed SBP conformation does not exist for transported substrates. Instead, SBPs sample a range of conformations that activate transport. Certain non-transported ligands leave the structure largely unaltered or trigger a conformation distinct from that of transported substrates. Intriguingly, in some cases, similar SBP conformations are formed by both transported and non-transported ligands. In this case, the inability for transport arises from slow opening of the SBP or the selectivity provided by the translocator. Our results reveal the complex interplay between ligand-SBP interactions, SBP conformational dynamics and substrate transport.

Monitoring the Structural Dynamics of U2 snRNA Via Single-Molecule Förster Resonance Energy Transfer

2018 ◽  
Author(s):  
Alexander Carl DeHaven
Keyword(s):  
Energy Transfer ◽  
Structural Dynamics ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Förster Resonance Energy Transfer ◽  
U2 Snrna ◽  
Folding Dynamics ◽  
The Impact

This thesis contains four topic areas: a review of single-molecule microscropy methods and splicing, conformational dynamics of stem II of the U2 snRNA, the impact of post-transcriptional modifications on U2 snRNA folding dynamics, and preliminary findings on Mango aptamer folding dynamics.

scholarly journals Conformational entropy of a single peptide controlled under force governs protease recognition and catalysis

2018 ◽  
Vol 115 (45) ◽  
pp. 11525-11530 ◽  
Author(s):  
Marcelo E. Guerin ◽  
Guillaume Stirnemann ◽  
David Giganti
Keyword(s):  
Single Molecule ◽  
Conformational Dynamics ◽  
Conformational Sampling ◽  
Enzymatic Reactions ◽  
Sequence Specificity ◽  
Proteomics Data ◽  
Conformational Entropy ◽  
Substrate Peptide ◽  
The Impact

An immense repertoire of protein chemical modifications catalyzed by enzymes is available as proteomics data. Quantifying the impact of the conformational dynamics of the modified peptide remains challenging to understand the decisive kinetics and amino acid sequence specificity of these enzymatic reactions in vivo, because the target peptide must be disordered to accommodate the specific enzyme-binding site. Here, we were able to control the conformation of a single-molecule peptide chain by applying mechanical force to activate and monitor its specific cleavage by a model protease. We found that the conformational entropy impacts the reaction in two distinct ways. First, the flexibility and accessibility of the substrate peptide greatly increase upon mechanical unfolding. Second, the conformational sampling of the disordered peptide drives the specific recognition, revealing force-dependent reaction kinetics. These results support a mechanism of peptide recognition based on conformational selection from an ensemble that we were able to quantify with a torsional free-energy model. Our approach can be used to predict how entropy affects site-specific modifications of proteins and prompts conformational and mechanical selectivity.

Conformational Dynamics of DNA Hairpins at Millisecond Resolution Obtained from Analysis of Single-Molecule FRET Histograms

2013 ◽  
Vol 117 (50) ◽  
pp. 16105-16109 ◽  
Author(s):  
Roman Tsukanov ◽  
Toma E. Tomov ◽  
Yaron Berger ◽  
Miran Liber ◽  
Eyal Nir
Keyword(s):  
Single Molecule ◽  
Conformational Dynamics ◽  
Dna Hairpins ◽  
Single Molecule Fret

scholarly journals Conformational dynamics of the ABC transporter McjD seen by single‐molecule FRET

2018 ◽  
Vol 37 (21) ◽  
Author(s):  
Florence Husada ◽  
Kiran Bountra ◽  
Konstantinos Tassis ◽  
Marijn Boer ◽  
Maria Romano ◽  
...  
Keyword(s):  
Abc Transporter ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Single Molecule Fret

scholarly journals Single Molecule FRET Studies of Protein Conformational Landscapes: 3 Prototypic Examples for the Relation Between Conformational Dynamics and Function

2011 ◽  
Vol 100 (3) ◽  
pp. 474a-475a
Author(s):  
Markus Richert ◽  
Dymitro Rodnin ◽  
Carola S. Hengstenberg ◽  
Thomas Peulen ◽  
Alessandro Valeri ◽  
...  
Keyword(s):  
Single Molecule ◽  
Conformational Dynamics ◽  
Single Molecule Fret ◽  
Dynamics And Function ◽  
And Function

scholarly journals Intramolecular dynamics of single molecules in free diffusion

2017 ◽  
Author(s):  
Charles Limouse ◽  
Jason C. Bell ◽  
Colin J. Fuller ◽  
Aaron F. Straight ◽  
Hideo Mabuchi
Keyword(s):  
Single Molecule ◽  
Conformational Dynamics ◽  
Correlation Spectroscopy ◽  
Biomolecular Systems ◽  
Optimal Position ◽  
Biochemical Processes ◽  
Fluorescence Correlation ◽  
Dna Molecule ◽  
Feedback Scheme ◽  
The Impact

AbstractBiomolecular systems such as multiprotein complexes or biopolymers can span several tens to several hundreds of nanometers, but the dynamics of such “mesocale” molecules remain challenging to probe. We have developed a single-molecule technique that uses Tracking Fluorescence Correlation Spectroscopy (tFCS) to measure the conformation and dynamics of molecular assemblies specifically at the mesoscale level (~100-1000 nm). tFCS is non-perturbative, as molecules, which are tracked in real-time, are untethered and freely diffusing. To achieve sub-diffraction spatial resolution, we use a feedback scheme which allows us to maintain the molecule at an optimal position within the laser intensity gradient. We find that tFCS is sufficiently sensitive to measure the distance fluctuations between two sites within a DNA molecule separated by distances as short as 1000 bp. We demonstrate that tFCS detects changes in the compaction of reconstituted chromatin, and can assay transient protein mediated interactions between distant sites in an individual DNA molecule. Our measurements highlight the impact that tFCS can have in the study of a wide variety of biochemical processes involving mesoscale conformational dynamics.

scholarly journals 631: Single-molecule FRET reveals CFTR conformational dynamics during channel gating

2021 ◽  
Vol 20 ◽  
pp. S299-S300
Author(s):  
P. Liyanage ◽  
K. Mun ◽  
S. Yarlagadda ◽  
Y. Huang ◽  
A. Naren
Keyword(s):  
Single Molecule ◽  
Conformational Dynamics ◽  
Channel Gating ◽  
Single Molecule Fret
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