scholarly journals Interpreting Transition Path Time Extrapolation by Single Molecule FRET with MD Simulations

2020 ◽  
Vol 118 (3) ◽  
pp. 510a
Author(s):  
Grace H. Taumoefolau ◽  
Robert B. Best
Keyword(s):  
Single Molecule ◽  
Md Simulations ◽  
Transition Path ◽  
Single Molecule Fret ◽  
Time Extrapolation

scholarly journals Transport mechanism of a glutamate transporter homologue GltPh

2016 ◽  
Vol 44 (3) ◽  
pp. 898-904 ◽  
Author(s):  
Yurui Ji ◽  
Vincent L.G. Postis ◽  
Yingying Wang ◽  
Mark Bartlam ◽  
Adrian Goldman
Keyword(s):  
Single Molecule ◽  
Transport Mechanism ◽  
Glutamate Transporter ◽  
Md Simulations ◽  
Research Progress ◽  
Pyrococcus Horikoshii ◽  
Single Molecule Fret ◽  
Neurotransmitter Glutamate ◽  
Central Nervous Systems ◽  
Recent Research Progress

Glutamate transporters are responsible for uptake of the neurotransmitter glutamate in mammalian central nervous systems. Their archaeal homologue GltPh, an aspartate transporter isolated from Pyrococcus horikoshii, has been the focus of extensive studies through crystallography, MD simulations and single-molecule FRET (smFRET). Here, we summarize the recent research progress on GltPh, in the hope of gaining some insights into the transport mechanism of this aspartate transporter.

scholarly journals The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor

2019 ◽  
Author(s):  
Michael V. LeVine ◽  
Daniel S. Terry ◽  
George Khelashvili ◽  
Zarek S. Siegel ◽  
Matthias Quick ◽  
...  
Keyword(s):  
Single Molecule ◽  
Substrate Binding ◽  
Md Simulations ◽  
Binding Pocket ◽  
Coupled Transport ◽  
Single Molecule Fret ◽  
Allosteric Mechanism ◽  
Specific Transport ◽  
Slc6 Family ◽  
The Stability

AbstractNeurotransmitter:sodium symporters (NSS) in the SLC6 family terminate neurotransmission by coupling the thermodynamically favorable transport of ions to the thermodynamically unfavorable transport of neurotransmitter back into presynaptic neurons. While a combination of structural, functional, and computational studies on LeuT, a bacterial NSS homolog, has provided critical insight into the mechanism of sodium-coupled transport, the mechanism underlying substrate-specific transport rates is still not understood. We present a combination of MD simulations, single-molecule FRET imaging, and measurements of Na+ binding and substrate transport that reveal an allosteric mechanism in which residues F259 and I359 in the substrate binding pocket couple substrate binding to Na+ release from the Na2 site through allosteric modulation of the stability of a partially-open, inward-facing state. We propose a new model for transport selectivity in which the two residues act as a volumetric sensor that inhibits the transport of bulky amino acids.

scholarly journals Local-to-global signal transduction at the core of the Mn2+ sensing riboswitch

2019 ◽  
Author(s):  
Krishna C Suddala ◽  
Ian R Price ◽  
Michal Janeček ◽  
Petra Kührová ◽  
Shiba Dandpat ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Metal Ions ◽  
Single Molecule ◽  
Md Simulations ◽  
Xanthomonas Oryzae ◽  
Manganese Ion ◽  
The Core ◽  
Ion Sensing ◽  
Single Molecule Fret ◽  
Global Signal

The widespread manganese-ion sensing yybP-ykoY riboswitch controls the expression of bacterial Mn2+ homeostasis genes. Here, we first determine the crystal structure of the ligand-bound yybP-ykoY riboswitch from Xanthomonas oryzae at 2.85 Å resolution, revealing two conformations with docked four-way junction (4WJ) and incompletely coordinated metal ions. In >50 μs of MD simulations, we observe that loss of divalents from the core triggers local structural perturbations in the adjacent docking interface, laying the foundation for signal transduction to the regulatory switch helix. Using single-molecule FRET, we unveil a previously unobserved extended 4WJ conformation that samples transient docked states in the presence of Mg2+. Only upon adding sub-millimolar Mn2+, however, can the 4WJ dock stably, a feature lost upon mutation of an adenosine contacting Mn2+ in the core. These observations illuminate how subtly differing ligand preferences of competing metal ions become amplified by the coupling of local with global RNA dynamics.

scholarly journals Measurement of Average Transition-Path Time for Protein Folding in Single Molecule FRET Experiments

2012 ◽  
Vol 102 (3) ◽  
pp. 217a-218a
Author(s):  
Hoi Sung Chung ◽  
Irina V. Gopich ◽  
Kevin McHale ◽  
John M. Louis ◽  
William A. Eaton
Keyword(s):  
Protein Folding ◽  
Single Molecule ◽  
Transition Path ◽  
Single Molecule Fret ◽  
Average Transition

scholarly journals Hierarchical dynamics in allostery following ATP hydrolysis monitored by single molecule FRET measurements and MD simulations

2021 ◽  
Author(s):  
Steffen Wolf ◽  
Benedikt Sohmen ◽  
Björn Hellenkamp ◽  
Johann Thurn ◽  
Gerhard Stock ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Single Molecule ◽  
Atp Hydrolysis ◽  
Md Simulations ◽  
Large Protein ◽  
Single Molecule Fret ◽  
Fluorescence Methods ◽  
Dynamics Simulations

We report on a study that combines advanced fluorescence methods with molecular dynamics simulations to cover timescales from nanoseconds to milliseconds for a large protein, the chaperone Hsp90.

scholarly journals Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Krishna C. Suddala ◽  
Ian R. Price ◽  
Shiba S. Dandpat ◽  
Michal Janeček ◽  
Petra Kührová ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Metal Ions ◽  
Single Molecule ◽  
Md Simulations ◽  
Xanthomonas Oryzae ◽  
Rna Dynamics ◽  
The Core ◽  
Single Molecule Fret ◽  
Global Signal ◽  
Structural Perturbations

Abstract The widespread Mn2+-sensing yybP-ykoY riboswitch controls the expression of bacterial Mn2+ homeostasis genes. Here, we first determine the crystal structure of the ligand-bound yybP-ykoY riboswitch aptamer from Xanthomonas oryzae at 2.96 Å resolution, revealing two conformations with docked four-way junction (4WJ) and incompletely coordinated metal ions. In >100 µs of MD simulations, we observe that loss of divalents from the core triggers local structural perturbations in the adjacent docking interface, laying the foundation for signal transduction to the regulatory switch helix. Using single-molecule FRET, we unveil a previously unobserved extended 4WJ conformation that samples transient docked states in the presence of Mg2+. Only upon adding sub-millimolar Mn2+, however, can the 4WJ dock stably, a feature lost upon mutation of an adenosine contacting Mn2+ in the core. These observations illuminate how subtly differing ligand preferences of competing metal ions become amplified by the coupling of local with global RNA dynamics.

scholarly journals Dynamics of Histone H3 Tails in Mononucleosomes Studied by Single-Molecule FRET and MD Simulations

2018 ◽  
Vol 114 (3) ◽  
pp. 256a-257a
Author(s):  
Kathrin Lehmann ◽  
Ruihan Zhang ◽  
Suren Felekyan ◽  
Ralf Kühnemuth ◽  
Katalin Toth
Keyword(s):  
Single Molecule ◽  
Histone H3 ◽  
Md Simulations ◽  
Single Molecule Fret

scholarly journals Two-way communication between SecY and SecA suggests a Brownian ratchet mechanism for protein translocation

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
William John Allen ◽  
Robin Adam Corey ◽  
Peter Oatley ◽  
Richard Barry Sessions ◽  
Steve A Baldwin ◽  
...  
Keyword(s):  
Single Molecule ◽  
Atp Hydrolysis ◽  
Protein Translocation ◽  
Md Simulations ◽  
Atp Binding ◽  
Nucleotide Exchange ◽  
Brownian Ratchet ◽  
Ratchet Mechanism ◽  
Single Molecule Fret ◽  
Directional Movement

The essential process of protein secretion is achieved by the ubiquitous Sec machinery. In prokaryotes, the drive for translocation comes from ATP hydrolysis by the cytosolic motor-protein SecA, in concert with the proton motive force (PMF). However, the mechanism through which ATP hydrolysis by SecA is coupled to directional movement through SecYEG is unclear. Here, we combine all-atom molecular dynamics (MD) simulations with single molecule FRET and biochemical assays. We show that ATP binding by SecA causes opening of the SecY-channel at long range, while substrates at the SecY-channel entrance feed back to regulate nucleotide exchange by SecA. This two-way communication suggests a new, unifying 'Brownian ratchet' mechanism, whereby ATP binding and hydrolysis bias the direction of polypeptide diffusion. The model represents a solution to the problem of transporting inherently variable substrates such as polypeptides, and may underlie mechanisms of other motors that translocate proteins and nucleic acids.

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