Protein Fluctuations and Cavity Changes Relationship

2018 ◽  
Vol 14 (2) ◽  
pp. 998-1008 ◽  
Author(s):  
German P. Barletta ◽  
Sebastian Fernandez-Alberti
Keyword(s):  
Protein Fluctuations

scholarly journals Quantitative single-cell live imaging links HES5 dynamics with cell-state and fate in murine neurogenesis

2018 ◽  
Author(s):  
Cerys S Manning ◽  
Veronica Biga ◽  
James Boyd ◽  
Jochen Kursawe ◽  
Bodvar Ymisson ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Live Imaging ◽  
Protein Quantification ◽  
Expression Change ◽  
Dynamic View ◽  
Transient Period ◽  
Gene Expression Dynamics ◽  
Transcription Factor Expression ◽  
Protein Fluctuations

AbstractDuring embryogenesis cells make fate decisions within complex tissue environments. The levels and dynamics of transcription factor expression regulate these decisions. Here we use single cell live imaging of an endogenous HES5 reporter and absolute protein quantification to gain a dynamic view of neurogenesis in the embryonic mammalian spinal cord. We report that dividing neural progenitors show both aperiodic and periodic HES5 protein fluctuations. Mathematical modelling suggests that in progenitor cells the HES5 oscillator operates close to its bifurcation boundary where stochastic conversions between dynamics are possible. HES5 expression becomes more frequently periodic as cells transition to differentiation which, coupled with an overall decline in HES5 expression, creates a transient period of oscillations with higher fold expression change. This increases the decoding capacity of HES5 oscillations and correlates with interneuron versus motor neuron cell fate. Thus, HES5 undergoes complex changes in gene expression dynamics as cells differentiate.

scholarly journals Neutron Scattering Reveals Protein Fluctuations in GPCR Activation

2016 ◽  
Vol 110 (3) ◽  
pp. 228a-229a
Author(s):  
Suchithranga M.D.C. Perera ◽  
Utsab Shrestha ◽  
Debsindhu Bhowmik ◽  
Udeep Chawla ◽  
Andrey V. Struts ◽  
...  
Keyword(s):  
Neutron Scattering ◽  
Gpcr Activation ◽  
Protein Fluctuations

scholarly journals Robust light harvesting by a noisy antenna

2018 ◽  
Vol 20 (6) ◽  
pp. 4360-4372 ◽  
Author(s):  
Pavel Malý ◽  
Alastair T. Gardiner ◽  
Richard J. Cogdell ◽  
Rienk van Grondelle ◽  
Tomáš Mančal
Keyword(s):  
Theoretical Model ◽  
Single Molecule ◽  
Light Harvesting ◽  
Single Molecule Spectroscopy ◽  
Protein Fluctuations

Ultrafast bulk and single-molecule spectroscopy experiments described by a single theoretical model show how protein fluctuations influence photosynthetic light harvesting.

scholarly journals Exploring the landscape of model representations

2020 ◽  
Vol 117 (39) ◽  
pp. 24061-24068 ◽  
Author(s):  
Thomas T. Foley ◽  
Katherine M. Kidder ◽  
M. Scott Shell ◽  
W. G. Noid
Keyword(s):  
Statistical Physics ◽  
Degrees Of Freedom ◽  
Large Scale ◽  
Coarse Graining ◽  
Order Parameters ◽  
Microscopic Model ◽  
Coarse Grained ◽  
Proper Order ◽  
Complex Phenomena ◽  
Protein Fluctuations

The success of any physical model critically depends upon adopting an appropriate representation for the phenomenon of interest. Unfortunately, it remains generally challenging to identify the essential degrees of freedom or, equivalently, the proper order parameters for describing complex phenomena. Here we develop a statistical physics framework for exploring and quantitatively characterizing the space of order parameters for representing physical systems. Specifically, we examine the space of low-resolution representations that correspond to particle-based coarse-grained (CG) models for a simple microscopic model of protein fluctuations. We employ Monte Carlo (MC) methods to sample this space and determine the density of states for CG representations as a function of their ability to preserve the configurational information, I, and large-scale fluctuations, Q, of the microscopic model. These two metrics are uncorrelated in high-resolution representations but become anticorrelated at lower resolutions. Moreover, our MC simulations suggest an emergent length scale for coarse-graining proteins, as well as a qualitative distinction between good and bad representations of proteins. Finally, we relate our work to recent approaches for clustering graphs and detecting communities in networks.

scholarly journals Myoglobin Dynamics Measured With Vibrational Echo Experiments

1999 ◽  
Vol 19 (1-4) ◽  
pp. 19-34 ◽  
Author(s):  
K. D. Rector ◽  
M. D. Fayer
Keyword(s):  
Active Site ◽  
Covalent Bond ◽  
Native Protein ◽  
Vibrational Dephasing ◽  
Pure Dephasing ◽  
Homogeneous Linewidth ◽  
The Fourier Transform ◽  
Vibrational Echo ◽  
Protein Fluctuations ◽  
Dephasing Rate

Ps infrared vibrational echo experiments on myoglobin and myoglobin mutants are presented. The vibrational dephasing experiments examine the influence of protein dynamics on the CO ligand, at the active site of myoglobin, from low temperature to physiologically relevant temperatures. The vibrational echo results are combined with measurements of the CO vibrational lifetime to yield the homogeneous pure dephasing. The pure dephasing is the Fourier transform of the homogeneous linewidth with the lifetime contribution removed. The mutant H64V protein's CO vibrational pure dephasing rate is ∼20% slower (narrower pure dephasing linewidth) than the native protein at all temperatures, although the only difference between the two proteins is the replacement of the native’s polar distal histidine by a non-polar valine. The mutant H93G(N-MeIm) pure dephasing is identical to the native's, despite the severing of the only covalent bond between the heme and the globin. These results provide insights into the mechanisms of the transmission of protein fluctuations to the CO ligand bound at the active site.

Protein Fluctuations as the Possible Origin of the Thermal Activation of Rod Photoreceptors in the Dark

2010 ◽  
Vol 132 (16) ◽  
pp. 5693-5703 ◽  
Author(s):  
Víctor A. Lórenz-Fonfría ◽  
Yuji Furutani ◽  
Toru Ota ◽  
Kazutomo Ido ◽  
Hideki Kandori
Keyword(s):  
Thermal Activation ◽  
Rod Photoreceptors ◽  
Protein Fluctuations

Ligand Migration and Protein Fluctuations in Myoglobin Mutant L29W†,‡

Biochemistry ◽  
2005 ◽  
Vol 44 (13) ◽  
pp. 5095-5105 ◽  
Author(s):  
Karin Nienhaus ◽  
Andreas Ostermann ◽  
G. Ulrich Nienhaus ◽  
Fritz G. Parak ◽  
Marius Schmidt
Keyword(s):  
Ligand Migration ◽  
Protein Fluctuations
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