Search engine for discovering works of Art, research articles, and books related to Art and Culture
Javascript must be enabled to continue!
Analysis of changes of cavity volumes in predefined directions of protein motions and cavity flexibility
View through CrossRef
Dynamics of protein cavities associated with protein fluctuations and
conformational plasticity is essential for their biological function.
NMR ensembles, Molecular Dynamics (MD) simulations combined with
Principal Component Analysis (PCA), and Normal Mode Analysis (NMA)
provide appropriate frameworks to explore functionally relevant protein
dynamics and cavity changes relationships. Within this context, we have
developed ANA (Analysis of Null Areas), an efficient method to calculate
cavity volumes. ANA is based on a combination of algorithms that
guarantees its robustness against numerical differentiations. This is a
unique feature with respect to other methods. Herein, we test ANA as a
biophysical and bioinformatic method to analyze different structural and
dynamics properties of cavities. In order to address this task, we have
developed an updated and improved version of ANA that expands it use to
quantify changes in cavity features, like volume and flexibility, due to
protein structural distortions performed on predefined biologically
relevant directions, e.g, directions of largest contribution to protein
fluctuations (PCA modes) obtained by MD simulations or ensembles of NMR
structures, collective NMA modes or any other direction of motion
associated with specific conformational changes. A web page has been
developed and its facilities are explained in detail, making the
software available to all users. Firstly, we show that ANA can be useful
to explore gradual changes of cavity volume and flexibility associated
with protein ligand binding. Secondly, we perform a comparison study of
the extent of variability between protein backbone structural
distortions, and changes in cavity volumes and flexibilities evaluated
for an ensemble of NMR active and inactive conformers of the epidermal
growth factor receptor (EGFR) structures. Finally, we compare changes in
size and flexibility between sets of NMR structures for different
homologous chains of dynein.
Title: Analysis of changes of cavity volumes in predefined directions of protein motions and cavity flexibility
Description:
Dynamics of protein cavities associated with protein fluctuations and
conformational plasticity is essential for their biological function.
NMR ensembles, Molecular Dynamics (MD) simulations combined with
Principal Component Analysis (PCA), and Normal Mode Analysis (NMA)
provide appropriate frameworks to explore functionally relevant protein
dynamics and cavity changes relationships.
Within this context, we have
developed ANA (Analysis of Null Areas), an efficient method to calculate
cavity volumes.
ANA is based on a combination of algorithms that
guarantees its robustness against numerical differentiations.
This is a
unique feature with respect to other methods.
Herein, we test ANA as a
biophysical and bioinformatic method to analyze different structural and
dynamics properties of cavities.
In order to address this task, we have
developed an updated and improved version of ANA that expands it use to
quantify changes in cavity features, like volume and flexibility, due to
protein structural distortions performed on predefined biologically
relevant directions, e.
g, directions of largest contribution to protein
fluctuations (PCA modes) obtained by MD simulations or ensembles of NMR
structures, collective NMA modes or any other direction of motion
associated with specific conformational changes.
A web page has been
developed and its facilities are explained in detail, making the
software available to all users.
Firstly, we show that ANA can be useful
to explore gradual changes of cavity volume and flexibility associated
with protein ligand binding.
Secondly, we perform a comparison study of
the extent of variability between protein backbone structural
distortions, and changes in cavity volumes and flexibilities evaluated
for an ensemble of NMR active and inactive conformers of the epidermal
growth factor receptor (EGFR) structures.
Finally, we compare changes in
size and flexibility between sets of NMR structures for different
homologous chains of dynein.
Related Results
Endothelial Protein C Receptor
Endothelial Protein C Receptor
IntroductionThe protein C anticoagulant pathway plays a critical role in the negative regulation of the blood clotting response. The pathway is triggered by thrombin, which allows ...
Fiber-cavity enhanced and high-fidelity optical memory in cold atom ensemble
Fiber-cavity enhanced and high-fidelity optical memory in cold atom ensemble
Entanglement between a photon and an atomic memory is an important tool for quantum repeater research. By using the Duan-Lukin-Cirac-Zoller (DLCZ) process in the atomic ensemble, q...
Will The "Regular Wave Concept" Yield Meaningful Motion Predictions For Offshore Structures?
Will The "Regular Wave Concept" Yield Meaningful Motion Predictions For Offshore Structures?
ABSTRACT
It has long been recognized that ocean waves, and therefore their induced motions and forces on structures, are random phenomena whose exact time cannot ...
Self-reliance and independently developed high-finesse spherical ultrastable optical reference cavity
Self-reliance and independently developed high-finesse spherical ultrastable optical reference cavity
Ultra-stable reference cavity with high finesse is a crucial component in a narrow-linewidth laser system which is widely used in time and frequency metrology, the test of Lorentz ...
Multiple Riser System for Shallow Water
Multiple Riser System for Shallow Water
Abstract
Shallow water and high wave induced ship motions create a challenging and harsh environment for flexible risers and umbilicals. Two new riser systems are...
The communicative construction of workplace flexibility stigma
The communicative construction of workplace flexibility stigma
Workplace flexibility is becoming more and more common in American workplaces. However, most of these policies are created for professional and white-collar workers. Scholars have ...
Steel Catenary Riser Design Based on Coupled Analysis Methodology
Steel Catenary Riser Design Based on Coupled Analysis Methodology
In a riser design, the traditionally assessment adopted by industry for attainment of platform motions applied to the top of riser consists in the use of de-coupled methodologies. ...
Steering Protein Fermentation in Pigs
Steering Protein Fermentation in Pigs
Protein fermentation in pigs has been associated with diarrhea through the presence of potentially toxic metabolites, including ammonia, branched chain fatty acids, biogenic amines...