scholarly journals A multiscale model of mechanotransduction by the ankyrin chains of the NOMPC channel

2019 ◽  
Vol 151 (3) ◽  
pp. 316-327 ◽  
Author(s):  
David Argudo ◽  
Sara Capponi ◽  
Neville P. Bethel ◽  
Michael Grabe
Keyword(s):  
Normal Mode Analysis ◽  
Multiscale Model ◽  
Force Balance ◽  
Mode Analysis ◽  
Sensory Cells ◽  
Force Transmission ◽  
Balance Analysis ◽  
Dynamics Simulations ◽  
External Forces ◽  
Electrical Impulses

Our senses of touch and hearing are dependent on the conversion of external mechanical forces into electrical impulses by the opening of mechanosensitive channels in sensory cells. This remarkable feat involves the conversion of a macroscopic mechanical displacement into a subnanoscopic conformational change within the ion channel. The mechanosensitive channel NOMPC, responsible for hearing and touch in flies, is a homotetramer composed of four pore-forming transmembrane domains and four helical chains of 29 ankyrin repeats that extend 150 Å into the cytoplasm. Previous work has shown that the ankyrin chains behave as biological springs under extension and that tethering them to microtubules could be involved in the transmission of external forces to the NOMPC gate. Here we combine normal mode analysis (NMA), full-atom molecular dynamics simulations, and continuum mechanics to characterize the material properties of the chains under extreme compression and extension. NMA reveals that the lowest-frequency modes of motion correspond to fourfold symmetric compression/extension along the channel, and the lowest-frequency symmetric mode for the isolated channel domain involves rotations of the TRP domain, a putative gating element. Finite element modeling reveals that the ankyrin chains behave as a soft spring with a linear, effective spring constantof 22 pN/nm for deflections ≤15 Å. Force–balance analysis shows that the entire channel undergoes rigid body rotation during compression, and more importantly, each chain exerts a positive twisting moment on its respective linker helices and TRP domain. This torque is a model-independent consequence of the bundle geometry and would cause a clockwise rotation of the TRP domain when viewed from the cytoplasm. Force transmission to the channel for compressions >15 Å depends on the nature of helix–helix contact. Our work reveals that compression of the ankyrin chains imparts a rotational torque on the TRP domain, which potentially results in channel opening.

scholarly journals Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis

2015 ◽  
Vol 7 (17) ◽  
pp. 2317-2331 ◽  
Author(s):  
Gautier Moroy ◽  
Olivier Sperandio ◽  
Shakti Rielland ◽  
Saurabh Khemka ◽  
Karen Druart ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Virtual Screening ◽  
Molecular Dynamics Simulations ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Conformational Ensemble ◽  
Dynamics Simulations

Mode-Resolved Thermal Conductivity of Freestanding and Supported Bismuth Telluride Quintuple Layer

2016 ◽  
Author(s):  
Cheng Shao ◽  
Hua Bao
Keyword(s):  
Heat Transfer ◽  
Thermal Conductivity ◽  
Bismuth Telluride ◽  
Normal Mode Analysis ◽  
Relaxation Times ◽  
Phonon Transport ◽  
Mode Analysis ◽  
Underlying Mechanisms ◽  
Dynamics Simulations ◽  
Phonon Properties

The successful exfoliation of atomically-thin bismuth telluride quintuple layer (QL) attracts tremendous interest in investigating the electron and phonon transport properties in this quasi-two-dimensional material. While experimental results show that thermal conductivity is significantly reduced in Bi2Te3 QL compared to the bulk phase, the underlying mechanisms for the reduction is still unclear. Also in some measurements, the Bi2Te3 QL is usually supported on the substrate and the effect of the substrate on heat transfer in Bi2Te3 QL is unknown. In this work, we have performed molecular dynamics simulations and normal mode analysis to study the mode-wise phonon properties in freestanding and supported Bi2Te3 QL. We found that the existing of substrate will decrease the phonon relaxation times in Bi2Te3 QL in the full frequency range. Thermal conductivity accumulation function for both freestanding and supported Bi2Te3 QL are constructed and compared. We found that half of heat transfer in freestanding Bi2Te3 QL contributed from phonons with mean free paths larger than 16.5 nm, while in supported Bi2Te3 QL this value is reduced to 11 nm. In both cases phonons with MFPs in the range of 10–30 nm are the dominate heat carriers, which contribute to 55% and 53% of thermal conductivity in freestanding and supported cases.

scholarly journals Dynamical Correlations Reveal Allosteric Sites in G Protein-Coupled Receptors

2020 ◽  
Vol 22 (1) ◽  
pp. 187
Author(s):  
Pedro Renault ◽  
Jesús Giraldo
Keyword(s):  
G Protein ◽  
Conformational Changes ◽  
Drug Targets ◽  
Normal Mode Analysis ◽  
G Protein Coupled Receptors ◽  
Mode Analysis ◽  
Allosteric Sites ◽  
Basic Hypothesis ◽  
Dynamics Simulations ◽  
G Protein Coupled

G protein-coupled Receptors (GPCRs) play a central role in many physiological processes and, consequently, constitute important drug targets. In particular, the search for allosteric drugs has recently drawn attention, since they could be more selective and lead to fewer side effects. Accordingly, computational tools have been used to estimate the druggability of allosteric sites in these receptors. In spite of many successful results, the problem is still challenging, particularly the prediction of hydrophobic sites in the interface between the protein and the membrane. In this work, we propose a complementary approach, based on dynamical correlations. Our basic hypothesis was that allosteric sites are strongly coupled to regions of the receptor that undergo important conformational changes upon activation. Therefore, using ensembles of experimental structures, normal mode analysis and molecular dynamics simulations we calculated correlations between internal fluctuations of different sites and a collective variable describing the activation state of the receptor. Then, we ranked the sites based on the strength of their coupling to the collective dynamics. In the β2 adrenergic (β2AR), glucagon (GCGR) and M2 muscarinic receptors, this procedure allowed us to correctly identify known allosteric sites, suggesting it has predictive value. Our results indicate that this dynamics-based approach can be a complementary tool to the existing toolbox to characterize allosteric sites in GPCRs.

scholarly journals The Chirality of Isotopomers of Glycine Compared using Next-Generation QTAIM

2021 ◽  
Author(s):  
Xing Nie ◽  
Yong Yang ◽  
Tianlv Xu ◽  
Malgorzata Biczysko ◽  
Steven Kirk ◽  
...  
Keyword(s):  
Stress Tensor ◽  
Electric Fields ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Electronic Charge ◽  
Next Generation ◽  
Promising Tool ◽  
External Forces ◽  
Mass Dependent ◽  
Alpha Carbon

The effect of the presence of a deuterium (D) or tritium (T) isotope bonded to the alpha carbon of glycine is determined without the need to apply external forces e.g. electric fields or using normal mode analysis. Isotopic effects were accounted for using the mass-dependent diagonal Born-Oppenheimer energy correction (DBOC) at the CCSD level of theory. We calculated the stress tensor trajectories of the dominant C-N bond within next generation quantum theory of atoms in molecules (NG-QTAIM). S-character chirality was discovered using the stress tensor trajectories, instead of the Cahn–Ingold–Prelog (CIP) rules, for ordinary glycine. The S-character chirality was preserved after the substitution of the H on the alpha carbon for a D isotope but transformed to R-character chirality after replacement with the T isotope. This reversal of the chirality depending on the presence of a single D or T isotope bound to the alpha carbon adds to the debate on the nature of the extraterrestrial origins of chirality in simple amino acids. We demonstrate that NG-QTAIM is a promising tool for understanding isotopic induced electronic charge density changes, useful in analysis of infrared (IR) or circular dichroism (CD) spectra explaining changes in mode couplings and bands intensities or sign.

scholarly journals Collective Mode Mining from Molecular Dynamics Simulations: A Comparative Approach

2018 ◽  
Vol 15 (03) ◽  
pp. 1850108 ◽  
Author(s):  
Vito Dario Camiola ◽  
Valentina Tozzini
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Normal Mode Analysis ◽  
Principal Component ◽  
Mode Analysis ◽  
Comparative Approach ◽  
Atomic Systems ◽  
Equilibrium Dynamics ◽  
Definition Of ◽  
Dynamics Simulations

The evaluation of collective modes is fundamental in the analysis of molecular dynamics simulations. Several methods are available to extract that information, i.e., normal mode analysis, principal component and spectral analysis of trajectories, basically differing by the quantity considered as the nodal one (frequency, amplitude, or pattern of displacement) and leading to the definition of different kinds of collective excitations and physical spectral observables. The different views converge in the harmonic regime and/or for homo-atomic systems. However, for anharmonic and out of equilibrium dynamics, different quantities bring different information, and only their comparison can give a complete view of the system behavior. To allow such a comparative analysis, we review and compare the different approaches, applying them in diverse combinations to two examples of physical relevance: graphene and fullerene C[Formula: see text].

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