scholarly journals Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain

Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1308
Author(s):  
Arvind Ramanathan ◽  
Akash Parvatikar ◽  
Srinivas C. Chennubhotla ◽  
Yang Mei ◽  
Sangita C. Sinha
Keyword(s):  
Long Range ◽  
Conformational Changes ◽  
Hydrophobic Interactions ◽  
Dynamic Simulations ◽  
Bh3 Domain ◽  
Long Range Interactions ◽  
Partial Unfolding ◽  
Binding Cleft ◽  
Inference Techniques ◽  
The Impact

Viral BCL2 proteins (vBCL2s) help to sustain chronic infection of host proteins to inhibit apoptosis and autophagy. However, details of conformational changes in vBCL2s that enable binding to BH3Ds remain unknown. Using all-atom, multiple microsecond-long molecular dynamic simulations (totaling 17 μs) of the murine γ-herpesvirus 68 vBCL2 (M11), and statistical inference techniques, we show that regions of M11 transiently unfold and refold upon binding of the BH3D. Further, we show that this partial unfolding/refolding within M11 is mediated by a network of hydrophobic interactions, which includes residues that are 10 Å away from the BH3D binding cleft. We experimentally validate the role of these hydrophobic interactions by quantifying the impact of mutating these residues on binding to the Beclin1/BECN1 BH3D, demonstrating that these mutations adversely affect both protein stability and binding. To our knowledge, this is the first study detailing the binding-associated conformational changes and presence of long-range interactions within vBCL2s.

scholarly journals Lineage-specific compaction of Tcrb requires a chromatin barrier to protect the function of a long-range tethering element

2014 ◽  
Vol 212 (1) ◽  
pp. 107-120 ◽  
Author(s):  
Kinjal Majumder ◽  
Olivia I. Koues ◽  
Elizabeth A.W. Chan ◽  
Katherine E. Kyle ◽  
Julie E. Horowitz ◽  
...  
Keyword(s):  
Long Range ◽  
Conformational Changes ◽  
Three Dimensional ◽  
Chromatin Conformation ◽  
Dynamic Changes ◽  
Architectural Elements ◽  
Receptor Locus ◽  
Long Range Interactions ◽  
Enhancer Function ◽  
Flanking Regions

Gene regulation relies on dynamic changes in three-dimensional chromatin conformation, which are shaped by composite regulatory and architectural elements. However, mechanisms that govern such conformational switches within chromosomal domains remain unknown. We identify a novel mechanism by which cis-elements promote long-range interactions, inducing conformational changes critical for diversification of the TCRβ antigen receptor locus (Tcrb). Association between distal Vβ gene segments and the highly expressed DβJβ clusters, termed the recombination center (RC), is independent of enhancer function and recruitment of V(D)J recombinase. Instead, we find that tissue-specific folding of Tcrb relies on two distinct architectural elements located upstream of the RC. The first, a CTCF-containing element, directly tethers distal portions of the Vβ array to the RC. The second element is a chromatin barrier that protects the tether from hyperactive RC chromatin. When the second element is removed, active RC chromatin spreads upstream, forcing the tether to serve as a new barrier. Acquisition of barrier function by the CTCF element disrupts contacts between distal Vβ gene segments and significantly alters Tcrb repertoires. Our findings reveal a separation of function for RC-flanking regions, in which anchors for long-range recombination must be cordoned off from hyperactive RC landscapes by chromatin barriers.

scholarly journals Singularities in the gravitational capture of dark matter through long-range interactions

2022 ◽  
Vol 2022 (01) ◽  
pp. 016
Author(s):  
Cristian Gaidau ◽  
Jessie Shelton
Keyword(s):  
Dark Matter ◽  
Long Range ◽  
Capture Rate ◽  
Thermal Motion ◽  
The Sun ◽  
Long Range Interactions ◽  
Population Iii Stars ◽  
Logarithmic Sensitivity ◽  
Gravitational Capture ◽  
The Impact

Abstract We re-examine the gravitational capture of dark matter (DM) through long-range interactions. We demonstrate that neglecting the thermal motion of target particles, which is often a good approximation for short-range capture, results in parametrically inaccurate results for long-range capture. When the particle mediating the scattering process has a mass that is small in comparison to the momentum transfer in scattering events, correctly incorporating the thermal motion of target particles results in a quadratic, rather than logarithmic, sensitivity to the mediator mass, which substantially enhances the capture rate. We quantitatively assess the impact of this finite temperature effect on the captured DM population in the Sun as a function of mediator mass. We find that capture of DM through light dark photons, as in e.g. mirror DM, can be powerfully enhanced, with self-capture attaining a geometric limit over much of parameter space. For visibly-decaying dark photons, thermal corrections are not large in the Sun, but may be important in understanding long-range DM capture in more massive bodies such as Population III stars. We additionally provide the first calculation of the long-range DM self-evaporation rate.

scholarly journals The Impact of Mutation L138F/L210F on the Orai Channel: A Molecular Dynamics Simulation Study

2021 ◽  
Vol 8 ◽  
Author(s):  
Xiaoqian Zhang ◽  
Hua Yu ◽  
Xiangdong Liu ◽  
Chen Song
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Calcium Release ◽  
Hydrophobic Interactions ◽  
Dynamics Simulation ◽  
Wild Type ◽  
Hydrophobic Region ◽  
In The Wild ◽  
Dynamics Simulations ◽  
The Impact

The calcium release-activated calcium channel, composed of the Orai channel and the STIM protein, plays a crucial role in maintaining the Ca2+ concentration in cells. Previous studies showed that the L138F mutation in the human Orai1 creates a constitutively open channel independent of STIM, causing severe myopathy, but how the L138F mutation activates Orai1 is still unclear. Here, based on the crystal structure of Drosophila melanogaster Orai (dOrai), molecular dynamics simulations for the wild-type (WT) and the L210F (corresponding to L138F in the human Orai1) mutant were conducted to investigate their structural and dynamical properties. The results showed that the L210F dOrai mutant tends to have a more hydrated hydrophobic region (V174 to F171), as well as more dilated basic region (K163 to R155) and selectivity filter (E178). Sodium ions were located deeper in the mutant than in the wild-type. Further analysis revealed two local but essential conformational changes that may be the key to the activation. A rotation of F210, a previously unobserved feature, was found to result in the opening of the K163 gate through hydrophobic interactions. At the same time, a counter-clockwise rotation of F171 occurred more frequently in the mutant, resulting in a wider hydrophobic gate with more hydration. Ultimately, the opening of the two gates may facilitate the opening of the Orai channel independent of STIM.

scholarly journals The impact of mutation L138F/L210F on the Orai channel: a molecular dynamics simulation study

2021 ◽  
Author(s):  
Xiaoqian Zhang ◽  
Hua Yu ◽  
Xiangdong Liu ◽  
Chen Song
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Calcium Release ◽  
Hydrophobic Interactions ◽  
Dynamics Simulation ◽  
Hydrophobic Region ◽  
Crac Channel ◽  
Dynamics Simulations ◽  
The Impact ◽  
Basic Region

The calcium release-activated calcium (CRAC) channel, composed of the Orai channel and the STIM protein, plays a crucial role in maintaining the Ca2+ concentration in cells. Previous studies showed that the L138F mutation in the human Orai1 creates a constitutively open channel independent of STIM, causing severe myopathy, but how the L138F mutation activates Orai1 is still unclear. Here, based on the crystal structure of Drosophila melanogaster Orai (dOrai), molecular dynamics simulations for the wild-type (WT) and the L210F (corresponding to L138F in the human Orai1) mutant were conducted to investigate their structural and dynamical properties. The results showed that the L210F dOrai mutant tends to have a more hydrated hydrophobic region (V174 to F171), as well as more dilated basic region (K163 to R155) and selectivity filter (E178). Sodium ions were located deeper in the mutant than in the WT. Further analysis revealed two local but essential conformational changes that may be the key to the activation. A rotation of F210, a previously undescribed feature, was found to result in the opening of the K163 gate through hydrophobic interactions. At the same time, a counter-clockwise rotation of F171 occurred more frequently in the mutant, resulting in a wider hydrophobic gate with more hydration. Ultimately, the opening of the two gates may facilitate the opening of the Orai channel independent of STIM.

scholarly journals Impact of pathogenic mutations of the GLUT1 glucose transporter on channel dynamics using ConsDYN enhanced sampling

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 322
Author(s):  
Halima Mouhib ◽  
Akiko Higuchi ◽  
Sanne Abeln ◽  
Kei Yura ◽  
K. Anton Feenstra
Keyword(s):  
Conformational Changes ◽  
Glucose Transporter ◽  
Pathogenic Mutation ◽  
Deficiency Syndrome ◽  
Coarse Grained ◽  
Strong Impact ◽  
Conformational States ◽  
Dynamic Simulations ◽  
Pathogenic Mutations ◽  
The Impact

Background: The solute carrier (SLC) family of membrane proteins is a large class of transporters for many small molecules that are vital for the cell. Several pathogenic mutations are reported in the glucose transporter subfamily SLC2, causing Glut1-deficiency syndrome (GLUT1DS1, GLUT1DS2), epilepsy (EIG2) and cryohydrocytosis with neurological defects (Dystonia-9). Understanding the link between these mutations and transporter dynamics is crucial to elucidate their role in the dysfunction of the underlying transport mechanism. Methods: Predictions from SIFT and PolyPhen provided an impression of the impact upon mutation in the highly conserved RXGRR motifs, but no clear differentiation could be made by these methods between pathogenic and non-pathogenic mutations. Therefore, to identify the molecular effects on the transporter function, insight from molecular dynamic simulations is required. We studied a variety of pathogenic and non-pathogenic mutations, using a newly developed coarse-grained simulation approach ‘ConsDYN’, which allows the sampling of both inward-open and outward-occluded states. To guarantee the sampling of large conformational changes, we only include conserved restraints of the elastic network introduced upon coarse-graining, which showed similar reference distances between the two conformational states (≤1 Å difference). Results: We capture the ‘conserved dynamics’ between both states using ConsDYN. Simultaneously, it allowed us to considerably lower the computational costs of our study. This approach is sufficiently sensitive to capture the effect of different mutations, and our results clearly indicate that the pathogenic mutation in GLUT1, G91D, situated at the highly conserved RXGRR motif between helices 2 and 3, has a strong impact on channel function, as it blocks the protein from sampling both conformational states.  Conclusions: Using our approach, we can explain the pathogenicity of the mutation G91D when we observe the configurations of the transmembrane helices, suggesting that their relative position is crucial for the correct functioning of the GLUT1 protein.

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