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Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane‐bound cytochrome P450 2B4

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Abstract Cytochrome P450 2B4 (CYP 2B4) is one of the best‐characterized CYPs and serves as a key model system for understanding the mechanisms of microsomal class II CYPs, which metabolize most known …hich metabolize most known drugs. The highly flexible nature of CYP 2B4 is apparent from crystal structures that show the active site with either a wide open or a closed heme binding cavity. Here, we investigated the conformational ensemble of the full‐length CYP 2B4 in a phospholipid bilayer, using multiresolution molecular dynamics (MD) simulations. Coarse‐grained MD simulations revealed two predominant orientations of CYP 2B4's globular domain with respect to the bilayer. Their refinement by atomistic resolution MD showed adaptation of the enzyme's interaction with the lipid bilayer, leading to open configurations that facilitate ligand access to the heme binding cavity. CAVER analysis of enzyme tunnels, AquaDuct analysis of water routes, and Random Acceleration Molecular Dynamics simulations of ligand dissociation support the conformation‐dependent passage of molecules between the active site and the protein surroundings. Furthermore, simulation of the re‐entry of the inhibitor bifonazole into the open conformation of CYP 2B4 resulted in binding at a transient hydrophobic pocket within the active site cavity that may play a role in substrate binding or allosteric regulation. Together, these results show how the open conformation of CYP 2B4 facilitates the binding of substrates from and release of products to the membrane, whereas the closed conformation prolongs the residence time of substrates or inhibitors and selectively allows the passage of smaller reactants via the solvent and water channels.

Authors: Sungho Bosco Han, Jonathan Teuffel, Goutam Mukherjee, Rebecca C. Wade

Date Published: 1st Oct 2024

Publication Type: Journal

Merger seismology: Distinguishing massive merger products from genuine single stars using asteroseismology

Abstract (Expand)

Products of stellar mergers are predicted to be common in stellar populations and can potentially explain stars with peculiar properties. When the merger occurs after the initially more massive star …ar has evolved into the Hertzsprung gap, the merger product may remain in the blue part of the Hertzsprung–Russell diagram for millions of years. Such objects could, therefore, explain the overabundance of observed blue stars, such as blue supergiants. However, it is currently not straightforward to distinguish merger products from genuine single stars or other stars with similar surface diagnostics. In this work, we made detailed asteroseismic comparisons between models of massive post-main-sequence merger products and genuine single stars to identify which asteroseismic diagnostics can be used to distinguish them. In doing so, we developed tools for the relatively young field of merger seismology. Genuine single stars in the Hertzsprung gap are fully radiative, while merger products have a convective He-burning core and convective H-burning shell while occupying similar locations in the Hertzsprung–Russell diagram. These major structural differences are reflected in lower asymptotic period spacing values for merger products and the appearance of deep dips in their period spacing patterns. Our genuine single-star models with masses above roughly 11.4 solar masses develop short-lived intermediate convective zones during their Hertzsprung gap evolution. This also leads to deep dips in their period spacing patterns. Because of the lack of a convective core, merger products and genuine single stars can be distinguished based on their asymptotic period spacing value in this mass range. We performed the comparisons with and without the effects of slow rotation included in the pulsation equations and conclude that the two types of stars are seismically distinguishable in both cases. The observability of the distinguishing asteroseismic features of merger products can now be assessed and exploited in practice.

Authors: J. Henneco, F. R. N. Schneider, S. Hekker, C. Aerts

Date Published: 1st Oct 2024

Publication Type: Journal

Merger seismology: Distinguishing massive merger products from genuine single stars using asteroseismology

Abstract (Expand)

Products of stellar mergers are predicted to be common in stellar populations and can potentially explain stars with peculiar properties. When the merger occurs after the initially more massive star … has evolved into the Hertzsprung gap, the merger product may remain in the blue part of the Hertzsprung–Russell diagram for millions of years. Such objects could, therefore, explain the overabundance of observed blue stars, such as blue supergiants. However, it is currently not straightforward to distinguish merger products from genuine single stars or other stars with similar surface diagnostics. In this work, we made detailed asteroseismic comparisons between models of massive post-main-sequence merger products and genuine single stars to identify which asteroseismic diagnostics can be used to distinguish them. In doing so, we developed tools for the relatively young field of merger seismology. Genuine single stars in the Hertzsprung gap are fully radiative, while merger products have a convective He-burning core and convective H-burning shell while occupying similar locations in the Hertzsprung–Russell diagram. These major structural differences are reflected in lower asymptotic period spacing values for merger products and the appearance of deep dips in their period spacing patterns. Our genuine single-star models with masses above roughly 11.4 solar masses develop short-lived intermediate convective zones during their Hertzsprung gap evolution. This also leads to deep dips in their period spacing patterns. Because of the lack of a convective core, merger products and genuine single stars can be distinguished based on their asymptotic period spacing value in this mass range. We performed the comparisons with and without the effects of slow rotation included in the pulsation equations and conclude that the two types of stars are seismically distinguishable in both cases. The observability of the distinguishing asteroseismic features of merger products can now be assessed and exploited in practice.

Authors: J. Henneco, F. R. N. Schneider, S. Hekker, C. Aerts

Date Published: 1st Oct 2024

Publication Type: Journal

The radial modes of stars with suppressed dipole modes

Abstract (Expand)

Context. The Kepler space mission provided high-quality light curves for more than 16 000 red giants. The global stellar oscillations extracted from these light curves carry information about the … interior of the stars. Several hundred red giants were found to have low amplitudes in their dipole modes (i.e. they are suppressed dipole-mode stars). A number of hypotheses (involving e.g. a magnetic field, binarity, or resonant mode coupling) have been proposed to explain the suppression of the modes, yet none has been confirmed. Aims. We aim to gain insight into the mechanism at play in suppressed dipole-mode stars by investigating the mode properties (linewidths, heights, and amplitudes) of the radial oscillation modes of red giants with suppressed dipole modes. Methods.We selected from the literature suppressed dipole-mode stars and compared the radial-mode properties of these stars to the radial-mode properties of stars in two control samples of stars with typical (i.e. non-suppressed) dipole modes. Results. We find that the radial-mode properties of the suppressed dipole-mode stars are consistent with the ones in our control samples, and hence not affected by the suppression mechanism. Conclusions. From this we conclude that (1) the balance between the excitation and damping in radial modes is unaffected by the suppression, and by extrapolation the excitation of the non-radial modes is not affected either; and (2) the damping of the radial modes induced by the suppression mechanism is significantly less than the damping from turbulent convective motion, suggesting that the additional damping originates from the more central non-convective regions of the star, to which the radial modes are least sensitive.

Authors: Q. Coppée, J. Müller, M. Bazot, S. Hekker

Date Published: 1st Oct 2024

Publication Type: Journal

Validation and Cross‑Species Comparison of scRNA‑seq Trajectory Inference Algorithms

Abstract

Not specified

Authors: Eric Laudemann, Alexandros Stamatakis

Date Published: 1st Oct 2024

Publication Type: Master's Thesis

Binarity at LOw Metallicity (BLOeM): A spectroscopic VLT monitoring survey of massive stars in the SMC

Abstract

Not specified

Authors: T. Shenar, J. Bodensteiner, H. Sana, P. A. Crowther, D. J. Lennon, M. Abdul-Masih, L. A. Almeida, F. Backs, S. R. Berlanas, M. Bernini-Peron, J. M. Bestenlehner, D. M. Bowman, V. A. Bronner, N. Britavskiy, A. de Koter, S. E. de Mink, K. Deshmukh, C. J. Evans, M. Fabry, M. Gieles, A. Gilkis, G. González-Torà, G. Gräfener, Y. Götberg, C. Hawcroft, V. Hénault-Brunet, A. Herrero, G. Holgado, S. Janssens, C. Johnston, J. Josiek, S. Justham, V. M. Kalari, Z. Z. Katabi, Z. Keszthelyi, J. Klencki, J. Kubát, B. Kubátová, N. Langer, R. R. Lefever, B. Ludwig, J. Mackey, L. Mahy, J. Maı́z Apellániz, I. Mandel, G. Maravelias, P. Marchant, A. Menon, F. Najarro, L. M. Oskinova, A. J. G. O’Grady, R. Ovadia, L. R. Patrick, D. Pauli, M. Pawlak, V. Ramachandran, M. Renzo, D. F. Rocha, A. A. C. Sander, T. Sayada, F. R. N. Schneider, A. Schootemeijer, E. C. Schösser, C. Schürmann, K. Sen, S. Shahaf, S. Simón-Dı́az, M. Stoop, S. Toonen, F. Tramper, J. Th. van Loon, R. Valli, L. A. C. van Son, A. Vigna-Gómez, J. I. Villaseñor, J. S. Vink, C. Wang, R. Willcox

Date Published: 1st Oct 2024

Publication Type: Journal

Protostellar spin-up and fast rotator formation through binary star formation

Abstract (Expand)

Context. Many fast-rotating stars (rotation periods of < 2 days) are found to be unresolved binaries with separations of tens of AU. This correlation between fast rotators and binarity leads to the …ween fast rotators and binarity leads to the question of whether the formation of binary stars inherently produces fast rotators. Aims. Our goal is to understand the spin evolution of protostars and whether the formation of companions plays a role in spinning up stars. Methods. We used magneto-hydrodynamic simulations to study the formation of multiple star systems from turbulent and non-turbulent protostellar cores. We tracked the angular momentum accreted by individual star and inner disc systems by using a sink (star) particle technique. We ran a resolution study to extrapolate protostellar properties. Results. We find in all simulations that the primary star can experience a spin-up event correlated with the formation of companions, namely fragmentation into binaries or higher-order systems. The primary star can spin up by up to 84% of its pre-fragmentation angular momentum and by up to 18% of its pre-fragmentation mass-specific angular momentum. The mechanism for the spin-up is gravitational disc instabilities in the circumstellar disc around the primary star, which leads to the accretion of material with high specific angular momentum. The simulations that experience the strongest disc instabilities fragment to form companions. Simulations with weaker spin-up events experience disc instabilities triggered by a companion flyby, and the disc instability in these cases typically does not produce further fragments (i.e. they remain binary systems). Conclusions. The primary star in multiple star systems can end up with a higher spin than single stars. This is because gravitational instabilities in the circumstellar disc around the primary star can trigger a spin-up event. In the strongest spin-up events, the instability is likely to cause disc fragmentation and the formation of companions. This spin-up mechanism, coupled with shorter disc lifetimes due to truncated circumstellar discs (and thus short spin-down times), may help produce fast rotators.

Authors: Rajika L. Kuruwita, Christoph Federrath, Marina Kounkel

Date Published: 1st Oct 2024

Publication Type: Journal

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