Enhancing OSA Assessment with Explainable AI.

Explainable Artificial Intelligence (xAI) is a rapidly growing field that focuses on making deep learning models interpretable and understandable to human decision-makers. In this study, we introduce xAAEnet, a novel xAI model applied to the assessment of Obstructive Sleep Apnea (OSA) severity. OSA is a prevalent sleep disorder that can lead to numerous medical conditions and is currently assessed using the Apnea-Hypopnea Index (AHI). However, AHI has been criticized for its inability to accurately estimate the effect of OSAs on related medical conditions. To address this issue, we propose a human-centric xAI approach that emphasizes similarity between apneic events as a whole and reduces subjectivity in diagnosis by examining how the model makes its decisions. Our model was trained and tested on a dataset of 60 patients' Polysomnographic (PSG) recordings. Our results demonstrate that the proposed model, xAAEnet, outperforms models with traditional architectures such as convolutional regressor, autoencoder (AE), and variational autoencoder (VAE). This study highlights the potential of xAI in providing an objective OSA severity scoring method.Clinical relevance- This study provides an objective OSA severity scoring technique which could improve the management of apneic patients in clinical practice.

Differential reactivity between two copper sites in peptidylglycine α-hydroxylating monooxygenase.

Peptidylglycine α-hydroxylating monooxygenase (PHM) catalyzes the stereospecific hydroxylation of the Cα of C-terminal glycine-extended peptides and proteins, the first step in the activation of many peptide hormones, growth factors, and neurotransmitters. The crystal structure of the enzyme revealed two nonequivalent Cu sites (Cu(M) and Cu(H)) separated by ∼11 Å. In the resting state of the enzyme, Cu(M) is coordinated in a distorted tetrahedral geometry by one methionine, two histidines, and a water molecule. The coordination site of the water molecule is the position where external ligands bind. The Cu(H) has a planar T-shaped geometry with three histidines residues and a vacant position that could potentially be occupied by a fourth ligand. Although the catalytic mechanism of PHM and the role of the metals are still being debated, Cu(M) is identified as the metal involved in catalysis, while Cu(H) is associated with electron transfer. To further probe the role of the metals, we studied how small molecules such as nitrite (NO(2)(-)), azide (N(3)(-)), and carbon monoxide (CO) interact with the PHM copper ions. The crystal structure of an oxidized nitrite-soaked PHMcc, obtained by soaking for 20 h in mother liquor supplemented with 300 mM NaNO(2), shows that nitrite anion coordinates Cu(M) in an asymmetric bidentate fashion. Surprisingly, nitrite does not bind Cu(H), despite the high concentration used in the experiments (nitrite/protein > 1000). Similarly, azide and carbon monoxide coordinate Cu(M) but not Cu(H) in the PHMcc crystal structures obtained by cocrystallization with 40 mM NaN(3) and by soaking CO under 3 atm of pressure for 30 min. This lack of reactivity at the Cu(H) is also observed in the reduced form of the enzyme: CO binds Cu(M) but not Cu(H) in the structure of PHMcc obtained by exposure of a crystal to 3 atm CO for 15 min in the presence of 5 mM ascorbic acid (reductant). The necessity of Cu(H) to maintain its redox potential in a narrow range compatible with its role as an electron-transfer site seems to explain the lack of coordination of small molecules to Cu(H); coordination of any external ligand will certainly modify its redox potential.

UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions.

Electron microscopy of a macromolecular structure can lead to three-dimensional reconstructions with resolutions that are typically in the 30-10 A range and sometimes even beyond 10 A. Fitting atomic models of the individual components of the macromolecular structure (e.g. those obtained by X-ray crystallography or nuclear magnetic resonance) into an electron-microscopy map allows the interpretation of the latter at near-atomic resolution, providing insight into the interactions between the components. Graphical software is presented that was designed for the interactive fitting and refinement of atomic models into electron-microscopy reconstructions. Several characteristics enable it to be applied over a wide range of cases and resolutions. Firstly, calculations are performed in reciprocal space, which results in fast algorithms. This allows the entire reconstruction (or at least a sizeable portion of it) to be used by taking into account the symmetry of the reconstruction both in the calculations and in the graphical display. Secondly, atomic models can be placed graphically in the map while the correlation between the model-based electron density and the electron-microscopy reconstruction is computed and displayed in real time. The positions and orientations of the models are refined by a least-squares minimization. Thirdly, normal-mode calculations can be used to simulate conformational changes between the atomic model of an individual component and its corresponding density within a macromolecular complex determined by electron microscopy. These features are illustrated using three practical cases with different symmetries and resolutions. The software, together with examples and user instructions, is available free of charge at http://mem.ibs.fr/UROX/.

Complex oligomeric structure of a truncated form of DdrA: a protein required for the extreme radiotolerance of Deinococcus.

In order to preserve their genome integrity, organisms have developed elaborate tactics for genome protection and repair. The Deinococcus radiodurans bacteria famous for their extraordinary tolerance toward high doses of radiations or long period of desiccation, possess some specific genes with unknown function which are related to their survival in such extreme conditions. Among them, ddrA is an orphan gene specific of Deinococcus genomes. DdrA, the product of this gene was suggested to be a component of the DNA end protection system. Here we provide a three-dimensional reconstruction of the Deinococcus deserti DdrA((1-160)) by electron microscopy. Although not functional in vivo, this truncated protein keeps its DNA binding ability at the wild-type level. DdrA((1-160)) has a complex three-dimensional structure based on a heptameric ring that can self-associate to form a larger molecular weight assembly. We suggest that the complex architecture of DdrA plays a role in the substrate specificity and favors an efficient DNA repair.

Geometric mismatches within the concentric layers of rotavirus particles: a potential regulatory switch of viral particle transcription activity.

Rotaviruses are prototypical double-stranded RNA viruses whose triple-layered icosahedral capsid constitutes transcriptional machinery activated by the release of the external layer. To understand the molecular basis of this activation, we studied the structural interplay between the three capsid layers by electron cryo-microscopy and digital image processing. Two viral particles and four virus-like particles containing various combinations of inner (VP2)-, middle (VP6)-, and outer (VP7)-layer proteins were studied. We observed that the absence of the VP2 layer increases the particle diameter and changes the type of quasi-equivalent icosahedral symmetry, as described by the shift in triangulation number (T) of the VP6 layer (from T = 13 to T = 19 or more). By fitting X-ray models of VP6 into each reconstruction, we determined the quasi-atomic structures of the middle layers. These models showed that the VP6 lattices, i.e., curvature and trimer contacts, are characteristic of the particle composition. The different functional states of VP6 thus appear as being characterized by trimers having similar conformations but establishing different intertrimeric contacts. Remarkably, the external protein VP7 reorients the VP6 trimers located around the fivefold axes of the icosahedral capsid, thereby shrinking the channel through which mRNA exits the transcribing rotavirus particle. We conclude that the constraints arising from the different geometries imposed by the external and internal layers of the rotavirus capsid constitute a potential switch regulating the transcription activity of the viral particles.

The concept of resolution in the domain of rotations.

The metric of the SO(3) group of rotations can be used to define the angular resolution of a function of rotations. The resolution is related to the degree of the highest representation present in the expansion of the function in terms of Wigner functions. The peculiar non-Euclidean metric of the rotation domain, however, implies that the terms which effectively contribute to the expansion vary through two-dimensional sections of the rotation domain and are within limiting resolution circles in two-dimensional reciprocal sections. This reconciles an economic sampling of the expansion with the acceleration provided by fast Fourier transform (FFT) techniques.

The catalytic copper of peptidylglycine alpha-hydroxylating monooxygenase also plays a critical structural role.

Many bioactive peptides require amidation of their carboxy terminus to exhibit full biological activity. Peptidylglycine alpha-hydroxylating monooxygenase (PHM; EC 1.14.17.3), the enzyme that catalyzes the first of the two steps of this reaction, is composed of two domains, each of which binds one copper atom (CuH and CuM). The CuM site includes Met(314) and two His residues as ligands. Mutation of Met(314) to Ile inactivates PHM, but has only a minimal effect on the EXAFS spectrum of the oxidized enzyme, implying that it contributes only marginally to stabilization of the CuM site. To characterize the role of Met(314) as a CuM ligand, we determined the structure of the Met(314)Ile-PHM mutant. Since the mutant protein failed to crystallize in the conditions of the original wild-type protein, this structure determination required finding a new crystal form. The Met(314)Ile-PHM mutant structure confirms that the mutation does not abolish CuM binding to the enzyme, but causes other structural perturbations that affect the overall stability of the enzyme and the integrity of the CuH site. To eliminate possible effects of crystal contacts, we redetermined the structure of wt-PHM in the Met(314)Ile-PHM crystal form and showed that it does not differ from the structure of wild-type (wt)-PHM in the original crystals. Met(314)Ile-PHM was also shown to be less stable than wt-PHM by differential scanning calorimetry. Both structural and calorimetric studies point to a structural role for the CuM site, in addition to its established catalytic role.

Thermodynamic calculations in biological systems.

The ability to compute intra- and inter-molecular interactions provides the opportunity to gain a deeper understanding of previously intractable problems in biochemistry and biophysics. This review presents three examples in which molecular dynamics calculations were used to gain insight into the atomic detail underlying important experimental observations. The three examples are the following: (1) Entropic contribution to rate acceleration that results from conformational constraints imposed on the reactants; (2) Mechanism of force unfolding of a small protein molecule by the application of a force that separates its N- and C-terminals; and (3) Loss of translational entropy experienced by small molecules when they bind to proteins.

Loss of translational entropy in molecular associations.

Molecular associations in solution are opposed by the loss of entropy (DeltaS) that results from the restriction of motion of each component in the complex. Theoretical estimates of DeltaS are essential for rationalizing binding affinities, as well as for calculating entropic contribution to enzyme catalysis. Recently a statistical-mechanical framework has been proposed for estimating efficiently the translational entropy loss (DeltaS(trsl)), while taking explicitly into account the complex intermolecular interactions between the solute and the solvent. This framework relates the translational entropy of a solute in solution to its "free volume," defined as the volume accessible to the center of mass of the solute in the presence of the solvent and calculated by using an extension of the cell model (CM) for condensed phases. The translational entropy of pure water, estimated with the CM algorithm, shows good agreement with the experimental information. The free volume of various solutes in water, calculated within the CM by using molecular dynamics simulations with explicit solvent, displays a strong correlation with the solutes' polar and total surface areas. This correlation is used to propose a parameterization that can be used to calculate routinely the translational entropy of a solute in water. We also applied the CM formalism to calculate the free volume and translational entropy loss (DeltaS(trsl)) on binding of benzene to a cavity in a mutant T4-lysozyme. Our results agree with previously published estimates of the binding of benzene to this mutant T4-lysozyme. These and other considerations suggest that the cell model is a simple yet efficient theoretical framework to evaluate the translational entropy loss on molecular association in solution.

Hydrophobicity maps of the N-peptide coiled coil of HIV-1 gp41.

Blocking HIV-1 viral entry into the host cell offers a promising new strategy for interfering with the HIV-1 life cycle. A major target of inhibitor design is to prevent binding of fusogenic gp41 C-peptides to the trimeric coiled coil of fusion-active N-peptides. Here, we map the hydrophobic character of the binding surface of the IQN17 peptide, a soluble analogue of the N-peptide coiled coil. The local binding affinity for a hydrophobic probe is determined by three methods: a hydrophobic force field, and molecular dynamics in solution analyzed by test particle insertion and inhomogeneous information theory. The regions of highest calculated hydrophobicity overlap with the positions of the hydrophobic anchor residues of the native C-peptides, and of two known inhibitors. Additional binding sites not exploited by these inhibitors are identified, and modifications for enhancing their binding affinity are suggested.