On the unknown proteins of eukaryotic proteomes

In order to study unknown proteins on a large scale, a reference system has been set up for the three major eukaryotic lineages, built with 36 proteomes as taxonomically diverse as possible. Proteins from 362 eukaryotic proteomes with no known homologue in this set were then analyzed, focusing noteworthy on singletons, that is, on unknown proteins with no known homologue in their own proteome. Consistently, according to Uniprot, for a given species, no more than 12% of the singletons thus found are known at the protein level. Also, since they rely on the information found in the alignment of homologous sequences, predictions of AlphaFold2 for their tridimensional structure are usually poor. In the case of metazoan species, the number of singletons seems to increase as a function of the evolutionary distance from the reference system. Interestingly, no such trend is found in the cases of viridiplantae and fungi, as if the timescale on which singletons are added to proteomes were different in metazoa and in other eukaryotic kingdoms. In order to confirm this phenomenon, further studies of proteomes closer to those of the reference system are however needed.Comment: 11 pages, 5 figure

Discrete breathers in nonlinear network models of proteins

We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a site-dependent process. Localized modes of nonlinear origin form spontaneously in the stiffest parts of the structure and display site-dependent activation energies. Our results provide a straightforward way for understanding the recently discovered link between protein local stiffness and enzymatic activity. They strongly suggest that nonlinear phenomena may play an important role in enzyme function, allowing for energy storage during the catalytic process.Comment: 4 pages, 5 figures. Minor change

A framework for the next generation of stationary cosmological models

According to a tired-light cosmological model where H(z) = H(0) (1 + z), the number density of galaxies has been nearly constant over the last 10 Gyr, at least, meaning that, as far as galaxies are concerned, the Universe has been stationary. On the other hand, an analysis of the luminosity distances of quasars and supernovae Ia shows that the Universe is far from being as transparent as assumed nowadays, the photon lifetime along the line-of-sight being one third of the Hubble time. The tired-light model advocated in the present study would be falsified if, for instance, the time-dilation of remote events were shown to have a general character, that is, if it were definitely observed for phenomenons other than the light-curves of supernovae Ia.Comment: 16 pages, 6 figures; one more figure, about time dilatio

No obvious change in the number density of galaxies up to z ≈ 3.5

The analysis of the cumulative count of sources of gamma-ray bursts as a function of their redshift strongly suggests that the number density of star-forming galaxies is roughly constant, up to z ≈ 3.5. The analysis of the cumulative count of galaxies in the Hubble Ultra Deep Field further shows that the overall number density of galaxies is constant as well, up to z ≈ 2 at least. Since ΛCDM does not seem able to cope with the age of old objects, both analyses were performed using a non-standard redshift-distance relationship

Les modes normaux de basse fréquence des protéines

Low-frequency normal modes often give useful information on the large-amplitude functional motions of proteins, as determined experimentally using, e.g., X-ray cristallography. This result seems to be quite robust, since it has been obtained using atomic-level description of proteins, as well as coarse-grained ones. Building upon this result, several applications have been proposed, in particular in the field of structural refinement. This text is a review of what has been achieved to date, with a particular emphasis on my own contributions. Among the most recent developments, attempts to complexify current elastic network models, by adding nonlinear terms, are evoked.Les mouvements de basse fréquence des protéines, tels qu'on peut les calculer via l'approximation des petits déplacements (approximation harmonique), ressemblent souvent beaucoup à des mouvements fonctionnels, tels qu'on peut les observer par cristallographie des rayons X. Ce résultat semble très robuste puisqu'il a été obtenu, tout d'abord, en partant d'une description des protéines à l'échelle atomique puis, plus récemment, de descriptions à "gros grains" (des modèles de type réseau élastique). S'appuyant sur ce constat, des applications variées ont été proposées, notamment pour faciliter la résolution de structures ou pour améliorer leur qualité (ajustement dans des enveloppes obtenues par cryomicroscopie électronique, remplacement moléculaire...). Ce mémoire est une revue des résultats obtenus, dans laquelle mes contributions sont plus particulièrement mises en avant. Parmi les développements les plus récents, sont évoquées des tentatives de faire le lien entre modèles à l'échelle atomique et modèles à gros grains, ou bien de complexifier ces derniers, en y incluant des termes anharmoniques