Meta-structure correlation in protein space unveils different selection rules for folded and intrinsically disordered proteins

The number of existing protein sequences spans a very small fraction of sequence space. Natural proteins have overcome a strong negative selective pressure to avoid the formation of insoluble aggregates. Stably folded globular proteins and intrinsically disordered proteins (IDP) use alternative solutions to the aggregation problem. While in globular proteins folding minimizes the access to aggregation prone regions IDPs on average display large exposed contact areas. Here, we introduce the concept of average meta-structure correlation map to analyze sequence space. Using this novel conceptual view we show that representative ensembles of folded and ID proteins show distinct characteristics and responds differently to sequence randomization. By studying the way evolutionary constraints act on IDPs to disable a negative function (aggregation) we might gain insight into the mechanisms by which function - enabling information is encoded in IDPs.

Long-lived States in an intrinsically disordered protein domain

Long-lived states (LLS) are relaxation-favoured eigenstates of J-coupled magnetic nuclei. LLS were measured, along with classical 1H and 15 N relaxation rate constants, in aminoacids of the N-terminal Unique domain of the c-Src kinase (USrc), which is disordered in vitro under physiological conditions. The relaxation rates of LLS are a probe for motions and interactions in biomolecules. LLS of the aliphatic protons of glycines, with lifetimes ca. four times longer than their spin-lattice relaxation times, are reported for the first time in an intrinsically disordered protein domain (IDP). LLS relaxation experiments were integrated with 2D spectroscopy methods, further adapting them for studies on proteins.

Effect of vaccination against gonadotrophin-releasing hormone, using Improvac®, on growth performance, body composition, behaviour and acute phase proteins

The objective of this study was to evaluate the effect of vaccination against GnRH on performance traits, pig behaviour and acute phase proteins. A total of 120 pigs (36 non-castrated males, NCM; 36 males to be vaccinated, IM; 24 castratedmales, CM; and 24 females, FE)were controlled in groups of 12 in pens with feeding stations allowing the recording of individual feed intake. The two vaccinations (Improvac®) were applied at a mean age of 77 and 146 days. All pigswere individually weighed every 3 weeks from the mean ages of 74 to 176 days and backfat thickness (BT) and loinmuscle depth (LD) were also recorded ultrasonically. Twelve group-housed pigs for each treatment were video recorded during 2 consecutive days at weeks 9, 11, 20, 21, 23 and 25 of age to score the number of inactive or active pigs in each treatment group by scan sampling. Aggressive behaviour by the feeder and away from the feeder, and mounting behaviour was also scored by focal sampling. Blood samples from 12 NCM, 12 CM and 12 IM were taken to determine the concentration of circulating acute phase protein Pig-MAP atweeks 1, 2, 4, 11, 13, 21 and 25 of age. After slaughter, the number of skin lesions on the left half carcasswas scored. IMpresented overall a higher growth rate and daily feed intake compared to NCM (Pb0.05),whereas their feed conversion ratios did not differ significantly. In comparison with CM, IM presented a better feed conversion ratio (Pb0.05), since their overall dailyweight gaindid not differ significantly, butIM ate less. Final leanmeat percentage of IM and CM was lower compared to that of NCM (Pb0.05). Activity, mounting and aggressive behaviour of NCM was higher than in IM, CM and FE after the second vaccination. Pig-MAP concentrationswere significantly elevated just after surgical castrationand after bothadministrations of the vaccine (Pb0.05), but concentrations subsequently decreased throughout time. Skin lesions of NCM were significantly higher compared to that of IM and FE (Pb0.05). The effects of vaccination were especially remarkable after the second dose, when the higher feed intake and lower activity of IM compared to NCMmight result in higher final body weight and more fat. Results from this study indicate that some welfare aspects such as a reduced aggression and mounting behaviour may be improved by vaccination against GnRH, together with productive benefits like adequate feed conversion ratio and daily weight gain.

Biophysical characterization of tubulin tyrosine ligase-like proteins on microtubule dynamics

Report for the scientific sojourn carried out at the Cell Biology and Biophysics Unit from the National Institutes of Health, from 2010 to 2012.

Distributed all-atom simulations of intrinsically unstructured proteins

The Computational Biophysics Group at the Universitat Pompeu Fabra (GRIB-UPF) hosts two unique computational resources dedicated to the execution of large scale molecular dynamics (MD) simulations: (a) the ACMD molecular-dynamics software, used on standard personal computers with graphical processing units (GPUs); and (b) the GPUGRID. net computing network, supported by users distributed worldwide that volunteer GPUs for biomedical research. We leveraged these resources and developed studies, protocols and open-source software to elucidate energetics and pathways of a number of biomolecular systems, with a special focus on flexible proteins with many degrees of freedom. First, we characterized ion permeation through the bactericidal model protein Gramicidin A conducting one of the largest studies to date with the steered MD biasing methodology. Next, we addressed an open problem in structural biology, the determination of drug-protein association kinetics; we reconstructed the binding free energy, association, and dissaciociation rates of a drug like model system through a spatial decomposition and a Makov-chain analysis. The work was published in the Proceedings of the National Academy of Sciences and become one of the few landmark papers elucidating a ligand-binding pathway. Furthermore, we investigated the unstructured Kinase Inducible Domain (KID), a 28-peptide central to signalling and transcriptional response; the kinetics of this challenging system was modelled with a Markovian approach in collaboration with Frank Noe’s group at the Freie University of Berlin. The impact of the funding includes three peer-reviewed publication on high-impact journals; three more papers under review; four MD analysis components, released as open-source software; MD protocols; didactic material, and code for the hosting group.

Impaired fast-spiking, suppressed cortical inhibition and increased susceptibility to seizures in mice lacking Kv3.2 K+ channel proteins

Voltage-gated K+ channels of the Kv3 subfamily have unusual electrophysiological properties, including activation at very depolarized voltages (positive to −10 mV) and very fast deactivation rates, suggesting special roles in neuronal excitability. In the brain, Kv3 channels are prominently expressed in select neuronal populations, which include fast-spiking (FS) GABAergic interneurons of the neocortex, hippocampus, and caudate, as well as other high-frequency firing neurons. Although evidence points to a key role in high-frequency firing, a definitive understanding of the function of these channels has been hampered by a lack of selective pharmacological tools. We therefore generated mouse lines in which one of the Kv3 genes, Kv3.2, was disrupted by gene-targeting methods. Whole-cell electrophysiological recording showed that the ability to fire spikes at high frequencies was impaired in immunocytochemically identified FS interneurons of deep cortical layers (5-6) in which Kv3.2 proteins are normally prominent. No such impairment was found for FS neurons of superficial layers (2-4) in which Kv3.2 proteins are normally only weakly expressed. These data directly support the hypothesis that Kv3 channels are necessary for high-frequency firing. Moreover, we found that Kv3.2 −/− mice showed specific alterations in their cortical EEG patterns and an increased susceptibility to epileptic seizures consistent with an impairment of cortical inhibitory mechanisms. This implies that, rather than producing hyperexcitability of the inhibitory interneurons, Kv3.2 channel elimination suppresses their activity. These data suggest that normal cortical operations depend on the ability of inhibitory interneurons to generate high-frequency firing.

SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements

Selenoproteins are a diverse group of proteinsusually misidentified and misannotated in sequencedatabases. The presence of an in-frame UGA (stop)codon in the coding sequence of selenoproteingenes precludes their identification and correctannotation. The in-frame UGA codons are recodedto cotranslationally incorporate selenocysteine,a rare selenium-containing amino acid. The developmentof ad hoc experimental and, more recently,computational approaches have allowed the efficientidentification and characterization of theselenoproteomes of a growing number of species.Today, dozens of selenoprotein families have beendescribed and more are being discovered in recentlysequenced species, but the correct genomic annotationis not available for the majority of thesegenes. SelenoDB is a long-term project that aims toprovide, through the collaborative effort of experimentaland computational researchers, automaticand manually curated annotations of selenoproteingenes, proteins and SECIS elements. Version 1.0 ofthe database includes an initial set of eukaryoticgenomic annotations, with special emphasis on thehuman selenoproteome, for immediate inspectionby selenium researchers or incorporation into moregeneral databases. SelenoDB is freely available athttp://www.selenodb.org.

Perpendicular magnetic anisotropy in chemically disordered FePd-FeV(100) alloy thin films

We find that the use of V(100) buffer layers on MgO(001) substrates for the epitaxy of FePd binary alloys yields to the formation at intermediate and high deposition temperatures of a FePd¿FeV mixed phase due to strong V diffusion accompanied by a loss of layer continuity and strong increase of its mosaic spread. Contrary to what is usually found in this kind of systems, these mixed phase structures exhibit perpendicular magnetic anisotropy (PMA) which is not correlated with the presence of chemical order, almost totally absent in all the fabricated structures, even at deposition temperatures where it is usually obtained with other buffer layers. Thus the observed PMA can be ascribed to the V interdiffusion and the formation of a FeV alloy, being the global sample saturation magnetization also reduced.

Dissipation in quasistatically driven disordered systems

This work presents an analysis of hysteresis and dissipation in quasistatically driven disordered systems. The study is based on the random field Ising model with fluctuationless dynamics. It enables us to sort out the fraction of the energy input by the driving field stored in the system and the fraction dissipated in every step of the transformation. The dissipation is directly related to the occurrence of avalanches, and does not scale with the size of Barkhausen magnetization jumps. In addition, the change in magnetic field between avalanches provides a measure of the energy barriers between consecutive metastable states

Wave propagation in a medium with disordered excitability

The effect of quenched disorder on the propagation of autowaves in excitable media is studied both experimentally and numerically in relation to the light-sensitive Belousov-Zhabotinsky reaction. The spatial disorder is introduced through a random distribution with two different levels of transmittance. In one dimension the (time-averaged) wave speed is smaller than the corresponding to a homogeneous medium with the mean excitability. Contrarily, in two dimensions the velocity increases due to the roughening of the front. Results are interpreted using kinematic and scaling arguments. In particular, for d = 2 we verify a theoretical prediction of a power-law dependence for the relative change of the propagation speed on the disorder amplitude.

Growth of unstable interfaces in disordered media

The effects of a disordered medium in the growth of unstable interfaces are studied by means of two local models with multiplicative and additive quenched disorder, respectively. For short times and large pushing the multiplicative quenched disorder is equivalent to a time-dependent noise. In this regime, the linear dispersion relation contains a destabilizing contribution introduced by the noise. For long times, the interface always gets pinned. We model the systematics of the pinned shapes by means of an effective nonlinear model. These results show good agreement with numerical simulations. For the additive noise we find numerically that a depinning transition occurs.

Percolation thresholds in chemical disordered excitable media

The behavior of chemical waves advancing through a disordered excitable medium is investigated in terms of percolation theory and autowave properties in the framework of the light-sensitive Belousov-Zhabotinsky reaction. By controlling the number of sites with a given illumination, different percolation thresholds for propagation are observed, which depend on the relative wave transmittances of the two-state medium considered.

Disordered backgammon model

In this paper we consider an exactly solvable model that displays glassy behavior at zero temperature due to entropic barriers. The new ingredient of the model is the existence of different energy scales or modes associated with different relaxational time scales. Low-temperature relaxation takes place by partial equilibration of successive lower-energy modes. An adiabatic scaling solution, defined in terms of a threshold energy scale e*, is proposed. For such a solution, modes with energy ee* are equilibrated at the bath temperature, modes with ee* remain out of equilibrium, and relaxation occurs in the neighborhood of the threshold e~e*. The model is presented as a toy example to investigate the conditions related to the existence of an effective temperature in glassy systems and its possible dependence on the energy sector is probed by the corresponding observable.

Understanding and modulating the competitive surface-adsorption of proteins through coarse-grained molecular dynamics simulations

It is now well accepted that cellular responses to materials in a biological medium reflect greatly the adsorbed biomolecular layer, rather than the material itself. Here, we study by molecular dynamics simulations the competitive protein adsorption on a surface (Vroman effect), i.e. the non-monotonic behavior of the amount of protein adsorbed on a surface in contact with plasma as functions of contact time and plasma concentration. We find a complex behavior, with regimes during which small and large proteins are not necessarily competing between them, but are both competing with others in solution ("cooperative" adsorption). We show how the Vroman effect can be understood, controlled and inverted.

ORMDL proteins are a conserved new family of endoplasmic reticulum membrane proteins

Background: Annotations of completely sequenced genomes reveal that nearly half of the genes identified are of unknown function, and that some belong to uncharacterized gene families. To help resolve such issues, information can be obtained from the comparative analysis of homologous genes in model organisms. Results: While characterizing genes from the retinitis pigmentosa locus RP26 at 2q31-q33, we have identified a new gene, ORMDL1, that belongs to a novel gene family comprising three genes in humans (ORMDL1, ORMDL2 and ORMDL3), and homologs in yeast, microsporidia, plants, Drosophila, urochordates and vertebrates. The human genes are expressed ubiquitously in adult and fetal tissues. The Drosophila ORMDL homolog is also expressed throughout embryonic and larval stages, particularly in ectodermally derived tissues. The ORMDL genes encode transmembrane proteins anchored in the endoplasmic reticulum (ER). Double knockout of the two Saccharomyces cerevisiae homologs leads to decreased growth rate and greater sensitivity to tunicamycin and dithiothreitol. Yeast mutants can be rescued by human ORMDL homologs. Conclusions: From protein sequence comparisons we have defined a novel gene family, not previously recognized because of the absence of a characterized functional signature. The sequence conservation of this family from yeast to vertebrates, the maintenance of duplicate copies in different lineages, the ubiquitous pattern of expression in human and Drosophila, the partial functional redundancy of the yeast homologs and phenotypic rescue by the human homologs, strongly support functional conservation. Subcellular localization and the response of yeast mutants to specific agents point to the involvement of ORMDL in protein folding in the ER.