Polymer-theory insights into biomolecular systems

Boosted by the technological advances in experimental techniques, cellular biology is nowadays facing the need for quantitative approaches in order to rationalize the huge amount of collected data. A particularly succesfull theoretical framework is provided by Polymer Theory which, combined with molecular simulations, can capture the essential features of biomacromolecules and describe the cellular processes they participate to. This thesis provides a compendium of works showing the strength of this combination. In a first project, we model the twisting properties of amyloid fibrils by means of a simple coarse-grained approach, based on the competition between elasticity and electrostatic repulsion of nearby portions of the fibrils. The model quantitatively recapitulates the evolution of fibril periodicity as a function of the ionic strength of the solution and of the fibril width. A universal mesoscopic structural signature of the fibrils emerges from this picture, predicting a general, parameter-free law for the periodicity of the fibrils which is validated on several experimental results. A second work is focused on the role played by mitochondrial Hsp70 chaperone in the import of cytoplasmic proteins. Particularly, we computed by means of molecular simulations the effective free-energy profile for substrate translocation upon chaperone binding. We then used the resulting free energy to quantitatively characterize the kinetics of the import process and outline the essential role played by Hsp70 in this context. Finally, in a third project we studied the shape properties of a polymer under tension, a physical condition typically realized both in single-molecule experiments and in vivo. By means of analytical calculations and Monte Carlo simulations, we develop a theoretical framework which quantitatively describes these properties, highlighting the interplay between external force and chain size in determining the spatial distribution of a stretched chain

Quantifying the role of chaperones in protein translocation by computational modelling

The molecular chaperone Hsp70 plays a central role in the import of cytoplasmic proteins into organelles, driving their translocation by binding them from the organellar interior. Starting from the experimentally-determined structure of the \textit{E. coli} Hsp70, we computed, by means of molecular simulations, the effective free-energy profile for substrate translocation upon chaperone binding. We then used the resulting free energy to quantitatively characterize the kinetics of the import process, whose comparison with unassisted translocation highlights the essential role played by Hsp70 in importing cytoplasmic proteins.Comment: 8 pages, 4 figure

Enhancement of cooperation in highly clustered scale-free networks

We study the effect of clustering on the organization of cooperation, by analyzing the evolutionary dynamics of the Prisoner's Dilemma on scale-free networks with a tunable value of clustering. We find that a high value of the clustering coefficient produces an overall enhancement of cooperation in the network, even for a very high temptation to defect. On the other hand, high clustering homogeneizes the process of invasion of degree classes by defectors, decreasing the chances of survival of low densities of cooperator strategists in the network.Comment: 4 pages, 3 figure

Beyond Freezing: Low Temperature Lipidic Cubic Phase As Biomimetic, Nanoconfining Matrix

Lipidic cubic phases (LCPs) are used in areas ranging from membrane biology to drug delivery. Because some membrane proteins are notoriously unstable at room temperature, and available LCPs undergo transformation to lamellar phases at low temperatures, the development of stable low-temperature LCPs for biophysical studies of membrane proteins is called for. A family of synthetic lipids with designed cyclopropyl modifications in the hydrophobic chains was synthesised in order to study the relationship between lipid molecular structure and mesophase behaviour. These lipids show a unique liquid-crystalline behaviour at low temperatures, enabling the use of LCP crystallisation in conditions never explored before.1 Please click Additional Files below to see the full abstract

Force-dependent elasticity of nucleic acids

The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The perturbation of the elasticity of NAs arising from these deformations is not properly considered by most theoretical frameworks. In this work, we introduce a novel method to assess the impact of mechanical stress on the elastic response of dsDNA and dsRNA through the analysis of the fluctuations of the double helix. Application of this approach to atomistic simulations reveals qualitative differences in the force dependence of the mechanical properties of dsDNA with respect to those of dsRNA, which we relate to structural features of these molecules by means of physically-sound minimalistic models.Comment: 6 pages, 2 figure

Force-dependent elasticity of nucleic acids

The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The perturbation of the elasticity of NAs arising from these deformations is not properly considered by most theoretical frameworks. In this work, we introduce a novel method to assess the impact of mechanical stress on the elastic response of dsDNA and dsRNA through the analysis of the fluctuations of the double helix. Application of this approach to atomistic simulations reveals qualitative differences in the force dependence of the mechanical properties of dsDNA with respect to those of dsRNA, which we relate to structural features of these molecules by means of physically-sound minimalistic modelsThe project that gave rise to these results received the support of a fellowship from “la Caixa” Foundation (ID 100010434) and from the European Union’s Horizon Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement no. 847648. The fellowship code is LCF/BQ/PI20/ 11760019. We acknowledge support from the Ministerio de Ciencia e Innovación (MICINN) through the project PID2020-115864RB-I00 and the “María de Maeztu” Programme for Units of Excellence in R&D (grant no. CEX2018-000805-M). We thank Laura R. Arriaga for helpful discussio

Godišnje promjene nekih pokazatelja mijene tvari u mliječnih krava na području Sredozemlja.

The seasonal rhythms reflect the ability of the endogenous adaptive mechanism to react in advance to the regular environmental changes associated with the seasons. It seems that these biochemical parameters are often influenced by a change in physiological status. The aim of this study was to assess the trend of annual variations of some biochemical parameters in dairy cows. The experimental subjects were ten dairy cows and the start of the experimental period coincided with the last month of pregnancy. These animals were monitored for one year and blood samples were collected every month. From the obtained sera, total bilirubin, blood urea nitrogen (BUN), creatinine, total cholesterol, non-esterified fatty acids (NEFA), tryglicerides, β-hydroxybutyrate, total proteins, calcium and phosphorus were assessed by means of an automated spectrophotometer. All the results were expressed as mean ± standard deviation (SD). Data were normally distributed (P<0.05, Kolmogorov-Smirnov test). One method of repeated measurement, the Analysis of Variance (ANOVA), was applied to determine the effect of time during the experimental period (12 months) and P values of <0.05 were considered statistically significant. Using cosinor-rhythmometry, three rhythmic parameters were determined: mesor (mean level), amplitude (half the range of oscillation) and acrophase (Φ, time of peak). A significant effect of time (P<0.0001) was shown for all the parameters, except for NEFA. After application of cosinor rhythmometry, only total bilirubin, creatinine, triglycerides and β-hydroxybutyrate showed a seasonal rhythm. In conclusion we can affirm that our results supplement the current information available about the circannual changes in the metabolic activity of these animals and help us to evaluate the adaptation of these animals to environmental changes, together with the metabolic effect of calving and lactation.Ritam promjene godišnjih doba utječe na endogeni adaptacijski mehanizam kako bi on unaprijed reagirao na sezonske promjene u okolišu. Čini se da promjene u fiziološkom stanju često utječu na biokemijske pokazatelje vezane uz taj mehanizam. Svrha je ovog istraživanja procijeniti utjecaj godišnjih promjena na neke biokemijske pokazatelje u mliječnih krava. U pokus je bilo uzeto 10 mliječnih krava, a sam je pokus započeo kad su one bile u posljednjem mjesecu bređosti. Krave su bile promatrane tijekom jedne godine, a krv im je bila uzimana svaki mjesec. Uzeti uzorci seruma bili su automatskim spekrofotometrom pretraženi na ukupni bilirubin, dušik iz ureje u krvi (BUN), kreatinin, ukupni kolesterol, neesterificirane masne kiseline, trigliceride, β-hidroksibutirat, ukupne bjelančevine te kalcij i fosfor. Rezultati su bili izraženi kao srednja vrijednost ± standardna devijacija (SD). Podatci su bili normalno distribuirani (P<0,05, Kolmogorov-Smirnov test). Za ponovljeno mjerenje bila je primijenjena analiza varijance (ANOVA) kako bi se odredio učinak vremena tijekom pokusnog razdoblja (12 mjeseci) te su P vrijednosti <0,05 smatrane statistički značajnima. Uporabom Cosinor ritmometrije određena su četiri ritmička pokazatelja: mesor (srednja vrijednost), amplituda (polovica područja oscilacije) i akrofaza (Φ, vršno vrijeme). Značajan učinak vremena (P<0,0001) dokazan je za sve pokazatelje, osim za neesterificirane masne kiseline. Nakon primjene cosinor ritmometrije samo su ukupni bilirubin, kreatinin, trigliceridi i β-hidroksibutirat pokazivali sezonski ritam. Zaključno se može potvrditi da rezulati predstavljaju doprinos aktualnim informacijama o godišnjim promjenama metaboličke aktivnosti u krava i pomažu vrednovanju njihove prilagodbe okolišnim promjenama kod teljenja i laktacije

Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here we combine complementary computational/theoretical approaches to elucidate the structural and thermodynamic details of the chaperone-induced expansion of a substrate protein, with a particular emphasis on the critical role played by ATP hydrolysis. We first determine the conformational free-energy cost of the substrate expansion due to the binding of multiple chaperones using coarse-grained molecular simulations. We then exploit this result to implement a non-equilibrium rate model which estimates the degree of expansion as a function of the free energy provided by ATP hydrolysis. Our results are in quantitative agreement with recent single-molecule FRET experiments and highlight the stark non-equilibrium nature of the process, showing that Hsp70s are optimized to convert effectively chemical energy into mechanical work close to physiological conditions

The Shape of a Stretched Polymer

The shape of a polymer plays an important role in determining its interactions with other molecules and with the environment, and is in turn affected by both of them. As a consequence, in the literature the shape properties of a chain in many different conditions have been investigated. Here, we characterize the shape and orientational properties of a polymer chain under tension, a physical condition typically realized both in single-molecule experiments and in vivo. By means of analytical calculations and Monte Carlo simulations, we develop a theoretical framework which quantitatively describes these properties, highlighting the interplay between external force and chain size in determining the spatial distribution of a stretched chain