Population reversal driven by unrestrained interactions in molecular dynamics simulations: A dialanine model

Standard Molecular Dynamics simulations (MD) are usually performed under periodic boundary conditions using the well-established "Ewald summation". This implies that the distance among each element in a given lattice cell and its corresponding element in another cell, as well as their relative orientations, are constant. Consequently, protein-protein interactions between proteins in different cells - important in many biological activities, such as protein cooperativity and physiological/pathological aggregation - are severely restricted, and features driven by protein-protein interactions are lost. The consequences of these restrictions, although conceptually understood and mentioned in the literature, have not been quantitatively studied before. The effect of protein-protein interactions on the free energy landscape of a model system, dialanine, is presented. This simple system features a free energy diagram with well-separated minima. It is found that, in the case of absence of peptide-peptide (p-p) interactions, the ψ = 150° dihedral angle determines the most energetically favored conformation (global free-energy minimum). When strong p-p interactions are induced, the global minimum switches to the ψ = 0° conformation. This shows that the free-energy landscape of an individual molecule is dramatically affected by the presence of other freely interacting molecules of its same type. Results of the study suggest how taking into account p-p interactions in MD allows having a more realistic picture of system activity and functional conformations.Fil: Pullara, Filippo. University of Pittsburgh; Estados Unidos. Fondazione RiMED; ItaliaFil: General, Ignacio. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Early stages of beta2-microglobulin aggregation and the inhibiting action of alphaB-crystallin

The interest of nucleation of protein crystals and aggregates (including oligomerization) spans from basic physics theory all the way to biophysics, nanophysics, clinical sciences, biotechnologies, food technologies and polymer-solvent interactions. Understanding nucleation within a theoretical framework capable of providing quantitative predictions and control of nucleation rates, or even the very occurrence of crystallization, is a long-sought goal of remarkable relevance to each of the above fields. A large amount of work has been aimed at such goal, but success has been so far rather limited. Work at our laboratory has more recently highlighted a direct link between nucleation rates and the universal scaling properties of concentration fluctuations occurring in the vicinity of a phase transition. The phase transition here concerned is that of non nucleated liquid-liquid demixing of the solution. This novel universality feature allows viewing nucleation processes within one and the same frame, and to capture all normalized nucleation rates on one and the same "master curve" for different proteins, as a function of one parameter only. The quantitative value of the latter is the result of the joint, non additive effects of protein composition, conformation and state (e.g. oligomers), as well as of the temperature of non nucleated liquid-liquid demixing of the solution at the given protein concentration and at the given conditions of the solution. The present work was undertaken for the purpose of ascertaining if (and if so, in what way) the universality feature can allow the quantitative prediction of nucleation rates changes caused by the addition to the solvent of additives empirically known for their strong effect on such rates, as well as the very occurrence of crystallization. To this purpose we have used PEG (polyethylene glycol), which is perhaps the most familiar and most-used additive, and have measured by static and dynamic light scattering the properties of concentration fluctuation of the system as a function of temperature, for various PEG concentration and polymerisation degrees. Experiments have shown that the action of PEG can in no way be accounted for in terms of changes of specific local contacts or of a one-to-one chaperone-like action. Instead, the effect of PEG is seen to be due to alteration of the thermodynamic properties of the solution. This leaves unchanged the universality features and consequently also the validity and predictive power of the master curve in the various conditions

Protein crystallization: universal thermodynamic vs. specific effects of PEG

The interest of nucleation of protein crystals and aggregates (including oligomerization) spans from basic physics theory all the way to biophysics, nanophysics, clinical sciences, biotechnologies, food technologies and polymer– solvent interactions. Understanding nucleation within a theoretical framework capable of providing quantitative predictions and control of nucleation rates, or even the very occurrence of crystallization, is a long-sought goal of remarkable relevance to each of the above fields. A large amount of work has been aimed at such goal, but success has been so far rather limited. Work at our laboratory has more recently highlighted a direct link between nucleation rates and the universal scaling properties of concentration fluctuations occurring in the vicinity of a phase transition. The phase transition here concerned is that of non nucleated liquid–liquid demixing of the solution. This novel universality feature allows viewing nucleation processes within one and the same frame, and to capture all normalized nucleation rates on one and the same ‘‘master curve’’ for different proteins, as a function of one parameter only. The quantitative value of the latter is the result of the joint, non additive effects of protein composition, conformation and state (e.g. oligomers), as well as of the temperature of non nucleated liquid–liquid demixing of the solution at the given protein concentration and at the given conditions of the solution. The present work was undertaken for the purpose of ascertaining if (and if so, in what way) the universality feature can allow the quantitative prediction of nucleation rates changes caused by the addition to the solvent of additives empirically known for their strong effect on such rates, as well as the very occurrence of crystallization. To this purpose we have used PEG (polyethylene glycol), which is perhaps the most familiar and most-used additive, and have measured by static and dynamic light scattering the properties of concentration fluctuation of the system as a function of temperature, for various PEG concentration and polymerisation degrees. Experiments have shown that the action of PEG can in no way be accounted for in terms of changes of specific local contacts or of a one-to-one chaperone-like action. Instead, the effect of PEG is seen to be due to alteration of the thermodynamic properties of the solution. This leaves unchanged the universality features and consequently also the validity and predictive power of the master curve in the various conditions

Lysozyme crystallization rates controlled by anomalous fluctuations

Nucleation of protein aggregates and crystals is a process activated by statistical fluctuations of concentration. Nucleation rates may change by several orders of magnitude upon apparently minor changes in the multidimensional space of parameters (temperature, pH, protein concentration, salt type and concentrations, additives). We use available data on hen egg lysozyme crystal induction times in different solution conditions. We measure by static and dynamic light scattering the amplitudes and lifetimes of anomalously ample and long-lived fluctuations occurring in proximity of the liquid-liquid demixing region of the given lysozyme solutions. This allows determining the related spinodal temperatures TS and ε=(T-TS)/TS. Experimental induction times appear to depend solely upon ε over many orders of magnitude. This is quantitatively accounted for in terms of an extended two-stage nucleation model, which jointly takes into consideration amplitudes, lifetimes and scaling properties of anomalous fluctuations. One and the same relation describes quantitatively and equally well the present case of lysozyme crystallization (the best studied case of protein crystallization) and that of sickle hemoglobin fiber formation (the best studied case of protein fiber formation). Comparison with other recent models shows that taking into account lifetimes of anomalous fluctuations allows capturing the essence of the observed behavior

Absorption band at 7.6 eV induced by γ-irradiation in silica glasses

Optical absorption of defects induced by γ-irradiation in both natural and synthetic silica is experimentally investigated in the vacuum-ultraviolet (UV) range. Our results show that γ-rays, in a dose range of 1000 Mrad, induce an absorption band centered at 7.6 eV, the so-called E band, whose growth kinetics is not related to γ-activated precursors but to defects of the glassy matrix directly induced via the breaking of Si-O bonds occurring under γ-irradiation. Moreover, we observe that γ-rays do not bleach the E band present in some silica samples before irradiation, so ruling out that the associated defects can be precursors of the paramagnetic E′ centers, also induced by γ-irradiation

Mechanisms of Activation and Subunit Release in Ca 2+ /Calmodulin-Dependent Protein Kinase II

Calcium/calmodulin-dependent protein kinase II is an enzyme involved in many different functions, including the so-called long-term potentiation, a mechanism that strengthens synapses in a persistent mode and is believed to be a basic cellular mechanism for memory formation. Here we study the conformational changes of the enzyme due to phosphorylation of some key residues that are believed to drive the transition from an inhibited to an active state; it is this active state the one associated with long-term potentiation. We found that the conformational changes could be explained in terms of three charged regions in the three main subdomains of the enzyme: the hub, linker, and kinase. The role of phosphorylation is to change the charge relation between them, turning on and off their interactions and switching between an attractive state (nonphosphorylated or inhibited) and a not attractive one (phosphorylated or active). We also show that phosphorylated subunits become less stable, and this could favor their release from the multimer, as has been already observed experimentally.Fil: Pullara, Filippo. University of Pittsburgh; Estados UnidosFil: Asciutto, Eliana Karina. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: General, Ignacio. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin