mRNA lipid nanoparticle phase transition

Crucial for mRNA-based vaccines are the composition, structure, and properties of lipid nanoparticles (LNPs) as their delivery vehicle. Using all-atom molecular dynamics simulations as a computational microscope, we provide an atomistic view of the structure of the Comirnaty vaccine LNP, its molecular organization, physicochemical properties, and insight in its pH-driven phase transition enabling mRNA release at atomistic resolution. At physiological pH, our simulations suggest an oil-like LNP core that is composed of the aminolipid ALC-0315 and cholesterol (ratio 72:28). It is surrounded by a lipid monolayer formed by distearoylphosphatidylcholine, ALC-0315, PEGylated lipids, and cholesterol at a ratio of 22:9:6:63. Protonated aminolipids enveloping mRNA formed inverted micellar structures that provide a shielding and likely protection from environmental factors. In contrast, at low pH, the Comirnaty lipid composition instead spontaneously formed lipid bilayers that display a high degree of elasticity. These pH-dependent lipid phases suggest that a change in pH of the environment upon LNP transfer to the endosome likely acts as trigger for cargo release from the LNP core by turning aminolipids inside out, thereby destabilizing both the LNP shell and the endosomal membrane.     

Cancer as a dynamical phase transition

Background

We review and extend the work of Rosen and Casti who discuss category theory with regards to systems biology and manufacturing systems, respectively.

Results

We describe anticipatory systems, or long-range feed-forward chemical reaction chains, and compare them to open-loop manufacturing processes. We then close the loop by discussing metabolism-repair systems and describe the rationality of the self-referential equation f = f (f). This relationship is derived from some boundary conditions that, in molecular systems biology, can be stated as the cardinality of the following molecular sets must be about equal: metabolome, genome, proteome. We show that this conjecture is not likely correct so the problem of self-referential mappings for describing the boundary between living and nonliving systems remains an open question. We calculate a lower and upper bound for the number of edges in the molecular interaction network (the interactome) for two cellular organisms and for two manufacturomes for CMOS integrated circuit manufacturing.

Conclusions

We show that the relevant mapping relations may not be Abelian, and that these problems cannot yet be resolved because the interactomes and manufacturomes are incomplete.     

Application of the phase transition theory to the description of fibrinogen-fibrin transition

A physical model of the kinetics of the fibrinogen--fibrin transition was constructed using the theory of phase transitions. It was shown that the model is consistent with the experimental data.     

Microbiome-related aspects of locust density-dependent phase transition

Locust plagues are a notorious, ancient phenomenon. These swarming pests tend to aggregate and perform long migrations, decimating cultivated fields along their path. When population density is low, however, the locusts will express a cryptic, solitary, non-aggregating phenotype that is not considered a pest. Although the transition from the solitary to the gregarious phase has been well studied, associated shifts in the locust's microbiome have yet to be addressed. Here, using 16S rRNA amplicon sequencing, we compared the bacterial composition of solitary desert locusts before and after a phase transition. Our findings revealed that the microbiome is altered during the phase transition, and that a major aspect of this change is the acquisition of Weissella (Firmicutes). Our findings led us to hypothesize that the locust microbiome plays a role in inducing aggregation behaviour, contributing to the formation and maintenance of a swarm. Employing a mathematical model, we demonstrate the potential evolutionary advantage of inducing aggregation under different conditions; specifically, when the aggregation-inducing microbe exhibits a relatively high horizontal transmission rate. This is the first report of a previously unknown and important aspect of locust phase transition, demonstrating that the phase shift includes a shift in the gut and integument bacterial composition.     

Molecular markers of phase transition in locusts

The changes accompanying the transition from the gregarious to the solitary phase state in locusts are so drastic that for a long time these phases were considered as distinct species. It was Boris Uvarov who introduced the concept of polyphenism. Decades of research revealed that phase transition implies changes in morphometry, the color of the cuticle, behavior and several aspects of physiology. In particular, in the recent decade, quite a number of molecular studies have been undertaken to uncover phase-related differences. They resulted in novel insights into the role of corazonin, neuroparsins, some protease inhibitors, phenylacetonitrile and so on. The advent of EST-databases of locusts （e.g. Kang et al., 2004） is a most encouraging novel development in physiological and behavioral locust research. Yet, the answer to the most intriguing question, namely whether or not there is a primordial molecular inducer of phase transition, is probably not within reach in the very near future.     

A phase transition model for hemolysis

A phase transition model of red cell membrane rupture is developed based on the interaction of lipid and water at the membrane surface. It is shown that when the membrane tension increases, the water concentration of the membrane surface must increase. When a critical concentration of water is reached, large pores may open up in the membrane surface, allowing the hemoglobin to escape.     

Properties of bilayer membranes in the phase transition or phase separation region

The increase in passive permeability of bilayer membranes near the phase transition temperature is usually explained as caused by either the increase in the amount of ‘boundary lipid’ present in the membrane, or by the increase in lateral compressibility of the membrane. Since both the amount of ‘boundary lipid’ and the lateral compressibility show a similar anomaly near the transition temperature, it is difficult to distinguish experimentally between the two proposed mechanisms.We have examined some details of both of the proposed pictures. The fluid-solid boundary energy, neglected in previous work, has been computed as a function of the domain size. For a single component uncharged lipid bilayer, the results rule out the existence of even loosely defined solid domains in a fluid phase, or vice versa. Thermodynamic fluctuations, which are responsible for anomalous behaviour near the phase transition temperature, are not intense enough to approximate the formation of a domain of the opposite phase.Turning next to lateral compressibility of bilayer membranes we have considered two-component mixtures in the phase separation region. We present the first calculation of lateral compressibility for such systems. The behaviour shows interesting anomalies, which should correlate with existing and future data on transport across membranes.     

Tracing dynamic biological processes during phase transition

Background

Phase transition widely exists in the biological world, such as transformation of cell cycle phases, cell differentiation stages, disease development, and so on. Such a nonlinear phenomenon is considered as the conversion of a biological system from one phenotype/state to another. Studies on the molecular mechanisms of biological phase transition have attracted much attention, in particular, on different genotypes (or expression variations) in a specific phase, but with less of focus on cascade changes of genes' functions (or system state) during the phase shift or transition process. However, it is a fundamental but important mission to trace the temporal characteristics of a biological system during a specific phase transition process, which can offer clues for understanding dynamic behaviors of living organisms.

Results

By overcoming the hurdles of traditional time segmentation and temporal biclustering methods, a causal process model (CPM) in the present work is proposed to study the biological phase transition in a systematic manner, i.e. first, we make gene-specific segmentation on time-course expression data by developing a new boundary gene estimation scheme, and then infer functional cascade dynamics by constructing a temporal block network. After the computational validation on synthetic data, CPM was used to analyze the well-known Yeast cell cycle data. It was found that the dynamics of the boundary genes are periodic and consistent with the phases of the cell cycle, and the temporal block network indeed demonstrates a meaningful cascade structure of the enriched biological functions. In addition, we further studied protein modules based on the temporal block network, which reflect temporal features in different cycles.

Conclusions

All of these results demonstrate that CPM is effective and efficient comparing to traditional methods, and is able to elucidate essential regulatory mechanism of a biological system even with complicated nonlinear phase transitions.

     

Revisiting phase transition during flowering in Arabidopsis

Single-phase transition during flowering has been suggested by Hempel and Feldman (1994) [Planta 192: 276]. When early flowering ecotypes of Arabidopsis were microscopically observed, a long day signal simultaneously induced the acropetal (bottom to top) production of flower primordia and the basipetal (top to bottom) differentiation of paraclades (axillary flowering shoots) from the axils of pre-existing leaf primordia. However, this model could not account for the production of an extra number of secondary shoots in the TERMINAL FLOWER 1 overexpressor line or AGL20 overexpressor line in Columbia background with a functional allele of FRIGIDA. We report here that Columbia with a functional allele of FRIGIDA under long days and Columbia under short days show an inflorescence-producing phase between the vegetative and the flower-producing phases, supporting two-step phase transition during flowering. In addition, a late-flowering mutant, fwa shows an inflorescence phase but fca, fy and fve follow a single-phase transition, suggesting flowering time mutations have different effects on phase transition during flowering.     

Non-isothermal pattern of phase transition in vesicle membranes

Phase transition of lipid molecules between liquid and crystalline states in the vesicle membrane has a non-isothermal pattern; it is spread in some temperature range, which depends on the vesicle size. With a change of phase transition the area which falls within a lipid molecule is changed. As a result elastic tensions appear in the membrane. They may account for the non-isothermal pattern of phase transition. The number of molecules in each state is calculated in relation to temperature, and the temperature range is calculated within which the phase transition is realized. The smaller is the vesicle radius, the higher is the temperature range value. Temperature relationship of the membrane heat capacity at non-isothermal phase transition is calculated. The obtained results well agree with the number of experimental data.     

Pressure-induced elevation of phase transition temperature in dipalmitoylphosphatidylcholine bilayers: An electron spin resonance measurement of the enthalpy of phase transition

The application of 136 atm of helium pressure to an aqueous dispersion of dipalmitoylphosphatidylcholine increased the temperature of the primary phase transition at 40.4 ± 0.2 °C by 3.0 °C. The lower temperature pretransition at 30.5 ± 0.5 °C, thought to be due to phosphate headgroup reorganization, was increased by 1.7 °C. Addition of 4% dipalmitoylphosphatidic acid to the dipalmitoylphosphatidylcholine affected the phase transition in the head group region more than in the hydrocarbon chain region. The pressure and temperature data obtained, taken together with the literature value for the bilayer volume expansion during solid-fluid phase transition, and inserted into the Clausius-Clapeyron equation yield a ΔH value of 8.8 kcal/mole for this phase transition. This value is within experimental error of the ΔH value obtained from differential scanning calorimetry and serves to support the validity of the data and the experimental technique. Phase transition was observed by electron spin resonance measurement of the exclusion of the small spin label Tempo (2,2,6,6-tetramethylpiperidine-N-oxyl) from the solid domains of the bilayer. This result offers a possible explanation for the direct antagonism by high pressure of the effects of the inhalation anesthetics.     

Disc formation in cholesterol-free liposomes during phase transition

Cryogenic transmission electron microscopy (cryo-TEM) images of lysolipid-containing thermosensitive liposomes (LTSL) revealed that open liposomes and bilayer discs appeared when liposomes were cycled through the gel (L_β′) to liquid-crystalline (L_α) phase transition. The amount of bilayer discs generated was dependent on the combined presence of PEG-lipid and lysolipid in the membrane. We hypothesize that micelle-forming membrane components stabilize the rim of bilayer openings and membrane discs that form when liposomes are cycled through T_C.     

Disc formation in cholesterol-free liposomes during phase transition

Cryogenic transmission electron microscopy (cryo-TEM) images of lysolipid-containing thermosensitive liposomes (LTSL) revealed that open liposomes and bilayer discs appeared when liposomes were cycled through the gel (Lbeta') to liquid-crystalline (Lalpha) phase transition. The amount of bilayer discs generated was dependent on the combined presence of PEG-lipid and lysolipid in the membrane. We hypothesize that micelle-forming membrane components stabilize the rim of bilayer openings and membrane discs that form when liposomes are cycled through TC.     

Kinetic investigations on the phase transition of phospholipid bilayers

Pressure-jump experiments were performed on vesicles and liposomes of dimyristoyl phosphatidylcholine and dipalmitoyl phosphatidylcholine following the time course of solution turbidity. For both lipids two relaxation effects were evaluated the time constants of which exhibit clear maxima at the midpoint of the phase transition. The time constants lie for vesicles in the 100 μs and 1 ms ranges and for liposomes in the 1 ms and 10 ms ranges. The processes are slightly faster for dimyristoyl phosphatidylcholine than for dipalmitoyl phosphatidylcholine. All relaxation times are concentration-independent. The time constant and amplitude behaviours indicate that all processes are cooperative in agreement with previous interpretations. It is demonstrated that cooperative units can be evaluated from the relaxation amplitudes. These are of the same order of magnitude as those obtained from static experiments. On the grounds of the present kinetic investigation we can state that the application of the linear Ising model to two-dimensional processes as attempted for the static lipid phase transition is inadequate.     

Ionic influences on the phase transition of dipalmitoylphosphatidylserine.

The ionization and phase behavior of 1,2-dipalmitoyl-sn-glycero-3-phosphoserine have been investigated under a variety of condtions by several different methods. As measured by turbidity changes, the temperature of the crystal-liquid crystal phase transition of this lipid is influenced by pH and mono- and divalent cation concentrations. The pH-transition temperature curve is congruent with the curve relating temperature to the degree of ionization of the carboxyl group of the crystalline form. The transition temperature falls from an upper plateau of 72 degrees C at low pH values, where the carboxyl group is fully protonated, to a lower plateau of 55 degrees C at high pH values, where this group is fully ionized. The apparent pK (pH at 50% ionization) of the crystalline form shifts from 6.0 to 4.6 to 3.7 with an increase of NaCl concentration from 10(-3) to 0.1 to l.0 M, respectively. These observations are in accord with a simple theoretical analysis that utilizes diffuse double layer theory and the influence of surface potential on surface concentration of protons. In qualitative terms, an increase in electrolyte concentration reduces the surface potential, the result of which is a diminution of the surface-bulk pH difference and a lowering of the apparent pK. Assuming an area of 50 A2/molecule, the intrinsic pKa (apparent pK corrected for surface pH) of the carboxyl group is 2.7. A 1000-fold change of NaCl concentration produces a very large change in surface potential without influencing the transition temperature of the ionized form of the lipid.