Formation of Peptide Bonds from Metastable versus Crystalline Phase: Implications for the Origin of Life

Formation of peptide bonds was attempted bythermal activation of dry amino acids from aqueous solutionthat simulated prebiotic evaporative environments. Theevaporation trend of amino acids solutions shows abifurcation and can lead to either a crystalline phase(near equilibrium) or a metastable non-crystalline phase(far from equilibrium). Only amino acids in this metastablephase are able to form peptide bonds by thermal activationat temperatures that are generated by solar radiationtoday. We suggest that this metastable phase is the idealinitial material to trigger amino acid assemblage withprotein-like structure because provide the driving force(supersaturation) for an intense interaction betweenmonomers of different amino acids and allows activation ofthese monomers in plausible prebiotic conditions.     

Registered and Antiregistered Phase Separation of Mixed Amphiphilic Bilayers

We derive a mean-field free energy for the phase behavior of coupled bilayer leaflets, which is implicated in cellular processes and important to the design of artificial membranes. Our model accounts for amphiphile-level structural features, particularly hydrophobic mismatch, which promotes antiregistration, in competition with the direct transmidplane coupling usually studied, which promotes registration. We show that the phase diagram of coupled leaflets allows multiple metastable coexistences, and we illustrate the kinetic implications of this with a detailed study of a bilayer of equimolar overall composition. For approximate parameters estimated to apply to phospholipids, equilibrium coexistence is typically registered, but metastable antiregistered phases can be kinetically favored by hydrophobic mismatch. Thus, a bilayer in the spinodal region can require nucleation to equilibrate, in a novel manifestation of Ostwald’s rule of stages. Our results provide a framework for understanding disparate existing observations in the literature, elucidating a subtle competition of couplings and a key role for phase-transition kinetics in bilayer phase behavior.     

Advances in Understanding Stimulus-Responsive Phase Behavior of Intrinsically Disordered Protein Polymers

Proteins and synthetic polymers can undergo phase transitions in response to changes to intensive solution parameters such as temperature, proton chemical potentials (pH), and hydrostatic pressure. For proteins and protein-based polymers, the information required for stimulus-responsive phase transitions is encoded in their amino acid sequence. Here, we review some of the key physical principles that govern the phase transitions of archetypal intrinsically disordered protein polymers (IDPPs). These are disordered proteins with repetitive amino acid sequences. Advances in recombinant technologies have enabled the design and synthesis of protein sequences of a variety of sequence complexities and lengths. We summarize insights that have been gleaned from the design and characterization of IDPPs that undergo thermo-responsive phase transitions and build on these insights to present a general framework for IDPPs with pH and pressure responsive phase behavior. In doing so, we connect the stimulus-responsive phase behavior of IDPPs with repetitive sequences to the coil-to-globule transitions that these sequences undergo at the single-chain level in response to changes in stimuli. The proposed framework and ongoing studies of stimulus-responsive phase behavior of designed IDPPs have direct implications in bioengineering, where designing sequences with bespoke material properties broadens the spectrum of applications, and in biology and medicine for understanding the sequence-specific driving forces for the formation of protein-based membraneless organelles as well as biological matrices that act as scaffolds for cells and mediators of cell-to-cell communication.     

The curious case of Skokholm: equilibrium,non‐equilibrium and a phase shift in an island landbird assemblage

Previous work has indicated that the landbirds of Skokholm island (Wales) are not in equilibrium as defined in MacArthur–Wilson's classic theory of island biogeography. This study takes a new dataset with over six decades of data and investigates equilibrium on Skokholm using cluster analysis to identify periods of turnover stability. The attributes of the identified periods were investigated in relation to the MacArthur–Wilson model using analyses of change in numbers of species, S, from one year to the next and measures of variability in S quantified for each of the periods identified together with a consideration of the dynamics in the numbers of species by habitat groupings. Cluster analysis identified four main periods of which two middle periods appeared to be in equilibrium but with a phase shift in‐between. The first and last periods showed non‐equilibrium dynamics but plots of species by habitat groupings suggested that this was due to habitat changes going on at those times. This decadal long dataset indicates that the landbirds of Skokholm exhibit periods of both equilibrium and non‐equilibrium with the latter attributable to habitat change. The apparent phase shift in the equilibrium number of species was unexpected within the framework of island biogeographic theory and not easily explained using the current MacArthur–Wilson framework. There is a need to integrate the theory of island biogeography with more recent work on alternative stable states, tipping points, and phase (or regime) shifts, together with equilibrium and non‐equilibrium dynamics, into a single framework.     

Dynamics of intracellular metabolites of glycolysis and TCA cycle during cell-cycle-related oscillation in Saccharomyces cerevisiae

In the present work LC-MS/MS was applied to measure the concentrations of intermediates of glycolysis and TCA cycle during autonomous, cell-cycle synchronized oscillations in aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae. This study complements previously reported oscillations in carbon dioxide production rate, intracellular concentrations of trehalose and various free amino acids, and extracellular acetate and pyruvate in the same culture. Of the glycolytic intermediates, fructose 1,6-bisphosphate, 2- and 3-phosphoglycerate, and phosphoenolpyruvate show the most pronounced oscillatory behavior, the latter three compounds oscillating out of phase with the former. This agrees with previously observed metabolic control by phosphofructokinase and pyruvate kinase. Although individually not clearly oscillating, several intermediates of the TCA cycle, i.e., alpha-ketoglutarate, succinate, fumarate, and malate, exhibited increasing concentration during the cell cycle phase with high carbon flux through glycolysis and TCA cycle. The average mass action ratios of beta-phosphoglucomutase and fumarase agreed well with previously determined in vitro equilibrium constants. Minor differences resulted for phosphoglucose isomerase and enolase. Together with the observed close correlation of the pool sizes of the involved metabolites, this might indicate that, in vivo, these reactions are operating close to equilibrium, whereby care must be taken due to possible differences between in vivo and in vitro conditions. Combining the data with previously determined intracellular amino acid levels from the same culture, a few clear correlations between catabolism and anabolism could be identified: phosphoglycerate/serine and alpha-ketoglutarate/lysine exhibited correlated oscillatory behavior, albeit with different phase shifts. Oscillations in intracellular amino acids might therefore be, at least partly, following oscillations of their anabolic precursors.     

Protein solubility modeling.

A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process.     

Equilibrium and non‐equilibrium phases in the radiation of Hakea and the drivers of diversity in Mediterranean‐type ecosystems

Mediterranean‐type ecosystems (MTEs) contain exceptional plant diversity. Explanations for this diversity are usually classed as either “equilibrium,” with elevated MTE diversity resulting from greater ecological carrying capacities, or “non‐equilibrium,” with MTEs having a greater accumulation of diversity over time than other types of ecosystems. These models have typically been considered as mutually exclusive. Here, we present a trait‐based explanatory framework that incorporates both equilibrium and non‐equilibrium dynamics. Using a large continental Australian plant radiation (Hakea) as a case study, we identify traits associated with niche partitioning in coexisting species (α‐traits) and with environmental filtering (β‐traits), and reconstruct the mode and relative timing of diversification of these traits. Our results point to a radiation with an early non‐equilibrium phase marked by divergence of β‐traits as Hakea diversified exponentially and expanded from the southwest Australian MTE into biomes across the Australian continent. This was followed from seven million years ago by an equilibrium phase, marked by diversification of α‐traits and a slowdown in lineage diversification as MTE‐niches became saturated. These results suggest that processes consistent with both equilibrium and non‐equilibrium models have been important during different stages of the radiation of Hakea, and together they provide a richer explanation of present‐day diversity patterns.     

The structure and behavior of defoliating insect/forest systems

Using four detailed and complex simulation models we derive a framework for predicting behavior of any defoliating insect/forest system. The framework uses simple and easily gathered biological information on four sets of state variables, each with a characteristic temporal scale, to predict presence, absence or form of key ecological processes acting on or between the variables. The combination of these key processes enables prediction of system equilibrium structure and this structure can be used to derive the temporal behavior of the system. Four qualitatively different classes of system behavior arise from the equilibrium structures. The framework is tested against twelve other systems and field invalidation experiments are outlined. Forest defoliator research and management implications are discussed.     

Scope and utility of hydrogen exchange as a tool for mapping landscapes

The ability to determine conformational parameters of protein-folding landscapes is critical for understanding the link between conformation, function, and disease. Monitoring hydrogen exchange (HX) of labile protons at equilibrium enables direct extraction of thermodynamic or kinetic landscape parameters in two limiting extremes. Here, we establish a quantitative framework for relating HX behavior to landscape. We use this framework to demonstrate that the range of predicted global HX behavior for the majority of a set of characterized two-state proteins under near-native conditions does not readily span between both extremes. For most, stability may be quantitatively determined under physiological conditions, with semiquantitative boundaries on kinetics additionally determined using modest experimental perturbations to shift HX behavior. The framework and relationships derived in the simple context of two-state global folding highlight the importance of understanding HX across the entire continuum of behavior, in order to apply HX to map landscapes.     

A predictive coarse-grained model for position-specific effects of post-translational modifications

Biomolecules undergo liquid-liquid phase separation (LLPS), resulting in the formation of multicomponent protein-RNA membraneless organelles in cells. However, the physiological and pathological role of post-translational modifications (PTMs) on the biophysics of phase behavior is only beginning to be probed. To study the effect of PTMs on LLPS in silico, we extend our transferable coarse-grained model of intrinsically disordered proteins to include phosphorylated and acetylated amino acids. Using the parameters for modified amino acids available for fixed-charge atomistic force fields, we parameterize the size and atomistic hydropathy of the coarse-grained-modified amino acid beads and, hence, the interactions between the modified and natural amino acids. We then elucidate how the number and position of phosphorylated and acetylated residues alter the protein’s single-chain compactness and its propensity to phase separate. We show that both the number and the position of phosphorylated threonines/serines or acetylated lysines can serve as a molecular on/off switch for phase separation in the well-studied disordered regions of Fused in Sarcoma (FUS) and DDX3X, respectively. We also compare modified residues to their commonly used PTM mimics for their impact on chain properties. Importantly, we show that the model can predict and capture experimentally measured differences in the phase behavior for position-specific modifications, showing that the position of modifications can dictate phase separation. In sum, this model will be useful for studying LLPS of post-translationally modified intrinsically disordered proteins and predicting how modifications control phase behavior with position-specific resolution.     

About deterministic extinction in ratio-dependent predator-prey models

Ratio-dependent predator-prey models set up a challenging issue regarding their dynamics near the origin. This is due to the fact that such models are undefined at (0, 0). We study the analytical behavior at (0, 0) for a common ratio-dependent model and demonstrate that this equilibrium can be either a saddle point or an attractor for certain trajectories. This fact has important implications concerning the global behavior of the model, for example regarding the existence of stable limit cycles. Then, we prove formally, for a general class of ratio-dependent models, that (0, 0) has its own basin of attraction in phase space, even when there exists a non-trivial stable or unstable equilibrium. Therefore, these models have no pathological dynamics on the axes and at the origin, contrary to what has been stated by some authors. Finally, we relate these findings to some published empirical results.     

A framework to open the black box of the use phase in circular economy life cycle assessments: The case of shell jacket reuse

Life cycle assessments of circular economy measures (CE LCA) of consumer products have been criticized for oversimplifying important aspects of the use phase such as user behavior and rebound effects, limiting our understanding of the environmental performance of circular economy measures. This study tests the usefulness of a framework designed to facilitate accounting for such aspects, by applying the framework to a case study of reuse of shell jackets enabled by “premium secondhand” outdoor stores. Methods for collecting use phase data were user surveys and interviews with store managers. Using the framework on this case study generated several novel insights which are interesting in themselves and as inputs to CE LCA. For instance, secondhand shell jackets have a significantly lower frequency of use during their first use span compared to the second and to shell jackets in the linear reference scenario. This implies that reuse in this case does not function as a mere use extension of otherwise similar use phases as is commonly assumed. The generation of such insights, which hitherto have been lacking in CE LCAs, points to the usefulness of the framework as a tool for opening the “black box” of the use phase in CE LCAs to improve understanding of the environmental performance of circular economy measures.     

Employing relative entropy techniques for assessing modifications in animal behavior

In order to make quantitative statements regarding behavior patterns in animals, it is important to establish whether new observations are statistically consistent with the animal's equilibrium behavior. For example, traumatic stress from the presence of a telemetry transmitter may modify the baseline behavior of an animal, which in turn can lead to a bias in results. From the perspective of information theory such a bias can be interpreted as the amount of information gained from a new measurement, relative to an existing equilibrium distribution. One important concept in information theory is the relative entropy, from which we develop a framework for quantifying time-dependent differences between new observations and equilibrium. We demonstrate the utility of the relative entropy by analyzing observed speed distributions of Pacific bluefin tuna, recorded within a 48-hour time span after capture and release. When the observed and equilibrium distributions are gaussian, we show that the tuna's behavior is modified by traumatic stress, and that the resulting modification is dominated by the difference in central tendencies of the two distributions. Within a 95% confidence level, we find that the tuna's behavior is significantly altered for approximately 5 hours after release. Our analysis reveals a periodic fluctuation in speed corresponding to the moment just before sunrise on each day, a phenomenon related to the tuna's daily diving pattern that occurs in response to changes in ambient light.     

Phase behavior of a monoacylglycerol: (myverol 18-99K)/water system

The phase behavior of Myverol 18-99K, a food emulsifier rich in monoacylglycerols, in combination with water has been determined. X-ray diffraction and polarized light microscopy (PLM) were used for phase identification and structure characterization. Phase behavior was established in the temperature range from -15 to 50 degrees C and in the composition range from dry to full hydration. Phases identified include the solid lamellar crystal (Lc) phase, the liquid fluid isotropic phase and three liquid crystal phases, the lamellar liquid crystal, the cubic-Ia3d and the cubic-Pn3m phase. Phase information is reported in the form of temperature-composition phase diagrams. It was collected under equilibrium conditions where measurements were made in the heating direction beginning with the Lc phase at -15 degrees C. Phase metastability was also examined in which the natural tendency of the liquid crystal phases to undercool was facilitated. Under this condition, both cubic phases were found to remain free of the solid Lc phase over a relatively wide range of hydration values down to 0 degrees C. The microstructure of the different phases and its dependence on temperature and hydration has been determined. Compositional analysis using thin layer chromatography and gas chromatography/mass spectrometry shows that Myverol 18-99K consists of 82% monoacylglycerols (86.6% monoolein, 7. 0% monostearin, 3.5% monopalmitin, 0.9% monoarachidin, 2.0% unidentified). The equilibrium and metastable phase diagrams of the Myverol 18-99K/water system show remarkable similarity to those reported for the monoolein/water system (Qiu, H., Caffrey, M., 2000. The phase diagram of the monoolein/water system: metastability and equilibrium aspects Biomaterials 21, 223-594.).     

Substrate conformational restriction and CD45-catalyzed dephosphorylation of tail tyrosine-phosphorylated Src protein

Hydrolysis of the tail phosphotyrosine in Src family members is catalyzed by the protein-tyrosine phosphatase CD45, activating Src family-related signaling pathways. Using purified recombinant phospho-Src (P-Src) (amino acid residues 83-533) and purified recombinant CD45 catalytic (cytoplasmic) domain (amino acid residues 565-1268), we have analyzed the kinetic behavior of dephosphorylation. A time course of phosphatase activity showed the presence of a burst phase. By varying the concentration of P-Src, it was shown that the amplitude of this burst phase increased linearly with respect to P-Src concentration. Approximately 2% of P-Src was shown to be rapidly dephosphorylated followed by a slower linear phase. A P-Src protein substrate containing a functional point mutation in the Src homology domain 2 (SH2) led to more rapid dephosphorylation catalyzed by CD45, and this reaction showed only a single linear kinetic phase. These results were interpreted in terms of a model in which P-Src exists in a relatively slow dynamic equilibrium between "closed" and "open" conformational forms. Combined mutations in the SH2 and SH3 domain or the addition of an SH3 domain ligand peptide enhanced the accessibility of P-Src to CD45 by biasing P-Src to a more open form. Consistent with this model, a phosphotyrosine peptide that behaved as an SH2 domain binding ligand showed approximately 100-fold greater affinity for unphosphorylated Src versus P-Src. Surprisingly, P-Src possessing combined SH3 and SH2 functional inactivating point mutations was dephosphorylated by CD45 more slowly compared with P-Src completely lacking SH3 and SH2 domains. Additional data suggest that the SH3 and SH2 domains can inhibit accessibility of the P-Src tail to CD45 by interactions other than direct phosphotyrosine binding by the SH2 domain. Taken together, these results suggest how activation of Src family member signaling pathways by CD45 may be influenced by the presence or absence of ligand interactions remote from the tail.     

Thermodynamic roles of basic amino acids in statherin recognition of hydroxyapatite

Salivary statherin is a highly acidic, 43 amino acid residue protein that functions as an inhibitor of primary and secondary crystallization of the biomineral hydroxyapatite. The acidic domain at the N-terminus was previously shown to be important in the binding of statherin to hydroxyapatite surfaces. This acidic segment is followed by a basic segment whose role is unclear. In this study, the role of the basic amino acids in the hydroxyapatite adsorption thermodynamics has been determined using isothermal titration calorimetry and equilibrium adsorption isotherm analysis. Single point mutations of the basic side chains to alanine lowered the binding affinity to the surface but did not perturb the maximal surface coverage and the adsorption enthalpy. The structural and dynamic properties of the single point mutants as characterized by solid-state NMR techniques were not altered either. Simultaneous replacement of all four basic amino acids with alanine lowered the adsorption equilibrium constant by 5-fold and the maximal surface coverage by nearly 2-fold. The initial exothermic phase of adsorption exhibited by native statherin is preserved in this mutant, along with the alpha-helical structure and the dynamic properties of the N-terminal domain. These results help to refine the two binding site model of statherin adsorption proposed earlier in our study of wild-type statherin (Goobes, R., Goobes, G., Campbell, C.T., and Stayton, P.S. (2006) Biochemistry 45, 5576-5586). The basic charges function to reduce protein-protein charge repulsion on the HAP surface, and in their absence, there is a considerable decrease in statherin packing density on the surface at binding saturation.     

FRET-based analysis of protein-nucleic acid interactions by genetically incorporating a fluorescent amino acid

Protein–nucleic acid interaction is an important process in many biological phenomena. In this study, a fluorescence resonance energy transfer (FRET)-based protein–DNA binding assay has been developed, in which a fluorescent amino acid is genetically incorporated into a DNA-binding protein. A coumarin-containing amino acid was incorporated into a DNA-binding protein, and the mutant protein specifically produced a FRET signal upon binding to its cognate DNA labeled with a fluorophore. The protein–DNA binding affinity was then measured under equilibrium conditions. This method is advantageous for studying protein-nucleic acid interactions, because it is performed under equilibrium conditions, technically easy, and applicable to any nucleic acid-binding protein.     

Protein instability during HIC: describing the effects of mobile phase conditions on instability and chromatographic retention

Hydrophobic interaction chromatography (HIC) is known to be potentially denaturing to proteins, but the effects of mobile phase conditions on chromatographic behavior are not well understood. In this study, we apply a model describing the effects of secondary protein unfolding equilibrium on chromatographic behavior, including the effects of salt concentration on both stability and adsorption. We use alpha-lactalbumin as a model protein that in the presence and absence of calcium, allows evaluation of adsorption parameters for folded and unfolded species independently. The HIC adsorption equilibrium under linear binding conditions and solution phase protein stability have been obtained from a combination of literature and new experiments. The effect of salt concentration on protein stability and the rate constant for unfolding on the chromatographic surface have been determined by fitting the model to isocratic chromatography data under marginally stable conditions. The model successfully describes the effects of added calcium and ammonium sulfate. The results demonstrate the importance of considering the effects on stability of mobile phase modifiers when applying HIC to marginally stable     

On the nature of calcium ion binding between phosphatidylserine lamellae

Ca2+ binding between phosphatidylserine (PS) lamellae gives rise to a phase with the composition Ca(PS)2. When aqueous Ca2+, hydrated PS, and Ca(PS)2 coexist at equilibrium, the aqueous Ca2+ concentration is invariant. At Ca2+ concentrations below this critical value, no binding of Ca2+ to PS is detected. Above this value, Ca2+ binds to PS to form Ca(PS)2. The invariant Ca2+ concentration is 0.14 microM for palmitoyloleoylphosphatidylserine (POPS) and 3.0 microM for dioleoylphosphatidylserine (DOPS). For the mixed acyl chain PS derived from bovine brain (BBPS) this Ca2+ concentration ranges from 0.25 to 0.7 microM. The observed phase behavior is described by the phase rule for the three-component system of water, Ca2+, and PS, with temperature and pressure constant. In order for Ca2+ to bind between PS lamellae to form the Ca(PS)2 phase, the aqueous Ca2+ concentration must be supersaturated. The equilibrium Ca2+ concentration is determined by dissolving Ca(PS)2 by use of Ca2+ chelators.