Self-assembly of bioelastomeric structures from solutions: mean-field critical behavior and Flory-Huggins free energy of interactions

The role of solvent in protein folding and in aggregation

We discuss features of the effect of solvent on protein folding andaggregation, highlighting the physics related to the particulate nature and the peculiar structure of the aqueous solvent, and the biological significance of interactions between solvent and proteins. To this purpose we use a generalized energy landscape of extended dimensionality. A closer look at the properties of solvent induced interactions and forces proves useful for understanding the physical grounds of `ad hoc' interactions and for devising realistic ways of accounting for solvent effects. The solvent has long been known to be a crucially important part of biological systems, and times appear mature for it to be adequately accounted for in the protein folding problem. Use of the extended dimensionality energy landscape helpseliciting the possibility of coupling among conformational changes and aggregation, such as proved by experimental data in the literature.

Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model

Proteins aggregate and precipitate from high concentration solutions in a wide variety of problems of natural and technological interest. Consequently, there is a broad interest in developing new ways to model the thermodynamic and kinetic aspects of protein stability in these crowded cellular or solution environments. We use a coarse-grained modeling approach to study the effects of different crowding agents on the conformational equilibria of proteins and the thermodynamic phase behavior of their solutions. At low to moderate protein concentrations, we find that crowding species can either stabilize or destabilize the native state, depending on the strength of their attractive interaction with the proteins. At high protein concentrations, crowders tend to stabilize the native state due to excluded volume effects, irrespective of the strength of the crowder-protein attraction. Crowding agents reduce the tendency of protein solutions to undergo a liquid-liquid phase separation driven by strong protein-protein attractions. The aforementioned equilibrium trends represent, to our knowledge, the first simulation predictions for how the properties of crowding species impact the global thermodynamic stability of proteins and their solutions.

Effect of T-R conformational change on sickle-cell hemoglobin interactions and aggregation

We compare the role of a conformational switch and that of a point mutation in the thermodynamic stability of a protein solution and in the consequent propensity toward aggregation. We study sickle-cell hemoglobin (HbS), the beta6 Glu-Val point mutant of adult human hemoglobin (HbA), in its R (CO-liganded) conformation, and compare its aggregation properties to those of both HbS and HbA in their T (unliganded) conformation. Static and dynamic light scattering measurements performed for various hemoglobin concentrations showed critical divergences with mean field exponents as temperature was increased. This allowed determining spinodal data points T(S)(c) by extrapolation. These points were fitted to theoretical expressions of the T(S)(c) spinodal line, which delimits the region where the homogeneous solution becomes thermodynamically unstable against demixing in two sets of denser and dilute mesoscopic domains, while remaining still liquid. Fitting provided model-free numerical values of enthalpy and entropy parameters measuring the stability of solutions against demixing, namely, 93.2 kJ/mol and 314 J/ degrees K-mol, respectively. Aggregation was observed also for R-HbS, but in amorphous form and above physiological temperatures close to the spinodal, consistent with the role played in nucleation by anomalous fluctuations governed by the parameter epsilon = (T - T(S))/T(S). Fourier transform infrared (FTIR) and optical spectroscopy showed that aggregation is neither preceded nor followed by denaturation. Transient multiple interprotein contacts occur in the denser liquid domains for R-HbS, T-HbS, and T-HbA. The distinct effects of their specific nature and configurations, and those of desolvation on the demixing and aggregation thermodynamics, and on the aggregate structure are highlighted.

Coarse-grained strategy for modeling protein stability in concentrated solutions. II: phase behavior

We use highly efficient transition-matrix Monte Carlo simulations to determine equilibrium unfolding curves and fluid phase boundaries for solutions of coarse-grained globular proteins. The model we analyze derives the intrinsic stability of the native state and protein-protein interactions from basic information about protein sequence using heteropolymer collapse theory. It predicts that solutions of low hydrophobicity proteins generally exhibit a single liquid phase near their midpoint temperatures for unfolding, while solutions of proteins with high sequence hydrophobicity display the type of temperature-inverted, liquid-liquid transition associated with aggregation processes of proteins and other amphiphilic molecules. The phase transition occurring in solutions of the most hydrophobic protein we study extends below the unfolding curve, creating an immiscibility gap between a dilute, mostly native phase and a concentrated, mostly denatured phase. The results are qualitatively consistent with the solution behavior of hemoglobin (HbA) and its sickle variant (HbS), and they suggest that a liquid-liquid transition resulting in significant protein denaturation should generally be expected on the phase diagram of high-hydrophobicity protein solutions. The concentration fluctuations associated with this transition could be a driving force for the nonnative aggregation that can occur below the midpoint temperature.

Time scale of protein aggregation dictated by liquid-liquid demixing

The growing impact of protein aggregation pathologies, together with the current high need for extensive information on protein structures are focusing much interest on the physics underlying the nucleation and growth of protein aggregates and crystals. Sickle Cell Hemoglobin (HbS), a point-mutant form of normal human Hemoglobin (HbA), is the first recognized and best-studied case of pathologically aggregating protein. Here we reanalyze kinetic data on nucleation of deoxy-HbS aggregates by referring them to the (concentration-dependent) temperature T(s) characterizing the occurrence of the phase transition of liquid-liquid demixing (LLD) of the solution. In this way, and by appropriate scaling of kinetic data at different concentrations, so as to normalize their spans, the apparently disparate sets of data are seen to fall on a master curve. Expressing the master curve vs. the parameter epsilon = (T - T(s)) / T(s), familiar from phase transition theory, allows eliciting the role of anomalously large concentration fluctuations associated with the LLD phase transition and also allows decoupling quantitatively the role of such fluctuations from that of microscopic, inter-protein interactions leading to nucleation. Referring to epsilon shows how in a narrow temperature span, that is at T - T(s), nucleation kinetics can undergo orders-of-magnitude changes, unexpected in terms of ordinary chemical kinetics. The same is true for similarly small changes of other parameters (pH, salts, precipitants), capable of altering T(s) and consequently epsilon. This offers the rationale for understanding how apparently minor changes of parameters can dramatically affect protein aggregation and related diseases.

Genetically directed synthesis and spectroscopic analysis of a protein polymer derived from a flagelliform silk sequence

The flagelliform silk protein underlies the unique elastomeric properties displayed by the capture spiral of arachnid webs. To investigate molecular mechanism underlying the elastomeric recovery of the capture spiral, a model polypeptide based upon the elastomeric repeat sequence of Nephila clavipes flagelliform silk protein has been synthesized using recombinant DNA techniques. Polypeptide 1 contains 11 repeats of the 25 amino acid sequence [(Gly-Pro-Gly-Gly-Ser-Gly-Pro-Gly-Gly-Tyr)(2)-Gly-Pro-Gly-Gly-Lys] and was expressed in Escherichia coli strain BL21(DE3) as a C-terminal fusion to a decahistidine leader sequence. A combination of (1)H-(1)H COSY, DEPT, (1)H-(13)C HETCOR, and (1)H-(13)C HMBC NMR spectroscopy was employed on polypeptides 1 and the [1-(13)C]glycine-labeled analogue 1G to assign the (1)H and (13)C NMR resonances of the amino acid residues comprising the flagelliform silk repeat sequence. The conformational properties of 1 in aqueous solution were investigated using a combination of CD, FTIR, VT-NMR, and two-dimensional NOESY NMR. These techniques were consistent with the presence of small but detectable population of beta-turn conformers between Gly(1) and Gly(4) of the pentapeptide units of 1. FTIR and CD studies of solid films of 1 indicated an increase in beta-turn population in the solid state, which coincided with the decrease in hydration level of the polypeptide. The spectroscopic information suggests that the pentapeptide segments of the flagelliform silk protein adopt a beta-turn conformation in the fiber and that the mechanism of elasticity may resemble that proposed for other beta-turn forming polypeptides including elastin.

Elastin: a representative ideal protein elastomer

During the last half century, identification of an ideal (predominantly entropic) protein elastomer was generally thought to require that the ideal protein elastomer be a random chain network. Here, we report two new sets of data and review previous data. The first set of new data utilizes atomic force microscopy to report single-chain force-extension curves for (GVGVP)(251) and (GVGIP)(260), and provides evidence for single-chain ideal elasticity. The second class of new data provides a direct contrast between low-frequency sound absorption (0.1-10 kHz) exhibited by random-chain network elastomers and by elastin protein-based polymers. Earlier composition, dielectric relaxation (1-1000 MHz), thermoelasticity, molecular mechanics and dynamics calculations and thermodynamic and statistical mechanical analyses are presented, that combine with the new data to contrast with random-chain network rubbers and to detail the presence of regular non-random structural elements of the elastin-based systems that lose entropic elastomeric force upon thermal denaturation. The data and analyses affirm an earlier contrary argument that components of elastin, the elastic protein of the mammalian elastic fibre, and purified elastin fibre itself contain dynamic, non-random, regularly repeating structures that exhibit dominantly entropic elasticity by means of a damping of internal chain dynamics on extension.

Interaction of processes on different length scales in a bioelastomer capable of performing energy conversion

This work concerns the aggregation properties of (Gly-Val-Gly-Val-Pro)(251) rec, a polypentapeptide reflecting a highly conserved repetitive unit of the bioelastomer, elastin. On raising the temperature of aqueous solutions above 25 degrees C, this polypeptide was already known to undergo concurrent conformational changes (hydrophobic folding), phase separation, and self-assembly with formation of aggregated three-stranded filaments composed of dynamic polypeptide helices, called beta-spirals. Aggregates obtained from the solution can be shaped into bands that acquire entropic elastic properties upon gamma-irradiation and can perform a variety of energy conversions. Previous studies have shown that aggregation is prompted by the (diverging) critical fluctuations of concentration occurring in the solution, in vicinity of its spinodal line. Here, we present combined circular dicroism (CD) and light scattering experiments, and independent fittings of experimental data to the theoretical spinodal and binodal (coexistence) lines. Results show the following logical and causal sequence of processes: (a) Smooth and progressive conformational changes promoted by concentration fluctuations occurring as temperature is raised "pull down" (in the temperature scale) the instability region of the solution. (b) This further promotes critical fluctuations. (c) The related locally high concentration prompts a further substantial conformational change ending in triple-helix formation and coacervation. (d) This intertwining of processes, covering different length scales (from that of individual peptides to the mesoscopic one of demixed regions), is related to the fact that solvent-induced interactions play a strong role over the entire scale span. These results concur with other recent ones in pointing out that process interactions over many length-scales probably reflect a frequent if not ubiquitous pattern in protein aggregation. This may be highly relevant to the desirable deep understanding of such phenomenon, whose interests cover many fields.

Interacting processes in protein coagulation

A strong interest is currently focused on protein self-association and deposit. This usually involves conformational changes of the entire protein or of a fragment. It can occur even at low concentrations and is responsible for pathologies such as systemic amyloidosis, Alzheimer's and Prion diseases, and other neurodegenerative pathologies. Readily available proteins, exhibiting at low concentration self-association properties related to conformational changes, offer very convenient model systems capable of providing insight into this class of problems. Here we report experiments on bovine serum albumin, showing that the process of conformational change of this protein towards an intermediate form required for coagulation occurs simultaneously and interacts with two more processes: mesoscopic demixing of the solution and protein cross-linking. This pathway of three interacting processes allows coagulation even at very low concentrations, and it has been recently observed also in the case of a nonpeptidic polymer. It could therefore be a fairly common feature in polymer coagulation/gelation. Proteins 1999;37:116-120.

Effects of solvent perturbation on gelation driven by spinodal demixing

We study effects of solvent perturbation on kinetic competition between spinodal demixing and gelation in agarose solutions at a concentration of 5 g/l. Two different cosolutes (tert-butyl alcohol and trimethyl amine N-oxide) known for altering in opposite way solvent-mediated interactions are chosen. By rheometry, static and dynamic light scattering experiments, we show that the cosolute presence shifts the boundary of the instability region of solution leaving unaffected temperature and polymer concentration values required for percolation. Results suggest that an appropriate choice of quenching temperature and solvent allows controlling the gelation time and the gel structural properties.

Collective properties of hydration: long range and specificity of hydrophobic interactions

We report results of molecular dynamics (MD) simulations of composite model solutes in explicit molecular water solvent, eliciting novel aspects of the recently demonstrated, strong many-body character of hydration. Our solutes consist of identical apolar (hydrophobic) elements in fixed configurations. Results show that the many-body character of PMF is sufficiently strong to cause 1) a remarkable extension of the range of hydrophobic interactions between pairs of solute elements, up to distances large enough to rule out pairwise interactions of any type, and 2) a SIF that drives one of the hydrophobic solute elements toward the solvent rather than away from it. These findings complement recent data concerning SIFs on a protein at single-residue resolution and on model systems. They illustrate new important consequences of the collective character of hydration and of PMF and reveal new aspects of hydrophobic interactions and, in general, of SIFs. Their relevance to protein recognition, conformation, function, and folding and to the observed slight yet significant nonadditivity of functional effects of distant point mutations in proteins is discussed. These results point out the functional role of the configurational and dynamical states (and related statistical weights) corresponding to the complex configurational energy landscape of the two interacting systems: biomolecule + water.

Mesoscopic gels at low agarose concentration: perturbation effects of ethanol

Aqueous agarose solutions at low concentrations (0.5 g/liter) were temperature quenched below the spinodal line to form mutually disconnected mesoscopic gels. In the presence of 6% ethanol, these solutions, obtained by quenching at the same temperature depth as in pure water, appear much more fluid, as determined by probe diffusion experiments. We show by static and dynamic light scattering that this can be explained by the solvent-mediated effects of ethanol, leading to a globular shape of mesoscopic agarose gels, rather than to an extended rodlike structure observed in pure water. Our findings show the significant effects of solvent perturbations on particle condensation and, therefore, may be useful in understanding the role of the solvent in the folding of biomolecules.

Self-assembly of biopolymeric structures below the threshold of random cross-link percolation

Self-assembly of extended structures via cross-linking of individual biomolecules often occurs in solutions at concentrations well below the estimated threshold for random cross-link percolation. This requires solute-solute correlations. Here we study bovine serum albumin. Its unfolding causes the appearance of an instability region of the sol, not observed for native bovine serum albumin. As a consequence, spinodal demixing of the sol is observed. The thermodynamic phase transition corresponding to this demixing is the determinative symmetry-breaking step allowing the subsequent occurrence of (correlated) cross-linking and its progress up to the topological phase transition of gelation. The occurrence of this sequence is of marked interest to theories of spontaneous symmetry-breaking leading to morphogenesis, as well as to percolation theories. The present results extend the validity of conclusions drawn from our previous studies of other systems, by showing in one single case, system features that we have hitherto observed separately in different systems. Time-resolved experimental observations of the present type also bring kinetic and diffusional processes and solute-solvent interactions into the picture of cross-link percolation.

Fractal aspects of elastin supramolecular organization

The supramolecular organisation of elastin and its soluble derivative alpha-elastin were studied by scanning and transmission electron microscopy. It was found a variety of different structures including filaments, fibrils, fibres, networks and dendritic, leaf-like forms. Self-similar patterns, extending for at least three orders of magnitude, were revealed, strongly suggesting the presence of fractal objects. The fractal dimension D was determined by using the box counting method.

Mesoscopic gel at low agarose concentration in water: a dynamic light scattering study

Previous work in our laboratory has shown that at very low agarose concentration in water gelation still occurs within mutually disconnected, high concentration regions generated by spinodal demixing. The freely diffusing particles obtained in these conditions are studied in the present work by depolarized dynamic light scattering and probe diffusion experiments. These particles are found to behave as large (in fact, mesoscopic) polymer fibers entangled in a continuously rearranged mesh with scaling parameters typical of partially flexible, neutral chains. The present results allow specifying the notion of mesoscopic gelation. They also reveal that the same symmetry-breaking mechanism that allows macroscopic gelation at polymer concentrations well below the threshold for random cross-link percolation generates additional and unexpected phenomena.

Effects of metal cations on coacervation of alpha-elastin

The quasi-elastic light scattering studies were carried out to investigate effects of metal cations such as Ca2+ and Na+ on the early stage of coacervation process of alpha-elastin, a chemical fragmentation product originated from the biological elastomeric protein elastin, in aqueous solutions. In particular, our attention was focused on changes of two types of dynamical behaviors found in the earlier work, which are a remarkable increase and a monotonous decrease in the hydrodynamic radius R of molecules with temperature for critical and off-critical concentrations of alpha-elastin, respectively. For the critical alpha-elastin concentration, an addition of Ca2+ was found to exert little effects on the steep temperature profile of R observed in the absence of Ca2+. On the other hand, an addition of a slight amount of Na+ resulted in a monotonous decrease in R, but its further addition restored a remarkable increase in R similar to the critical behaviors in the salt-free system. In the case of off-critical sample, the addition of either Ca2+ or Na+ above a certain concentration induced a change in R from a monotonous decrease to a remarkable increase. For both critical and off-critical concentrations of alpha-elastin, Ca2+ and Na+ brought about an elevation and a lowering of the temperature at which the sample started to be turbid, respectively.