Thermodynamic aspects of biopolymer functionality in biological systems,foods, and beverages

Molecular mimicry and molecular symbiosis are proposed to be the main factors controlling thermodynamic activity and phase behavior of macromolecular compounds in foods, beverages, and chyme. Molecular mimicry implies a chemical resemblance of hydrophilic surfaces of globular proteins with their chemical information hidden in the hydrophobic interior and low excluded volume of the globules. The molecular mimicry contributes to the efficiency of enzymes. Molecular symbiosis means that interactions attraction or repulsion) between biopolymer molecules greatly differing in conformation (globular and rod-like) favor the biological efficiency of one of them at least. The symbiosis is based on excluded volume effects of macromolecules in mixed solutions. Association-dissociation of rod-like macromolecules can dictate thermodynamic activity of an enzyme in the mixed solution. Thermodynamic incompatibility is typical of food macromolecules, whose denaturation, association, complexing, and chemical modification reduce their mimicry and co-solubility. Foods are normally phase-separated systems with highly volume-occupied phases. The phase-separated nature of the gel-like chyme is important to the efficiency of digestion of mixed diets. Phase separation of biopolymer mixtures, presumably, underlies mechanisms of nonspecific immune defense. The phase behavior-functionality relationships is presented through concrete examples of some foods (such as milk products, low-fat spreads, ice cream, wheat and rye doughs, thermoplastic extrudates, etc.), beverages (tea and coffee), and chyme.     

Excluded volume as a determinant of macromolecular structure and reactivity

The effect of excluded volume on the thermodynamic activity of globular macromolecules and macromolecular complexes in solution is studied in the hard-particle approximation. Activity coefficients are calculated as a function of the fraction of total volume occupied by macromolecules using relations obtained from scaled particle and lattice models. Significant and readily observable effects are predicted to occur as the fraction of volume occupied by globular macromolecules increases, including the following: (i) Compact quasi-spherical macromolecular conformations become increasingly energetically favored over extended anisometric conformations. (ii) Self- and heteroassociation processes are enhanced, particularly those leading to the formation of compact quasi-spherical aggregates. (iii) Depending upon the details of the reaction mechanism, the rate of an enzyme-catalyzed reaction may monotonically decrease, go through a maximum, or exhibit more complex behavior. A given degree of volume occupancy by larger macromolecules is predicted to have less effect on the structure and self-association of smaller macromolecules than the same degree of volume occupancy by smaller macromolecules has on the structure and self-association of larger macromolecules.     

Origins of globular structure in proteins

Thermodynamic incompatibility of polymers in a common solvent is possibly a driving force for formation and evolution of globular protein structures. Folding of polypeptide chains leads to a decrease in both excluded volume of molecules and chemical differences between surfaces of globular molecules with chemical information hidden in the hydrophobic interior. Folding of polypeptide chains results in 'molecular or thermodynamic mimicry' of globular proteins and in at least more than 10-fold higher phase separation threshold values of mixed protein solutions compared to those of classical polymers. Unusually high co-solubility might be necessary for efficient biological functioning of proteins, e.g. enzymes, enzyme inhibitors, etc.     

Size-dependent studies of macromolecular crowding on the thermodynamic stability,structure and functional activity of proteins: in vitro and in silico approaches

BackgroundThe environment inside cells in which proteins fold and function are quite different from that of the dilute buffer solutions often used during in vitro experiments. The presence of large amounts of macromolecules of varying shapes, sizes and compositions makes the intracellular milieu extremely crowded.Scope of reviewThe overall concentration of macromolecules ranges from 50 to 400 g l^− 1, and they occupy 10–40% of the total cellular volume. These differences in solvent conditions and the level of crowdedness resulting in excluded volume effects can have significant consequences on proteins' biophysical properties. A question that arises is: how important is it to examine the roles of shape, size and composition of macromolecular crowders in altering the biological properties of proteins? This review article aims at focusing, gathering and summarizing all of the research investigations done by means of in vitro and in silico approaches taking into account the size-dependent influence of the crowders on proteins' properties.Major conclusionsAltogether, the internal architecture of macromolecular crowding environment including size, shape and concentration of crowders, appears to be playing an extremely important role in causing changes in the biological processes. Most often the small sized crowders have been found more effective crowding agents. However, thermodynamic stability, structure and functional activity of proteins have been governed by volume exclusion as well as soft (chemical) interactions.General significanceThe article provides an understanding of importance of internal architecture of the cellular environment in altering the biophysical properties of proteins.     

Probing the combination of erlotinib hydrochloride,an anticancer drug,and human serum albumin: Spectroscopic,molecular docking,and molecular dynamic analyses

Human serum albumin (HSA) is a globular and monomeric protein in plasma that transports many drugs and compounds. Binding of some drugs to HSA can lead to changes in its stability and biological function. We investigated the binding interactions between erlotinib hydrochloride (Erlo) and HSA. Erlo is used to treat lung, pancreatic, and some other cancers. Experimental data showed that the fluorescence emission of the protein was quenched by Erlo using a static quenching mechanism. The calculation of the binding constant, K_b (1.57 × 10⁵ M⁻¹ at 300 K), confirmed the existence of a moderate binding interaction between Erlo and HSA. The interaction was enthalpy driven, spontaneous, and exothermic. The calculated thermodynamic parameters in agreement with simulation and molecular docking data showed that van der Waals and hydrogen bond forces played an important role in the interaction process. Molecular docking results indicated that Erlo has more affinity to bind to subdomain IIA (site I) of HSA. Molecular dynamics simulation analysis showed that the protein is stable in the presence of Erlo under simulation conditions.     

MD Simulations of Liquids with Td,Oh Molecular Symmetry

Abstract

A new method is proposed for the calculation of intermolecular interactions in Molecular Dynamics simulations of liquids with T_d, O_h molecular symmetry. The new algorithm is based on the separation of the pair potential into a short-range and a long-range contribution described by a site-site and a spherical centre-centre potential model respectively using an additional cutoff distance. Test calculations for the Lennard-Jones fluids CCl₄ and SF₆ show significant savings in CPU time. We compare thermodynamic properties, pair correlation functions and a few dynamic autocorrelation functions obtained with the novel strategy with results of the commonly used algorithm for systems containing 864 molecules. Since no significant differences appear the new algorithm may be suggested as a useful contribution to the area of Molecular Dynamics simulation of liquids with these rather high molecular symmetries.     

Critical Examination of the Colloidal Particle Model of Globular Proteins

Recent studies of globular protein solutions have uniformly adopted a colloidal view of proteins as particles, a perspective that neglects the polymeric primary structure of these biological macromolecules, their intrinsic flexibility, and their ability to sample a large configurational space. While the colloidal perspective often serves as a useful idealization in many cases, the macromolecular identity of proteins must reveal itself under thermodynamic conditions in which the native state is no longer stable, such as denaturing solvents and high protein concentrations where macromolecules tend to have screened excluded volume, charge, and hydrodynamic interactions. Under extreme pH conditions, charge repulsion interactions within the protein chain can overcome the attractive hydrogen-bonding interactions, holding it in its native globular state. Conformational changes can therefore be expected to have great significance on the shear viscosity and other rheological properties of protein solutions. These changes are not envisioned in conventional colloidal protein models and we have initiated an investigation of the scattering and rheological properties of model proteins. We initiate this effort by considering bovine serum albumin because it is a globular protein whose solution properties have also been extensively investigated as a function of pH, temperature, ionic strength, and concentration. As we anticipated, near-ultraviolet circular dichroism measurements and intrinsic viscosity measurements clearly indicate that the bovine serum albumin tertiary structure changes as protein concentration and pH are varied. Our findings point to limited validity of the colloidal protein model and to the need for further consideration and quantification of the effects of conformational changes on protein solution viscosity, protein association, and the phase behavior. Small-angle Neutron Scattering measurements have allowed us to assess how these conformational changes influence protein size, shape, and interprotein interaction strength.     

First-Year Evaluation of Mexico’s Tax on Nonessential Energy-Dense Foods: An Observational Study

BackgroundIn an effort to prevent continued increases in obesity and diabetes, in January 2014, the Mexican government implemented an 8% tax on nonessential foods with energy density ≥275 kcal/100 g and a peso-per-liter tax on sugar-sweetened beverages (SSBs). Limited rigorous evaluations of food taxes exist worldwide. The objective of this study was to examine changes in volume of taxed and untaxed packaged food purchases in response to these taxes in the entire sample and stratified by socioeconomic status (SES).ConclusionsHousehold purchases of nonessential energy-dense foods declined in the first year after the implementation of Mexico’s SSB and nonessential foods taxes. Future studies should evaluate the impact of the taxes on overall energy intake, dietary quality, and food purchase patterns (see S1 Abstract in Spanish).     

Preparation of Biopolymer Aerogels Using Green Solvents

Although the first reports on aerogels made by Kistler¹ in the 1930s dealt with aerogels from both inorganic oxides (silica and others) and biopolymers (gelatin, agar, cellulose), only recently have biomasses been recognized as an abundant source of chemically diverse macromolecules for functional aerogel materials. Biopolymer aerogels (pectin, alginate, chitosan, cellulose, etc.) exhibit both specific inheritable functions of starting biopolymers and distinctive features of aerogels (80-99% porosity and specific surface up to 800 m²/g). This synergy of properties makes biopolymer aerogels promising candidates for a wide gamut of applications such as thermal insulation, tissue engineering and regenerative medicine, drug delivery systems, functional foods, catalysts, adsorbents and sensors. This work demonstrates the use of pressurized carbon dioxide (5 MPa) for the ionic cross linking of amidated pectin into hydrogels. Initially a biopolymer/salt dispersion is prepared in water. Under pressurized CO₂ conditions, the pH of the biopolymer solution is lowered to 3 which releases the crosslinking cations from the salt to bind with the biopolymer yielding hydrogels. Solvent exchange to ethanol and further supercritical CO₂ drying (10 - 12 MPa) yield aerogels. Obtained aerogels are ultra-porous with low density (as low as 0.02 g/cm³), high specific surface area (350 - 500 m²/g) and pore volume (3 - 7 cm³/g for pore sizes less than 150 nm).     

Macromolecular diffusion in crowded solutions.

The effects of crowding on the self or tracer diffusion of macromolecules in concentrated solutions is an important but difficult problem, for which, so far, there has been no rigorous treatment. Muramatsu and Minton suggested a simple model to calculate the diffusion coefficient of a hard sphere among other hard spheres. In this treatment, scaled particle theory is used to evaluate the probability that the target volume for a step in a random walk is free of any macromolecules. We have improved this approach by using a more appropriate target volume which also allows the calculation to be extended to the diffusion of a hard sphere among hard spherocylinders. We conclude that, to the extent that proteins can be approximated as hard particles, the hindrance of globular proteins by other proteins is reduced when the background proteins aggregate (the more so the greater the decrease in particle surface area), the hindrance due to rod-shaped background particles is reduced slightly if the rod-like particles are aligned, and the anisotropy of the diffusion of soluble proteins among cytoskeletal proteins will normally be small.     

Quantification of Excluded Volume Effects on the Folding Landscape of Pseudomonas aeruginosa Apoazurin In Vitro

Proteins fold and function inside cells that are crowded with macromolecules. Here, we address the role of the resulting excluded volume effects by in vitro spectroscopic studies of Pseudomonas aeruginosa apoazurin stability (thermal and chemical perturbations) and folding kinetics (chemical perturbation) as a function of increasing levels of crowding agents dextran (sizes 20, 40, and 70 kDa) and Ficoll 70. We find that excluded volume theory derived by Minton quantitatively captures the experimental effects when crowding agents are modeled as arrays of rods. This finding demonstrates that synthetic crowding agents are useful for studies of excluded volume effects. Moreover, thermal and chemical perturbations result in free energy effects by the presence of crowding agents that are identical, which shows that the unfolded state is energetically the same regardless of method of unfolding. This also underscores the two-state approximation for apoazurin’s unfolding reaction and suggests that thermal and chemical unfolding experiments can be used in an interchangeable way. Finally, we observe increased folding speed and invariant unfolding speed for apoazurin in the presence of macromolecular crowding agents, a result that points to unfolded-state perturbations. Although the absolute magnitude of excluded volume effects on apoazurin is only on the order of 1–3 kJ/mol, differences of this scale may be biologically significant.     

Methods for Assessment of Dietary Lead Exposure of the Inner-City Population

Abstract

Assessment of dietary lead exposure of individuals begins with the determination of food and beverage intake by the individuals, and concludes with an evaluation of the lead content of the foods and beverages consumed. Of several techniques available for assessment of dietary intake, the 24-hour food recall is recommended as the method of choice for assessing current dietary lead intakes in inner-city populations. The three-day food record can be used among cooperative and motivated subjects, while the dietary history method is available for assessing long-term intakes in the past. The unavailability of lead content values of a large number of foods will to a large extent restrict the use of these methods in large-scale dietary lead exposure studies. Until the time that such data becomes available, the most accurate estimates of lead intake can be provided by chemical analysis of duplicate samples of foods consumed, as is currently done. However, this method is feasible only for small samples.     

Chemical Potential,Partial Enthalpy and Partial Volume of Mixtures by NPT Molecular Dynamics

Abstract

Equilibrium NPT molecular dynamics computer simulations have been used to determine the chemical potential, partial enthalpy and partial volume of model Ar-Kr mixtures using newly devised non-intrusive particle insertion and particle swap techniques [P. Sindzingre et al. Chemical Physics, 129 (1989) 213]. In this report we examine, for the first time, in some detail the relative convergence statistics of the particle swap and particle insertion methods for these properties for binary Lennard-Jones (LJ) mixtures. Both species are represented by single-site Lennard-Jones pair potentials with Lorentz-Berthelot rules for the cross-species interactions. We show that, over the whole phase diagram and especially in the vicinity of the fluid-solid coexistence line, the particle swap method gives significantly better statistics than the particle insertion method for the difference in chemical potential of the two species, partial enthalpy and partial volume of each species. Also, we find that, using the particle swap method, the difference in the chemical potential converges more rapidly than the differences in the partial enthalpy and volume.     

Thermodynamic functions of biopolymer hydration. I. Their determination by vapor pressure studies,discussed in an analysis of the primary hydration process

The primary hydration process of native biopolymers is analyzed in a brief review of the literature, pertaining to various aspects of biopolymer–water systems. Based on this analysis, a hydration model is proposed that implies that the solution conformation of native biopolymers is stable at and above a critical degree of hydration (h_p′ = 0.06–0.1 g H₂O/g polymer). This water content corresponds to the fraction of strongly bound water, and amounts to ～20% of the primary hydration sphere. In order to test this model, detailed sorption–desorption scanning experiments were performed on a globular protein (α-chymotrypsin). The results obtained are consistent with the proposed hydration model. They show that under certain experimental conditions, sorption isotherms can be obtained that do not exhibit hysteresis. These data represent equilibrium conditions and are thus accessible to thermodynamic treatment. Valid thermodynamic functions, pertinent to the interaction of water with biopolymers in their solution state, can be obtained from these sorption experiments.     

Quantification of Excluded Volume Effects on the Folding Landscape of Pseudomonas aeruginosa Apoazurin In?Vitro

Proteins fold and function inside cells that are crowded with macromolecules. Here, we address the role of the resulting excluded volume effects by in vitro spectroscopic studies of Pseudomonas aeruginosa apoazurin stability (thermal and chemical perturbations) and folding kinetics (chemical perturbation) as a function of increasing levels of crowding agents dextran (sizes 20, 40, and 70 kDa) and Ficoll 70. We find that excluded volume theory derived by Minton quantitatively captures the experimental effects when crowding agents are modeled as arrays of rods. This finding demonstrates that synthetic crowding agents are useful for studies of excluded volume effects. Moreover, thermal and chemical perturbations result in free energy effects by the presence of crowding agents that are identical, which shows that the unfolded state is energetically the same regardless of method of unfolding. This also underscores the two-state approximation for apoazurin’s unfolding reaction and suggests that thermal and chemical unfolding experiments can be used in an interchangeable way. Finally, we observe increased folding speed and invariant unfolding speed for apoazurin in the presence of macromolecular crowding agents, a result that points to unfolded-state perturbations. Although the absolute magnitude of excluded volume effects on apoazurin is only on the order of 1–3 kJ/mol, differences of this scale may be biologically significant.     

Efficient Test Molecule Sampling in Molecular Simulation

Abstract

Excluded volume map sampling (EVMS) is a particularly efficient means of performing test molecule sampling to estimate or impose chemical potential in molecular simulations. This paper discusses the motivation and applications of excluded volume map sampling, presents computer code demonstrating its implementation, and gives an example of its application.     

Bacillus mojavensis strain 32A, a bioflocculant-producing bacterium isolated from an Egyptian salt production pond

Bacillus mojavensis strain 32A that exhibited 96.11% flocculation efficiency for clay suspensions was selected from other 15 comparative strains. Under growth condition, strain 32A was able to produce 5.2 g/L of purified biopolymer. Its constituent was mainly polysaccharide and protein with proportional of 98.4-1.6% respectively. FTIR spectrum was confirming its chemical analysis. This biopolymer attain very fast sedimentation rate. The cost-effective biopolymer and CaCl₂ dosages were 3 mg/L and 5 ml/L respectively that posed 89.7% flocculation efficiency. These dosages were suitable only for clay concentrations ?5 g/L. The maximum flocculation efficiency of the biopolymer recorded at pH 1.0 of clay suspension. The too high (>75 °C) or too low (<25 °C) clay suspension temperature was unfavorable for the biopolymer flocculation performance. The biopolymer solution utilized high thermal stability over the temperature range of 5-60 °C. Furthermore, its pH stability recorded at pH range of 5-9.     

Why Were Polysaccharides Necessary?

The main idea of this paper is that the primordial soup may be modelled by food systems whose structure-property relationship is based on non-specific interactions between denatured biopolymers. According to the proposed hypothesis, polysaccharides were the first biopolymers that decreased concentration of salts in the primordial soup, 'compatibilised' and drove the joint evolution of proto-biopolymers. Synthesis of macromolecules within the polysaccharide-rich medium could have resulted in phase separation of the primordial soup and concentration of the polypeptides and nucleic acids in the dispersed phase particles. The concentration of proto-biopolymer mixtures favoured their cross-linking in hybrid supermacromolecules of conjugates. The cross-linking of proto-biopolymers could occur by hydrophobic, electrostatic interactions, H-bonds due to freezing aqueous mixed biopolymer dispersions and/or by covalent bonds due to the Maillard reaction. Cross-linking could have increased the local concentration of chemically different proto-biopolymers, fixed their relative positions and made their interactions reproducible. Attractive-repulsive interactions between cross-linked proto-biopolymer chains could develop pairing of the monomer units, improved chemical stability (against hydrolysis) and led to their mutual catalytic activity and coding. Conjugates could probably evolve to the first self-reproduced entities and then to specialized cellular organelles. Phase separation of the primordial soup with concentration of conjugates in the dispersed particles has probably resulted in proto-cells.