Macromolecular crowding and its consequences.

Incompatible pairs of polymers separate into two phases in aqueous solution above a few percentage points total concentration. Protein pairs can also produce phase separation, but at somewhat higher concentrations. In this chapter, we explore the effect of high background concentrations of macromolecules on phase separation of pairs of species which would not be at sufficiently high concentration to separate in the absence of the uninvolved species. Effects produced by such high background concentrations are known as macromolecular crowding. Dramatic enhancements in various association reactions due to crowding have been predicted and observed but its effects on phase separation in biological mixtures typical of the cytoplasm have not been examined. Here, we describe a calculation based on the Flory-Huggins treatment of concentrated polymer solutions that sheds some light on this issue. We find that a background of 20 wt % of a high molecular weight species greatly reduces the concentrations needed to produce phase separation in a mixture of two incompatible macromolecules if one is more hydrophobic than the other. Given the high total concentration of macromolecules in cytoplasm, it is perhaps surprising that phases have not been observed. This issue is discussed and some explanations offered.

In vivo study and thermodynamic investigation of two lanthanum complexes, La(dpp)3 and La(XT), for the treatment of bone resorption disorders.

Bone density diseases such as osteoporosis affect a significant number of people worldwide. Lanthanide ions are functional mimics of calcium ions, able to substitute for Ca2+ in the bone mineral component, hydroxyapatite (HAP). Bone undergoes a continuous remodelling cycle and lanthanides can affect this cycle, exerting a positive influence on bone mineral. We have been engaged in efforts to find new lanthanide containing complexes as active agents for treatment of these diseases and have identified two lead compounds, 3-hydroxy-1,2-dimethylpyridin-4(1H)-one (Hdpp) and a phosphinate-EDTA derivative, bis[[bis(carboxymethyl)amino]-methyl]phosphinate (H5XT). In this paper, we report in vivo data for the first time for the two lead compounds. The pharmacokinetics of La(dpp)3 suggest the complex is rapidly cleared from plasma. We demonstrate that La3+ accumulates in the bone following IV dose of either La(dpp)3 or La(XT) and we have investigated the influence of each chelating ligand on the incorporation of La3+ into HAP using ITC and HAP-binding studies.

The role of a conserved tyrosine residue in high-potential iron sulfur proteins.

Conserved tyrosine-12 of Ectothiorhodospira halophila high-potential iron sulphur protein (HiPIP) iso-I was substituted with phenylalanine (Y12F), histidine (Y12H), tryptophan (Y12W), isoleucine (Y12I), and alanine (Y12A). Variants Y12A and Y12I were expressed to reasonable levels in cells grown at lower temperatures, but decomposed during purification. Variants Y12F, Y12H, and Y12W were substantially destabilized with respect to the recombinant wild-type HiPIP (rcWT) as determined by differential scanning calorimetry over a pH range of 7.0-11.0. Characterization of the Y12F variant by NMR indicates that the principal structural differences between this variant and the rcWT HiPIP result from the loss of the two hydrogen bonds of the Tyr-12 hydroxyl group with Asn-14 O delta 1 and Lys-59 NH, respectively. The effect of the loss of the latter interaction is propagated through the Lys-59/Val-58 peptide bond, thereby perturbing Gly-46. The delta delta GDapp of Y12F of 2.3 kcal/mol with respect to rcWT HiPIP (25 degrees C, pH 7.0) is entirely consistent with the contribution of these two hydrogen bonds to the stability of the latter. CD measurements show that Tyr-12 influences several electronic transitions within the cluster. The midpoint reduction potentials of variants Y12F, Y12H, and Y12W were 17, 19, and 22 mV (20 mM MOPS, 0.2 M sodium chloride, pH 6.98, 25 degrees C), respectively, higher than that of rcWT HiPIP. The current results indicate that, although conserved Tyr-12 modulates the properties of the cluster, its principle function is to stabilize the HiPIP through hydrogen bonds involving its hydroxyl group and electrostatic interactions involving its aromatic ring.

Nanogram-level micro-volume DNA assay based on the monomeric cyanine dye PO-PRO-3 iodide.

Several commercially available DNA-staining dyes can yield highly sensitive fluorimetric assays under optimized conditions. However, the high cost of most dyes, coupled with the need for elaborate or expensive instrumentation and/or mL sample volumes, makes assays of this type very costly for routine use. We present a rapid, highly sensitive double-stranded DNA assay based on the new and relatively inexpensive monomeric cyanine dye PO-PRO-3. This dye exhibits maximum excitation/emission wavelengths that are compatible with one of the standard filter sets available on multi-well plate fluorimeters such as the Pandex FCA. The assay does not depend on DNA tertiary structure and is relatively insensitive to protein contamination (up to 1 mg/mL protein), although the bound dye fluorescence does diminish significantly at ionic strengths above approximately 25 mM. Under the assay conditions described here, subnanogram detection limits (in 60-microL sample volumes) are achievable. This assay makes high-sensitivity DNA quantification cost-effective and convenient for many routine analytical applications.

Performance of succinylacetone assays and their associated proficiency testing outcomes.

BACKGROUND: Succinylacetone (SUAC) is the primary metabolic marker for hepatorenal tyrosinemia. MATERIALS AND METHODS: We used results reported for dried-blood-spot proficiency testing (PT) specimens and hepatorenal tyrosinemia patients' newborn screening (NBS) samples to demonstrate analytic biases in SUAC recoveries and differences in presumptive clinical classifications. RESULTS: SUAC recoveries from non-kit and NeoBase™ kit tandem mass spectrometry methods were markedly different. Kit users that set high cutoff values submitted discordant clinical assessments of "within normal limits" for PT specimens enriched with 10-15 µmol SUAC/L in blood. SUAC levels in tyrosinemia patients' NBS samples analyzed by NeoBase™ kit were lower than those in samples analyzed by non-kit methods. CONCLUSIONS: From 2009 to 2011, analytic biases in SUAC recoveries were consistent. Discordant clinical assessments of PT specimens were associated with high cutoff values for NeoBase™ kit results. Method-related differences in SUAC concentrations of tyrosinemia patients' samples were consistent with those of PT specimens.

Analysis of compression of polymer mushrooms using self-consistent field theory.

A number of new technologies, including new-generation biomaterials and chromatography resins, are based on passivation and modification of surfaces by terminally attaching polymer chains to the surface. However, little is known about these systems at the molecular level. In this work the compression of a single end-grafted polymer chain (or mushroom) by a disc of finite radius was investigated using a self-consistent field (SCF) lattice model. In accordance with results predicted using scaling theory [Subramanian et al., Europhys. Lett. 29 (1995) 285 and Macromolecules 29 (1996) 4045], the compressed chain undergoes a smooth escape transition. However, under the assumption of angular symmetry, a first-order escape transition of the end-grafted chain is not observed, suggesting that the formation of a tether is required for the predicted phase transition. Segment density distributions and compression energies are calculated in a cylindrical lattice. The energy required to compress a chain increases monotonically as the disc is moved closer to the surface and becomes independent of chain length at strong compressions where the work of compression involves only confinement of the tether joining the escaped chain fraction to the grafting point.

Analysis of brush-particle interactions using self-consistent-field theory.

Non-specific protein adsorption can be reduced by attaching polymer chains by one end to a sorbent surface. End-grafted polymer modified surfaces have also found application in size-based chromatographic bioseparations. To better understand how to tailor surfaces for these applications, a numerical SCF model has been used to calculate theoretical results for the polymer density distribution of interacting polymer chains around a solute particle positioned at a fixed distance from a surface. In addition, the excess energy required to move the particle into the polymer chains (interaction energy) is calculated using a statistical mechanical treatment of the lattice model. The effect of system variables such as particle size, chain length, surface density and Flory interaction parameters on density distributions and interaction energies is also studied. Calculations for the interaction of a solute particle with a surface covered by many polymer chains (a brush) show that the polymer segments will fill in behind the particle quite rapidly as it moves toward the surface. When there is no strong energetic attraction between the polymer and solute we predict that the interaction energy will be purely repulsive upon compression due to losses in conformational entropy of the polymer chains. Above a critical chain length, which depends upon particle size, a maximum in the force required to move the particle toward the surface is observed due to an engulfment of the particle as chains attempt to access the free volume behind the particle. If an attraction exists between the polymer and solute, such that a minimum in the interaction energy is seen, the optimum conditions for solute repulsion occur at the highest surface density attainable. Long chain length can lead to increased solute concentration within the polymer layer due to the fact that an increased number of favourable polymer-solute contacts are able to occur than with short chains at a similar entropic penalty.

Characterization of an oligonucleotide-binding fluorescent ligand for application in affinity purification of dsDNA.

The fluorescent probe PO-PRO-3 was investigated as a potential ligand for the affinity immobilization and purification of genomic or plasmid DNA fragments. Affinities and mechanisms for PO-PRO-3 binding to superhelical and linearized pUC 18 plasmid DNA were examined through measurement of binding isotherms, continuous-variation analysis, and DNA titrations. In addition, the effects of DNA conformation, protein and RNA contaminants, solvent polarity, and ionic strength are examined with the aim of optimizing binding and elution conditions and of assigning limits to the range of applicability of the affinity purification.

Solvent dielectric effects on protein dynamics.

Electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations were used to investigate the dynamics of alpha-chymotrypsin in solvents ranging in dielectric constant from 72 to 1.9. EPR measurements showed that motions in the vicinity of two spin-labeled amino acids (Met-192 and Ser-195) decreased dramatically with decreasing solvent dielectric constant, a trend consistent with changes in the electrostatic force between charged residues of the protein. EPR results and MD simulations revealed a very similar functional dependence between rates of motion in the protein and the dielectric constant of the bulk solvent; however, predicted motions of protein atoms were markedly faster than measured motions of the spin labels. MD calculations for dielectric constants of 5 and 72 showed the greatest differences near the outer surface of the protein. In general, at the lower dielectric constant many atoms of the protein move more slowly, and many of the slowest residues are near the exterior. These results suggest that altered dynamics may contribute to the unusual properties--e.g., modified stereoselectivities--of enzymes in nearly dry organic solvents.

Surface diffusion of cellulases and their isolated binding domains on cellulose.

The surface diffusion rate of bacterial cellulases from Cellulomonas fimi on cellulose was quantified using fluorescence recovery after photobleaching analysis. Studies were performed on an exo-beta-1-4-glycanase (Cex), an endo-beta-1-4-glucanase (CenA), and their respective isolated cellulose-binding domains (CBDs). Although these cellulose-binding domains bind irreversibly to microcrystalline cellulose, greater than 70% of bound molecules are mobile on the cellulose surface. Surface diffusion rates are dependent on surface coverage and range from a low of 2 x 10(-11) to a maximum of 1.2 x 10(-10) cm2/s. The fraction of mobile molecules increases only slightly with increasing fractional surface coverage density. Results demonstrate that the packing of C. fimi cellulases and their isolated binding domains onto the cellulose surface is a dynamic process. This suggests that the exclusion of potential CBD binding sites on the cellulose due to steric effects of neighboring bound CBDs may not fully explain the apparent negative cooperativity exhibited in CBD adsorption isotherms. Comparison with the kinetics of cellulase hydrolysis of crystalline substrate suggests that surface diffusion rates do not limit cellulase activity.

Extractive bioconversions in aqueous two-phase systems: enzymatic hydrolysis of casein proteins.

Partition coefficients in poly(ethylene glycol)/dextran aqueous two-phase systems are reported for mixed-casein and its components, alpha, beta and kappa casein. Rates of casein proteolysis by alpha-chymotrypsin and by trypsin are reported in single-phase and aqueous two-phase reactor systems. The advantages resulting from selective partitioning of substrates, enzymes, and products are examined in terms of relative volumetric reaction rates.

Binding of the cellulose-binding domain of exoglucanase Cex from Cellulomonas fimi to insoluble microcrystalline cellulose is entropically driven.

Isothermal titration microcalorimetry is combined with solution-depletion isotherm data to analyze the thermodynamics of binding of the cellulose-binding domain (CBD) from the beta-1,4-(exo)glucanase Cex of Cellulomonas fimi to insoluble bacterial microcrystalline cellulose. Analysis of isothermal titration microcalorimetry data against two putative binding models indicates that the bacterial microcrystalline cellulose surface presents two independent classes of binding sites, with the predominant high-affinity site being characterized by a Langmuir-type Ka of 6.3 (+/-1.4) x 10(7) M-1 and the low-affinity site by a Ka of 1.1 (+/-0.6) x 10(6) M-1. CBDCex binding to either site is exothermic, but is mainly driven by a large positive change in entropy. This differs from protein binding to soluble carbohydrates, which is usually driven by a relatively large exothermic standard enthalpy change for binding. Differential heat capacity changes are large and negative, indicating that sorbent and protein dehydration effects make a dominant contribution to the driving force for binding.

Interaction of polysaccharides with the N-terminal cellulose-binding domain of Cellulomonas fimi CenC. 1. Binding specificity and calorimetric analysis.

The carbohydrate-binding specificity of the N-terminal cellulose-binding domain (CBDN1) from Cellulomonas fimi beta-1,4-glucanase C (CenC) was investigated using affinity electrophoresis, binding assays and microcalorimetry in parallel with NMR and difference ultraviolet absorbance spectroscopy [Johnson, P.E., Tomme, P., Joshi, M.D., & McIntosh, I., P. (1996) Biochemistry 35, 13895-13906]. Binding of CBDN1 on insoluble cellulose is distinctly different from other cellulose-binding domains. CBDN1 binds amorphous cellulose (phosphoric acid-swollen) with high affinity (Kr = 5.1 L g-1), binds Avicel weakly and does not bind highly crystalline bacterial or tunicin cellulose. Moreover, CBDN1 binds soluble cellooligosaccharides and beta-1,4-linked oligomers of glucose such as hydroxyethycellulose, soluble beta-1,3-1,4-glucans from barley and oat, but has no affinity for alpha-1,4-, beta-1,3-, or beta-1,6-polymers of glucose. This is the first report of a cellulose-binding domain with strong and specific affinity for soluble glycans. The thermodynamics for binding of CBDN1 to oligosaccharides, soluble glycans, and phosphoric acid-swollen cellulose were investigated by titration microcalorimetry. At least four beta-1,4-linked glucopyranosides are required to detect binding. For larger glucans, with five or more glucopyranoside units, the binding constants and standard free energy changes are virtually independent of the glucan chain length, indicating that cellopentaose completely fills the binding site. Binding is moderately strong with binding constants ranging from 3,200 +/- 500 M-1 for cellotetraose, to 25,000 +/- 3,000 M-1 for the larger sugars. The reactions are controlled by favorable standard free enthalpy changes which are compensated in a linear fashion by a significant decrease in entropy. A predominance of polar interactions such as hydrogen bonding together with van der Waals interactions provide the major driving forces for the binding event.

Size exclusion chromatography does not require pores.

Separation of macromolecules on the basis of their molecular weight by size exclusion chromatography has long been considered to be caused by the geometry-dependent partition of macromolecules between a continuous phase and the porous interior of a gel or cross-linked bead. The volume of a pore accessible to a solute is limited by its relative dimensions, so larger molecules will have access to a smaller volume and will remain in a bead for a shorter time than smaller solutes. Our recent alternate picture proposes that the partition coefficient can be calculated from a thermodynamic model for the free energy of mixing of the solute with the gel phase. Size-dependent exclusion caused by the unfavorable entropy of mixing associated with the partition is predicted; the magnitude of the effect is modified by enthalpic interactions between the solute and the gel phase. This concept is extended here to describe the partition of macromolecules into a layer of terminally attached polymer chains grafted onto a solid bead. Both simple mean field and self-consistent field theory calculations predict size-dependent entropic exclusion. Experimental results obtained with neutral polymer chains grafted onto solid polystyrene latex beads confirm the predictions.

Driving forces for phase separation and partitioning in aqueous two-phase systems.

A set of simple analytical equations, derived from the Flory-Huggins theory, are used to identify the dominant driving forces for phase separation and solute (e.g., protein) partitioning, in the absence and presence of added electrolyte, in every general class of aqueous two-phase systems. The resulting model appears to capture the basic nature of two-phase systems and all trends observed experimentally. Case studies are used to identify fundamental differences in and the magnitudes of enthalpic and entropic contributions to partitioning in polymer-polymer (e.g., PEG-dextran), polymer-salt, and thermoseparating polymer-water (e.g., UCON-water) two-phase systems. The model therefore provides practitioners with a better understanding of partition systems, and industry with a simple, fundamental tool for selecting an appropriate two-phase system for a particular separation.

Thermostability and irreversible activity loss of exoglucanase/xylanase Cex from Cellulomonas fimi.

The activity of the beta-1,4-glycanase Cex (EC 3.2.1.91) from Cellulomonas fimi is investigated in connection with its industrial application in cellulose hydrolysis and its potential use in cellosaccharide synthesis. Catalytic activity measurements as a function of temperature, complemented with differential scanning calorimetry (DSC) data, are used to characterize the thermostability of the protein and the influence of interdomain interactions. The data suggest that the enzyme is irreversibly deactivated in one of two possible ways: (1) through a low-temperature route characterized by first-order kinetics; or (2) through a high-temperature route characterized by an initial reversible step followed by an irreversible step. Melting temperatures (Tm) of Cex and p-33 (the isolated catalytic domain of Cex) as estimated by DSC are 64.2 and 64.0 degrees C, respectively, suggesting that the binding and catalytic domains of the protein fold independently. Kinetic parameters (Km, kcat, and kcat/Km) of Cex for the hydrolysis of p-nitrophenyl beta-D-cellobioside (pNPC) were determined at temperatures ranging from 15 to 80 degrees C. As demanded by reversible mass-action thermodynamics, the Tm of Cex in the presence of excess ligand as determined from activity-temperature data is ca. 66.55 degrees C, more than 2 degrees C higher than the Tm for Cex under ligand-free conditions. The effect of temperature on the rate constant has been determined using Arrhenius plots. Combined with irreversible deactivation half-life data and DSC data, the results are used to evaluate a model, based on a theory developed by Hei et al. (1993), for predicting the time-dependent activity and active-state stability of the protein under a range of potential operating conditions.

Binding site analysis of cellulose binding domain CBD(N1) from endoglucanse C of Cellulomonas fimi by site-directed mutagenesis.

Endoglucanase C (CenC), a beta1,4 glucanase from the soil bacterium Cellulomonas fimi, binds to amorphous cellulose via two homologous cellulose binding domains, termed CBD(N1) and CBD(N2). In this work, the contributions of 10 amino acids within the binding cleft of CBD(N1) were evaluated by single site-directed mutations to alanine residues. Each isolated domain containing a single mutation was analyzed for binding to an insoluble amorphous preparation of cellulose, phosphoric acid swollen Avicel (PASA), and to a soluble glucopyranoside polymer, barley beta-glucan. The effect of any given mutation on CBD binding was similar for both substrates, suggesting that the mechanism of binding to soluble and insoluble substrates is the same. Tyrosines 19 and 85 were essential for tight binding by CBD(N1) as their replacement by alanine results in affinity decrements of approximately 100-fold on PASA, barley beta-glucan, and soluble cellooligosaccharides. The tertiary structures of unbound Y19A and Y85A were assessed by heteronuclear single quantum coherence (HSQC) spectroscopy. These studies indicated that the structures of both mutants were perturbed but that all perturbations are very near to the site of mutation.