EVIDENCE FROM PHYSICAL CHEMISTRY REGARDING THE SIZE AND SHAPE OF PROTEIN MOLECULES FROM ULTRA-CENTRIFUGATION, DIFFUSION, VISCOSITY, DIELECTRIC DISPERSION, AND DOUBLE REFRACTION OF FLOW

SEDNTERP: a calculation and database utility to aid interpretation of analytical ultracentrifugation and light scattering data

Proper interpretation of analytical ultracentrifugation (AUC) data for purified proteins requires ancillary information and calculations to account for factors such as buoyancy, buffer viscosity, hydration, and temperature. The utility program SEDNTERP has been widely used by the AUC community for this purpose since its introduction in the mid-1990s. Recent extensions to this program (1) allow it to incorporate data from diffusion as well as AUC experiments; and (2) allow it to calculate the refractive index of buffer solutions (based on the solute composition of the buffer), as well as the specific refractive increment (dn/dc) of proteins based on their composition. These two extensions should be quite useful to the light scattering community as well as helpful for AUC users. The latest version also adds new terms to the partial specific volume calculations which should improve the accuracy, particularly for smaller proteins and peptides, and can calculate the viscosity of buffers containing heavy isotopes of water. It also uses newer, more accurate equations for the density of water and for the hydrodynamic properties of rods and disks. This article will summarize and review all the equations used in the current program version and the scientific background behind them. It will tabulate the values used to calculate the partial specific volume and dn/dc, as well as the polynomial coefficients used in calculating the buffer density and viscosity (most of which have not been previously published), as well as the new ones used in calculating the buffer refractive index.

Subunit Flexibility of Multimeric von Willebrand Factor/Factor VIII Complexes

Von Willebrand factor (VWF) is a plasma glycoprotein that participates in platelet adhesion and aggregation and serves as a carrier for blood coagulation factor VIII (fVIII). Plasma VWF consists of a population of multimers that range in molecular weight from ∼ 0.55 MDa to greater than 10 MDa. The VWF multimer consists of a variable number of concatenated disulfide-linked ∼275 kDa subunits. We fractionated plasma-derived human VWF/fVIII complexes by size-exclusion chromatography at a pH of 7.4 and subjected them to analysis by sodium dodecyl sulfate agarose gel electrophoresis, sedimentation velocity analytical ultracentrifugation (SV AUC), dynamic light scattering (DLS), and multi-angle light scattering (MALS). Weight-average molecular weights, M _w, were independently measured by MALS and by application of the Svedberg equation to SV AUC and DLS measurements. Estimates of the Mark-Houwink-Kuhn-Sakurada exponents , α_s, and α_D describing the functional relationship between the z-average radius of gyration, , weight-average sedimentation coefficient, s _w, z-average diffusion coefficient, D _z , and M _w were consistent with a random coil conformation of the VWF multimer. Ratios of to the z-average hydrodynamic radius, , estimated by DLS, were calculated across an M _w range from 2 to 5 MDa. When compared to values calculated for a semi-flexible, wormlike chain, these ratios were consistent with a contour length over 1000-fold greater than the persistence length. These results indicate a high degree of flexibility between domains of the VWF subunit.

Conformation of the von Willebrand factor/factor VIII complex in quasi-static flow

Von Willebrand factor (VWF) is a plasma glycoprotein that circulates noncovalently bound to blood coagulation factor VIII (fVIII). VWF is a population of multimers composed of a variable number of ∼280 kDa monomers that is activated in shear flow to bind collagen and platelet glycoprotein Ibα. Electron microscopy, atomic force microscopy, small-angle neutron scattering, and theoretical studies have produced a model in which the conformation of VWF under static conditions is a compact, globular “ball-of-yarn,” implying strong, attractive forces between monomers. We performed sedimentation velocity (SV) analytical ultracentrifugation measurements on unfractionated VWF/fVIII complexes. There was a 20% per mg/ml decrease in the weight-average sedimentation coefficient, s_w, in contrast to the ∼1% per mg/ml decrease observed for compact globular proteins. SV and dynamic light scattering measurements were performed on VWF/fVIII complexes fractionated by size-exclusion chromatography to obtain s_w values and z-average diffusion coefficients, D_z. Molecular weights estimated using these values in the Svedberg equation ranged from 1.7 to 4.1 MDa. Frictional ratios calculated from D_z and molecular weights ranged from 2.9 to 3.4, in contrast to values of 1.1–1.3 observed for globular proteins. The Mark–Houwink–Kuhn–Sakurada scaling relationships between s_w, D_z and molecular weight, s=k′Mas and D=k″MaD, yielded estimates of 0.51 and –0.49 for a_s and a_D, respectively, consistent with a random coil, in contrast to the a_s value of 0.65 observed for globular proteins. These results indicate that interactions between monomers are weak or nonexistent and that activation of VWF is intramonomeric.

Thermodynamic Characterization of Free and Surface Water of Colloidal Unimolecular Polymer (CUP) Particles Utilizing DSC

Colloidal Unimolecular Polymer (CUP) particles are spheroidal, 3–9 nm with charged groups on the surface and a hydrophobic core, which offer a larger surface water fraction to improve the analysis of its characteristics. Differential scanning calorimetry (DSC) was performed to determine the characteristics of surface water. These properties include the amount of surface water, the layer thickness, density, specific heat of the surface water above and below the freezing point of water, melting point depression of free water, effect of charge density and particle size. The charge density on the CUP surface was varied as well as the molecular weight which controls the particle diameter. The surface water is proportional to the weight fraction of CUP <20%. Analogous to recrystallization the CUP particles were trapped in the ice when rapidly cooled but slow cooling excluded the CUP, causing inter-molecular counterion condensation and less surface water. The density of surface water was calculated to be 1.023 g/mL to 1.056 g/mL depending on the surface charge density. The thickness of surface water increased with surface charge density. The specific heat of surface water was found to be 3.04 to 3.07 J/g·K at 253.15 K and 3.07 to 3.09 J/g·K at 293.15 K. The average area occupied by carboxylate and ester groups on the CUP surface were determined.

Electroviscous contribution to the rheology of colloidal unimolecular polymer (CUP) particles in water

The rheological characteristics of anionic colloidal unimolecular polymer (CUP) particles in water were investigated. The intrinsic viscosities were determined for CUPs with different molecular weights as a function of volume fraction. The specific viscosities were measured and fit with models considering hydrodynamic interaction and electroviscous effects. The rheological characteristics were consistent with a surface layer of water which increases with the particle size or molecular weight of CUPs. The effective charges on the surface of particle were calculated and correlated with the rheological behavior of the CUP particles from the dilute to semidilute range, a volume fraction of 0.0001-0.08.

Backbone rigidity and static presentation of guanidinium groups increases cellular uptake of arginine-rich cell-penetrating peptides

In addition to endocytosis-mediated cellular uptake, hydrophilic cell-penetrating peptides are able to traverse biological membranes in a non-endocytic mode termed transduction, resulting in immediate bioavailability. Here we analysed structural requirements for the non-endocytic uptake mode of arginine-rich cell-penetrating peptides, by a combination of live-cell microscopy, molecular dynamics simulations and analytical ultracentrifugation. We demonstrate that the transduction efficiency of arginine-rich peptides increases with higher peptide structural rigidity. Consequently, cyclic arginine-rich cell-penetrating peptides showed enhanced cellular uptake kinetics relative to their linear and more flexible counterpart. We propose that guanidinium groups are forced into maximally distant positions by cyclization. This orientation increases membrane contacts leading to enhanced cell penetration.

Cell-penetrating peptides can deliver molecular cargoes into living cells, and cross biological membranes by transduction—a non-endocytic mechanism. Here, the transduction efficiency of cyclic arginine-rich peptides is shown to be higher than that of more flexible linear peptides.

The Size, Shape and Hydration of Cetomacrogol 1000 Micelles

Cetomacrogol solutions have been studied by three techniques. The micellar weight in water has been found from light-scattering experiments to be 101,000; the micelles appear to be spherical. Viscosity measurements can be interpreted in terms of micellar hydration, and 1.96 g. water appear to hydrate 1 g. of cetomacrogol. A similar amount of hydration (1.92 g. water per g. cetomacrogol) can be calculated from the diffusion coefficient. A check on the micellar weight was obtained from the diffusion and viscosity results, giving 96,000, in good agreement with the result from light-scattering.

Water Compartments in Cells

Human experience in the macrobiological world leads scientists to visualize water compartments in cells analogous to the bladder in the human pelvis or ventricles in the brain. While such water-filled cellular compartments likely exist, the volume contributions are insignificant relative to those of biomolecular hydration compartments. The purpose of this chapter is to identify and categorize the molecular water compartments caused by proteins, the primary macromolecular components of cells. The categorical changes in free energy of water molecules on proteins cause these compartments to play dominant roles in osmoregulation and provide important adjuncts to fundamental understanding of osmosensing and osmosignaling mechanisms. Water compartments possess differences in molecular motion, enthalpy, entropy, freezing point depression, and other properties because of electrostatic interaction of polar water molecules with electric fields generated by covalently bound pairs of opposite charge caused by electronegative oxygen and nitrogen atoms of the protein. Macromolecules, including polypeptides, polynucleotides, and polysaccharides, are stiff molecular chains with restricted folding capacities due to inclusion of rigid ring structures or double amide bonds in the backbone sequence. This creates "irreducible spatial charge separation" between positive and negative partial charges, causing elevated electrostatic energy. In the fully hydrated in vivo state of living cells the high dielectric coefficient of water reduces protein electrostatic free energy by providing polar "water bridge networks" between charges, thereby creating four measurably different compartments of bound water with distinct free energy differences.

Importance of head group polarity in controlling aggregation properties of cationic gemini surfactants

Cationic gemini surfactants have been extensively studied in the recent past and the effect of chain length, spacer length and nature on aggregation behavior has been examined. But the effect of variation in head group polarity on micellization has not been examined. Hence, the effect of head group polarity of the butane-1,4-bis(dodecyldimethylammonium bromide) surfactants on aggregation properties is studied through conductance, surface tension, viscosity, and small-angle neutron scattering (SANS) measurements. The critical micellar concentration (cmc), average degree of micelle ionization (beta(ave)), minimum area per molecule of surfactant at air-water interface (A(min)), surface excess concentration (Gamma(max)) and Gibbs free energy change of micellization (DeltaG degrees (mic)) of the surfactants were determined from conductance and surface tension data. The aggregation numbers (N), dimension of micelle (b/a), effective fractional charge per monomer (alpha) were determined from SANS and hydration of micelle (h(m)) from viscosity data. The increasing head group polarity of gemini surfactant having spacer chain length of 4 methylene units promotes micellar growth, leading to decrease in cmc, beta(ave), DeltaG degrees (mic) and increase in N and b/a. This is well supported by the observed increase in hydration (h(m)) of micelle with increase in aggregation number (N) and dimension (b/a) of micelle. The Kraft temperature (k(T)), foamability and foam stability as a function of head group polarity of gemini surfactants were also examined.

Crystallohydrodynamics of protein assemblies: Combining sedimentation, viscometry, and x-ray scattering

Crystallohydrodynamics describes the domain orientation in solution of antibodies and other multidomain protein assemblies where the crystal structures may be known for the domains but not the intact structure. The approach removes the necessity for an ad hoc assumed value for protein hydration. Previous studies have involved only the sedimentation coefficient leading to considerable degeneracy or multiplicity of possible models for the conformation of a given protein assembly, all agreeing with the experimental data. This degeneracy can be considerably reduced by using additional solution parameters. Conformation charts are generated for the three universal (i.e., size-independent) shape parameters P (obtained from the sedimentation coefficient or translational diffusion coefficient), nu (from the intrinsic viscosity), and G (from the radius of gyration), and calculated for a wide range of plausible orientations of the domains (represented as bead-shell ellipsoidal models derived from their crystal structures) and after allowance for any linker or hinge regions. Matches are then sought with the set of functions P, nu, and G calculated from experimental data (allowing for experimental error). The number of solutions can be further reduced by the employment of the D max parameter (maximum particle dimension) from x-ray scattering data. Using this approach we are able to reduce the degeneracy of possible solution models for IgG3 to a possible representative structure in which the Fab domains are directed away from the plane of the Fc domain, a structure in accord with the recognition that IgG3 is the most efficient complement activator among human IgG subclasses.

The hydration problem in solution biophysics: an introduction

The background and purpose of the British Biophysical Society Discussion meeting, The Hydration Problem in Solution Biophysics, held at the University of Glasgow, 12 September 2000, is described, particularly in relation to previous meetings in this field. Whereas a study of the nature and dynamic properties of water associated with a molecule is an important topic by itself, the collection of papers based on this meeting focus mainly on its affect in interpreting biophysical data in terms of macromolecular shape in a solution environment, particularly under dilute and very dilute systems. The techniques considered are largely hydrodynamically or thermodynamically based and supplemented by molecular modeling strategies; but in the context of how these could be used in conjunction with techniques like X-ray crystallography, NMR and neutron scattering.

Comparative investigations of biopolymer hydration by physicochemical and modeling techniques

The comparative investigation of biopolymer hydration by physicochemical techniques, particularly by small-angle X-ray scattering, has shown that the values obtained differ over a wide range, depending on the nature of the polymer and the environmental conditions. In the case of simple proteins, a large number of available data allow the derivation of a realistic average value for the hydration (0.35 g of water per gram of protein). As long as the average properties of proteins are considered, the use of such a default value is sufficient. Modeling approaches may be used advantageously, in order to differentiate between different assumptions and hydration contributions, and to correctly predict hydrodynamic properties of biopolymers on the basis of their three-dimensional structure. Problems of major concern are the positioning and the properties of the water molecules on the biopolymer surface. In this context, different approaches for calculating the molecular volume and surface of biopolymers have been applied, in addition to the development of appropriate hydration algorithms.

Analysis of thermodynamic non-ideality in terms of protein solvation

The effects of thermodynamic non-ideality on the forms of sedimentation equilibrium distributions for several isoelectric proteins have been analysed on the statistical-mechanical basis of excluded volume to obtain an estimate of the extent of protein solvation. Values of the effective solvation parameter delta are reported for ellipsoidal as well as spherical models of the proteins, taken to be rigid, impenetrable macromolecular structures. The dependence of the effective solvated radius upon protein molecular mass exhibits reasonable agreement with the relationship calculated for a model in which the unsolvated protein molecule is surrounded by a 0.52-nm solvation shell. Although the observation that this shell thickness corresponds to a double layer of water molecules may be of questionable relevance to mechanistic interpretation of protein hydration, it augurs well for the assignment of magnitudes to the second virial coefficients of putative complexes in the quantitative characterization of protein-protein interactions under conditions where effects of thermodynamic non-ideality cannot justifiably be neglected.

Limited tryptic hydrolysis of pea legumin: molecular mass and conformational stability of legumin-T

The investigation of hydrodynamic and thermodynamic properties and the determination of the molecular mass of legumin-T, the product of limited tryptic hydrolysis of the 11-S-globulin from pea seeds, was carried out to ascertain the structural relationship to globulin-T's from other legumin-like proteins. The obtained legumin-T preparation has a molecular mass M(W)=260+/-10 kDa and M(S,D)=270+/-20 kDa. The secondary structure of legumin-T is characterised by a high percentage of beta-sheet conformation, comparable to that of native legumin and a reduced percentage of helical conformation. The conformational stability of legumin-T evaluated by equilibrium unfolding in the presence of guanidinium chloride was only slightly reduced in comparison to the native legumin, whereas the calorimetrically determined denaturation enthalpy and Gibbs energy of denaturation were found to be increased for legumin-T. These physicochemical properties are very similar to those of faba bean legumin-T.

Purification and partial characterization of the phospholipase A2 and co-lytic factor from sea anemone (Aiptasia pallida) nematocyst venom

Functional nematocysts of one specific morphological class, the penetrant microbasic mastigophores, were isolated from the sea anemone, Aiptasia pallida. These nematocysts contain a multicomponent venom composed of several proteins, including those with neurotoxic, hemolytic, and lethal activities. Hemolytic activity is produced by at least three synergistic venom proteins. One of these proteins is identified as a phospholipase A2 (EC 3.1.1.4) which exists in two isozymic forms, alpha and beta, with molecular weights of 45,000 and 43,000, respectively. The beta isozyme has been purified to homogeneity. It is a single-chained glycoprotein with an isoelectric point (pI) of 8.8 and represents 70% of the phospholipase activity of the venom. The activity of the beta isozyme is relatively labile and is inactivated by 3.5 M urea or by heating at 45 degrees C. It is most stable at pH 4.0 and loses 50% of its activity at pH values below 3.5 and above 8.0. A second venom protein has also been purified. It is essential for the hemolytic activity of the venom and is termed co-lytic factor (CLF). It is a monomeric glycoprotein having a pI of 4.5. CLF has a molecular weight of approximately 98,000, a sedimentation coefficient of 4.8 S, and is prolate in shape, having a frictional ratio of about 1.6. CLF constitutes about 1.25% of the total venom protein and is assayed by reversing fatty acid inhibition of the venom hemolysis activity.

Effect of the ionic environment on the molecular structure of bacteriophage SPP1 portal protein

Bacteriophage SPP1 portal protein is a large cyclical homo-oligomer composed of 13 subunits. The solution structure and assembly behavior of this protein with high-point rotational symmetry was characterized. The purified protein was present as a monodisperse population of 13-mers, named gp6H, at univalent salt concentrations in the hundred millimolar range (>/= 250 mM NaCl) or in the presence of bivalent cations in the millimolar range (>/= 5 mM MgCl2). Gp6H had a slightly higher sedimentation coefficient, a smaller shape-dependent frictional ratio, and a higher rate of intersubunit cross-linking in the presence of magnesium than in its absence. In the absence of bivalent cations and at univalent salt concentrations below 250 mM, the 13-mer molecules dissociated partially into stable monomers, named gp6L. The monomer had a somewhat different shape from the subunit present in the 13-mer, but maintained a defined tertiary structure. The association-dissociation equilibrium was mainly between the monomer and the 13-mer with a minor population of intermediate oligomers. Their interconversion was strongly influenced by the ionic environment. Under physiological conditions, the concentration of Mg2+ found in the Bacillus subtilis cytoplasm (10-50 mM) probably promotes complete association of gp6 into 13-mer rings with a compact conformation.

COVOL: an interactive program for evaluating second virial coefficients from the triaxial shape or dimensions of rigid macromolecules

An interactive program is described for calculating the second virial coefficient contribution to the thermodynamic nonideality of solutions of rigid macromolecules based on their triaxial dimensions. The FORTRAN-77 program, available in precompiled form for the PC, is based on theory for the covolume of triaxial ellipsoid particles [Rallison, J. M., and S.E Harding. (1985). J. Colloid Interface Sci. 103:284-289]. This covolume has the potential to provide a magnitude for the second virial coefficient of macromolecules bearing no net charge. Allowance for a charge-charge contribution is made via an expression based on Debye-Hückel theory and uniform distribution of the net charge over the surface of a sphere with dimensions governed by the Stokes radius of the macromolecule. Ovalbumin, ribonuclease A, and hemoglobin are used as model systems to illustrate application of the COVOL routine.

Secondary structure and shape of plasma sex steroid-binding protein--comparison with domain G of laminin results in a structural model of plasma sex steroid-binding protein

We have analyzed the secondary structure, shape and dimensions of plasma sex steroid-binding protein (SBP) by CD, size-exclusion chromatography and electron microscopy. CD spectra show extrema at 186 nm and 216 nm characteristic for beta-sheet structures. Analysis with different algorithms indicates 15% alpha-helix, 43% beta-sheet and 10-16% beta-turn structures. An irreversible structural change is observed upon heating above 60 degrees C, which correlates with the loss of steroid-binding activity. As the SBP sequence shows similarity with domains of several multidomain proteins, including laminins, we evaluated the structure of domain G of laminin-1. The CD spectrum shows extrema at 200 nm and 216 nm. Deconvolution results in 13% alpha-helix, 32% beta-sheet and 15% beta-turn structures. Steroid-binding assays indicate that laminin and fragments thereof have no activity. Size-exclusion chromatography reveals that SBP has an extended shape and can be modeled as a cylinder with a length and diameter of 23 nm and 3 nm, respectively. This shape and the dimensions are in agreement with the appearance on electron micrographs. We propose a model for the structure of SBP in which two monomers assemble head to head with the steroid-binding site located in the center of the rod-like particle.

Physico-chemical characterization of legumin-T from faba bean (Vicia faba L)

Legumin-T, the high-molecular mass product of limited tryptic hydrolysis of faba bean legumin, was investigated using hydrodynamic methods, static light scattering, fluorescence and ultraviolet spectroscopy. The following physico-chemical parameters were determined in a high-ionic strength buffer system: molecular mass, 2.4 x 10(5) g/mol; sedimentation coefficient, SO20 = 10.8 x 10(-13)Si; diffusion coefficient, DO20 = 4.1 x 10(-7) cm2 s-1; intrinsic viscosity, [eta] = 3.51 mL/g; partial specific volume, v = 0.719 mL/g; frictional ratio, f/f0 = 1.22; shape factor, beta = 2.17 x 10(6). Conformational changes during the formation of legumin-T can be deduced from the fluorescence emission and UV spectra.

Capillary electrophoresis of S. nuclease mutants

The electrophoretic migration behavior of 12 S. nuclease variants from Staphylococcus aureus with small but well defined structural differences from site directed mutation was investigated in free solution capillary electrophoresis at pH 2.8 to 9.5. The nucleases are basic proteins; the pI and the M(r) of the wild type are 10.3 and 16.811 kd, respectively. With specially selected oligoamino buffers and with an inert, hydrophilic wall coating in 75 microns I.D. quartz capillary tubes, most of the proteins could be separated by CZE without interference by wall adsorption even at pH 9.5 where the selectivity was the highest. At pH 2.8, 4.1 and 7.0, S. nucleases are known to be in the random coil, "swollen" and the tight native state. Assuming that in a given state, i.e., at a certain pH, the molecular radii of the nucleases are the same, their hydrodynamic radii were calculated from their pertinent electrophoretic mobilities. The respective radii of 50.1, 26.8, and 25.0 Angstrum thus obtained agreed very well with the corresponding radii of gyration obtained from X-ray scattering. In fact, from the electrophoretic mobilities at pH 9.5, the existence of a hitherto unknown swollen basic state of the nuclease having a hydrodynamic radius of 30.5 Angstrum was postulated. In addition, a method was described to evaluate the valence of the protein at different pH from their pertinent electrophoretic mobilities. A general advantage of this method is that only the differences between the valences of the mutants and the wild type are needed; and for none of the proteins is required the knowledge of the actual valence. The results of the methods allowed the construction of a pH profile of the protein's valence. For the wild type, this profile was compared to the H+ titration curve and the agreement was excellent. Both methods employed some novel structure-electrophoretic mobility relationships and the predicted protein properties compared remarkably well to the values obtained by exoelectrophoretic methods such as pH titration and X-ray scattering. Surprisingly, certain S. nucleases having the same valence could also be readily separated by CZE in some cases under the same conditions used for the others. Close examination of appropriate X-ray crystallography and/or NMR data indicated subtle differences in the molecular structure of these proteins that could be responsible for slight alteration in their hydrodynamic radii.(ABSTRACT TRUNCATED AT 400 WORDS)

On the hydrodynamic analysis of macromolecular conformation

Hydrodynamics provides a powerful complementary role to the traditional "high resolution" techniques for the investigation of macromolecular conformation, especially in dilute solution, conditions which are generally inaccessible to other structural techniques. This paper describes the state of art of hydrodynamic representations for macromolecular conformation, in terms of (1) simple but straightforward ellipsoid of revolution modelling; (2) general triaxial ellipsoid modelling; (3) hydrodynamic bead modelling; (4) the ability, especially for polydisperse macromolecular systems, to distinguish between various conformation types; (5) analysis of macromolecular flexibility.

Three-dimensional model and quaternary structure of the human eye lens protein gamma S-crystallin based on beta- and gamma-crystallin X-ray coordinates and ultracentrifugation

A 3-dimensional model of the human eye lens protein gamma S-crystallin has been constructed using comparative modeling approaches encoded in the program COMPOSER on the basis of the 3-dimensional structure of gamma-crystallin and beta-crystallin. The model is biased toward the monomeric gamma B-crystallin, which is more similar in sequence. Bovine gamma S-crystallin was shown to be monomeric by analytical ultracentrifugation without any tendency to form assemblies up to concentrations in the millimolar range. The connecting peptide between domains was therefore built assuming an intramolecular association as in the monomeric gamma-crystallins. Because the linker has 1 extra residue compared with gamma B and beta B2, the conformation of the connecting peptide was constructed by using a fragment from a protein database. gamma S-crystallin differs from gamma B-crystallin mainly in the interface region between domains. The charged residues are generally paired, although in a different way from both beta- and gamma-crystallins, and may contribute to the different roles of these proteins in the lens.

Effect of temperature on the propylamine transferase from Sulfolobus solfataricus, an extreme thermophilic archaebacterium. 1. Conformational behavior of the oligomeric enzyme in solution

The effect of temperature on the molecular structure of propylamine transferase from Sulfolobus solfataricus has been investigated. Sulfolobus solfataricus is an extreme thermophilic archaebacterium with an optimum living condition at 90 degrees C. The enzyme is an oligomeric (trimer) protein of molecular mass 112 kDa. The frictional ratio for the native protein suggests an irregularly shaped compact globular structure. The protein matrix is well organized as suggested by far ultraviolet circular dichroism at 25 degrees C (18% alpha helix, 43% beta structure, 19% beta bends and 20% unordered: root mean square = 7). Structural effects of temperature were investigated over 25-85 degrees C. The protein retains its quaternary structure in this temperature range. A highly reversible subtle conformational transition was detected by numerous structure-dependent techniques over 40-50 degrees C, with a midpoint centered at 45 degrees C. Functional data also support this view. In fact, two enzyme forms, characterized by different catalytic properties, are present in solution. The Arrhenius plot suggests the occurrence of two different activation-energy-dependent processes, one at a temperature higher and one at a temperature lower than 45 degrees C. The transition has been considered as a molecular switch between two protein populations at equilibrium with different functional and structural properties, temperature modulated. A physiological role for the molecular switch has also been postulated. The protein also shows some subtle and reversible spectroscopic changes around 75 degrees C. The molecular basis of the thermophilic nature of this enzyme seems to reside in its capability to dynamically couple catalytic and structural events to the thermal properties of the ambient medium.

Escherichia coli sigma 70 and NusA proteins. II. Physical properties and self-association states

In this paper we examine the physical properties and potential for self-association of the Escherichia coli transcription factors, sigma 70 and NusA. We show, by a combination of chemical crosslinking, equilibrium and velocity sedimentation, quasi-elastic light scattering, and small-angle X-ray scattering that NusA exists as a monomer at KCl concentrations between 0.01 and 1.5 M, and that sigma 70 exists as a monomer at KCl concentrations between 0.1 and 1.5 M. The shape and hydration characteristics of each of these monomeric proteins are also examined. The results serve as background for the companion paper in which a thermodynamic analysis is made of the interactions of these transcription factor with E. coli core RNA polymerase in solution and as a component of the functional transcription complex.

Purification, physicochemical characterization, and immunohistochemical localization of a major 11.7 S glycoprotein from the jelly coats of the anuran Lepidobatrachus laevis

Embryos of the frog Lepidobatrachus laevis are encased by a fertilization envelope and two jelly layers, termed J1 (innermost) and J2 (outermost). From preparations of total jelly solubilized from cleavage-stage embryos by a solution of alkaline beta-mercaptoethanol we have purified one jelly coat glycoprotein to homogeneity via FPLC gel permeation chromatography on Superose 6H. The purified glycoprotein was 94% protein and 6% carbohydrate, had an s0(20),w of 11.7 S, with a molecular weight of 245,000 measured by sedimentation equilibrium and 263,000 by gel permeation chromatography. SDS-PAGE revealed that the glycoprotein is composed of a single subunit near 29,700 molecular weight; thus we propose that eight of these subunits comprise the native molecule. Amino acid analysis of the glycoprotein indicated a high content of Glx + Asx (32.4 mole%), a low content of basic amino acids (Arg + Lys = 12.2 mole%), and a single cysteine residue per subunit. The N-terminal amino acid was threonine and the sequence of the first twenty amino acids was determined. Monospecific antisera to the glycoprotein were prepared in rabbits and were used to immunohistochemically localize the glycoprotein throughout the matrix of both jelly layers. Antiserum against the glycoprotein had virtually no effect on the fertilizability of jellied eggs in vitro; thus we hypothesize that the glycoprotein fulfills a structural role in both jelly layers.

Purification and characterization of scatter factor

Scatter factor is a fibroblast-derived protein which disrupts and scatters epithelial colonies and enhances the local movement of individual epithelial and endothelial cells. The factor purified from mouse fibroblasts by cation-exchange and reverse phase chromatography is a dimer of 57 kD and 30 kD protein subunits (A and B subunits), is active at picomolar concentrations and requires intact intra- and/or inter-chain disulphide bonds for activity. In serum-free conditioned medium the factor is highly aggregated but in the presence of high-salt buffers or protein denaturants elutes from gel filtration columns with an apparent Mr of approximately 50 kD. From a combination of molecular sieving and ultracentrifugation studies, a calculated Mr of 61.4 kD is obtained for native mouse scatter factor, a value which agrees well with the Mr estimates obtained by SDS-PAGE (62-67 kD). Mouse fibroblast scatter factor is a heparin-binding, basic protein (pI 8.5-9.5) which contains N-linked carbohydrates which are not, however, essential for activity. The factor has no metallo- or serine protease activity and there is no evidence so far that its junctional-breaking activity involves proteolytic cleavage of surface molecules on target cells. Scatter factor is either identical or closely related to hepatocyte growth factor/hepatopoietin A (a potent mitogen for rat hepatocytes recently purified from human and rabbit serum and rat platelets). The factor is thus an effector of mesenchymal-epithelial interactions which affects the movement or the growth of different epithelia.

Genetic engineering of EcoRI mutants with altered amino acid residues in the DNA binding site: physicochemical investigations give evidence for an altered monomer/dimer equilibrium for the Gln144Lys145 and Gln144Lys145Lys200 mutants

We have genetically engineered the Arg200----Lys mutant, the Glu144Arg145----GlnLys double mutant, and the Glu144Arg145Arg200----GlnLysLys triple mutant of the EcoRI endonuclease in extension of previously published work on site-directed mutagenesis of the EcoRI endonuclease in which Glu144 had been exchanged for Gln and Arg145 for Lys [Wolfes et al. (1986) Nucleic Acids Res. 14, 9063]. All these mutants carry modifications in the DNA binding site. Mutant EcoRI proteins were purified to homogeneity and characterized by physicochemical techniques. All mutants have a very similar secondary structure composition. However, whereas the Lys200 mutant is not impaired in its capacity to form a dimer, the Gln144Lys145 and Gln144Lys145Lys200 mutants have a very much decreased propensity to form a dimer or tetramer depending on concentration as shown by gel filtration and analytical ultracentrifugation. This finding may explain the results of isoelectric focusing experiments which show that these two mutants have a considerably more basic pI than expected for a protein in which an acidic amino acid was replaced by a neutral one. Furthermore, while wild-type EcoRI and the Lys200 mutant are denatured in an irreversible manner upon heating to 60 degrees C, the thermal denaturation process as shown by circular dichroism spectroscopy is fully reversible with the Gln144Lys145 double mutant and the Gln144Lys145Lys200 triple mutant. All EcoRI endonuclease mutants described here have a residual enzymatic activity with wild-type specificity, since Escherichia coli cells overexpressing the mutant proteins can only survive in the presence of EcoRI methylase. The detailed analysis of the enzymatic activity and specificity of the purified mutant proteins is the subject of the accompanying paper [Alves et al. (1989) Biochemistry (following paper in this issue)].

Dissociation of ferritins

Apoferritins prepared from horse spleen and heart and rat heart and liver were dissociated by treatment with acetic acid (pH 1.3-3.0). Sedimentation velocity studies showed that apoferritins of spleen and liver (16-17 S) and heart (18-19 S) dissociated into material sedimenting near 3.2 S. Sedimentation equilibrium measurements determined that most of the material had a molecular weight of 38,000-43,000, corresponding to subunit dimers. Failure to dissociate into subunit monomers was confirmed by gel chromatography on Sephadex G-75 and G-150. With the exception of boiling in sodium dodecyl sulfate, further treatments with 0.1-0.4 M KCl, NaCl, 4-9 M urea, 0.01-0.5 M KSCN, 0.1-0.5% Triton X-100, 5-52% dimethylsulfoxide, 10% ethylene glycol, or 0.1% trifluoroacetic acid all failed to cause dissociation into individual subunits, as did exposure to 6 M guanidine-HCl or formic acid, or prior succinylation and/or nitration of the protein. Reassociation occurred between pH 4 and 7 but was not aided by the addition of Fe(II) or reducing agents. It is concluded that ferritins readily dissociate to subunit dimer units and that further dissociation does not occur without full denaturation of the protein.

A calcium-insoluble 6.4 S protein derived from sea urchin cortical granule exudate

A major protein component of the sea urchin, Strongylocentrotus purpuratus, cortical granule exudate has been purified and characterized. In the absence of divalent cations, the native, soluble protein has a sedimentation coefficient at infinite dilution of 6.4 S and a molecular weight from sedimentation equilibrium measurements of 2.8 +/- 0.3 X 10(5). These and other data indicate that the protein assumes an elongated, rod-like structure in solution. The protein is greater than 95% homogeneous as judged by agarose- and sodium dodecyl sulfate-gel electrophoresis. In the latter experiments, the protein shows a relative molecular weight of 1.8 X 10(5) and is clearly distinct from the 11.6 S protein described earlier which shows two bands corresponding to 3.2 X 10(5) and 2.1 X 10(5). The 6.4 S protein is the major protein of the calcium-insoluble fraction of cortical granule exudate and contributes to the formation of the extracellular investments of the sea urchin embryo. Using a light-scattering assay, we show that the purified protein retains the ability to aggregate in the presence of divalent cations mirroring its assembly in vivo. Calcium ion alone is able to initiate this reaction and the rate of precipitation increases with calcium concentration. Magnesium alone is ineffective in this regard but, in combination, the two ions act synergistically. Strontium and barium can substitute for calcium, but higher concentrations of the former cations are required to produce an equivalent effect.

Isolation and partial characterization of rhizolysin, a high molecular weight protein with hemolytic activity, from the jellyfish Rhizostoma pulmo

A new cytolysin has been isolated from the nematocysts of the jellyfish, Rhizostoma pulmo, and named rhizolysin. The hemolysin has a mol. wt of approximately 260,000, a sedimentation coefficient of 10.3 S and is rod-shaped with a calculated axial ratio of about 1:5. It appears to be composed of three subunits with a pI value near 7.8. Rhizolysin shows no phospholipase A activity, nor an induction period for its hemolytic activity and is completely inhibited by sucrose. The optimum pH was 6.75. The mu value calculated from the Arrhenius plot is 5940 cal/mole. Rhizolysin was inhibited by cholesterol and less by sphingomyelin.