Globular Protein Molecules Research Articles

Building models of globular protein molecules from their amino acid sequences: I. Theory

Proteins are polyelectrolytes, and their tertiary structures can be made compact only if their ionized residues are placed on the surface. This paper begins with a description of the electrostatic restoring forces responsible for this spatial distribution of ionized residues in proteins, and it discusses some consequences of strong restoring forces for the tertiary structure. The electrostatic forces display behaviour usually attributed only to hydrophobic interactions. However, unlike other noncovalent interactions, these restoring forces depend on the positions of amino acid residues within the globular molecule. Electrostatic interactions appear to have a major influence on the low-resolution features of protein tertiary structure.

Mechanical properties of globular proteins gels: 1. Incipient gelation behaviour

It has long been known that globular protein molecules in concentrated aqueous solution can be converted into a different form by heating or use of denaturing agents. Under certain conditions of pH and ionic strength, elastic gels are formed. This work describes kinetic measurements of viscosity and elasticity close to the gel point (sol-gel transition) in bovine serum albumin solutions. These studies and optical rotation measurements near the gel point lend support to the conclusions of earlier structural studies on this system, that the gel is fibrillar in nature.

Fine structure of the gap junction in the tunicate heart.

The plasma membranes of the tunicate heart exhibit an abundance of macular gap junctions distributed widely over the membrane surface. A study of these junctions by the freeze-etch technique was undertaken in an effort to elucidate the fine structure of this important membrane modification in a primitive heart. In cross or near-cross fractured junctions the junctional particles in contiguous membranes appear to be paired in register and to meet in the midline. In favorable face views, the junctional particles are seen to be disposed in hexagonal array. The individual particles display a distinct rosette-like substructure consistent with a six-membered ring of globular protein molecules clustered around a central channel. Similar junctional-type particles can be found in nonjunctional areas of membrane suggesting that the transport mechanism which they may represent is not restricted to the gap junction.

Orientation distribution of globular protein molecules in a two-dimensional lattice: II. Thermal effect

The effect of the thermal fluctuation on the orientation distribution pattern of globular protein molecules in a two-dimensional lattice was investigated by the method of computer simulation. A set of interaction parameters was assigned to interaction sites on each molecule and the interaction energy between two molecules was given by the product of the parameters of facing sites. Orientation fluctuation was assumed to take place with the probability proportional to the Boltzmann factor. Patterns having different degrees of order appeared with the change of temperature. The entropy and other thermodynamic quantities of these patterns were calculated, and gradual and transitional changes of the pattern were discussed in comparison with the case of simple atoms or molecules.

Orientation distribution of globular protein molecules in a two-dimensional lattice: II. Thermal effect

Orientation distribution of globular protein molecules in a two-dimensional lattice: II. Thermal effect

Two cis-prolines in the Bence-Jones protein Rei and the cis-pro-bend

FEBS LettersVolume 48, Issue 2 p. 235-237 Full-length articleFree Access Two cis-prolines in the Bence-Jones protein Rei and the cis-pro-bend Robert Huber, Robert Huber Max-Planck-Institut für Biochemie und Physikalisch-Chemisches Institut der Technischen Universität, 8033 Martinsried bei München, GermanySearch for more papers by this authorWolfgang Steigemann, Wolfgang Steigemann Max-Planck-Institut für Biochemie und Physikalisch-Chemisches Institut der Technischen Universität, 8033 Martinsried bei München, GermanySearch for more papers by this author Robert Huber, Robert Huber Max-Planck-Institut für Biochemie und Physikalisch-Chemisches Institut der Technischen Universität, 8033 Martinsried bei München, GermanySearch for more papers by this authorWolfgang Steigemann, Wolfgang Steigemann Max-Planck-Institut für Biochemie und Physikalisch-Chemisches Institut der Technischen Universität, 8033 Martinsried bei München, GermanySearch for more papers by this author First published: November 15, 1974 https://doi.org/10.1016/0014-5793(74)80475-8Citations: 60AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article.Citing Literature Volume48, Issue2November 15, 1974Pages 235-237 ReferencesRelatedInformation

The Structure of a Lipid-Cytochrome c Membrane

In the preceding paper a theory has been developed for the X-ray diffraction pattern from a lipid bilayer coated with protein molecules. In this paper the validity of the theory is tested. After adding cytochrome c to a preparation of lipid vesicles both vesicles and, in lesser amount, a multilayered structure are found. The expected cross-interference ripple is evident, and a computed profile shows the added protein at the surface of an unchanged lipid bilayer. The results confirm the structure proposed by others on the basis of rather indirect chemical and X-ray data. Protein coating a lipid bilayer is a possible structure for natural membranes. These results demonstrate that globular protein molecules can be detected at the surfaces of a lipid bilayer.

Orientation distribution of globular protein molecules in a two-dimensional lattice: Computer simulation

In order to see the relationship between the monomer structure and the polymer structure of protein, stable patterns of the orientation distribution of globular molecules in a two-dimensional lattice were investigated by a computer. A set of interaction parameters was given to interaction sites distributed on the surface of the molecule and the energy was assumed to be given by the sum of products of parameters belonging to the facing sites of neighbouring molecules. Patterns having different degrees of order were obtained under various sets of interaction parameters. The response of the pattern to the environmental condition was also simulated and the gradual and transitional changes of the pattern were found.

Restrictions of sequence on the thickness of globular protein molecules.

A model for globular protein molecules based on a linear and random sequence of polar and nonpolar amino acids was developed. Polar amino acids were assumed to be always in contact with the aqueous solvent, while nonpolar amino acids were assumed to have a tendency to be buried. Considerations of amino-acid dimensions indicated that only runs of four or more nonpolar amino acids in a row could allow some amino acids to be more than 1-nm (10-A) removed from the surface of the protein. The expected volume fraction of a protein molecule that could be more than 1-nm removed from the surface was obtained with the assumption of a random sequence. Calculation of this volume fraction for a number of simple geometric shapes indicated that some nonpolar amino acids must be exposed to solvent and that the maximum average thickness of globular proteins should be 3-4 nm. Good agreement with published protein dimensions was obtained.

Biological membrane structure. II. A detailed model for the retinal rod outer segment membrane.

A model, based on the available chemical, electron microscopic, and x-ray diffraction data, has been developed for the structure of the retinal rod outer segment membranes. The model consists of a double layer of globular protein molecules, with lipid bilayer filling the spaces between the proteins. The electron density across the membrane has been calculated and shown to be in agreement with that found by x-ray diffraction. The protein molecules "float" half submerged in a lipid field; this serves to orient them in the same way at all times relative to incident radiation in the intact retina.

Size distribution of protein polymers

Theoretical analyses were made on the size distribution of tubular or helical polymers of globular protein molecules in the reversible polymerization. In the true final equilibrium, polymerization approximates to a kind of crystallization and the average degree of polymerization becomes very large; nevertheless, the size distribution is of a simple exponential type, the same as found in macromolecular chemistry ( Flory, 1953). Even when spontaneous nucleation is inhibited and the number of polymers is given, the final distribution must tend towards the exponential type. Free energy due to deviation of the size distribution from the true equilibrium was calculated. It is very much smaller than the main free energy coming from the monomer-polymer equilibrium. Kinetics showed that polymerization having characteristics of crystallization usually consists of three stages—nucleation, growth and redistribution of polymer size. In the first and second stages where the rate of depolymerization is negligible, the concentration of monomers approaches closely to the equilibrium value. In the third stage, where both polymerization and depolymerization take place nearly at the same rate, the size distribution is slowly transformed into the exponential type. The relaxation time for such redistribution was estimated as a function of rate constants and the average degree of polymerization under various conditions. All of the theoretical results are quantitatively in good agreement with experimental data on polymerization of globular proteins such as actin and flagellin. Brief analyses were added on the size distribution of two-dimensional membraneous polymers and distorted polymers.

Planar liquid-like arrangement of photopigment molecules in frog retinal receptor disk membranes

Low-angle X-ray diffraction arising from 40 to 50 Å particles within wet frog retinal receptor disk membranes at 26 °C was not consistent with a planar crystalline lattice of the particles within the disk membranes. The nature of the diffraction suggested the possibility of a planar liquid-like arrangement of the particles. Such an arrangement is supported by the observation that the planar ordering of the particles is easily altered by their interaction with globular protein molecules non-specifically adsorbed to the disk membranes. In view of the above, we obtained diffraction patterns from our wet disk membrane preparations at several temperatures between 4.5 and 42.5 °C, and applied a Fourier analysis to the diffracted intensities appropriate for a planar liquid-like arrangement of the 40 to 50 Å particles. The analysis gave the planar radial distribution function description of the supposed planar liquid-like arrangement of the particles. These radial distribution functions, derived from the diffracted intensities, were examined in terms of their shape and variation with temperature, and compared with the known predictions from statistical mechanics for a liquidlike arrangement of particles whose pair potential contains both attractive and repulsive terms. This comparison for the derived radial distribution functions demonstrated that the observed diffraction data from the 40 to 50 Å particles were indeed consistent with a planar liquid-like arrangement of these particles within the disk membrane. Our radial distribution function analysis allowed model scattering factors for the particles to be tested. It was found that only hard sphere cross-sectional electron densities for the particle with diameters of 40 to 44 Å or reasonably hard, soft-sphere cross-sectional electron densities, with a core of uniform electron density 38 to 40 Å in diameter and a total diameter of 44 to 46 Å, gave good agreement. A similar analysis was applied to the diffracted intensities arising from the antirhodopsin molecules adsorbed to the wet disk membranes which had been treated with our antirhodopsin serum and is discussed relative to the preceding paper (Blasie, Worthington & Dewey, 1969). A comparison of the radial distribution functions for the antirhodopsin molecules adsorbed to the antirhodopsin serum treated disk membranes and the 40 to 50 Å particles of the untreated disk membranes at identical temperatures showed the particles to be the photopigment molecules. The mathematical derivation of the planar radial distribution function and a critical evaluation of the errors involved are presented in the Appendices.

Effect of modifications in conformation of protein molecules on structure of mitochondrial membranes

New methods for preparing tissues for electron microscopy were worked out with the aim of limiting as far as possible conformational changes in the protein molecules. The proteins were stabilized by intermolecular cross-linking with glutaraldehyde, dehydrated by short treatment with ethylene glycol, and embedded in Vestopal W or in hydroxypropylmethacrylate. Such treatment appeared to affect the native conformation of proteins less than dehydration by means of air drying with or without previous cross-linking. The mitochondrial membrane elements showed a particulate structure with a range of dimensions of the particles which closely corresponds to that of membrane proteins as judged from their molecular weights. A rectangularly shaped particle measuring 60 × 100 A was frequently observed in the mitochondrial membranes. Intentional denaturation of the tissue by heat or low pH resulted in a membrane structure similar to that observed in conventionally prepared tissues. The results conform with the concept that cellular membranes consist of a two-dimensional array of globular protein molecules and lipoprotein complexes. A continuous light layer of uniform thickness which characterizes the unit membrane structure and which has been interpreted as consisting of a continuous lipid bilayer could be observed only after extensive denaturation of the membrane proteins. The triple-layered unit membrane pattern of membranes, therefore, appears to be the result of extensive denaturation of membrane proteins.

Evidence for order in the structure of alpha-elastin.

THE structure of elastin, the insoluble constituent protein of elastic fibres occurring in the intercellular spaces of connective tissues, has been investigated and different models have been proposed. While a fibril structure is supported by electron microscope results1–3, the rubber-like properties of the water swollen elastin have been interpreted as evidence for a cross-linked network of randomly coiled chains4–6. According to Partridge7,8, elastin should be composed of globular protein molecules arranged in a tetrahedral packing, but Ramachandran9,10 has suggested a collagen-like triple helical structure on the basis of X-ray analysis and of amino-acid composition.

Physicochemical properties of S-zone and base proteins in gluten.

Some of the physicochemical properties (solubility, viscosity, sedimentation) and the amino acid composition of the isolated S-zone and base proteins from soft-wheat gluten were studied. The S-zone proteins are homogeneous in size, of low molecular weight (about 20,000), and high intrinsic viscosity in buffer of pH 3,5, having stable structures whose unique solubility properties are related to their atypical amino acid content. The base protein molecules exist in a more folded conformation, having the properties of globular protein molecules. The protein–protein interactions, aggregation, and unfolding conformation of S-zone proteins are major contributing factors at neutral pH to the rheological properties of wheat flour, such as viscosity, elasticity, and cohesiveness.

Globular protein molecules: their structure and dynamic propertiesby J. Segal, K. Dornberger-Schiff and A. Kalaidjiev

<i>Globular protein molecules: their structure and dynamic properties</i>by J. Segal, K. Dornberger-Schiff and A. Kalaidjiev

Globular Protein Molecules: their Structure and Dynamic Properties by J. Segal, K. Dornberger-Schiff and A. Kalaidjiev

Globular Protein Molecules: their Structure and Dynamic Properties by J. Segal, K. Dornberger-Schiff and A. Kalaidjiev

Measurement of globular protein molecules by electron microscopy.

A series of molecular species with approximately spherical shape and with molecular weights between 35,000 and 250,000 were shadowed with platinum while resting on a cleaved mica surface. They were backed, stripped from the surface, and examined by electron microscopy. Materials examined were: pepsin, liver alcohol dehydrogenase, yeast alcohol dehydrogenase, glutamic dehydrogenase, polyhedral virus protein (insect), fibrinogen substructure, alkaline phosphatase, and microsomal particles from Escherichia coli. Measurements were made of widths perpendicular to the shadowing direction and heights were deduced from shadow lengths. For those molecular species with well established molecular weights the average heights correlate very well with the diameter of the theoretical sphere but the average widths are too great by 50 to 80 A due to the lateral growth of the deposited metal. Although the distortion in shape of shadowed particles is relatively large, with standardized conditions for shadowing, it is possible to make allowance for the distortion and to obtain reasonably reliable estimates of the dimensions of spherical organic particles down to a molecular weight of about 35,000.

The charge and deformation of protein molecules

AbstractThe density of like‐charged groups distributed along the molecules of proteins is much lower than in molecules of polyelectrolytes. From this it follows that the degree of deformation of the protein molecules resulting from the charge is much less. In buffered solutions—if the correction for hydration (measured by the compressibility method) is taken into account—the shape of gelatin particles (as measured by viscosity) practically does not depend on the pH, while in unbuffered solutions it varies roughly in proportion to the fourth to fifth root of the number of charges. For molecules of serum albumin and egg albumin the deformation is proportional to the 25th to 30th root of the number of charges, i.e., completely negligible. This comparison also shows that the deformation of the threadlike molecules of gelatin occurs much more easily than with the firmly molecules of the globular proteins. For globular proteins the following expression has been derived where E is the modulus of elasticity, n the number of charges inthe molecule, m the relative elongation of the molecule, a0, b0, and S the semi‐axes and surface of the ellipsoidal molecule and κ the reciprocal thickness of the ionic atmosphere. A value of E = 10–40 kg./mm.2 was calculated according to this relation for the molecules of these globular proteins (for soft rubber E = 0.14 kg./mm.2, for polyamides 70–80 kg./mm.2, for ebonite 50–80 kg./mm.2, etc.). These results for the first time quantitatively characterize the high rigidity of the molecules of globular proteins.

The thicknesses of hemoglobin and bovine serum albumin molecules as unimolecular layers adsorbed onto films of barium stearate.

The following work, which describes a method of measuring one dimension of some protein molecules, is based on the determination of the apparent thickness of a unimolecular layer of globular protein molecules adsorbed from solution onto a metallic slide covered with an optical gauge of barium stearate. Langmuir [1, 2] and Rothen [3] have published a few results obtained by such a technique, but have not exploited the method thoroughly. A complete set of experimental data has been obtained by Clowes [4] on insulin and protamine. He studied the effects of pH and time of exposure on the thickness of layers of protamine and insulin adsorbed onto slides covered with barium stearate and conditioned with uranyl acetate. He found that the pH was responsible for large variations in the thickness of the adsorbed layers and that the thickness of insulin layers adsorbed onto a protamine base was dependent on the concentration of the insulin. Since Clowes found thicknesses as high as 100 A. for protamine and 400 A. for insulin, he was without doubt usually dealing with multilayers.