Globular protein

Proteins can be divided into two large groups on the basis of conformation (a) fibrillar (fibrous) or scleroproteins, and (b) folded or globular proteins. 

The entire peptide chain is packed or arranged within a single regular structure for a variety of fibrous proteins. Examples are wool keratin (a-helix), silk fibroin (P-sheet structure) and collagen (a triple hehx). Stabilization of these structures is achieved by intermolecular bonding (electrostatic interaction and disulfide linkages, but primarily hydrogen bonds and hydrophobic interactions). 

Amino acid a-Helix (Pa) Pleated sheet (Pp) P-Turn (Pt) 

Pro and Gly are important building blocks of turns. Arginine does not prefer any of the three structures. By means of such data it is possible to forecast the expected conformations for a given amino acid sequence. 

Folding of the peptide chain packs it densely by formation of a large number of intermolecu-lar noncovalent bonds. Data on the nature of the bonds involved are provided in Table 1.25. 

For other, larger proteins, the release was very slow - in 100 hours no more than 5% of loaded catalyse, urease, glucose oxidase or hemoglobin were released. 

Soluble proteins have a more complex structure than the fibrous, completely insoluble structural proteins. The shape of soluble proteins is more or less spherical (globular). In their biologically active form, globular proteins have a defined spatial structure (the native conformation). If this structure is destroyed (denaturation see p. 74), not only does the biological effect disappear, but the protein also usually precipitates in insoluble form. This happens, for example, when eggs are boiled the proteins dissolved in the egg white are denatured by the heat and produce the solid egg white. 

To illustrate protein conformations in a clear (but extremely simplified) way, Richardson diagrams are often used. In these diagrams, a-helices are symbolized by red cylinders or spirals and strands of pleated sheets by green arrows. Less structured areas of the chain, including the p-turns, are shown as sections of gray tubing. 

The native conformation of proteins is stabilized by a number of different interactions. Among these, only the disulfide bonds (B) represent covalent bonds. Hydrogen bonds, which can form inside secondary structures, as well as between more distant residues, are involved in all proteins (see p. 6). Many proteins are also stabilized by complex formation with metal ions (see pp. 76, 342, and 378, for example). The hydrophobic effect is particularly important for protein stability. In globular proteins, most hydrophobic amino acid residues are arranged in the interior of the structure in the native conformation, while the polar amino acids are mainly found on the surface (see pp. 28, 76). 

Disulfide bonds arise when the SH groups of two cysteine residues are covalently linked as a dithiol by oxidation. Bonds of this type are only found (with a few exceptions) in extracellular proteins, because in the interior of the cell glutathione (see p.284) and other reducing compounds are present in such high concentrations that disulfides would be reduc- 

Koolman, Color Atlas of Biochemistry, 2nd edition 2005 Thieme All rights reserved. Usage subject to terms and conditions of license. 

The amide I band has been examined by Elliott et al. (1950) in native and denatured insulin, by Elliott et al. (1957) in lysozyme, and by Ambrose et al. (1951) in water-soluble silk. The band at 3200 cm has also been investigated. Beer et al. (1959) have given a comprehensive list of proteins studied up to 1959, along with characteristic absorption bands. Bamford et al. (1956) have reviewed work done up to 1956 in the region between 5000 and 4500 cm (combination band of the N—H stretching frequency and that of the amide I or amide II band). The infrared dichroic properties of crystals of hemoglobin and ribonuclease have been observed in this region (Elliott and Ambrose, 1951 Elliott, 1952). 

Myoglobin in DjO at pD 6.6 (corrected to 7.0) has an amide I band at 1650 cm, characteristic of a-helical structure. Myoglobin is known to have at least 77% a-helical structure (Kendrew et al., 1960). Timasheff and Susi s (1966) data indicate that in DjO solution the )S-conformation and the a-helical conformation produce amide I bands at the same frequencies as in dry films. Randomly folded proteins (a -casein and denatured ) -lactoglobulin) give rise to a sharp band centering at 1643 cm 

Slow hydrogen-deuterium exchange (see Chapter 11) of native -lactoglobulin in DjO, pD 1.0 (corrected to 1.4) allowed the amide II band ( 1550 cm ) to remain and be seen in one sample of the lactoglobulin (Fig. 10.18, top curve) which was run immediately after preparation. The presence of this band shows that the native protein must be quite compact. No such bands are observed in denatured lactoglobulin or in a -casein, which have loose randomly folded structures. 

The spectra of other genetic variants, )S-lactoglobulins B and C, were also found by TimashdT and Susi (1966) to be identical with the data for lactoglobulin A, suggesting very similar secondary structures. 

Synthetic Polypeptides and Nontransferability of Conformation Frequencies to Corresponding Conformations of Globular Proteins 

But this is only part of the story. Since the early 1950 s protein structures have been studied by X-iay dJfiraction in many laboratories throughout the world. Protein crystallography has come of age. Almost forty independent high-resolution (3.5 A or better) structure analyses have now been successfully elucidated. The principal references for this impressive list are given in Table 1. 

A very wide variety of globular proteins has proved amenable to crystallization and A -ray analysis. The earlier successful analyses concerned stable 

Subtilisins BPN and Novo 15, 51 High potential iron protein 95 

Recently, a number of proteins including cytochromes, ferrodoxin, and flavodoxin, which are involved in electron-transfer reactions, have been 

The range in size and function of the proteins studied by A -ray techniques means that protein crystallography is beginning to play an important role in extending our understanding of most biological systems. 

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The behaviour of tliese systems is similar to tliat of suspensions in which short-range attractions are induced by changing solvent quality for sterically stabilized particles (e.g. [103]). Anotlier case in which narrow attractions arise is tliat of solutions of globular proteins. These crystallize only in a narrow range of concentrations [104]. 

Baker E N and Flubbard R E 1984 Hydrogen bonding in globular proteins Prog. Biophys. Molec. Biol. 44 97-179... 

Flaynes C A and Norde W 1994 Globular proteins at solld/llquid Interfaces Colloids Surf. B 2 517-66... 

Fig. 2. Correlation between predicted and experimental pKaS in 4 globular proteins...

Water-soluble globular proteins usually have an interior composed almost entirely of non polar, hydrophobic amino acids such as phenylalanine, tryptophan, valine and leucine witl polar and charged amino acids such as lysine and arginine located on the surface of thi molecule. This packing of hydrophobic residues is a consequence of the hydrophobic effeci which is the most important factor that contributes to protein stability. The molecula basis for the hydrophobic effect continues to be the subject of some debate but is general considered to be entropic in origin. Moreover, it is the entropy change of the solvent that i... 

Cohen F E, M J E Sternberg and W R Taylor 1982 Analysis and Prediction of the Paclung oi. i-E a iinst a /3-Sheet in the Tertiary Structure of Globular Proteins. Journal of AdoljcuLir E 156 821-862. 

Gamier J, D Osguthorpe and B Robson 1978. Analysis of the Accuracy and ImpUcatiotrs of Simple Mel for Predicting the Secondary Structure of Globular Proteins. Journal of Mokadar Biology 120 97-i... 

Nlng Q and T J Sejnowsld 1988. Predicting the Secondary Structure of Globular Proteins Using Neural Network Models. Journal of Molecular Biology 202 865-888. 

M J1990. Calculation of Conformational Ensembles from Potentials of Mean Force. An Approach o the Knowledge-Based Prediction of Local Structures in Globular Proteins. Journal of Molecular Siology 213 859-883. 

Many globular proteins are enzymes They accelerate the rates of chemical reactions m biological systems but the kinds of reactions that take place are the fundamental reactions of organic chemistry One way m which enzymes accelerate these reactions is by bringing reactive func tions together m the presence of catalytically active functions of the protein... 

Globular protein (Section 27 20) An approximately spheri cally shaped protein that forms a colloidal dispersion in water Most enzymes are globular proteins Glycogen (Section 25 15) A polysaccharide present in animals that IS denved from glucose Similar in structure to amy lopectin... 

Dill, KA. Theory for the folding and stability of globular proteins. Biochemistry 24 1501-1509, 1985. 

Hydrogen bonding stabilizes some protein molecules in helical forms, and disulfide cross-links stabilize some protein molecules in globular forms. We shall consider helical structures in Sec. 1.11 and shall learn more about ellipsoidal globular proteins in the chapters concerned with the solution properties of polymers, especially Chap. 9. Both secondary and tertiary levels of structure are also influenced by the distribution of polar and nonpolar amino acid molecules relative to the aqueous environment of the protein molecules. Nonpolar amino acids are designated in Table 1.3. 

Equation (8.97) shows that the second virial coefficient is a measure of the excluded volume of the solute according to the model we have considered. From the assumption that solute molecules come into surface contact in defining the excluded volume, it is apparent that this concept is easier to apply to, say, compact protein molecules in which hydrogen bonding and disulfide bridges maintain the tertiary structure (see Sec. 1.4) than to random coils. We shall return to the latter presently, but for now let us consider the application of Eq. (8.97) to a globular protein. This is the objective of the following example. 

Fig. 10. Selectivity curves A—D for Sephadex G-75, G-lOO, G-150, and G-200, respectively, for globular proteins.

The Stokes-Einstein equation has already been presented. It was noted that its vahdity was restricted to large solutes, such as spherical macromolecules and particles in a continuum solvent. The equation has also been found to predict accurately the diffusion coefficient of spherical latex particles and globular proteins. Corrections to Stokes-Einstein for molecules approximating spheroids is given by Tanford. Since solute-solute interactions are ignored in this theory, it applies in the dilute range only. 

Direct experiment-simulation quasielastic neutron scattering comparisons have been perfonned for a variety of small molecule and polymeric systems, as described in detail in Refs. 4 and 18-21. The combination of simulation and neutron scattering in the analysis of internal motions in globular proteins was reviewed in 1991 [3] and 1997 [4]. 

MI Sippl. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures m globular proteins. I Mol Biol 213 859-883, 1990. 

M Vasquez. Modeling side-chain conformation. Curr Opm Stiaict Biol 6 217-221, 1996. JM Thornton. Disulphide bridges m globular proteins. J Mol Biol 151 261-287, 1981. 

FI Schrauber, F Eisenhaber, P Argos. Rotamers To be or not to be An analysis of ammo acid side-chain conformations m globular proteins. J Mol Biol 230 592-612, 1993. 

MJ McGregor, SA Islam, MJE Sternberg. Analysis of the relationship between side-chain conformation and secondary structure m globular proteins. J Mol Biol 198 295-310, 1987. 

J Skolmck, A Kolinski. Simulations of the folding of a globular protein. Science 250 1121-1125, 1990. 

C Mumenthaler, W Braun. Pi edictmg the helix packing of globular proteins by self-coirecting distance geometry. Protein Sci 4 863-871, 1995. 

N Qian, TJ Sejnowski. Predicting the secondary structure of globular proteins using neural network models. J Mol Biol 202 865-884, 1988. 

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