Structure of Material Proteins

Until recently, research work on the structure, properties and applications of proteins were mainly considered within the scientific field of Food Science. To reach a better understanding of properties and to define the potential applications of material proteins, it is essential to compare their structural features with those of chemically synthesised organic polymers used to produce plastic materials. Novel research on nonfood uses of agricultural resources, and especially on material proteins , has led to the application of Polymer Science concepts and tools to investigate the structure-function relationships of these macromolecular organisations. This involves  

Proteins (except homopolymers or copolymers in which one or two monomers are repeated) are heteropolymers comprising more than 20 different amino acids, each 

Amino acid Relative hydrophobocity Polarity Aminoacid Relative hydrophobocity Polarity 

Adapted from J. A. Koihias, Journal of Agricultural and Food Chemistry, 1996,44,10,3143 [10]  

The molecular diversity means that proteins have considerable potential for the formation of various interactions and links that differ according to their position, nature and/or energy [11,12]. This heterogeneous structure provides many reaction sites for potential crosslinking or chemical grafting - it even facilitates modification of the film-forming properties and end-product properties. The amino acid sequence formed by peptide bonds is called the primary structure. 

In organic polymers, macromolecules can form regular crystal network type arrangements. These arrangements have a marked effect on the properties of polymers, especially their mechanical strength. For proteins, a-helix or (3-sheet secondary structures are highly 

Proteins Nomenclature of main subunits Molecular Weight (kDa) Ref 

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Proteases are used in many industrial areas as well as basic research. They are classified by their mechanism of catalysis. Proteases are used in the pharmacological, food and other consumer industries to convert raw materials into a final product or to alter properties of the raw material. In biomedical research, proteases are used to study the structure of other proteins and for nthesis of peptides. The choice of a protease for an application depends in part on its specificity for peptide bonds, activity and stability. Technical advances in protein engineering have enabled alteration of these properties and allowed proteases to be used more effectively. Some easily obtained proteases can be modified so that they can substitute for proteases whose supply is limited. 

Linus Pauling, in 1954, received the Nobel Prize for his insights into the structure of materials, mainly proteins. Pauling showed that only certain conformations are preferred because of intermolecular and intramolecular hydrogen bonding. While we know much about the structures of natural macromolecules, there is still much to be discovered. 

Semisynthesis can be defined as the use of fragments of proteins, or intact proteins themselves, as ready-made intermediates in the chemical synthesis of proteins. Many modifications to the native structure of a protein can be expected to have profound effects, and produce materials of the greatest academic or practical value, but only involve a change of one or a few atoms out of the thousands that often go to make up the complete molecule. If a semisynthetic method can be found to incorporate, at the correct site, a small synthetic fragment carrying the wanted change, there is no need to go to the trouble of constructing the rest of the molecule when it has already been preformed for us biosynthetically. 

A typical molecular analysis of various micro-organisms is shown in Table 5.9U ) Most of the elemental composition of cells is found in three basic types of materials—proteins, nucleic acids and lipids. In Table 5.10, the molecular composi-tion of a bacterium is shown in more detail. Water is the major component of the cell and accounts for 80-90 per cent of the total weight, whilst proteins form the next most abundant group of materials and these have both structural and functional properties. Most of the protein present will be in the form of enzymes. Nucleic acids are found in various forms—ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Their primary function is the storage, transmission and... 

The peptide linkages between amino acids form the primary structure of the protein. The primary structure is all that the nucleotide sequence of the genetic material determines, and therefore the primary structure contains all information necessary to specify the complete three-dimensional conformation. 

Crystals of the material are grown, and isomorphous derivatives are prepared. (The derivatives differ from the parent structure by the addition of a small number of heavy atoms at fixed positions in each — or at least most — unit cells. The size and shape of the unit cells of the parent crystal and the derivatives must be the same, and the derivatization must not appreciably disturb the structure of the protein.) The relationship between the X-ray diffraction patterns of the native crystal and its derivatives provides information used to solve the phase problem. 

Hydration of biopolymers is a mechanism for stabilizing these materials (Fig. 2.78). When proteins are conpletely dry, they tend to decompose. One way of evaluating hydration in polyions is to measure the dielectric constant of a solution containing a dissolved protein as a function of concentration at radio frequency. The dielectric constant falls with increase in concentration and the water per polyion can be calculated by assuming that water bound to the protein no longer makes any contribution to the dielectric constant. Thus, Buchanan calculated the irrotationally bound water from such expaiments. Some of this water is hidden in cavities within the structure of the protein molecule. 

The recent discovery of a large number of different proteolytic enzymes capable of degrading elastin has provided a very valuable tool for the study of the structure of the protein, and by means of controlled degradation—coupled with modem techniques for the examination of the split products—it should be well within the present compass to obtain an unambiguous representation of this unique material. Such a project, if successfully concluded, would form a firm basis for many urgent investigations in the study of connective tissue diseases, in leather chemistry, and food science. 

Matsui et al. [235,236] have recently used zeolites with a higher Si/Al ratio (i.e., Na-BEA) for the purification of nucleic acids and proteins due to the electrostatic and hydrophobic interactions between biopolymers and zeolites. In addition, the activity and structure of the proteins are preserved even under denaturing conditions, thus emerging as promising materials for biochemical and biotechnological applications. 

The role of proteins as enzymes in controlling a cellular activity was known much before its structure was elucidated. The conceptual breakthrough in deciphering the structure of a protein as a linear array of amino acids came from the enunciation of the one-gene enzyme concept. This conceptual breakthrough was materialized by certain technical advances. The technical advances included the development of machines for the analysis of the amino acid composition and for the determination of the sequence of the amino acids in a protein. With the help of these machines, the structure of proteins was elucidated one protein at a time for several years. Later,... 

To determine these complicated structures the only general method available is X-ray diffraction of the single crystals of these materials. Although the structure of small proteins (molecular weight (MW) less than about 10000 daltons (D)) can be determined in solution with nuclear magnetic resonance (NMR) spectroscopy and the assembly of proteins in a complex can be studied with electron microscopy, only X-ray diffraction can give the three-dimensional structure of small as well as large proteins with a precision of about 0.1-0.2 A. 

For spectroscopic determinations of the amounts of protein material it should be noted that SOD absorbs, in the UV region, with a maximum at 265 nm. Different extinction coefficients were found for various isoenzymes, as a consequence of the different primary sequence. For example, Emax is 15,900 M cm, for the human enzyme, and 10,300 Af cm for the bovine enzyme (2, 103). In the visible region of the electronic spectrum the holoenzyme has an absorption maximum at 680 nm [e = 300 M cm (2)]. The CU2E2 enz5nme has a typical absorption with A ,ax at 700 nm, at pH 6 (183). The two metal binding sites in SOD are largely determined by the tertiary structure of the protein, so that a number of M2N2SOD derivatives can be prepared (Fig. 25) with coordination properties similar to those seen for Cul Zn SOD and Cu Zn SOD. 

Connective tissue, which consists primarily of fibroblasts, produces extracellular matrix materials that surround cells and tissues, determining their appropriate position within the organ (see Chapter 49). These materials include structural proteins (collagen and elastin), adhesive proteins (fibronectin), and glycosaminoglycans (heparan sulfate, chondroitin sulfate). The unique structures of the proteins and carbohydrates found within the extracellular matrix allow tissues and organs to carry out their many functions. A loss of these supportive and barrier functions of connective tissue sometimes leads to significant clinical consequences, such as those that result from the microvascular alterations that lead to blindness or renal failure, or peripheral neuropathies in patients with diabetes mellitus. 

Plasma proteins are adsorbed to the surfaces of carbon, polystyrene, and a series of polyetherurethanes of increasing surface energy from both a static and a flowing milieu. The conformations of the individual protein molecules and the structure of the protein films formed are studied by electron microscopy. The conformation of individual protein molecules and the structure of the adsorbed films are found to be dependent upon the surfaces to which they are adsorbed, and the flow conditions under which the protein solutions contact the materials. 

Sequencing monomer distributions, determining the composition of copolymers, and relating them to material properties is one of the most common demands posed to polymer analysts. The concept of copolymer sequence may have a double meaning. In fact, in proteins, nucleic acids, and other biopolymers, the comonomer units are aligned into a well-determined sequence that is constant for each copolymer chain contained in a specific material. The sequence of amino acids in a protein is invariant, and it is usually called the "primary" structure of the protein. 

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