Proteins versatility

Rzepecki, L.M. and Waite, J.H. (1991) DOPA proteins versatile varnishes and adhesives from marine fauna, in Bioorganic Marine Chemistry, vol. 4 (ed. P.J. Scheuer), Springer-Verlag, Berlin, Heidelberg, pp. 119-148. 

Controllcd-Currcnt Coulomctry The use of a mediator makes controlled-current coulometry a more versatile analytical method than controlled-potential coulome-try. For example, the direct oxidation or reduction of a protein at the working electrode in controlled-potential coulometry is difficult if the protein s active redox site lies deep within its structure. The controlled-current coulometric analysis of the protein is made possible, however, by coupling its oxidation or reduction to a mediator that is reduced or oxidized at the working electrode. Controlled-current coulometric methods have been developed for many of the same analytes that may be determined by conventional redox titrimetry. These methods, several of which are summarized in Table 11.9, also are called coulometric redox titrations. 

Gel-permeation media are extremely versatile and may be used for separation of particles such as vimses (Fig. 11) as well as proteins (34). Separations of proteins and other particles having sizes equivalent to a molecular weight of 40 x 10 are possible using the agar-based Sepharose-type gel. This particular gel has a limited temperature range for operation, however. It melts upon heating to 40°C (34). 

The side chains of the 20 different amino acids listed in Panel 1.1 (pp. 6-7) have very different chemical properties and are utilized for a wide variety of biological functions. However, their chemical versatility is not unlimited, and for some functions metal atoms are more suitable and more efficient. Electron-transfer reactions are an important example. Fortunately the side chains of histidine, cysteine, aspartic acid, and glutamic acid are excellent metal ligands, and a fairly large number of proteins have recruited metal atoms as intrinsic parts of their structures among the frequently used metals are iron, zinc, magnesium, and calcium. Several metallo proteins are discussed in detail in later chapters and it suffices here to mention briefly a few examples of iron and zinc proteins. 

Alpha helices are sufficiently versatile to produce many very different classes of structures. In membrane-bound proteins, the regions inside the membranes are frequently a helices whose surfaces are covered by hydrophobic side chains suitable for the hydrophobic environment inside the membranes. Membrane-bound proteins are described in Chapter 12. Alpha helices are also frequently used to produce structural and motile proteins with various different properties and functions. These can be typical fibrous proteins such as keratin, which is present in skin, hair, and feathers, or parts of the cellular machinery such as fibrinogen or the muscle proteins myosin and dystrophin. These a-helical proteins will be discussed in Chapter 14. 

Proteins are a diverse and abundant class of biomolecules, constituting more than 50% of the dry weight of cells. This diversity and abundance reflect the central role of proteins in virtually all aspects of cell structure and function. An extraordinary diversity of cellular activity is possible only because of the versatility inherent in proteins, each of which is specifically tailored to its biological role. The pattern by which each is tailored resides within the genetic information of cells, encoded in a specific sequence of nucleotide bases in DNA. 

Regulation of enzyme activity is achieved in a variety of ways, ranging from controls over the amount of enzyme protein produced by the cell to more rapid, reversible interactions of the enzyme with metabolic inhibitors and activators. Chapter 15 is devoted to discussions of enzyme regulation. Because most enzymes are proteins, we can anticipate that the functional attributes of enzymes are due to the remarkable versatility found in protein structures. 

The initial discoveries of the extension of the aromatic ring of the ortho-phthalaldehyde (OPA) to a naphthalene-2,3-dicarboxaldehyde (NBA) and the substitution of cyanide (CN ) for 2-ME as the nucleophile have provided the Center with a much more versatile reagent system (5,11), which maintains the sensitivity for primary aliphatic amines and amino acids, and now is known to form fluorescent products with oligopeptides, proteins, and other related analytes that possess a primary amine function (Equation 1). 

Fig. 6. A schematic view of the [3Fe-4S] Emd [4Fe-4S] cores, as versatile structures. The absence of one site leads to the formation of a [3Fe-4S] core. The cubane structure can incorporate different metals (in proteins, M = Fe, Co, Zn, Cd, Ni, Tl, Cs), and S, N, O may be coordinating atoms from hgands (Li). The versatihty csm be extended to higher coordination number at the iron site and a water molecule can even be a ligand, exchangeable with substrate (as in the case of aconitase (,87)). The most characteristic binding motifs are schematically indicated, for different situations proteins accommodating [3Fe-4S], [4Fe-4S], [3Fe-4S] + [4Fe-4S], and [4Fe-4S] -I- [4Fe-4S] clusters. A disulfide bridge may replace a cluster site (see text).

The nanostructured molecular arrangements from DNA developed by Seeman may find applications as biological encapsulation and drug-delivery systems, as artificial multienzymes, or as scaffolds for the self-assembling nanoscale fabrication of technical elements. Moreover, DNA-protein conjugates may be anticipated as versatile building blocks in the fabrication of multifunctional supramolecular devices and also as highly functional-... 

Complex peptide mixmres can now be analyzed without prior purification by tandem mass spectrometry, which employs the equivalent of two mass spectrometers linked in series. The first spectrometer separates individual peptides based upon their differences in mass. By adjusting the field strength of the first magnet, a single peptide can be directed into the second mass spectrometer, where fragments are generated and their masses determined. As the sensitivity and versatility of mass spectrometry continue to increase, it is displacing Edman sequencers for the direct analysis of protein primary strucmre. 

Burkhard P, Stetefeld J, Strelkov SV Coiled coils A highly versatile protein folding motif. Trends Cell Biol 2001 11 82. Collinge J Prion diseases of humans and animals Their causes and molecular basis. Annu RevNeurosci 2001 24 519. 

Protein phosphorylation-dephosphorylation is a highly versatile and selective process. Not all proteins are subject to phosphorylation, and of the many hydroxyl groups on a protein s surface, only one or a small subset are targeted. While the most common enzyme function affected is the protein s catalytic efficiency, phosphorylation can also alter the affinity for substrates, location within the cell, or responsiveness to regulation by allosteric ligands. Phosphorylation can increase an enzyme s catalytic efficiency, converting it to its active form in one protein, while phosphorylation of another converts it into an intrinsically inefficient, or inactive, form (Table 9—1). 

Lowry, O.H. Rosebrough, N.J. Farr, A.L. and Randall, R.J. Protein measurement with folin phenol reagent. J Biol Chem 193 265-275, 1951. Munson, P.J.. and Rodbard, D. LIGAND A versatile computerized approach for characterization of ligand binding systems. Anal Biochem 107 220-237. 1980. 

Despite the availability of fast computers and efficient codes for accurate quantum chemistry calculations, it is not likely in the near future that we will be able to study chemical reactions in proteins taking all the proteins atoms into quantum mechanical calculations. Hybrid methods in which different parts of large molecular systems are treated by different theoretical levels of methods are likely to play a key role in such studies for the coming decade or more. The ONIOM method we have developed is a versatile hybrid method that allows combining different quantum mechanical methods as well as molecular mechanics method in multiple layers, some features of... 

Table 1 summarizes several of the experimental methods discussed in this chapter. A need exists for new or revised methods for transport experimentation, particularly for therapeutic proteins or peptides in polymeric systems. An important criterion for the new or revised methods includes in situ sampling using micro techniques which simultaneously sample, separate, and analyze the sample. For example, capillary zone electrophoresis provides a micro technique with high separation resolution and the potential to measure the mobilities and diffusion coefficients of the diffusant in the presence of a polymer. Combining the separation and analytical components adds considerable power and versatility to the method. In addition, up-to-date separation instrumentation is computer-driven, so that methods development is optimized, data are acquired according to a predetermined program, and data analysis is facilitated. 

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