Location in proteins

Fluorescence is not widely used as a general detection technique for polypeptides because only tyrosine and tryptophan residues possess native fluorescence. However, fluorescence can be used to detect the presence of these residues in peptides and to obtain information on their location in proteins. Fluorescence detectors are occasionally used in combination with postcolumn reaction systems to increase detection sensitivity for polypeptides. Fluorescamine, o-phthalaldehyde, and napthalenedialdehyde all react with primary amine groups to produce highly fluorescent derivatives.33,34 These reagents can be delivered by a secondary HPLC pump and mixed with the column effluent using a low-volume tee. The derivatization reaction is carried out in a packed bed or open-tube reactor. 

Double duty. Degradation signals are commonly located in protein regions that also facilitate protein-protein interactions. Explain why this coexistence of two functions in the same domain might be useful. 

Recently, Shimahara et al. [57] observed a very interesting behavior of histidine 64 in HCA 11. Usually, as illustrated in Figure 14.15a, imidazole rings of histidines are located in protein surfaces sticking into water exhibit a large equilibrium constant K of tautomerism, that is, the proton is preferentially bound to N-1 forming the x-tautomer. The it-tautomer where the proton is bound to N-3 is non-dominant. 

An increasing number of diseases are known to be linked to defects in receptor stmcture, function, or coupling. The defects may He at several locations in the stmcture of the receptor, which may alter its abiHty either to bind dmgs, to be inserted into the membrane, or to couple to effectors (including G-proteins) in the coupling protein or in the presence of autoantibodies, which can proceed to activate, block, or lyse the receptors and its components (96—99). 

Janin, J., Chothia, C. Domains in proteins definitions, location and structural principles. Methods Enzymol. 115 420-430, 1985. 

Cell membrane The cell membrane is composed of about 45% lipid and 55% protein. The lipids form a bilayer that is a continuous nonpolar hydrophobic phase in which the proteins are embedded. The cell membrane is a highly selective permeability barrier that controls the entry of most substances into the cell. Important enzymes in the generation of cellular energy are located in the membrane. 

With a knowledge of the methodology in hand, let s review the results of amino acid composition and sequence studies on proteins. Table 5.8 lists the relative frequencies of the amino acids in various proteins. It is very unusual for a globular protein to have an amino acid composition that deviates substantially from these values. Apparently, these abundances reflect a distribution of amino acid polarities that is optimal for protein stability in an aqueous milieu. Membrane proteins have relatively more hydrophobic and fewer ionic amino acids, a condition consistent with their location. Fibrous proteins may show compositions that are atypical with respect to these norms, indicating an underlying relationship between the composition and the structure of these proteins. 

Proteoglycans may be soluble and located in the extracellular matrix, as is the case for serglycin, versican, and the cartilage matrix proteoglycan, or they may be integral transmembrane proteins, such as syndecan. Both types of proteoglycan... 

The mechanism of the lysozyme reaction is shown in Figures 16.36 and 16.37. Studies using O-enriched water showed that the Ci—O bond is cleaved on the substrate between the D and E sites. Hydrolysis under these conditions incorporates into the Ci position of the sugar at the D site, not into the oxygen at C4 at the E site (Figure 16.36). Model building studies place the cleaved bond approximately between protein residues Glu and Asp. Glu is in a nonpolar or hydrophobic region of the protein, whereas Asp is located in a much more polar environment. Glu is protonated, but Asp is ionized... 

The space inside the inner mitochondrial membrane is called the matrix, and it contains most of the enzymes of the TCA cycle and fatty acid oxidation. (An important exception, succinate dehydrogenase of the TCA cycle, is located in the inner membrane itself.) In addition, mitochondria contain circular DNA molecules, along with ribosomes and the enzymes required to synthesize proteins coded within the mitochondrial genome. Although some of the mitochondrial proteins are made this way, most are encoded by nuclear DNA and synthesized by cytosolic ribosomes. 

Proteins are complex molecules that give cells structure and act as both enzymes and motors within cells. Proteins are long strings of amino acids folded in specific three-dimensional formations. There are twenty different animo acids in our bodies. DNA, the genetic material located in the cell nucleus, carries information for the order of the amino acids in each protein. Indeed, in the simplest sense, a gene is the... 

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