Mean amino acid residue weight

The ratio of the volume of the active site to that of the whole protein is —5 27,000/110 = 0.02 this is so because the mean amino acid residue weight is —110. If we assume that the enzyme is spherical, the above volume ratio corresponds to a surface-area ratio of (0.02)2/3 x 0.5. The factor 0.5 accounts for the fact that half of the active-site residues face outward and contribute also to the total surface area the other half faces in toward the interior of the enzyme. The answer is 0.04, or 4 percent of the surface area. 

Protein concentrations were approximately 0.4%. Circular dichroism data were presented as mean residue ellipticity [0], in degrees X cm x decimole . The same mean residue weight 112.4 was employed for native lysozyme and its ozonized products, since the deviation caused by the ozonolysis of few amino acid residues of lysozyme is far less than the experimental error. 

The iV-terminal groups in elastin fibers and the two derived proteins were estimated by the fluorodinitrobenzene technique. The elastin of the fibers contained 0.29 moles of iV-terminal residues in 100,000 gm and the a- and /3-proteins contained 24.4 and 32.5 moles of i f-terminals respectively in the same weight of protein. By comparison with the molecular weight of these samples it was deduced that -protein consists of molecules composed on the average of two chains, each containing 27 amino acid residues the a-protein has, as a mean value, 17 such chains containing 35 residues each. 

Most natural polypeptide chains contain between 50 and 2000 amino acid residues and are commonly referred to as proteins. Peptides made of small numbers of amino acids are called oligopeptides or simply peptides. The mean molecular weight of an amino acid residue is about 110, and so the molecular weights of most proteins are between 5500 and 220,000. We can also refer to the mass of a protein, which is expressed in units of daltons one dalton is equal to one atomic mass unit. A protein with a molecular weight of 50,000 has a mass of 50,000 daltons, or 50 kd (kilodaltons). 

Figure 5.9. Experimental data for development of the T,-based hydrophobicity scale. The general composition for the protein-based polymer is poly [f,(GXGVP),fv(GVGVP)], where X is the guest amino acid residue to be evaluated and fx and E are mole fractions wherein fj -i- E = 1. Part A contains the raw data for a number of guest residues substituted at a mole fraction of 0.2, which means 4 substituted residues per 100 residues of poly(GVGVP). The experimental conditions were 40mg/ml of polymer of a molecular weight of about 100,000 Da in 0.15 N NaCl and 0.01 M phosphate at pH 7.4. Experimental T,-values were obtained as shown in part A for fx = 0.2, and additional polymers were characterized with different fx values such that a plot of fx versus T, could be constructed as in part B. Extrapolation of the linear plots in part B to fx = 1 gave the T,-values that became the basis for the T,-based hydrophobicity scale given in Table 5.1. (Adapted with permission from Urry. )...

Because the Edman degradation does not cleave the peptide bonds in the protein, it can be repeated to sequentially identify the amino acids from the N-terminal amino acid of the molecule. The yield of the Edman degradation approaches 100%, and sequences of 30 residues of a polypeptide can be determined from 5-picomole (5 X 10" mole) samples. This means that the sequence of a peptide with 30 amino acid residues, with a molecular weight of about 3000, can be determined from a 15 nanogram sample ... 

Volume = Volume enclosed by van der Waals radii Mass = molecular weight of nonionized amino acid minus that of water both adopted from Creighton (1993) HP scale = degree of hydrophobicity of amino acid side chains, based on Kyte Doolittle (1982) Surface Area = mean fraction buried, based on Rose et al. (1985) and Secondary structure propensity = the normalized frequencies for each conformation, adopted from Creighton (1993), is the fraction of residues of each amino acid that occurred in that conformation, divided by this fraction for all residues. 

Residues of amino acid per 1000 total residues. Assuming mean residue weight is 91. 

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