Amino acid residues parameters

Physical-chemical characteristics of prion proteins are evident after assigning different parameters, including hydrophobicity, charge, and molecular weight to the amino acid residues (Inouye and Kirschner, 1991, 1998) (Table II, Fig. 5). The sequences among different animals... 

Aleshin and coworkers (49) have reported the X-ray crystal structure at 2.2-A resolution of a G2-type variant produced by Aspergillus awamori. Meanwhile, an attempt was made to determine the amino acid residues that participate in the substrate binding and catalysis provided by G2 of A. niger (52). The results of the chemical approach indicated that the Asp-176, Glu-179, and Glu-180 form an acidic cluster crucial to the functioning of the enzyme. This conclusion was then tested by site-specific mutagenesis of these amino acid residues, which were replaced, one at a time, with Asn, Gin, and Gin, respectively (53). The substitution at Glu-179 provided an inactive protein. The other two substitutions affected the kinetic parameters but were not of crucial importance to the maintenance of activity. The crystal structure (49) supports the conclusion that Glu-179 functions as the catalytic acid but Asp-17 6 does not appear to be a good candidate for provision of catalytic base. Thus, there still exists considerable uncertainty as to how the disaccharide is accepted into the combining site for hydrolysis. Nevertheless, the kind of scheme presented by Svensson and coworkers (52) almost surely prevails. 

Hilvert s group used the same hapten [26] with a different spacer to generate an antibody catalyst which has very different thermodynamic parameters. It has a high entropy of activation but an enthalpy lower than that of the wild-type enzyme (Table 1, Antibody 1F7, Appendix entry 13.2a) (Hilvert et al., 1988 Hilvert and Nared, 1988). Wilson has determined an X-ray crystal structure for the Fab fragment of this antibody in a binary complex with its TSA (Haynes et al., 1994) which shows that amino acid residues in the active site of the antibody catalyst faithfully complement the components of the conformationally ordered transition state analogue (Fig. 11) while a trapped water molecule is probably responsible for the adverse entropy of activation. Thus it appears that antibodies have emulated enzymes in finding contrasting solutions to the same catalytic problem. 

To verify such a steric effect a quantitative structure-property relationship study (QSPR) on a series of distinct solute-selector pairs, namely various DNB-amino acid/quinine carbamate CSPpairs with different carbamate residues (Rso) and distinct amino acid residues (Rsa), has been set up [59], To provide a quantitative measure of the effect of the steric bulkiness on the separation factors within this solute-selector series, a-values were correlated by multiple linear and nonlinear regression analysis with the Taft s steric parameter Es that represents a quantitative estimation of the steric bulkiness of a substituent (Note s,sa indicates the independent variable describing the bulkiness of the amino acid residue and i s.so that of the carbamate residue). For example, the steric bulkiness increases in the order methyl < ethyl < n-propyl < n-butyl < i-propyl < cyclohexyl < -butyl < iec.-butyl < t-butyl < 1-adamantyl < phenyl < trityl and simultaneously, the s drops from -1.24 to -6.03. In other words, the smaller the Es, the more bulky is the substituent. The obtained QSPR equation reads as follows ... 

The rates of formation of various cyclic peptides and DKPs have been documented and shown to be affected by a wide range of physicochemical and structural parameters. Goolcharran and Borchardt examined the effects of exogenous (i.e., pH, temperature, buffer species, and concentration) and endogenous (i.e., primary sequences) factors affecting the rate of cyclic dipeptide formation, using the dipeptide analogues of X-Pro-/)-nitroaniline (X-Pro-/>NA where X represents the amino acid residue of the respective cyclic dipeptide). 

The determination of fluorescence parameters of peptides requires the presence of either natural fluorescent amino acid residues (intrinsic fluorescence) or of extrinsic fluorescent probes covalently attached to the peptide at appropriate sites. The use of extrinsic fluorescent probes is mandatory in cases where the conformational or rotational behavior of a peptide is examined in the presence of proteins that contain intrinsic fluorescent amino acids. 

For the evaluation of g23 values, Peppas et al. first calculated the acid-base interaction parameter of every constituent amino acid residue, g23, according to the method of Lee and Richards [17]. 

In order to improve this reaction, a proper understanding of all parameters affecting product yield is desired. Clearly, the high enzyme consumption is a major obstacle for an efficient and economically feasible process. A likely cause of the inefficient use of DERA in this conversion is enzyme deactivation resulting from a reaction of the substrates and (by-) products with the enzyme. In general, aldehydes and (z-halo carbonyls tend to denature enzymes because of irreversible reactions with amino acid residues, especially lysine residues. From the three-dimensional structure it is known that DERA contains several solvent-accessible lysine residues [25]. Moreover, the complicated reaction profile as shown in Scheme 6.5 indicates the potential pitfalls of this reaction. 

Since the Zimm-Bragg parameters o and s of the naturally occurring amino acids (In water) cannot be obtained from studies of the helix-coil transition in homopolymers, because of experimental difficulties, a technique Is developed to circumvent these problems. It involves the study of the thermally induced transition curves for random copolymers of "guest amino acid residues in a water-soluble host" po y(amino acid). The data may be interpreted with the aid of suitable theories for the helix-coil transition in random copolymers to obtain a and s for the "guest" residues. It is shown in this paper that, for the usual ranges of parameters found for polylamino acids), one of the two lowest order approximations (corresponding to earlier treatments by Lifson and Allegra) is completely adequate. In essence, the low-order approximations hoid if o and s for the two constituents of the copolymer do not differ appreciably from each other. 

The final R-factor and structural parameters exceed the standards described in Section I and attest to the high quality of this model. Atom locations are precise to an average of 0.34 A. about one-fifth of a carbon-carbon covalent bond length. The plot of temperature factors shows greater variability and range for side-chain atoms, as expected, and shows no outlying values. The model defines the positions of all amino-acid residues in the protein. 

Ultraviolet (UV) and visible spectra, also known as electronic spectra, involve transitions between different electronic states. The accessible regions are 200-400 nm for UV and 400-750 nm for visible spectra. The groups giving rise to the electronic transitions in the accessible regions is termed chromophores, which include aromatic amino acid residues in proteins, nucleic acid bases, NAD(P)H, flavins, hemes, and some transition metal ions. Two parameters characterize an absorption band, namely the position of peak absorption Wmax) and the extinction coefficient (e), which is related to concentrations of the sample by the Beer-Lambert law ... 

From the set of geometrical parameters given in Section III, it is possible to compute the cartesian coordinates of each atom of an amino acid residue in a coordinate system fixed on the particular residue. But, since the position of every residue with respect to every other one in a polypeptide chain can be varied by varying all of the iff a, and y/s (see Fig. 2),... 

Answer Using the parameters from Problem 3 (3.6 AA/turn, 5.4 A/turn), we can calculate that there are 0.67 AA/A along the axis of a helix. Thus, a helix of length 45 A (sufficient to span the membrane) requires a minimum of (45 A) (0.67 AA/A) = 30 amino acid residues. 

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