Amino acid residue side chains

Gel permeation chromatography of protein linear random coils in guanidinium chloride allows simultaneous resolution and molecular weight analysis of polypeptide components. Column calibration results are expressed in terms of a log M vs. Kd plot or of effective hydrodynamic radius (Re/). For linear polypeptide random coils in 6M GuHCl, Re is proportional to M0 555, and M° 555 or Re may be used interchangeably. Similarly, calibration data may be interpreted in terms of N° 555 (N is the number of amino acid residues in the polypeptide chain), probably the most appropriate calibration term provided sequence data are available for standards. Re for randomly coiled peptide heteropolymers is insensitive to amino acid residue side-chain composition, permitting incorporation of chromophoric, radioactive, and fluorescent substituents to enhance detection sensitivity. 

Thus, these flavin-dependent monooxygenases demonstrate the capacity of enzymes to modify the pK of reactants through specific interactions of amino acid residue side-chains with the substrate. In principle, the catalytic process depicted in Fig. 4.81 is impossible outside the active site of the enzyme, since in solution at any given pH the simultaneous generation of both the protonated C(4a)-hydroperoxyflavin and the deprotonated para-hydroxybenzoate substrate would be impossible due to the pK values of these two reactants. The enzyme provides a way for simultaneous generation of the activated protonated C(4a)-hydroperoxyflavin cofactor and the activated deprotonated substrate. 

Figure 1.16 Depiction of (3-strand and (3-sheet from triose phosphate isomerase (chicken muscle) (pdb Itim). (a) CA stick Display of a-carbon backbone (side view), atoms and bonds of amino acid side-chains are rendered in ball and stick representation with carbon (grey), nitrogen (blue) and oxygen (red). (3-strand is shown to illustrate "zig-zag" extended conformation (b) Ball and stick representation of (3-sheet (side view) is shown with carbon (grey), nitrogen (blue) and oxygen (red) to illustrate "zig-zag" pleating and to show regular arrangement of amino acid residue side chains in close juxtaposition.

Figure 1.20 Stereo-defined structures of /3-sheets, (a) Three stranded parallel /3-sheet structure showing hydrogen bonding relationship between parallel p-strands. The N—H donor of each peptide link is able to form a hydrogen bond with the C=0 acceptor of a peptide link in a parallel /3-strand. Shading is used to demonstrate pleating and emphasise amino acid residue side-chain orientations with respect to the sheet and with respect to each other. Peptide backbone bonds are colour coded in the same way as Figs. 1.6 1.8. Arrows define N to C chain directions (b) three stranded antiparallel /3-sheet structure as for (a) except that hydrogen bonding occurs between peptide links in neighbouring antiparallel /3-strands.

For the synthesis of most dipeptides, protection of amino-acid residue side-chain functional groups will also be appropriate in order to avoid additional undesirable side reactions. 

Figure 8.3 a-Chymotrypsin. (a) Hydrolytic reaction catalyzed by -chymotrypsin, where amino acid residue side chain R2 is hydrophobic or aromatic in character (b) ribbon display structure of a-chymotrypsin (bovine pancreatic) (pdb 4cha) in which key active site residues D102, H57 and S195 (left to right) involved in biocatalysis are shown (yellow) rendered in a tube display style (See Fig. 8.50... 

Protein conformation at an oil/water interface is not fully understood. Model structures have been proposed based on the polarity of amino acid residue side chains, which depict the polypeptide chain in three segments trains of amino acid... 

The formation of an enzyme-substrate complex involves a close, complementary htting of the atoms of the amino-acid-residue side chains that make up the active site of the enzyme with the atoms of the substrate. Since stereoisomers have different spatial arrangements of their atoms, only a single stereoisomer of the substrate usually fits into the active site in a form capable of being acted upon by the enzyme. 

In addition to predicting the backbone conformation correctly, one also needs to predict the conformation of the attached amino acid residue side chains. The rotational conformations of these side chains are referred to as rotamers. The side-chain orientation of amino acid residues typically occupy one of several discrete conformations.The maximum number of possible rotamers for a protein is... 

While the reviewer is prepared to admit the correspondence between the compressibility of a spread film of a protein and the chemical composition of the protein as expressed by the hydrophobic and hydrophilic character of the amino acid residues he feels that the correspondence is due to at least two causes First, a dehydration of the film as it is compressed and second, an orientation of the amino acid residue side chains. The relative importance of these two factors is a legitimate subject of controversy. Both factors should be very dependent on the hydrophobic and hydrophilic nature of the amino acid residues. There is, however, no evidence that at pressures below the collapse pressure any groups are forced out of the film in the sense of Langmuir and Waugh. 

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