Amino Acid Composition and Sequence

Each polypeptide chain is cleaved into smaller fragments, and the amino acid composition and sequence of each fragment are determined. 

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. 

Implicit in the presumption of folding pathways is the existence of intermediate, partially folded conformational states. The notion of intermediate states on the pathway to a tertiary structure raises the possibility that segments of a protein might independently adopt local and well-defined secondary structures (a-helices and /3-sheets). The tendency of a peptide segment to prefer a particular secondary structure depends in turn on its amino acid composition and sequence. 

The amino acid compositions and sequences of the /3-strands in porin proteins are novel. Polar and nonpolar residues alternate along the /3-strands, with polar residues facing the central pore or cavity of the barrel and nonpolar residues facing out from the barrel where they can interact with the hydrophobic lipid milieu of the membrane. The smallest diameter of the porin channel is about 5 A. Thus, a maltodextrin polymer (composed of two or more glucose units) must pass through the porin in an extended conformation (like a spaghetti strand). 

Most enzymes consist of several identical or different subunits. It is known that subunits of similar activity but different origin, which therefore differ in size and amino acid composition and sequence, replace each other in oligomeric enzymes, leading to the formation of enzyme chimeras of catalytic activity 47). The feasibility... 

Montecucchi PC, de Castiglione R, Piani S, Gozzini L, Erspamer V. Amino acid composition and sequence of dermorphin, a novel opiate-like peptide from the skin of Phyllomedusa sauvagei. Int J Peptide Protein Res 1981 17 275-283. 

The CD spectra of nine proteins in 6 M Gdm-HCl were studied by Cortijo etal. (1973). Those proteins with disulfide bridges were reduced and carboxymethylated. The spectra of individual proteins were not reported, but the range of values at wavelengths from 240 to 210 nm was given. The [0]222 values ranged from —800 to —2400 deg cm2/dmol. From this substantial variation, Cortijo etal. (1973) concluded that the proteins studied are not true random coils in 6 M Gdm-HCl, because random coils should have CD spectra essentially independent of amino acid composition and sequence. The observed variation was attributed to differences in the conformational distribution between allowed regions of the Ramachandran map or to residual interactions between different parts of the chain that are resistant to Gdm-HCl denaturation. 

Experimental and theoretical approaches are now converging on the polyproline II backbone conformation as the most stable structure for short alanine peptides in water. It becomes of urgent importance to determine the energy differences between polyproline II and other possible backbone conformations, as well as to determine how amino acid composition and sequence affect backbone conformation. 

Differences in protein function result from differences in amino acid composition and sequence. Some variations in sequence are possible for a particular protein, with little or no effect on function. 

HEach protein is uniquely characterized by its amino acid composition and sequence. A protein s amino acid composition is defined simply as the number of each type of amino acid composing the polypeptide chain. To discover a protein s amino acid composition it is necessary to (1) break down the polypeptide chain into its constituent amino acids, (2) separate the resulting free amino acids according to type, and (3) measure the quantities of each amino acid. 

The unique Hyp residue may be important both at the molecular and higher-order structure levels in collagen. Bacteria and viruses lack prolyl hydroxylase and have no hydroxyproline in their collagen-like domains. The significant differences in their amino acid composition and sequence compared to animal collagens suggest the use of alternative stabilization strategies for the triple helix (Rasmussen et al., 2003). 

The surfaces of proteins are mostly hydrophilic. Although the majority of the hydrophobic residues tend to be buried in the interior of the protein, some hydrophobic regions are also found on the surface (Voet and Voet, 1995 Ladisch, 2001). The level of surface hydrophobicity differs from one protein to another, mainly as a consequence of the amino acid composition and sequence. Difference in surface hydrophobicity is the property exploited in hydrophobic interaction chromatography (HIC) and reverse phase chromatography (RPC). 

The transit peptide of the type-L phosphorylase isozyme of potato amyloplast has the following amino acid composition and sequence ... 

Depending on the nature of the protein and the protease used, progressive proteolysis can liberate bitter peptides from proteins, the bitterness of which is a function of amino acid composition and sequence as well as the peptide chain length (Adler-Nissen, 1986b). An excellent review of the chemistry of bitterness has been published (Roy, 1997) and the reader is directed to this for more details. 

Ramachandran plots serve to answer the question of why the a-helical or the pleated sheet structures have the properties that they do however, the plots do not serve to predict whether a given polypeptide chain will assume the a-helical, the pleated sheet, or a random conformation. Anfinsen and his colleagues have proposed that it is the amino acid composition and sequence in a given peptide chain that determine the conformation the chain assumes. Ideally, we should be able to look at an amino acid sequence of a protein and then... 

Proteins are macromolecules with different levels of structural organization. The primary structure of proteins relates to the peptide bonds between component amino acids and also to the amino acid sequence in the molecule. Researchers have elucidated the amino acid sequence in many proteins. For example, the amino acid composition and sequence for several milk proteins is now well established (Swaisgood 1982). 

B.2.6 Determination of Amino Acid Composition and Sequence in Peptides.200... 

VII. Amino Acid Composition and Sequence Homologies in Lysozyme and a-LACTALBUMiN... 

Neurokinin A and B are both decapeptides discovered by Kimura et al. (142) from the porcine spinal cord. Both have very similar amino acid composition and sequence homology to the undecapeptide substance P, and they also have similar biological activities as substance P. They are potent bronchoconstrictors, constrict smooth muscle, and activate the micturition reflex. 

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