Arrangement of amino acids

No sequence homologies can be detected. This is, perhaps, not surprising. The X-ray structure analysis of lysozyme by Phillips has shown that the polypeptide chain is folded in a way which puts none of the amino acids in sequential vicinity of the catalytic Asp-52 and Glu-37 that are near to the bound substrate. Comparable folding patterns can probably be realized with widely differing arrangements of amino acids, and thus the apparent lack of homologies. 

Figure 11.2 The secondary structure of proteins. The simplest spatial arrangement of amino acids in a polypeptide chain is as a fully extended chain (a) which has a regular backbone structure due to the bond angles involved and from which the additional atoms, H and O, and the amino acid residues, R, project at varying angles. The helical form (b) is stabilized by hydrogen bonds between the —NH group of one peptide bond and the —CO group of another peptide bond. The amino acid residues project from the helix rather than internally into the helix.

Sanger, F. (1952). Arrangements of amino acids in proteins. Adv. in Protein Chem. 7,1-67. 

Secondary structure is the regular arrangement of amino acid residues in a segment of a polypeptide chain, in which each residue is spatially related to its neighbors in the same way. 

The polypeptide backbone does not assume a random three-dimensional structure, but instead generally forms regular arrangements of amino acids that are located near to each other in the linear sequence. These arrangements are termed the secondary structure of the polypeptide. The a-helix, 3-sheet, and 3-bend are examples of secondary structures frequently encountered in proteins. [Note The collagen helix, another example of secondary structure, is discussed on p. 43.]... 

The arrangement of amino acids in polypeptide chains is determined by the arrangement of codons in messenger RNA molecules. 

Material Conversion - Natural and Artificial Enzymes Enzymes perform highly selective and highly efficient molecular conversion based on sophisticated three-dimensional arrangements of amino acids. Artificial enzyme mimics can be constructed using cyclodextrins and Hpid bilayer membranes. 

The primary stmcture gives rise to higher order levels of structure (secondary, tertiary, quaternary) and all enzymes have a three-dimensional folded structure of the polymer chain (or chains). This tertiary structure forms certain arrangements of amino acid groups that can behave as centers for catalytic reactions to occur (denoted as active sites). How an active site in an enzyme performs the chemical reaction is described in Vignette 4.2.1. 

Proteins are basically formed from one or more chains of polypeptides (with a particular primary structure). The chains of amino acids in proteins, being very long, can coil and fold. This spatial arrangement of amino acids is described by the secondary and tertiary structures of proteins. The arrangement of the amino acids that are near one another in the linear sequence is described by the secondary structure. For example, the amino acids may generate a helical structure (a-helix) such that the amino acids chain forms a tridimensional rod, and the amino acids that are four units apart can have hydrogen bonds between their N-H and C=0 groups. An example of a stereo view of an a-helix... 

Another typical secondary structure is the p-sheet. Tertiary structure describes the spatial arrangement of amino acid residues that are far apart (such as folding of parts of the protein connected by disulfidic bonds). 

Because there are only 20 different amino acids that form proteins, it might seem reasonable to think that only a limited number of different protein structures are possible. But a protein can have from 50 to a thousand or more amino acids, arranged in any possible sequence. To calculate the number of possible sequences these amino acids can have, you need to consider that each position on the chain can have any of 20 possible amino acids. Eor a peptide that contains n amino acids, there are 20" possible sequences of the amino acids. So a dipeptide, with only two amino acids, can have 20, or 400, different possible amino acid sequences. Even the smallest protein containing only 50 amino acids has 20, or more than 1 x 10, possible arrangements of amino acids It is estimated that human cells make between 80 000 and 100 000 different proteins. You can see that this is only a very small fraction of the total number of proteins possible. 

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