Regularities in the Primary Structure

Cserzo M, Simon I. Regularities in the primary structure of proteins. Int. J. Pept. Prot. Res. 1989 34 184-195. 

The steric relations of residues nearby in the primary structure which give rise to local regularities of conformation. These structures are maintained by hydrogen bonds between peptide bond carbonyl oxygens and amide hydrogens. The major secondary structural elements are the helix and the beta strand. (Characteristic bond type hydrogen.)... 

Another characteristic of the secondary structure of protein includes the occurrence of hydrophobic amino acids clustered on the surface of globular proteins. It seems that hydrophobic amino acids occur regularly as the 20th amino acid in the primary structure of the peptide. These amino acids are rotated on an angle of 100° on the axis of the protein such that the globular proteins have all hydrophobic amino acids clustered to one side on the helical surface of protein, whereas the other end of the globular protein contains polar amino acids. Thus, it is possible to generate a wheel of amino acids in a protein in which the hydrophobic amino acids are clustered on one side of the helix, and the other side contains polar amino acids. 

Isotactic Type of polymeric molecular structure that contains sequences of regularly spaced asymmetric atoms that are arranged in similar configuration in the primary polymer chain. Materials having isotactic molecules are generally in a highly crystalline form. 

As in the case of protein structure (Chapter 4), it is sometimes useful to describe nucleic acid structure in terms of hierarchical levels of complexity (primary, secondary, tertiary). The primary structure of a nucleic acid is its covalent structure and nucleotide sequence. Any regular, stable structure taken up by some or all of the nucleotides in a nucleic acid can be referred to as secondary structure. All structures considered in the remainder of this chapter fall under the heading of secondary structure. The complex folding of large chromosomes within eukaryotic chromatin and bacterial nucleoids is generally considered tertiary structure this is discussed in Chapter 24. 

There are different classes of protein sequence databases. Primary and secondary databases are used to address different aspects of sequence analysis. Composite databases amalgamate a variety of different primary sources to facilitate sequence searching efficiently. The primary structure (amino acid sequence) of a protein is stored in primary databases as linear alphabets that represent the constituent residues. The secondary structure of a protein corresponding to region of local regularity (e.g., a-helices, /1-strands, and turns), which in sequence alignments are often apparent as conserved motifs, is stored in secondary databases as patterns. The tertiary structure of a protein derived from the packing of its secondary structural elements which may form folds and domains is stored in structure databases as sets of atomic coordinates. Some of the most important protein sequence databases are PIR (Protein Information Resource), SWISS-PROT (at EBI and ExPASy), MIPS (Munich Information Center for Protein Sequences), JIPID (Japanese International Protein Sequence Database), and TrEMBL (at EBI). ... 

Moreover, different molecules of the same biopolymer may vary in the proportion and distribution of these units, and the whole substance should be considered as a continuum of molecules transitional between two or more extreme structures.95 Hence, for complete elucidation of the primary structure, it is necessary to identify the repeating units present in a galactan molecule and to determine their distribution or sequence. It is clear that the procedure of structural analysis becomes much more difficult for less regular polysaccharides.16... 

The goal of protein-structure prediction is to derive the tertiary structure of the protein (defined as the manner in which the protein is bent or folded in three dimensions) given the sequence of amino acids (referred to as the primary structure). In between the primary and tertiary structure is the secondary structure which consists of regularly recurring arrangements of the protein chain in one-dimension (i e, a-helices and (3-sheets)... 

---