Antiparallel Conformation and Tertiary Structure of Protein
The tertiary structure of a protein is the overall fold of the polypeptide chain so that it forms a certain 3-dimensional structure. For example, the tertiary structure of an enzyme is often dense, globular in shape. A tertiary structure is a combination of a variety of secondary structures. Tertiary structures are usually lumps. Some protein molecules can interact physically without covalent bonds to form stable oligomers (for example dimers, trimers, or quarters) and form quaternary structures.
These folds are controlled by hydrophobic interactions, but the structure can be stable only if the parts of the protein are locked into place by specific tertiary interactions, such as salt bridges, hydrogen bonds, and tight side chain packaging and disulfide bonds.
The tertiary structure of a protein is an overlapping layer over a secondary structural pattern consisting of irregular twists of bonds between side chains (R groups) of various amino acids (Figure 9). This structure is a three-dimensional conformation that refers to the spatial relationship between secondary structures. This structure is stabilized by four types of bonds, namely hydrogen bonds, ionic bonds, covalent bonds, and hydrophobic bonds. In this structure, hydrophobic bonds are very important for proteins. Amino acids that have hydrophobic properties will bind to the inside of globular proteins that don't bind to water, while amino acids that are hodrophilic in general will be on the outer surface of the surface that binds to the surrounding water (Murray et al, 2009; Lehninger et al., 2004).
Secondary structure
The secondary structure of proteins is regular, the pattern of repeated folds of the protein skeleton. The two most patterns are alpha helix and beta sheet. The secondary structure of proteins is the local three-dimensional structure of various amino acid sequences in proteins that are stabilized by hydrogen bonds. Various forms of secondary structures, for example, are as follows:
alpha helix (α-helix, "torsion-alpha"), in the form of a twisted chain of amino acids shaped like a spiral;
beta-sheet (β-sheet, "beta-plate"), in the form of wide sheets composed of a number of amino acid chains bound together through hydrogen bonds or thiol (S-H) bonds;
beta-turn, (β-turn, "beta-indentation"); and gamma-turn, (γ-turn, "gamma-indentation").
The secondary structure is a combination of the primary structure which is linearly stabilized by hydrogen bonds between the CO = and NH groups along the polypeptide spine. One example of a secondary structure is α-helical and β-pleated (Figures 4 and 5). This structure has segments in the polypeptide that are twisted or folded repeatedly. (Campbell et al., 2009; Conn, 2008).
Secondary structure
The α-helical structure is formed between each of the carbonyl oxygen atoms in a peptide bond with hydrogen attached to the amide group in a peptide bond of four amino acid residues along the polypeptide chain (Murray et al, 2009).
In the secondary structure β-pleated is formed through hydrogen bonds between linear regions of the polypeptide chain. β-pleated two forms are found, namely antiparrel and parallel (Figures 6 and 7). Both are different in terms of the hydrogen bonding pattern. In the form of antiparrel conformation has a bond conformation of 7 Å, while conformation in the parallel form is shorter which is 6.5 Å (Lehninger et al, 2004). If this hydrogen bond can be formed between two separate polypeptide chains or between two regions in a single chain that folds itself which involves four amino acid structures, then it is known as β turn shown in Figure 8 (Murray et al, 2009).
Tertiary structure and quaternary structure
Some proteins are composed of more than one polypeptide chain. Quartener structures describe different subunits that are used together to form protein structures.
The quaternary structure is a picture of the arrangement of sub-units or protein promoters in space. This structure has two or more of the protein sub-units with tertiary structures that will form functional protein complexes. the bonds that play a role in this structure are noncovalent bonds, namely electrostatic, hydrogen and hydrophobic interactions. Proteins with quaternary structures are often referred to as multimeric proteins. If a protein composed of two subunits is called a dimeric protein and if it is made up of four subunits it is called a tetrameric protein (Figure 10) (Lodish et al., 2003; Murray et al, 2009).