Proteins are chains of amino acids that fold into a three-dimensional shape. Each protein has a particular structure essential to bind with a high degree of specificity to one or more molecules and to carry out its function; thus, function is directly associated with the structure of protein.
2.1 PROTEIN STRUCTURES
There are four levels of protein structure: primary, secondary, tertiary, and quaternary. These levels also reflect their temporal sequence. Proteins are synthesized as a primary sequence and then fold into secondary, tertiary and to quaternary structures.
2.1.1 Primary structure
A primary structure of a protein comprises of linear sequence of amino acids. The sequence is written from the amino-terminal end of the first amino acid to the carboxyl-terminal end of the same sequence in which the protein is synthesized. From the primary structure, various properties of a protein is derived. Encoded in the sequence is the ability of the protein to fold into its secondary, tertiary, and quaternary structures, and thus to be able to carry out a function. The function of a protein is exhibited only when the protein has achieved its three-dimensional shape. Figure 2.1 shows the primary structure of influenza virus hemagglutinin protein.
Figure 2.1: Primary structure of influenza virus hemagglutinin protein
2.1.2 Secondary structure
Secondary structures arise from hydrogen bond interactions between amino acids across the chain. Near neighbor steric hindrances restricts the conformational freedom of the local region of the polypeptide chain and lead to two main types of protein secondary structure: the alpha (??) helix and the beta (??) strand.
?? helix is shaped like a spiral staircase, with each step representing a single amino acid. Each 3.6 amino acids complete a 360-degree turn in the helix. If a helical portion of a protein contained 36 amino acids, there would be 10 complete turns in the helix. Each amino acid projects an R group to the outside of the staircase. Helices of proteins vary in length from 5 to 40 amino acids with an average of about 10. Certain proteins are made up entirely of helices (with loops connecting helices).
As the name “strand” implies, the amino acids of the ?? strand form a linear structure. However, the bond angles along the peptide backbone produce a regular zigzag pattern within this linear structure. Adjacent R groups project in opposite directions. When amino acid sequences fold into a three-dimensional structure of strands, one amino acid R group will then project to the interior of the protein and the adjacent R group will project to the outside (to the water environment). ?? strands of proteins may be arranged adjacent to each other like strings on an instrument to form what is termed a ?? sheet. The ?? strands of a ?? sheet may be parallel in orientation (all the sequences running from amino- to carboxyl-terminal) or antiparallel (strands alternate in orientation). Figure 2.2 shows ?? helix & ?? sheet structures.
To form a complete protein, the helices or strands must be joined together through the amino acid sequence are called “loops.” Loops connect similar segments of ?? helices and ?? strands using two or three proteins. Some loop regions can be very long, consisting of up to twenty-one amino acids; but, commonly, between two and ten amino acids.
Figure 2.2 Secondary structures- ?? helix & ?? sheet
2.1.3 Tertiary structure
Protein tertiary structure is protein’s geometric shape. The tertiary structure will have a single polypeptide chain, called backbone, with one or more protein secondary structures, the protein domains. Side chains of amino acid interact in number of ways. The interactions of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure. Tertiary structures may assemble into a quaternary structure.
Tertiary structure is subdivided into certain portions called motifs and domains. Motifs are simple combinations of secondary structures that occur in different proteins exhibiting same functionality. An example, helix-loop helix, consists of two antiparallel helices at about a 60-degree angle to each other connected by a loop. One type of zinc finger motif consists of a single ?? helix opposite two ?? strands in an antiparallel arrangement. Another motif common to DNA binding to two parallel ?? helices. A single polypeptide chain may fold into one or more domains. Two ?? sheets (each of four antiparallel ?? strands) form a “?? barrel” structure domain that is repeated to efficiently carry out overall function of a protein (Devlin 1997). Figure 2.3 shows motifs, domains and tertiary structure of protein.
(sources: http://oregonstate.edu/instruct/bb450/fall14/stryer7/2/figure_02_46.jpg, http://swissmodel.expasy.org/course/text/chapter4.htm, http://en.wikipedia.org/wiki/Zinc_finger)
Read more: http://www.biologyreference.com/Po-Re/Protein-Structure.html#ixzz3HcgdJ7nX
Figure 2.3 Protein tertiary structure, motifs and domains
2.1.4 Quaternary structure
Quaternary structure is the three-dimensional structure of a multi-subunit protein and how the subunits fit together. In this context, the quaternary structure is stabilized by non-covalent interactions and disulfide bonds as in the tertiary structure. Complexes of two or more polypeptides are called multimers. Specifically it would be called a dimer if it contains two subunits, a trimer, when three subunits, a tetramer, when four subunits and a pentamer if it contains five subunits and so on. The subunits are frequently related to one another by symmetry operations, such as a 2-fold axis in a dimer.
Multimers made up of identical subunits are referred to with a prefix of “homo-” and those made up of different subunits are referred to with a prefix of “hetero-” as in literature Bruce et al (2002). Figure 2.4 shows a homo-dimer and a hetero-dimer.