Protein structure

Proteins are amino acid chains, made up from 20 different L-α-amino acids, also referred to as residues, that fold into unique three-dimensional protein structures. The shape into a which a protein naturally folds is known as its native state, which is determined by its sequence of amino acids. Below about 40 residues the term peptide is frequently used. A certain number of residues is necessary to perform a particular biochemical function, and around 40-50 residues appears to be the lower limit for a functional domain size. Protein sizes range from this lower limit to several thousand residues in multi-functional proteins. However, the current estimate for the average protein length is around 300 residues. Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into a an actin filament. Large protein complexes with RNA are found in the ribosome particles, which are in fact 'ribozymes'.

Secondary structure elements

The polypeptide chain of a protein seldom forms just a random coil. Remember that proteins have either a chemical (enzymes) or structural function to fulfill.

~ ~ ~ ~ ~ ~ ~ ~ ~ ~

High specificity requires an intricate arrangement of 3-dimensional interactions and therefore a defined conformation of the polypeptide chain. In fact, some neurodegenerative diseases like Huntington's may be related to random coil formation in certain proteins. The two most common secondary structure arrangements are the right-handed alpha helix and the beta sheet, which can be connected into a larger tertiary structure (or fold) by turns and loops of a variety of types. These two secondary structure elements satisfy a strong hydrogen bond network within the geometric constraints of the bond angles ω, ψ, and φ. The β-sheets can be formed by parallel or, most common, antiparallel arrangement of individual β-strands.

Related Topics:
Random coil formation - Secondary structure - Alpha helix - Beta sheet - Tertiary structure

~ ~ ~ ~ ~ ~ ~ ~ ~ ~

Only the atoms of the backbone are involved in secondary structure, not the amino acid side chains ("R groups")

~ ~ ~ ~ ~ ~ ~ ~ ~ ~

Turns, loops and a few other secondary structure elements such as a 3-10

~ ~ ~ ~ ~ ~ ~ ~ ~ ~

helix complete the picture. We have now enough pieces to assemble a complete protein, displaying its typical tertiary structure.

~ ~ ~ ~ ~ ~ ~ ~ ~ ~