Globular Proteins: Difference between revisions

Globular proteins have a 3D molecular structure that has a shape that is anywhere from a sphere to a cigar.  Usually the structure of a globular protein is divided into three or four levels.  The primary structure is simply the sequence of amino acids forming the peptide chain.  The peptide chain can be folded in an ordered and repetitive fashion, and the structures with ordered and repetitive conformations are called [[Secondary_structure|secondary structures]].  [[Helices_in_Proteins|Helices]], [[Sheets in Proteins|β-sheets]] and [[Turns in Proteins|turns]] are three important types of secondary structures.  Turns are classified as a secondary structure even though their structures are ordered but not repetitive.  The tertiary structure is the overall 3D structure of a globular protein and is produced by folding the helices and sheets upon themselves with turns and [[Loops in Proteins|loops]] forming the folds.  Some globular proteins have a quaternary structure, and it is formed when two or more globular protein molecules (monomer) join together and form a multimeric unit.  [[Hemoglobin]] is a good example of a protein that has a quarternary structure.  The tertiary structure of many globular proteins can be characterized by the number of layers of peptide backbone which are present and the attractive forces which are generated by these layers.<ref name='Garret'>Biochemistry, 4th ed., R. H. Garrett & C. M. Grisham, Thomson/Brooks/Cole, pages 167-170.</ref>  Other important characteristics in the absence of backbone layers are the presence of disulfice bonds, of chelated metal ions or of intrinsically unstructured segments <ref name='Garret'/>.  The objective of this page is to introduce the tertiary structures of globular proteins by illustrating these characteristics of globular proteins.

The ribbons representing the backbones show the two layers of α-helices.  The <scene name='Globular_Proteins/Two_layers_phobic/1'>hydrophobic side chains</scene> are shown in ball and stick with one layer colored green and the other cyan. Notice that these side chains are mostly located between the layers and that few are on the exterior of the molecule. The <scene name='Globular_Proteins/Two_layers_polar/1'>polar residues</scene> are now ball & stick, and they tend to be on the surface of the molecule where they can associate with <scene name='Globular_Proteins/Two_layers_water/1'>water</scene>.  More clearly see polar groups on the surface by <scene name='Globular_Proteins/Two_layers_polar_rot/1'>rotating structure</scene> so that axis of helix aligns with z-axis, compare this scene with a similarly aligned display of the hydrophobic side chains.

Some proteins are intrinsically unstructured. Most do have secondary structures, but these structural components are not folded back on themselves resulting in a more extended conformation without a tertiary structure.  Most of the examples are not complete proteins but are protein fragments, and at least these fragments, if not the whole protein, can be considered unordered segments. However, when these fragments bind to other proteins they become ordered segments, and can be crystallized for x-ray crystallographic study.  When these proteins bind to other proteins, since they do not have a compact structure, the binding occurs over a relatively large surface areas of the intrinsically unstructured proteins.  Examples will illustrate the extended conformation as well as the large binding surface.  When viewing the unbound unstructured proteins below, realize that they are modeled as being bound to another protein and not as a free protein, and therefore their conformations are determined by the binding site which they occupy.  If the proteins or protein fragments were actually free and unbound, since they are unordered, the individual molecules would have a range of conformations and not just one.