So what is so important about SHAPE?

 
 

In the example above, each of the tools can be used to perform some kind of function - hammering a nail, driving a screw, cutting a piece of pipe, turning a bolt, etc.  The FUNCTION depends on the SHAPE - especially the shape of the part which is used to actually do the work.   A saw is not much good for pounding a nail, nor is a hammer good for cutting wood.  Also if we change the shape of the pipe wrench, the function of the tool is destroyed, because it no longer "fits".     CLICK ON THE IMAGE TO SEE IT FULL SIZE.

 
 

In the same way, the FUNCTION of a protein usually depends upon its SHAPE.   This is because a protein, just like a tool,  must also have the proper "fit" in order to work.  An enzyme, for example catalyzes a chemical reaction ....... in order to do this, the chemical (the substrate) must fit into the active site of the enzyme.  When this does happen, the reaction proceeds rapidly (the reaction is catalyzed).    Also ........ just like a tool ....... if we change the shape of the protein, its function is destroyed, because the substrate no longer "fits" in.    CLICK ON THE IMAGE TO SEE IT FULL SIZE. NOTE:     When the shape of a protein is changed ............. then it can't perform its function .............  if the function is not performed, the result is often an aberrant phenotype  .........  we call it a genetic disease!  Examples are:   Phenylketonuria (PKU), Tay Sachs Disease, Sickle Cell Anemia, Cystic Fibrosis, and Huntington's Disease.

So why do proteins have SHAPE? ......... we already know!

But now we also understand how this SHAPE  allows proteins to perform a FUNCTION  which than results in a PHENOTYPE !!!
 

Two examples of this concept:  Arabinose Transporter Protein;  Hexokinase
 

This is an Arabinose Binding Protein (ABP) from the common gut bacterium Escherichia coli.  The protein's function is to transport a sugar called Arabinose across the cell membrane.   The secondary structures form a tertiary structure with a SHAPE which fits the shape of Arabinose and allows it to bind to the protein.  CLICK ON THE IMAGE TO SEE IT FULL SIZE. Secondary structures:   Alpha helix is shown as pink ribbons;  Beta pleated sheet as gold ribbons; Random coil as thin blue/white ribbons. Ligand: Arabinose is shown in white. Binding Site:   Individual atoms of the amino acids which form the binding site of the protein are shown.

 

This is a detailed view of the binding site of ABP.  Note how closely the individual atoms fit to the shape of the Arabinose molecule.  The fit between the ligand and the binding site is very close!  CLICK ON THE IMAGE TO SEE IT FULL SIZE ........... view it in STEREO!

 

Another example which shows how a helix, b pleated sheet and random coil pack together to form tertiary structure is this  space filling model of the enzyme fructose 1,6 hexokinase. Hexokinase catalyzes the first reaction in Glycolysis which phosphorylates glucose.  This image also shows how the tertiary structure results in a characteristic shape of the enzyme molecule.  CLICK ON THE IMAGE TO SEE IT FULL SIZE. From Biology Hypertextbook, http://esg-www.mit.edu:8001/esgbio/chapters.html     Note:  the SHAPE of hexokinase is  different from the shape of Arabinose Binding Protein!  *** WHY? ***  Because the PRIMARY STRUCTURE is different .... so the SECONDARY STRUCTURES which form it are different ... so they pack together differently to form a TERTIARY STRUCTURE ( a SHAPE!) which is different.