Re: What precisely does an inhibitor do to a protease enzym to denature it?

Inhibition and denaturation are two different things.  When an enzyme is 
denatured, it is essentially destroyed.  This is typically accomplished by 
heating, or by the action of strong acids or bases.  When an enzyme (which 
is a protein) is denatured, it loses its particular three-dimensional shape 
and becomes a more or less linear polymer of amino acids.  This process is 
usually irreversible.

By contrast, an inhibitor, such a metal ion in your example, or a particular 
chemical compound, typically acts by occupying the catalytic site of an 
enzyme.  This prevents the enzyme’s natural substrate from entering the 
catalytic site.  You can think of this as someone occupying a phone booth, 
which prevents someone else from entering the booth to use the telephone.  
Once the inhibitor leaves the catalytic site, the enzyme will regain its 
ability to bind its substrate and perform catalysis.  Of course, the 
situation is more complicated than this, since the catalytic site of an 
enzyme has very specific shape and electrostatic properties.  A phone booth 
may be entered by anyone.  But the catalytic site of an enzyme will only 
accommodate a chemical species with a molecular shapes and size, or charge, 
that falls within certain limits.  The inhibitor, like the natural 
substrate, must fit properly into the catalytic site in order to remain 
bound there.  This is why, for instance, in your case, certain metal ions 
will inhibit trypsin, but not others.