Protein terminology

by Steve Alexander

This information was extracted from Homebrew Digest #2375, March 15, 1997

Harlan Bauer writes about proteins enzymes and terminology ...

What I'm trying to get a handle on is what terms refer to what weight proteins? IOW, from the following lists, what is the correct order from largest to smallest molecular weight? And which would go under the headings: heavy, medium and low molecular weight proteins and the enzymes that catalyze the reaction? (I realize these enzymes are classes of enzyme and that there are a lot of specific enzymes represented by each class.)

Let's do the easy (and first thing) first. PROTEINS:

You forgot hordein and glutelin - these four names form a functional classification of proteins. Albumins are water soluable globulin is salt water soluable, hordein is soluable in warm ethanol and glutelin isn't soluable in the above. Hordein is a plant store of amino acids - the amount of hordein falls and the amount other peptides rises throughout malting.

>"true" proteins
excluding non-amino nitrogen and simple amino acids as well as excluding proteins compounded with lipids and sugars. BTW - cell walls are full of peptoglycans and peptolipids [thanks to Jeff Renner for pointing out the difference between cell walls and cell membranes re yeast - I wasn't making the proper distinction in a previous post.]

Don't know ??

Peptone is the one that doesn't quite fit. A lot of culture media for microorganisms list peptone as an ingredient. Peptone is a degraded beef muscle tissue, which includes a lot of proteins and amino acids but isn't well characterized. but ...

Proteose and peptone are also used to denote the non-amino acid nitrogen containing fraction of an Osborne degradation of protein according to M&BS. The fact that they represent non-amino nitrogen is sufficient for my purposes. I'd look up the Osbourne degradation for more detail.

Peptide - an amino acid polymer in which the individual amino acid residues are linked by amide bonds.

Amide - compound containing the -CONR functional group. (R represents a radical that indivuates the particular amino acid)

         R-C--NH2   Amide

Amide bond - links amides, as in the dipeptide ...

         O        O
         ||       ||
      |        |
      R'       R'' 
Polypeptide - generally refers to peptides smaller than proteins. Sometimes referenced as 2 to 30 amino acids linked.

Protein - a large peptide containing 50 or more amino acid residues.

ENZYMES: Common Names -
The naming of enzymes is a confusing thing. Common names for enzymes are based in all sorts of things tho' often because of a natural source: Alpha-amylase is also spitase because of its presence in saliva, Beta-amylase goes by maltase because of its presence in malt, Proteases papain and ficinase because of their presence in papaya and figs. Common names for enzymes are also taken from their substrate, their product and their common uses. I have a list of 23 common names for alpha-amylase!

With a given field of use, common names often make useful handles for communication purposes. If we were all discussing the George Fix 40-60-70 mash schedule we might coin names like '40ases' and '60ases' to refer to the enzymes active at the various temperature steps. Common names are, by themselves, uninformative. Common names for enzymes aren't cast in stone - make up a name if it suits your purpose. Everyone else does.

Systematic Names -
There are 6 broad classes of enzymes: hydrolases, isomerases, ligases, lyases, oxidoreductases and transferases. Within the 6 broad classes above there are subclasses, for example under the class of hydrolases (which break bonds by hydrolysis) there are amylases, lipases, nucleases and proteases among others. These subclasses can be further dissected.

The systematic names for enzymes have two parts, the first part defines the substrate, the material or specific chemical bond on which they act, and the second part defines the enzyme class (above) with an '-ase' suffix. Thus beta-amylase is systematically name '1-4-alpha-D-glucan maltohydrolase, while alpha-amylase is '1-4-alpha-D-glucan glucanohydrolase'. 'beta-amylase' and 'alpha-amylase' are listed as the 'recommended' names.

EC classification -
Sometime in the 1950's, when the discovery rate of new enzymes was skyrocketing, an international committee was formed to classify the nomenclature (naming) of enzymes. In addition to the systematic naming convention an EC (Enzyme Committee) numerical classification was created. Beta-amylase is thus EC, and alpha-amylase is EC The initial 3 refers to the hydrolases, the 2 in the second position is for glucanases, the 1 indicates a sub-sub category that is subclass specific and the final 1 & 2 are for the specific enzyme modality - it's method of action. The proteases are listed under EC3.4.x.x.

Springer-Verlag Press publishes a set of 7 or 8 volumes of ring-bound EC classifications with a short set of properties and references. Each volume is 4 to 6 inches thick and updates are sent out regularly. The Springer-Verlag is a great source from which to launch a search.

Let's be perfectly clear on one point. All of the alpha-amylase whether from barley or beans or bacteria or mice or men are classed as EC These enzymes do have different physical properties - different molecular weight, different temperature optima, different pH optima different co-factors. What they share is the same (or at least very similar) mechanisms of acting on their substrate. Enzymes are classified by function, not structure. And alpha-amylase from sources seemingly as similar as wheat and barley DO have different physical properties!

Back to the questions from Harlan Bauer -

Harlan asks specifically about the names protease, proteinase and peptidase. Without context these are common names and so the author, like Alice's Red Queen, can choose the meaning he/she likes.

Note tho' that 'protease' is a recognised subclass of hydrolases which are enzymes involved the the hydrolytic elimination of a bond in protein. Proteinase, as a common name would most likely refer to any enzyme that acts on proteins and so could include not only the hydrolase.proteases, but also ligases, lyases ... .

The mashing enzymes that we are most concerned with, the amylases, proteases and glucanases are classed as hydrolases - that is they catalyse the hydrolysis of bonds in amylose and proteins respectively. I believe that there are also some ligases involved in protein breakdown too.

Peptidase is -often- used to refer to proteases that snip off only small peptides, or just amino acids from a protein. There is an analogy with beta-amylase which snips maltose from the non-reducing end of a polysaccharide and a pepidase snipping amino acids from a protein. Beta-amylase is also called an exo-amylase because is act on the external or end of a polysaccharide. Alpha amylase is an endo-amylase because it can act on interior bonds of a saccharide. Similar for endo- and exo-protease or peptidase.

In an extremely interesting note on pp 270 of M&BS it is stated that in infusion mashes [enzymatic] proteolysis accounts for about half of the TSN (total soluable nitrogen) and alpha-amino nitrogen in the wort. This is attributed to heat-stabile endo-peptidases(!!) acting in conjunction with heat stable carboxypeptidases. It'd be interesting to read more on this.

Your question implied that certain proteases will only attack amide bonds in selective weight proteins. I don't believe that this is the case. It's just that exo-proteases will only produce small bits, and endo-proteases will be more effective at reducing large proteins into small and medium sized bits for statistical reasons alone. To repeat the anolgy above, alpha-amylase is effective in breaking big polysaccharides into medium sized ones - but alpha-amylase will also measurably break dextrins into yet simpler sugars ! I'm not aware of a significant molecular size contraint on the substrate for the proteases.

As a ballpark figure, amino acids range from a molecular weight of 89 to 204 and probably average around 133 or so. M&BS divide proteins into classes of <5000MW, 5-10,000MW, 10-50000MW, 50-100000MW and >100000MW. These 5 categories would translate roughly into <30 amino acid residues, 30-60 aminos, 60-300aminos, 300-600 aminos and >600 amino acids. As a point of comparison the mashing enzymes have estimateed molecular weights from 60,000 to 200,000 perhaps 450 to 1500 amino acids in their structure. Some as small as 213 amino acids tho'.

How big is a haze forming protein ?? I don't know. There are probably factors other than protein size to be considered in haze formation.

Steve Alexander,