The Fresh Loaf

News & Information for Amateur Bakers and Artisan Bread Enthusiasts

Guess its time to learn about enzyme problems

clazar123's picture

Guess its time to learn about enzyme problems

I seem to be having some issues lately with a bread I have been making for several years. The problem I am having is that after the bulk ferment, it seems the gluten is falling apart. It rises to about double but at that time the gluten is just about falling apart.I can't put any tension on it or it pulls apart.Shaping is a very gentle process (more like forming a clay loaf) and then it is a race to see if I will get anything but a brick before it falls apart totally. It cannot be allowed to fully proof  or it will totally collapse into a puddle.The last few loaves have been rather dense and chewy but still barely edible.Toasting helps.

I can't figure out what the variable is that is causing the issues with this particular loaf because I use a similar preferment for all my loaves, I use a little of the same rye in all my loaves and I have made WW sandwich bread (using the same WW,preferment,and rye) and none of the other loaves have done this. In fact, I use ALL the other ingredients (except the spices) in one or the other of my other loaves-gluten development is just fine. SO what do you think is happening with this particular loaf?

Any ideas?

***EDIT: Actually, now that I think about it, I added the rye to the recipe about 4 months ago but this problem started about 2 months ago.***

Here is the recipe:

NOTE: The bulk ferment is anywhere from3 hours to an overnight retard in the refrigerator and continued the next am.Sometimes, life happens and the breadmaking process is interrupted. This time it was mixed,refrigerated right from the mixer for 4 hours then removed to room temp (78F) and achieved double in 2 more hours. ALready deteriorating!

The WW flour is home milled hard red spring wheat and this particular batch was milled about 2-3 weeks ago. I have had 2 different rye flours in use and the problem has existed with both rye flours.


A dense, flavorful yet hearty loaf with aromatic spices and tangy fruit. Makes 2 loaves.

375F Needs a bold dark crust






1 cup


Mix and set 6-12 hours


1 cup


(evening before)

Starter (active)





Red Whole Wheat

(Bread needs the flavor of RED WW)         

4 cups

526 (130 g/cup)

Home ground on pastry setting

Rye Flour

4 tbsp


Adds non-gluten forming starch and loaf is loftier. Can be eliminated but reduce fluids


½ c




1 tsp




½ tsp



Yeast-SAF Gold (osmotolerant) works best

½-1 ½ tsp yeast

1 ½ tsp =5g

Amount dependent on time needed to complete loaf


1 ½ tsp salt



Mix dry ingredients in mixing bowl.


1 C




¼-1/2  C

82-110 g

Adjust to desired sweetness





Mix wet ingredients in separate bowl and add all preferment and above wet ingredients to dry ingredients.

When all flour incorporated, add the additional water below so dough is slightly sticky.





Mix well to develop gluten. Dough should be slightly sticky and after resting will become less so.

Rest 30 minutes then add fruit/nuts and incorporate well.

Golden Raisins

¾ C


Mix dough thoroughly to develop gluten, then incorporate fruit and   nuts.


¾ C



Chopped Walnuts

¾ C







Rise to double, degas, put in oiled pan and proof.

Bake to bold color.

BreadBro's picture

Is it possible that your starter is no longer acidic enough to combat the enzymes in the rye flour? Maybe you could substitute buttermilk for the regular milk to increase the acidity of the dough.

Mini Oven's picture
Mini Oven

Welcome to the club!   ... but before you panic, throw some vit C into the dough.  Nico has been telling me about it.  And Yes, I think the enzymes rapidly increase and break down the dough before the rye gets enough sour.  Try also adding cider vinegar or buttermilk as BreadBro suggests.  Rye can increase activity while sitting in a moist environment, developing too many enzymes.  More apt to happen on the bottom shelf with high humidity in a paper bag.  I was dealing with it just before I left Chile after a very wet Summer and Fall.  It can be harvested too late, or absorb moisture during storage, before or after milling.  Try acidifying the rye before adding to the rest of the dough and see if that does the trick.  

Was dabbling with lemon juice but never solved my problem before I left Chile.  I was nuking my loaves to set them.  It was compounded by the fact that I was baking 100% Rye.   Be sure your starter tastes sour before using it even if it rises and goes flat it may not be acid enough.


clazar123's picture

My rye FLour

The rye I am currently using has been in my cupboard for a while-plenty of time to absorb water from our unusually wet weather this last year. I believe it is a Hodsgen Mill organic stone ground rye. Someone gave it to me when she went carb-free and it has been stored in a plastic bag. I don't know if the texture makes a difference but it seems to be a bit coarser ground than the last bit of unbranded organic rye flour from a bulk bin. Both seemed to cause a problem, though. Oddly, adding rye seemed to work just fine for the first few months. Rye seemed to add nicely to the texture and loft of the dough when used in a small amount. Loved it!

Vit C

I had read one of the threads where nico suggested vit c and I did  try this twice..  I crushed up a 500mg vit c tablet and used just a small portion of it.  The odd thing is that the 1st time I did this, the dough texture seemed better! I thought I was onto the solution but the second time I did it, I was back to square one.

The preferment:

One time,I did try adding the rye flour to the preferment. Disaster! That batch just liquified.The preferment was nice and active, though.

I mix my preferment at bedtime, let it sit overnight and use it the next AM-usually about 8-9AM. So it has sat at room temp (anywhere from68F-75F) for about 8-12 hours and is bubbly and active when I use it. I haven't tasted my preferment in a long time but I remember it used to taste not mouth puckering but definitely acidic. I will have to taste it again. Smells good!

Buttermilk/Lemon juice/Rye sour

I have tons of VERY sour kefir and whey available-that culture knows no bounds! Would doing a separate rye/kefir overnight soak work to deactivate some of these enzymes? How long does it need to soak to do that? How sour does it have to be in order to be effective?

I started adding rye to this recipe because I wanted the fiber rye provides and the starchiness it added to a rather dense loaf. I'd like to learn to work with it as an additive to my doughs. Interestingly, I add about the same amount of the same rye flour to my "French" loaf and have no problems. That loaf also uses the same preferment,AP flour, and is either leavened with all preferment or a small amount of yeast to control production time. It never has a problem with enzymes.

Does WW flour either add to the enzyme issue when mixed with rye?

My enzyme education continues! 


pmccool's picture

makes me wonder if perhaps the pre-ferment isn't running away from you in warmer temperatures.  An 8-12 hour fermentation at 68F probably won't produce any noticeable gluten damage.  The same fermentation at 75F might produce the kind of gluten problems that you are encountering.  Maybe.

Another thing to consider.


FlourChild's picture

Your formula doesn't have much rye in it, so to determine if it is the rye flour that is causing the problem, you could bake this bread substituting whole spelt or whole wheat for the rye and see if that cures the issue.

If it does not, try grinding your wheat flour on the day you will use it.  I have read that home ground whole wheat flours need to be used within a day or two or else properly aged for a number of weeks, otherwise the enzymes won't be right.

If that still doesn't solve the problem, you could isolate the starter as a cause by baking the bread with a commercial yeast pre-ferment instead of the levain.  If it turns out that the enzyme activity of the starter is the problem, you could switch to a very dry hydration (50% or less) and consider salting it for a few feeding cycles, to see if that tames the enzymes.

My money is on the home ground wheat flour :)

dabrownman's picture

I don't think that the tiny amount of rye you are using could be the problem for the drastic change in your dough.  You can put it in the levain build where the acid environment there should neutralize any problem this small amount of rye might pose.  More likely there is a problem with the home milled WW.

clazar123's picture

Over the last few years I have sporadically had an issue like this but always overcame it.

I developed a similar problem after I started using kefir in my WW sandwich loaf. There was no rye in that at the time and when I switched to regular milk the problem went away.

I also had the probelm with WW when I did a long,cool first fermentation in a totally naturally levained dough-no rye and no kefir in it.

The commonalities are home milled hard red spring wheat of various ages (some fresh milled that day and some several weeks old), active natural levain, sometimes kefir/whey (home fermented). I would say that common to all the recipes that had difficulties was the WW and the starter (in various applications-some preferments and some volume builds as part of the recipe)

So in all these acid environments, my home milled WW seemed to have an issue. Is that typical? Any way to prevent that?

FlourChild's picture

@Does the acid environment awaken enzymes?  I'm not certain, but I don't think so.  It does make nutrients in the wheat more bio-available and should help to tighten up the gluten.  Water awakens enzymes.

It sounds from your description like it could be a combination of home milled flour that is the wrong age and, possibly, allowing your starter to overripen (Paul's idea, above).  Does the problem crop up when the weather is warm?  How are you determing the right time to use your starter/levain/bulk ferment?  It's possible that you need to do more to account for warmer temps.  Pull back on seed amounts and/or shorten fermentation times (or find a cooler spot).

Try baking the recipe with flour milled the same day you mix the bread, and also be very careful not to allow your starter, levain, and bulk ferment to go too long.  

You  could try using a young starter:  for the feed before you mix your levain, feed your starter enough flour to last at least 18 hours or as much as 24 hours (right now- summer temps- for my starter this is a 1:10 ratio of seed to flour), but then take what you need to mix the levain after only 12 hours- before the starter is fully ripe.  Using a young starter should help reduce any runaway enzyme levels.

After using a young starter to mix your levain, also keep a watch on both the levain and the bulk ferment, don't let the levain go past its peak rise, and don't let the bulk ferment go past double in volume.

clazar123's picture

I have some ideas to try and first and foremost, I need to pay more attention to what I am doing to solve this problem or at least to determine what the problem really is. When bread production is going on in between daily life events, production techniques can be inconsistent. 

First I am going to try the recipe without the rye and see what happens. If I get 2 good bakes in, I know wherein the problem lies.

If that is not successful, I will try using freshly millled flour and going for a shorter preferment time in this warmer weather.

I'm going to go for  parallell problem solving on using kefir in my WW sandwich loaf. Use freshly milled flour and a shorter preferment time and see how that goes.

Thanks to all for information . Now starts the experimental phase and that can take a few weeks when baking is done on weekends only, esp with a holiday this weekend (4th of July in the USA-Independence Day).  

Have a safe and fun holiday!

clazar123's picture

I made my "Breakfast Bread" last weekend and eliminated the rye flour. I had also run out of WW flour so I milled a fresh batch. This time I froze the wheat berries before milling to reduce the flour heatup, esp when it is so warm here now. So I changed 2 things and the loaves came out wonderful-no premature tearing-fermented,proofed and baked up deliciously.

So this weekend is going to be a WW bake-probably sandwich bread. I think I will NOT add rye and see what happens. If I am ambitious, I may do a miniloaf with WW and rye to see if there is a difference.

clazar123's picture

I had milled flour 3 weeks ago and made sure to freeze the kernels before milling to reduce heating the flour during the milling process. I believe that has made a big difference in the performance of this batch of WW flour. I still did not add any rye to the batch of Breakfast Bread I made yesterday but the dough behaved beautifully and I have to say this was the best batch I've made in a long time. Of course, it is the batch where I measured nothing and threw everything together (made so often I could probably do it in my sleep).

This is home milled WW that is 3 weeks old but the wheat berries were frozen prior to grinding and it was milled in smaller batches to prevent overheating of the flour. To answer the next question- I have a Wondermill (Whispermill) and it does tend to generate a lot of heat when it is set on fine(Pastry). This is esp a problem in summer.

Lesson learned -probably heat damage to the flour with home milling. So from now on-8cups wheat berries (my mill capacity) in a Ziploc and in the freezer at least 24 hours in advance and mill in several smaller batches.