Gauger and Mercer: Bifunctional Proteins and Protein Sequence Space

Design

(S. Joshua Swamidass) #75

2 posts were merged into an existing topic: Side Comments on Gauger and Mercer


(Ann Gauger) #78

I was not.

Perhaps you have this confused with my talk about binding as being inadequate as an enzyme. That di not apply to your enzyme. I said that you modified the binding pocket which is not the same as portraying as mere binding.

I have spent as much time as I can on this this morning. Take a look at my later posts and then we can talk more about your paper later.


Side Comments on Gauger and Mercer
(John Mercer) #79

No. I am making much of your citing a paper that cherry-picks two studies from the thousands of the relevant ones in the literature.


(John Mercer) #80

Actually, it’s considerably more than that, but the kludged system for modifying side chains to ones not incorporated during protein synthesis doesn’t look very intelligently designed.


(John Mercer) #81

I’m not talking about your goal nor your work, Dr. Gauger!!!

I’m talking about the relevance of OUR data to YOUR claims about sequence space:

So, given that you keep changing the focus away from the relevance of our work to your claims, I don’t think “Let’s try to focus” is out of line.


(John Mercer) #83

Then when I point out that we barely-intelligently designed a protein that uses different substrates, you try to pass it off as not relevant. Odd.


(John Mercer) #84

Let’s discuss our papers in relationship to your claims about sequence space, as Swamidass’s title indicates.


(John Mercer) #85

The quote from the paper you pointed me to is,
Two experimental studies provide reliable data for estimating the proportion of protein sequences that perform specified functions.

Why only two, Dr. Gauger? Aren’t there really thousands of relevant studies?


(Ann Gauger) #86

I can’t just discuss your work when it is clear you don’t understand mine. But I will discuss your work if you agree to review what we mean by a change in chemistry, especially in terms of the kins of enzymes that have to be explained. That’s the nub of the issue. If you are going to claim your work is relevant to mine, you need to know what we were testing.

Since I am not “allowed” to protest the tone of this discussion, might i ask the @moderator to remind everyone what the rules of peace science are supposed to be while I am gone?


#87

Except that is not what Axe measured. What Axe measured is the probability of a few amino acid changes resulting in specific beta-lactamase activity when starting with a specific protein. This can’t be used to find the entire functional space for beta-lactamases, and it certainly can’t be used to find the total space of functional proteins. In fact, using the methods used by Axe to define function we would have to conclude that no human proteins have function because none of them break down beta-lactam antibiotics.


(John Mercer) #88

No, you were very explicitly misrepresenting our work as mere binding, not activity:

That post was a reply to me, so it’s clear that the antecedent of “your” and “you” in that sentence is me. :wink:


(John Mercer) #89

Exactly.

Dr. Gauger seems to have this bizarre idea of scientific discussions, in which two sides only cite the papers they think support their position.

Now, I propose that we discuss the relevance of our work, in which we rigorously measured enzymatic activity (and for fun the irony that we were intelligent designers) to Dr. Gauger’s global claim quoted twice above.


(Ann Gauger) #90

@Mercer

Here’s what I said. “In your example, you made a single change to the binding pocket that allowed a modified substrate to bind.”

Here’s what I did not say. “In your example, you only made a single change to the binding pocket that allowed a modified substrate to bind.”

Or “In your example, you merely made a single change to the binding pocket that allowed a modified substrate to bind.”


(John Mercer) #91

Why not? Do you think that is how real scientific discussions proceed?

Do you think that when I anonymously review a grant application or a manuscript, I can’t do so without citing my own work?

I would say that you are moving the goalposts. I’m not sure why we should only discuss what you now claim to be a nub, when I am proposing that we discuss what you claimed to be the crux:

No, I don’t, as I’m not claiming that my lab work is relevant to your lab work.

I’m claiming that it is extremely relevant to your big question quoted above, "Take one specific protein interaction: How much substitution can it tolerate and remain functional?”

As you wrote, it’s the crux of the issue.


(Ann Gauger) #92

@Mercer @T_aquaticus

@T_aquaticus

I don’t think you have understood Axe’s paper.That’s the most charitable I can be: you either don’t understand or are mischaracterizing. Your last sentence makes it clear. Axe estimates the prevalence of sequences that adopt a specific functional fold; he doesn’t expect every protein to be a beta lactamase. You must know that.

In his experimental case he used a particular beta lactamase and calculated the proportion of possible sequences with that fold that could carry out that function. He then went on to generalize, making use of 2 studies with similar approaches, namely the use of mutagenesis to determine what proportion of sequences can carry out that fold’s function after mutagenesis. His paper was an estimate–it says so in the title. The methodology of the paper and its results were deemed worthy to be published in MBE.

@Mercer
Were there other studies using similar approaches back in 2004? I don’t know. Do you? And it wasn’t my paper.


(John Mercer) #93

I’m quoting a question you wrote in 2015:

We published our series of papers from 1999 through 2008, so it is unclear what point you’re trying to make about 2004 here.

Let’s discuss the relevance of our papers to your question from 2015 quoted above.


(Ann Gauger) #94

@Mercer
Ah. Now I see. You want to discuss a post written on ENV. Is this the one? “Test of Functional Sequence Space Shows Less Tolerance for Mutations than Expected.” I didn’t write that.

I though we were discussing your work in the context of my 2011 paper. This has not been my question: **Take one specific protein interaction: How much substitution can it tolerate and remain functional?" I didn’t write it.

From what I have read, proteins can tolerate about 10% of their sequence being changed before complete catastrophic collapse.

My question has been how many mutations does it take to shift function?


(John Mercer) #95

Which is not very relevant to the question posed in 2015, particularly since function was not measured.

Let’s discuss the relevance of our papers to the question from 2015 quoted above.

Sorry, my mistake. You did, however, write this:
“So unless functional sequences are easy to find (very common), and/or are clustered together (easily reachable from one functional island to another), explaining current protein diversity without design is impossible.”
https://evolutionnews.org/2013/08/protein_evoluti/

It’s pretty much the same thing. So let’s discuss how our results from 1999-2008 relate to your claim made in 2013.


(Ann Gauger) #96

@Mercer

What’s it to be. Choose one question and one paper that’s relevant to yours. It’s not professional, as you say, to play games like changing topics every other post. I am playing whack a mole, not having a legitimate discussion. As I said before, 2004, 2011, 2015?


#97

So how does Axe determine if a fold is functional?