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  • JOANNE STUBBE: This is the second recitation

  • on cholesterol, and it's really focused

  • on this question of how do you sense cholesterol

  • in a membrane?

  • So that's really a tough problem.

  • And they've developed new tools, and that's

  • what we're going to be talking about-- what the tools are,

  • and whether you would think they were

  • adequate to be able to address this question about what kinds

  • of changes in concentration of cholesterol.

  • Number one, can you measure them?

  • And number two, what effects do they have,

  • in terms of whether you're going to turn on cholesterol

  • biosynthesis and uptake, because you need more cholesterol,

  • or you're going to turn the whole thing off?

  • So we've been focusing, as we've described

  • in the last few lectures, in the endoplasmic reticulum.

  • And what would the cholesterol--

  • what kinds of changes in cholesterols

  • did they see in the experiments they were doing in this paper?

  • What were the range of changes that they saw?

  • AUDIENCE: 3% to 10%?

  • JOANNE STUBBE: Yeah, so see, something low.

  • Say they were trying to do this same experiment in the plasma

  • membrane-- how do we know it's the ER membrane that

  • does this sensing?

  • That's what the whole paper is focused on,

  • that's what everything we've focused on in class.

  • Say you wanted to do a similar kind of experiment

  • in the plasma membrane, do you remember

  • what I said about the levels of cholesterol?

  • So they distributed throughout the cell, in all membranes.

  • Where is the most cholesterol?

  • So if you don't remember, it's the plasma membrane.

  • So say, instead of having 7% or 8% of the lipids cholesterol,

  • say you had 40%--

  • that's an over-exaggeration-- do you

  • think this kind of an experiment would be hard to do,

  • that they've talked about in this paper?

  • So you would want to do this-- if you

  • tried to do the same experiment with the plasma membrane?

  • So the key issue that you need to think about,

  • is go back and look at the changes--

  • they did a whole bunch of different experiments.

  • The numbers are squishy, but they came up

  • with numbers that reproduced themselves, I thought,

  • in an amazing way.

  • But now say you wanted to do this

  • in the plasma membrane, where the levels of cholesterol

  • are much higher.

  • Do you think it would be easy to do?

  • Using the same tech techniques that

  • are described, that we're going to discuss, or not?

  • And what would the issues be?

  • Yeah?

  • AUDIENCE: So they had to deplete the cholesterol

  • from the membrane, and so that would probably

  • be hard to deplete it to a level that's low enough, so that you

  • don't get the activity.

  • Right?

  • JOANNE STUBBE: So, I don't know.

  • So that's an interesting question.

  • So you'd have to deplete--

  • so that's going to be it, we're going

  • to have to control the cholesterol levels.

  • But what change-- if you looked at the changes

  • in levels of cholesterol in the ER, how much did they change?

  • They change from what to what?

  • From-- 2% to 7%.

  • Say that you were in that same range of change that

  • was going to turn on a switch in the plasma membrane.

  • And say you could control the levels.

  • Do you think it would be easy to see that?

  • So you start with 40%, say, that's the norm.

  • Say the change was very similar to what

  • you see in the change in the ER--

  • do you think that would be easy to detect?

  • No, because now you have two big numbers,

  • and there's a huge amount of error

  • in this method of analysis.

  • So those are the kinds of things I'm trying

  • to get you to think about.

  • I don't know why it's the ER--

  • I mean, everybody's focused on the ER.

  • Could cholesterol and other organelles

  • have a different regulatory mechanism?

  • Or somehow be connected, still, to what's going on in the ER?

  • Could be-- I mean, you start out with the simplest model

  • you can get and you test it, but then as you learn more,

  • or we have more and more technology,

  • we learn new things, you go back and you revisit and rethink

  • about what's going on.

  • So the key question is, it's really

  • this switch of having cholesterol

  • that keeps it in the membrane, or not having cholesterol.

  • And the question is, what are the differences

  • in the levels that allow turn on of cholesterol-- biosynthesis

  • and LDL biosynthesis, which then allows uptake of cholesterol

  • from the diet?

  • OK, so that's the question.

  • And what does this look like?

  • And people hadn't measured this by any method,

  • and this model I've gone through a number of times in class

  • today, so I'm not going to go through it again.

  • Hopefully you all know that in some form in your head,

  • or you have the picture in front of you so you can remember it.

  • So these are the questions I want to pose,

  • and I want you guys to do the talking today.

  • And what I'm going to do is, I have most of the figures

  • on my PowerPoint, so we can bring them up and look at them.

  • And you can tell me what you see.

  • And then everybody might be seeing something different--

  • and so we're thinking about this differently,

  • and maybe we come to some kind of consensus about

  • whether these experiments were carried out well or not.

  • So one of the first things-- so these

  • will be the general things, and then we'll step through them.

  • But they wanted to perturb the cellular cholesterol levels.

  • And how did they end up doing that?

  • Did that make sense?

  • We talked a little bit about this already.

  • I mean, what did they use as tools to do that?

  • AUDIENCE: [INAUDIBLE]

  • JOANNE STUBBE: So you need to speak louder,

  • because I really am deaf.

  • Sorry.

  • AUDIENCE: So just, right here, they

  • were careful of the amount of cholesterol present in this?

  • JOANNE STUBBE: So that's one place,

  • so they can deplete cholesterol for the media.

  • But then what did they do?

  • So the whole paper is about this-- how did they

  • control the [INAUDIBLE]?

  • Let's assume that they can do that,

  • and they got good at that.

  • I think a lot of people have used that method,

  • and so they can deplete media.

  • So how did they deplete cholesterol?

  • There was some unusual ways to deplete cholesterol

  • in this paper.

  • Did any of you pick up on that?

  • AUDIENCE: A chemical that could bind to cholesterol.

  • JOANNE STUBBE: So did you think that was unusual?

  • Did any of you look up what that was?

  • AUDIENCE: It was a kind of carbohydrate

  • that can bind to cholesterol.

  • JOANNE STUBBE: Yeah, so but what was interesting about it,

  • it was hydroxypropyl--

  • remember HP, cyclodextrin.

  • We're going to look at this in a minute.

  • But what do we know--

  • what was the other molecule they used to add cholesterol back?

  • AUDIENCE: Another form of that molecule is--

  • JOANNE STUBBE: So methyl-cyclodextrin--

  • I'm going to show you the structure,

  • but they aren't very different.

  • So have any of you ever heard of cyclodextrin before?

  • People won the Nobel Prize for that, Don Cram won it,

  • Breslow spent his whole life studying host guest

  • interactions.

  • So you guys, I don't know what you teach you now anymore,

  • but that used to be something that was taught a lot,

  • host guest interactions, trying to understand

  • weak non-covalent interactions as the basis for understanding

  • catalysis.

  • But to me, that was--

  • immediately when I saw this, what the heck's going on?

  • So then I Googled it, and immediately--

  • and I don't know anything about hydroxypropyl-- you Google it,

  • you look it up.

  • And then you look at it, and if you were a chemist

  • and you were really interested in the molecular interactions,

  • you might make a model of it.

  • And then see, what is the difference between that one

  • little group, when you look at the structure, it's amazing.

  • And that's the basis of most of the experiments.

  • So you need to believe that they figured that out.

  • And that's not in this paper, so if you really cared about it

  • you would have to go back and read earlier papers,

  • and see what are the experiments that led them

  • to focus on these molecules?

  • How else did they end up getting cholesterol levels back

  • into the cell?

  • Do you remember what the other method was?

  • So we'll come back and we'll talk about this in a minute--

  • so that was one of the methods.

  • AUDIENCE: They added two kind of sterols.

  • JOANNE STUBBE: OK, so they did add two kind of sterols--

  • and they tried to figure out, this

  • is another unknown, what was the difference between the sterols?

  • Simply a hydroxyl group.

  • OK, so if you looked at this, cholesterol is this guy.

  • And then they had something like this guy--

  • 25, and remember where [INAUDIBLE] the side chain,

  • hanging out of the little [? cheer ?] system you have.

  • I don't think they learned very much from that.

  • And in fact, in your problem set,

  • you had all of these different cholesterol analogs.

  • I mean, I think we still really don't get it.

  • That's complicated-- we talked about this in class.

  • You have these transmembrane helices--

  • what is it that's actually the signaling agent?

  • So people are still asking that question,

  • and we haven't quite gotten that far.

  • But if you've read the reading, for HMG CoA reductase

  • degradation, which is what we we're

  • going to be talking about in class,

  • the signaler is not the sterile, it's lanosterol.

  • OK, and where have you seen lanosterol?

  • The biosynthetic pathway has lanosterol

  • sitting in the middle.

  • It's not all that different, structurally, from cholesterol.

  • You need to go back in, they all have four-membered rings,

  • they have different extra methyl groups.

  • So people are trying to sort that out.

  • I don't think we really know.

  • But how well?

  • So you're right, they use sterols.

  • They didn't use that, they didn't see very much difference

  • with the sterols.

  • What was the other way, which is sort of unusual,

  • that they added cholesterol back into the system.

  • So they could add it back with the methyl cyclodextrin--

  • they told you that that worked, and if you believe that--

  • and you look at the data-- it looked like that was happening.

  • Nobody remembers?

  • OK, well, we'll get to that in a little bit.

  • OK, so the question we're focusing on

  • is what are the changes in concentrations

  • of cholesterol in the ER?

  • So what method did they use to try

  • to separate the ER membranes from all the other membranes?

  • AUDIENCE: They first separated the [INAUDIBLE]----

  • JOANNE STUBBE: They separated the what?

  • AUDIENCE: The sterols and the nucleus in the [INAUDIBLE]..

  • JOANNE STUBBE: OK, so that's good.

  • You can separate out the nucleus,

  • and you could do that by ultracentrifugation-- we've

  • seen that used in different kinds of ultracentrifugation.

  • We've seen the different particles,

  • the lipoproteins in the diet, how do we separate those?

  • We talked about that in class briefly,

  • you haven't had any papers to read.

  • But what was the method of separation?

  • If you look at all those particles--

  • remember we had a little cartoon of all the particles,

  • and we focused on LDL, which is the particle that

  • has the most cholesterol.

  • So that's why everybody is focusing on that.

  • What was the basis of the separation?

  • AUDIENCE: Was it sucrose screening?

  • JOANNE STUBBE: Was the what?

  • AUDIENCE: Was it a sucrose screening--

  • the ultracentrifugation?

  • JOANNE STUBBE: You need to--

  • AUDIENCE: Did they use a sucrose screening,

  • like ultracentrifugation?

  • JOANNE STUBBE: Yeah, ultracentrifugation.

  • But how did the--

  • AUDIENCE: For the sucrose screening?

  • JOANNE STUBBE: Yeah, OK, so they have different density

  • gradients. , OK so that's going to be a key thing,

  • and that's because if you look at the composition,

  • they have different amounts of proteins,

  • different amounts of fats.

  • And they have different-- they float differently.

  • So that's the method that they're going to use here.

  • Is that a good method?

  • Can you think of a better method?

  • So in order to understand the switch for cholesterol,

  • you've got to be able to measure the changes in cholesterol.

  • Not an easy problem, because cholesterol is

  • really insoluble in everything.

  • And so how much is really in there,

  • and how does it change under different sets of conditions?

  • So is this a good method?

  • What do you think?

  • We'll look at the method in a little more detail, when

  • I pull up the figures, but what did you

  • think when you read the paper?

  • AUDIENCE: Seems a pretty good method,

  • other than that they're slightly different

  • any other like properties different from the membrane

  • than say, press on golgi bodies and ER.

  • So it's like the only one I can think of.

  • JOANNE STUBBE: Yeah, so the question is, you

  • could you separate?

  • Even separating the nucleus from the cytosol is not so trivial.

  • But these methods are really gross methods,

  • and during the centrifugation, things diffuse.

  • So if you're having close separations,

  • it's a equlibrating down this thing.

  • And so you're getting your proteins,

  • or your lipids are spreading out.

  • Is there anything else any of you experience with insoluble--

  • this is what we're dealing with, is an insoluble mess,

  • and how do you how do you separate things in a way

  • that you have control over it so that you

  • can address the key questions in this paper?

  • Nobody thought about anything else?

  • Did you like this method?

  • Were you convinced by the data?

  • AUDIENCE: I mean, like I couldn't necessarily

  • think of something better.

  • I don't know, I guess the thing that

  • sketches me out the most about it just like how--

  • I'm not really familiar with the method.

  • I haven't done this myself, so I don't

  • know how that process affects the membrane integrity.

  • JOANNE STUBBE: So that's an incredibly important question,

  • because lipids confuse.

  • They can mix.

  • The question is, what are the rate constants for all of that?

  • And we don't really teach very much

  • in the introductory courses about lipids,

  • and they're partitioning between other membranes and fusion,

  • and all that stuff.

  • But if you think about it, that's what the cell is, right?

  • How do you get a plasma membrane,

  • and all these membranes around all these little organelles--

  • that's an amazing observation.

  • And we've seen in class already, what

  • have we seen to get LDL receptor from here to the plasma

  • membrane?

  • How do we have to do that?

  • We had to use these little vesicles.

  • So you're generating something over here,

  • it goes through the Golgi stack.

  • Again, another set of membranes has

  • got to come out the different levels of the Golgi stack.

  • And then it's still got to get into the plasma membrane,

  • and fuse, and dump its cargo.

  • So I think it's an amazing process.

  • And people interested in evolution,

  • this is one of the major things people are focused on

  • is, how can you make cells, little fake cells,

  • artificial cells, that can replicate themselves.

  • You can make it, and they're going

  • to have to divide and fuse.

  • And it's exactly the same problem here.

  • And so this question of fluidity is an extremely important

  • question.

  • And a lot of people that focus on lipids--

  • which is not a popular thing to study, because it's so hard--

  • it's incredibly important.

  • And people that look at membrane proteins,

  • they almost always have lipids on them.

  • And when you do them yourself, you

  • have a detergent, which is not a real lipid--

  • does that change the property?

  • So all of these questions, I think,

  • are really central to what happens

  • in the membranes, which is a lot of stuff inside the cell.

  • So I think it's good to question what they did.

  • I think their results turned out to be quite interesting.

  • But we'll come back--

  • I think that was a hard problem.

  • And so we'll come back and we'll look at this.

  • And so then, let's say that we could end up separating things.

  • Then the question is, what was the key type of measurement

  • they made, where they could correlate the changes

  • in cholesterol levels--

  • we talked about, you can control perhaps the cholesterol

  • levels with the cyclodextrin.

  • But then, how did they correlate the changes

  • in the cholesterol levels in the membrane

  • with this transcriptional regulation?

  • Which, that is what happens with the steroid-responsive

  • element-binding protein, the transcription factor.

  • So what happens in that process?

  • What are the changes in the SRE BP

  • dependent on the concentrations of the cholesterol?

  • And how did they take advantage of that

  • in answering this question about what the cholesterol

  • levels were that allowed you to turn on transcription

  • of LDL receptor, and HMG CoA reductase.

  • So what's the major assay?

  • We'll look at that, as well.

  • So if you go back and you look at the model,

  • what happens in this model?

  • All right, here we go--

  • what happens in this model?

  • What's happening to SREBP?

  • AUDIENCE: It has completely changed

  • and exposed [INAUDIBLE].

  • JOANNE STUBBE: No, that's SCAP--

  • SCAP, that's this guy.

  • OK?

  • So SCAP, that's a key player.

  • That's what we talked about.

  • I know the names are all confusing.

  • You're going to need to write these down to remember.

  • The names are very confusing.

  • Yeah?

  • AUDIENCE: So the SCAP SREBP, whatever you call it,

  • complex move signal g-apperatus then part of it's cleaved

  • and moves to the nucleus?

  • JOANNE STUBBE: Right, so how could you

  • take advantage of that?

  • This is the key observation that they're taking advantage of,

  • to ask the question--

  • since this whole process is dependent on the concentration

  • of cholesterol.

  • If you have high cholesterol, there's

  • no way you want this to happen-- you want to shut it off.

  • If you have low cholesterol, you want to turn these guys on.

  • So this movement is the key.

  • And what do we see, if we look at what

  • happens to this protein, SREBP, what happens to it

  • during this process?

  • It gets cleaved.

  • And how could you monitor that cleavage?

  • How do they do it in the paper?

  • AUDIENCE: They used a--

  • was it a [? florifor-- ?] or is that the homework?

  • JOANNE STUBBE: They could use a [? florifor, ?] they

  • didn't do that.

  • They did a what?

  • AUDIENCE: They were able to separate the [INAUDIBLE] gel?

  • JOANNE STUBBE: So it can be operated by a gel.

  • So to me, this is quite an easy assay.

  • Because if you look at this--

  • I don't remember what the molecular weight is,

  • but it's a lot smaller over here.

  • And so, that turns out to be a great assay.

  • So that part of their analysis, I think,

  • was a really smart part of the analysis.

  • And so then the question becomes,

  • can you quantitate all of this?

  • So if you have a lot of cholesterol,

  • this doesn't happen.

  • And so everything is bigger, and resides in the membrane.

  • You could even probably look at that.

  • Whereas, when the cholesterol is really lower, things go there.

  • And it's everything in between.

  • The question is, what is the concept--

  • can you measure if you have X% cholesterol in the ER,

  • how much do you have to decrease it to see a change or a switch

  • in where this protein goes?

  • So I think the experimental design is actually

  • amazingly creative.

  • But then you see the data of the other side.

  • And what I want to do now is focus on what the issues are.

  • So we're going to come back and look at,

  • how did they look at SREBP?

  • So you could look at this a number

  • of ways-- you could look at this by protein gel directly.

  • How else do people look at proteins using westerns?

  • What's a western?

  • Anybody know what a western analysis is?

  • Didn't I ask you that at the beginning of class?

  • How else do you detect proteins?

  • You've seen this in the first half of the semester a lot.

  • Yeah, antibodies.

  • So if you have antibodies to this--

  • and we'll talk about this, because the western analysis,

  • which people use all the time, and there are so

  • many issues with it, that I think

  • I want you to think about what the issues are.

  • And then you correlate the two--

  • changing the levels of cholesterol.

  • Which they measure by mass spec after separation

  • and purification of lipids, and the cleavage.

  • And they plot the data, and that's

  • where they got the analysis from.

  • So the first thing that you want to do-- the first thing,

  • and the key to everything, is separation of the membranes.

  • And so, this is a cartoon of when you put something,

  • you load something on the top, and you have a gradient,

  • and the gradient could be made of a number of things.

  • Have any of you ever run these kinds of gradients?

  • OK, so you can make them out of glycerol,

  • you can make them out of sucrose--

  • did anybody look at how these gradients were made?

  • Did you read the experimental carefully enough

  • to look at that?

  • Yeah, how do you make a sucrose gradient?

  • You have no idea?

  • But yeah, so layering.

  • So what you really like to do is have a continuous gradient,

  • or something.

  • But sucrose is incredibly viscous.

  • So if you were trying to make a linear gradient,

  • which you could do by mixing two things

  • of different concentrations-- if you could get them to stir

  • really well, and then add it in, and you

  • could generate a gradient.

  • But it's so hard to do, that what happens

  • is they end up layering it.

  • So they make X%, Y%, Z%, they put it down.

  • And then they try to layer something on top of it.

  • And then they put whatever the interest in at the top,

  • and then they centrifuge it.

  • So what are the issues?

  • Do you think this is what the gradient would look like?

  • So what are the issues when you're

  • doing this, when you layer it?

  • And this is why the data--

  • which we'll talk about in a minute--

  • is the data, or part of the issue is this method.

  • That's why you need to think about the method.

  • And there are better ways to do this.

  • And it really depends on what you're trying to separate.

  • So if this band--

  • say these were two bands, you wouldn't really

  • get very much separation at all.

  • If there were two separate things

  • that sedimented under these conditions very close together.

  • So what would happen when you're sedimenting this?

  • Does anybody have any idea how long it takes?

  • Do you think you'd do this in a centrifuge,

  • you spin it for three minutes, and then--

  • so sometimes you sediment these things for 16, 20 hours.

  • So what happens during the sedimentation?

  • That might make this more challenging,

  • in terms of separating what you want to separate?

  • AUDIENCE: I'm not sure, but it [INAUDIBLE] diffusion.

  • JOANNE STUBBE: Yeah, so exactly, you have diffusion.

  • And even when you've layered things on top of each other

  • like that, you start to have diffusion.

  • And if you shake up the tube a little bit, it's all over.

  • So how do you prepare these things is not--

  • so people still use these methods,

  • but I would like to see better methods.

  • And so they tried one method with sucrose,

  • and then that wasn't good enough.

  • We'll look at the data.

  • So they went to a second method.

  • And where did they come up with this?

  • I have no idea where they came up with this,

  • but there was an MD PhD student in our class

  • who had seen this and one of his classes,

  • and they use it and some blood test.

  • So I think that's probably where these guys got it from,

  • because Brown and Goldstein are both MDs.

  • But again, it's just another way to make a gradient.

  • And I'm not sure why this gradient works

  • as effectively as it does.

  • But the first gradient didn't work so great,

  • and we'll look at that data.

  • So then they added on a few more steps,

  • because they weren't happy with the level of separation.

  • So looking at membranes, I think this

  • is going to be more and more looking at membranes,

  • because membranes, you have two leaflets--

  • the lipids and the leaflets are different.

  • Do you think that affects the biology?

  • I guarantee you it affects the biology in ways

  • that we would really like to understand that I don't

  • think we understand very well.

  • When you isolate a membrane protein, have any of you

  • ever isolated a membrane protein?

  • So you have an insoluble--

  • it's in this lipid system.

  • How do you think you get it out, so you

  • can go through the steps, a protein purification

  • that you've talked about, or you have probably done

  • in an introductory lab course?

  • What is the first thing you need to do?

  • Yeah, solubalize it.

  • And how do you solubalize it?

  • AUDIENCE: With a detergent.

  • JOANNE STUBBE: Yeah, with some kind of detergent.

  • It's like what you saw with a kilo microns, or the bile acids

  • that we talked about.

  • So you can use different-- and people have

  • their own favorite detergents.

  • But again, that changes things.

  • But otherwise, you can't purify anything

  • unless you happen to have a membrane where

  • the only protein in the membrane is

  • the one you're interested in, which, of course, doesn't

  • exist.

  • So anyhow, they went through that.

  • And then what did they end up seeing?

  • So they went through different steps,

  • and they separate them into different-- the supernate,

  • or the light and the heavy membrane fractions.

  • And then they have to analyze it.

  • And so the question is, how do they

  • analyze to tell how well these separations actually worked?

  • What was the method that they did

  • to determine whether they separated

  • the ER from the plasma membrane, from the Golgi stacks,

  • from the lisosomes, from the peroxisomes.

  • So they have all we have all these little organelles

  • in there.

  • What did they do to test each one of these fractions?

  • Let me ask you this question-- how do you think they got the--

  • how do you how did they get the material out of these gradients

  • to do the experiments that I was just talking about.

  • So they want to analyze what's in each of these bands.

  • How did they get it out of this tube?

  • AUDIENCE: Would they use a Pasteur filter?

  • JOANNE STUBBE: So what do you think?

  • You just stick it down in and suck it out?

  • Well, I mean, yes, so what do you think?

  • You could do that--

  • you open the top, you stick it in, you carefully stick it in.

  • If you can see it.

  • Lots of times you can see these lipids, because they're opaque,

  • or something.

  • So you can see.

  • Or, if you still hope your sucrose layers, lots of times

  • they layer in between the different concentrations

  • of the sucrose, and you see white stuff precipitating.

  • So you could conceivably stick a pipe head from the top

  • and suck it out.

  • AUDIENCE: But that would perturb all the other layers.

  • JOANNE STUBBE: Absolutely it would

  • perturb all the other layers.

  • So here you're doing something-- it's already

  • a very hard experiment, because they're all being perturbed

  • anyhow, because of diffusion.

  • So is there any other way you could think

  • about separating these things?

  • And so, the hint is that they use plastic tubes.

  • So these things are not glass.

  • Most centrifuges--

  • AUDIENCE: Freeze it?

  • Cut it?

  • JOANNE STUBBE: Well, so you don't do that, that could be--

  • OK, so you could.

  • But you then have to, if you were cutting it,

  • you still have to get it out of the tube.

  • Unless you had a saw that didn't have any vibrations when

  • you were cutting it, of course, which would not happen.

  • But if you look here in this cartoon,

  • so I gave you this, what are they doing here?

  • They're sticking a syringe in through the side of the tube.

  • And that's still what people use.

  • So you can suck out-- if you can see something.

  • So you have to be able to see in some way

  • to know where to suck it out, so you might have a way, actually,

  • in doing ultracentrifugations.

  • I think with the lipids you can see them by eyeball,

  • but you might look at absorption.

  • If they have proteins, you could monitor absorption

  • through the gradient, and that might tell you

  • how to fractionate things.

  • But anyhow, that's also an issue.

  • Because before they can do the next step in the analysis,

  • they've got to get the material out.

  • So they've got the material out in each of these steps,

  • and then, how do they look at this?

  • They can pull it out.

  • So what are they looking for?

  • To tell them how effective this method is.

  • AUDIENCE: Maybe some specific markers for each protein.

  • JOANNE STUBBE: Exactly.

  • So what are they--

  • to do that, what they're going to have to do

  • is, before we look at the details of the method,

  • I want to go through a western blot.

  • So what do we know about a western blot?

  • AUDIENCE: I have a quick question about the method here.

  • JOANNE STUBBE: About the which method?

  • AUDIENCE: The lysis method [INAUDIBLE]

  • ball bearing homogenizer.

  • So they're literally putting these cells in something

  • like a bunch of ball bearings?

  • JOANNE STUBBE: Yeah, you could do that.

  • There's a lot of ways to crack open cells.

  • I don't know which one's the best--

  • mammalian cells are really easy to open.

  • Sometimes what I like to do is freeze

  • and thaw them-- sometimes you have

  • like a little mortar and pestle, or something like that.

  • But that's-- I mean, yeast cells, you roll them.

  • You have to have enough cells so you can do something.

  • If you only have a tiny amount of cells,

  • it makes it really challenging with beads,

  • because it covers the beads.

  • AUDIENCE: Do you have any issues with any of the different types

  • of membranes that--

  • JOANNE STUBBE: Sticking to that?

  • Absolutely.

  • I'm sure you have to look at all of that kind of stuff.

  • So how you choose, that's an important thing

  • to look at, how you choose to crack open the cells.

  • And it's the same with bacterial cells--

  • there are three or four ways to crack open the cells.

  • And I can tell you only one of them really works efficiently.

  • And a lot of people, when they use some of the others,

  • they do something and they assume it works,

  • but they never check to see whether the cell

  • walls have been cracked open.

  • A lot of times they haven't, and so what you get out

  • is very, very low levels of protein,

  • because you haven't cracked open the cell.

  • So figuring out-- mammalian cells are apparently,

  • I haven't worked with those myself,

  • but they're apparently much easier

  • to disrupt than bacteria.

  • Or if you look at fungi--

  • fungi are really hard to crack open, yeast.

  • So anyhow, that's an important thing to look at.

  • So every one of these things, again, the devil

  • is in the details.

  • But when you're doing your own research,

  • it doesn't matter what method you're looking at.

  • The first time around, you need to look at it in detail,

  • and convince yourself that this is a good way

  • to chase this down.

  • And you look at it in detail the first time around.

  • And when you convince yourself it's

  • working really well, and doing what you want to do,

  • then you just use it.

  • And that's the end of it.

  • You don't have to go back and keep thinking about this over

  • and over again.

  • So the method we're going to use is a western blot.

  • So we've got this stuff out, and have you all

  • run SDS page shells?

  • OK, so SDS page shells separate proteins how?

  • AUDIENCE: Based on size...

  • JOANNE STUBBE: By the what?

  • AUDIENCE: It separates into a a charge gradient, and then--

  • not a charge gradient, but--

  • JOANNE STUBBE: Not charge.

  • AUDIENCE: That's what drives the protein, but...

  • JOANNE STUBBE: Right, but it's based on size,

  • because it's coded--

  • every protein ratio is coded with this detergent, sodium

  • dodecyl sulfate, which makes them migrate pretty

  • much like the molecular weight.

  • But if you've done these, it's not exactly

  • like the molecular weight.

  • You can do standards where you know the molecular weight,

  • you can do a standard curve, and then

  • you see where your protein migrates.

  • And sometimes they migrate a little faster, sometimes

  • a little slower, but it's OK.

  • So you run this, and then what do you do?

  • Does anybody know what you do next, to do a western?

  • AUDIENCE: You need to use the membrane to...

  • JOANNE STUBBE: Right, so the next thing

  • they did was they used--

  • I'm going to put all of these up-- so they transferred it

  • to a membrane.

  • And why did they have to transfer it to a membrane

  • to do this analysis?

  • This is an extra step.

  • And it turns out--

  • we're going to look at an antibody interacting

  • with a protein.

  • Why don't we just look at the antibody interacting

  • with the protein to start with?

  • AUDIENCE: It doesn't have access to the protein.

  • JOANNE STUBBE: Right, it doesn't have very good access.

  • It's really not very efficient.

  • So people found, pretty much by trial and error,

  • that you needed to transfer this to a membrane.

  • I mean, we have hundreds of kinds of membranes.

  • How did they choose nitrocellulose?

  • If any of you have one run westerns,

  • you remember what kind of a membrane you used?

  • Did you use nitrocellulose?

  • You do this in undergraduate class, don't you?

  • You don't do a western?

  • We used to do--

  • AUDIENCE: Did it once in undergrad class.

  • JOANNE STUBBE: Yeah, in what kind of a membrane?

  • Was it in biology?

  • AUDIENCE: Yes, biology.

  • JOANNE STUBBE: So what membrane?

  • Do you remember what the membrane was?

  • AUDIENCE: I think it was-- it was not nitrocellulose.

  • JOANNE STUBBE: It's not nitrocellulose.

  • So this PVDF, polyvinyl difluoride is the standard one

  • that people use now.

  • It works much better than nitrocellulose-- this paper is

  • really old, and so they're looking at nitrocellulose.

  • So then they do this.

  • And then, what do they do next?

  • They have an antibody--

  • we'll look at the details of this in a minute--

  • that can recognize the protein, that

  • can find it on the membrane.

  • And then what we're going to see is--

  • you still can't see anything really,

  • because you don't have very much material there.

  • And you can't observe--

  • you don't have enough to stain, oftentimes, by Coomassie,

  • so you're going to have to amplify the signal.

  • So then you're going to make an antibody to an antibody.

  • And then you have to figure out how to,

  • then, amplify the signal.

  • And we'll look at that in a second.

  • Is this what-- you ran a western, is

  • this what westerns look like?

  • AUDIENCE: I remember, we first [INAUDIBLE]

  • non-specific proteins to occupy the sites.

  • JOANNE STUBBE: Yeah, so that's good,

  • you have to block everything, if you're using crude extract.

  • So in this case, we would be using the crude mixture--

  • well, not a crude mixture, it's been

  • fractured by the ultracentrifugation that's

  • been fractionated.

  • But you still have mixtures of proteins in there.

  • Have any of you ever looked at westerns in a paper?

  • Or even the papers you had to read?

  • The paper on the PC--

  • go look at the PCK--

  • PCSK9 paper, that had westerns in it.

  • What do you see?

  • Do people show you something that looks like this?

  • And if they did show you that, what would it look like?

  • So you have an antibody that's specific for the protein

  • of interest, whatever that is-- supposedly specific.

  • What do you see?

  • What do you think you see?

  • Do you think antibodies are specific?

  • I think I have an example of a typical western.

  • AUDIENCE: I don't think they're as specific as [INAUDIBLE]

  • JOANNE STUBBE: Yeah.

  • Yeah.

  • So when you look at a paper, you should pay attention

  • to this when you read a paper, if you're doing anything

  • in biology, what do you see?

  • You never see a gel, ever.

  • What you see is a slice of a gel where they cut off

  • this-- the way they cut up all this stuff and all this stuff.

  • The reason they do that is because it's a hell of a mess.

  • So let me just show you a typical--

  • I don't care what kind of an antibody

  • you're using, in crude extracts, it's a mess.

  • Because you have non-specific interactions.

  • We'll just look at that.

  • So that would be something like you might see-- depending

  • on how much antibody you have.

  • So when you see this, the reason everybody

  • reports data like that now.

  • So it looks like it's really clean, but in reality--

  • I think if it is dirty as that, then in my opinion,

  • I would make you publish the whole gel.

  • But people don't do that.

  • They just cut off the little band

  • they're interested in-- they can see it change in concentration

  • using this method.

  • But you should be aware of the fact that antibodies in general

  • aren't as specific as you think they're going to be.

  • Yeah?

  • AUDIENCE: Are they required to report the whole gel in

  • supplementals?

  • JOANNE STUBBE: I mean, I think, it probably

  • depends on the journal, and it probably

  • depends on the reviewer.

  • But I would say, we're going away from data--

  • is something that is a pet peeve for me.

  • And all the data, which I think is all right,

  • is published in supplementary information,

  • as opposed to the paper.

  • I think if you have something really dirty,

  • you should publish in the paper, in the main body of the paper.

  • If you have something that's really clean,

  • and it looks like that, it's fine with me.

  • You don't even have to publish it,

  • if you could believe what people were saying.

  • Because people know what this looks like,

  • a lot of people-- everybody uses westerns.

  • But if it's a real mess, then you

  • need to let your reader know that this is not

  • such an easy experiment, and it's not so clear-cut.

  • That's what your objective is, is to show people

  • the data from which you drew your conclusions.

  • And then they can draw their own conclusions,

  • which may be different.

  • So let's look at the apparatus to do this.

  • So how do you get from here to here?

  • So you have a gel, you run the gel, a polyacrylamide gel--

  • what do you do?

  • AUDIENCE: Put the membrane on the gel.

  • JOANNE STUBBE: So you put the membrane on the gel.

  • And what do you do?

  • AUDIENCE: [INAUDIBLE] applying charges to.

  • JOANNE STUBBE: Yeah, so you're transferring it

  • based on applying a voltage across this system.

  • So here's your gel.

  • And here's your membrane, nitrocellulose membrane.

  • And then they have filter paper above the gel,

  • and below the membrane.

  • Why do you think they have the filter paper there?

  • When you ran the gel, did you have filter paper?

  • AUDIENCE: Yes.

  • JOANNE STUBBE: Yeah.

  • How do you think they decide how to do this transfer?

  • Do you think is a straightforward?

  • Do you run it for an hour, do you run it for five hours,

  • do you run it for 15 minutes?

  • What is the voltage you use to do the transfer?

  • Do you think any of that is hard to figure out?

  • So how do you figure that out?

  • Somebody told you that this is a good way to do it?

  • Yeah, so that might be a place you start.

  • So you do it because somebody gave you a recipe.

  • But then what do you need to do to make

  • sure this recipe is correct?

  • AUDIENCE: Find out what conditions

  • that work for what you're working on.

  • JOANNE STUBBE: Right, and then how do you do that?

  • So that's true, every protein is going to be different.

  • And if you have a protein--

  • if you have a clean protein, versus a mess of proteins,

  • and you try to do this transfer, the transfer conditions

  • will be different.

  • So for example, if you really want

  • to look at the concentration of something inside the cell,

  • in the crude extracts, you never compare it

  • to a standard with clean protein,

  • because this transfer is different.

  • So you need-- in the back of your mind,

  • if you care about quantitating this,

  • you need to understand the basis of the transfer.

  • So why do you think they have these filter papers here?

  • So this goes back to what controls

  • you would do to see whether your transfer was working.

  • So what would you look for?

  • Did you do this?

  • What did you do?

  • What did you do with the filter papers in your--

  • AUDIENCE: You want to filter all to the SDS molecules...

  • JOANNE STUBBE: You did what?

  • AUDIENCE: You want to filter all--

  • JOANNE STUBBE: No, that's not what you do.

  • I mean, you might want to do some of that,

  • too, but in terms of thinking about whether your transfer is

  • successful--

  • figuring out the conditions to blot from the gel

  • to a piece of paper is not trivial.

  • And there is a standard way that you do this, initially, to try.

  • But then you have to make sure that that method is working.

  • And lots of times it doesn't work.

  • So it's something that's going to be experimentally

  • determined.

  • So the question is, what would you

  • think would happen if you did this for six or seven hours?

  • Whereas, a normal blot would take two hours?

  • AUDIENCE: Would be transferred onto the filter paper?

  • JOANNE STUBBE: Right, it would go right into the filter paper,

  • or even off the filter paper.

  • So what you do is you take the filter paper out,

  • you look for protein being bound.

  • What about the gel?

  • What do you do with the gel after your experiment's over?

  • AUDIENCE: Make sure a protein's not on it?

  • JOANNE STUBBE: Right, make sure that the protein is not on it.

  • So these are simple controls, but these

  • are the controls you always do until you work out

  • the conditions to make sure this works.

  • And it's pretty critical to make sure you have good transfer.

  • So then, so this is the antibody thing that they do.

  • Has anybody thought about these kinds of assays?

  • You've seen them, I think, already in class.

  • But what's wrong with this picture?

  • The target protein, what's wrong with this picture

  • in the target?

  • So here's your nitrocellulose filter paper.

  • What's wrong with this cartoon?

  • Should be unfolded, yeah.

  • So you're doing SDS page, it's unfolded.

  • So then we react it with an antibody.

  • Presumably we have a good antibody,

  • but you've already learned in the first half

  • of this course that having really good antibodies is not

  • so trivial--

  • you can get them, but most of the time

  • they are not specific if you're looking at crude extracts.

  • They have little epitopes they recognize,

  • if you're using monoclonals that could

  • be present in other proteins.

  • And furthermore, how are you detecting something?

  • An antibody as a protein, it has absorption of 280.

  • Again, this is too low to see, so putting an antibody on it

  • is still going to be too low to detect.

  • So how do you detect your signal?

  • So have you done this?

  • I'm surprised they don't do this in your introductory class--

  • they don't do westerns, at all.

  • So what you're looking at is an antibody to an antibody.

  • So you put your antibody on, that's

  • specific for your protein.

  • And then you make an antibody in another organism

  • that can specifically recognize antibodies in general.

  • So if this is to a mouse, you make it to go and isolate that.

  • And then what you do is derivatize the second antibody

  • with what?

  • A protein?

  • That can function as a catalyst.

  • AUDIENCE: Why can't you just derivatize the first antibody?

  • JOANNE STUBBE: Well, what?

  • What did you say?

  • AUDIENCE: It's more expensive?

  • JOANNE STUBBE: Well, no, I don't know whether it's

  • more expensive or not.

  • But--

  • AUDIENCE: Well, because you'd have to derivatize

  • every primary antibody.

  • JOANNE STUBBE: So you'd have the derivatize every

  • primary antibody, and so this is a standard procedure.

  • You could derivatize the primary antibody.

  • So that's not a bad question.

  • And so what you're doing now, you

  • can buy these commercially, so they have rabbit, rabbit,

  • mouse, whatever, antibodies.

  • And the key is the amplification of the signal,

  • and you use enzymes to amplify the signal.

  • Does anybody know what the enzymes

  • are, what the enzymes do to amplify the signal?

  • AUDIENCE: You can covert the molecule to a blue molecule...

  • JOANNE STUBBE: To something that's colored.

  • So does anybody know what that horseradish peroxidase--

  • have you ever heard of horseradish peroxidase?

  • So that's a heme iron-- we're going

  • to be talking about heme irons pretty soon,

  • and hydrogen peroxide.

  • It makes a chemically very reactive iron oxide

  • species, that can oxidize a dye that changes color.

  • And it has extremely high extinction coefficients.

  • So you can see it, and it does it catalytically

  • and the lifetime of the dye is long enough.

  • So it accumulates, and you can get really

  • amplification of your signal.

  • Or you can use a phosphatase that

  • liberates something that's highly colored, again,

  • and you can see it.

  • So this is a standard method that everybody uses.

  • And so, that's our gel.

  • So now we're looking at sort of--

  • at the end already-- but we're looking at these gels,

  • and what do you see through the different steps?

  • So if we look through the first gradient,

  • through the sucrose gradient, that gets us through DNE.

  • And if you look, say, at lane E--

  • our goal is to separate proteins that

  • are specifically localized in each one of these membranes.

  • So you need to believe that's true,

  • that people have selected the right group of proteins

  • to look for.

  • And you notice they do more than one.

  • So they look at multiple proteins.

  • Why do you think--

  • do you think it's easy to select the proteins to look for?

  • And why or why not?

  • So, they obviously have selected a group of proteins,

  • and I think most people would agree that they've selected

  • a good group of proteins.

  • But what do we know now about proteins,

  • do they stay in one place?

  • No, they move around.

  • But some might be present in very low amounts,

  • sometimes in much higher amounts.

  • And so you need to have more than one protein as a control

  • to make sure you're looking in the right region.

  • And what do you see in E?

  • If you look over here, it tells you what the organelle is.

  • And if you look at this protein, this

  • is localized to the lisosomes-- we talked about that in class.

  • If you looked at this protein, it's

  • localized to the peroxisomes.

  • So in addition to the ones we care about, the ER proteins,

  • we're also getting proteins that are

  • localized in other membranes.

  • So that's when they went to the next method,

  • and they added on another gradient

  • to try to separate out, again, the lysosomal

  • and the peroxisomal proteins.

  • And you can see they were pretty successful at this.

  • There's none of these proteins left in this gradient.

  • So that's good.

  • And they took it a step further.

  • Do you remember what this is?

  • What are they looking for down here, in this?

  • AUDIENCE: Enzymatic activity.

  • JOANNE STUBBE: Yeah, so enzymatic activity

  • is localized in certain organelles.

  • So they again did a second experiment

  • to look at all of that.

  • So they were very careful in this,

  • they figured out how to separate.

  • And that's the key thing for them

  • to analyzing the concentration of cholesterol

  • in these membranes.

  • And what they looked at-- we're over time--

  • but is the concentration of cholesterol compared

  • to the total amount of lipids.

  • And how did they do that analysis?

  • Gene Kennedy, who's at Harvard Medical School--

  • he's in his 90s, now-- really trained all the lipid

  • chemists in the whole country.

  • And they figured out many years ago

  • how to separate lipid fractions with methanol, chloroform

  • extract, something that you guys probably haven't though

  • about at all.

  • But we're really pretty good at separating things,

  • and it's nothing more than an extraction

  • like you do as organic chemist to purify and separate things.

  • We've figured that out.

  • And so then they use mass spec to allow them to quantitate

  • the amount of glycerol.

  • And then in the end, so they use mass spec, these western blots,

  • and they can change the concentration

  • of the cholesterol and do the experiments over and over

  • again, to see what happens.

  • And when they do that, this is the picture of cyclodextrin.

  • So you can see the only difference is this group here

  • versus that with a methyl.

  • And one, so this is hydroxypropryl--

  • hydroxypropionyl cyclodextrin-- so

  • it's like a cavity like this.

  • And the other only other change here is a methyl group,

  • removing that.

  • And they have very different properties

  • about binding and releasing cholesterol, which somebody

  • had to do a lot of studying on to be able to ensure that they

  • can use it to remove cholesterol,

  • and then to add it back to the media.

  • And so you have to think about the exchange kinetics,

  • you have to think about a lot of things.

  • This is not trivial to set this up,

  • to figure out how to control the levels of cholesterol.

  • And then what they do is, this is like a typical assay,

  • and this is the end.

  • What you can do is this, removes cholesterol,

  • and you can see it change.

  • This reports on low levels of cholesterol,

  • which is happening over here, allows the protein

  • to move to the nucleus where it's smaller.

  • And that's how they do the correlation-- the correlation

  • between the levels in the nucleus

  • and the levels of cholesterol.

  • So I thought this was a pretty cool paper.

  • And these kinds of methods, I think,

  • will be applicable to a wide range of things

  • if people ever do biochemistry, looking

  • at the function of membranes.

  • So, OK, guys.

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