AT A GLANCE
NAME: Michael Snyder
POSITION: Professor, Yale University; co-founder of Protometrix
What is version 2.0 of the proteome chip going to look like?
Even though we haven’t got 6,200 clones, we are almost there. You may wonder why we made aminoterminal tags, and the reason is, the primers existed for that. When we started this, we had no money and there was one postdoc doing this. Eric [Phizicky at the University of Rochester] and I are going to join forces to make C-terminal fusion proteins, which I think is going to be much more valuable for the membrane proteins. At the end of the day we’ll have an N-terminal fusion set and a C-terminal fusion set. The N-terminal set actually fits on half of a slide, and so the C-terminal one could presumably fit on the other half. I don’t know whether version 2.0 will or will not be optimized for membrane proteins. There are probably always a few that will be very difficult to get, and it won’t be cost-effective to get them down as full-length. The other thing you have to remember is, the annotation of yeast is not perfect. We will always be discovering new genes that were missed by the annotation. But having said that, I’d be surprised if we don’t hit 95 percent of the information, I hope within a year.
How will you deal with membrane proteins?
I think there are a number of obvious ways to try. Will you be able to set up lipid environments on a solid surface to do binding assays? The answer almost certainly is yes. I think it’s doable, but I think it remains to be shown. Some of the [yeast] membrane proteins, by the way, are active. Two of the protein kinases are actually membrane proteins. The polytopic membrane proteins will be the most challenging — the multiple spanners, the G-protein coupled receptors. But even in a membrane protein you have soluble domains, and even if they are aggregating, some of the soluble domains would probably still be showing up on the chip.
What assays are you planning for your proteome chip?
As an example, we probed with some lectins, like wheat germ agglutinin, which recognizes N-acetyl glucosamine. We can find all the modified proteins that way. And in principle, you can do this for phosphoproteins as well [using phosphospecific antibodies]. We have also probed with GTP and ATP. There are many small molecules and many drugs that we would love to know the targets of. I am involved with a new company called Protometrix that’s involved in this whole area.
How difficult will it be to do this with human proteins?
One big factor in our success for yeast was that we express yeast proteins in yeast. One thing that surprised me was how many of our proteins were active. The fact that most of our protein kinases were active was pretty remarkable. It still remains to be seen what level of function we’ll have for the human proteins as we go about expressing these in various systems. That will be a little more challenging than yeast. When I started this, especially with the [yeast] protein kinases, so many people came up to me and told me so many reasons why that wasn’t going to work. Everybody knows proteins are unstable, you can’t store them very well, they don’t work on solid supports. Had we listened to all these people back when we started, we would be nowhere. We just jumped in with both feet and did it. And I think the same will be true for human [proteins]. I think one could get a first human proteome chip without too much effort. Will it be 100 percent active in all assays? No. Will we get certain kinds of assays working, simple binding assays? The answer almost certainly is going to be yes.
Where do you see the protein chip field going?
Ultimately there will be protein chips for every single organism. The first step will be sets of classes of proteins, then there will be uni-proteomes, where you have one representative of every single gene. The criticism that everybody used to raise, and they still do, [is that] there are probably millions of proteins in humans when you consider alternative splicing. I would say just having representatives is not going to have all the information but will be very valuable for lots of things. Another thing that would be very valuable is the uni-domain set. The combination of the two would be a great first start for biology. Ultimately you’ll buy these things from companies. I think the protein chip field will move faster [than DNA chips] because I think the market place is more aggressive, and we obviously would like to see Protometrix be a big player in this area.