From owner-biophysics@net.bio.net Sun Oct 04 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.cwix.com!205.252.116.205!howland.erols.net!newsfeed.fast.net!uunet!in1.uu.net!hearst.acc.Virginia.EDU!murdoch.acc.Virginia.EDU!avery.med.Virginia.EDU!mdz4c From: Matthew David Zimmerman Newsgroups: bionet.biophysics Subject: Re: protein folding Date: Mon, 5 Oct 1998 15:24:58 -0400 Organization: University of Virginia Lines: 37 Message-ID: References: <6v780i$1dn$1@nnrp1.dejanews.com> NNTP-Posting-Host: avery.med.virginia.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <6v780i$1dn$1@nnrp1.dejanews.com> On Sun, 4 Oct 1998 fromm@nauticom.net wrote: > Regarding protein folding, what I thought I knew: sometimes proteins will > fold correctly on their own---sequence determines geometry---and sometimes > they need help from "chaperones."A friend who does biological mathematics > claims that there's more to it thanthat. Namely, he says that a _random_ > sequence will probably not foldwell at all. That is, the proteins are > "special" in that they have goodfolding properties, among all possible > (long) polypeptides. (Even theones that use chaperones probably do a lot of > the folding on their own,I'd guess.) The conventional explanation would be > "chemical" evolution: sequences that don't fold well, their genes are > selected against.Is this claim about protein folding, namely that the > proteins are a[very small] subset of long polypeptides which are special > because theyhave good folding properties, true?-- Stephen J. Fromm > First let me say that I don't know the answer to that. The idea makes sense, though, especially considering that most long polypeptides have an abundance of secondary structure, even in regions that are not functionally acitve. I believe the current model of protein folding is that individual secondary strutures and other stable domains spontaneously fold first and then coalesce[sp?] into a molten globule that in some cases requires chaperone assistance. These secondary structures cut down the degrees of freedom in which the polypeptide can move to a major extent, and thus (I would think) the time in which the folding process can be completed. Chances are that most random sequences would not have a well-defined pattern of secondary structure regions and would then take an unreasonably long time to fold. YOu could probably also apply this same argument to hydrophobic/hydrophilic regions as well. This is just a guess, though... Matthew D Zimmerman University of Virginia Interdisciplinary Program of Biophysics http://hsc.virginia.edu/~mdz4c mdz4c @ virginia . edu --------------------------------------------------------------- "All the world's a stage... most of us are just stagehands." .