Path: utzoo!utgpu!news-server.csri.toronto.edu!bonnie.concordia.ca!uunet!zephyr.ens.tek.com!uw-beaver!stowe.cs.washington.edu!pauld From: pauld@stowe.cs.washington.edu (Paul Barton-Davis) Newsgroups: bionet.molbio.proteins Subject: Re: protein design using computational methods Keywords: protein folding, computational methods, molecular dynamics Message-ID: <1991May17.005953.12252@beaver.cs.washington.edu> Date: 17 May 91 00:59:53 GMT References: <719@mixcom.COM> <2158@fcs280s.ncifcrf.gov> Sender: news@beaver.cs.washington.edu (USENET News System) Organization: Computer Science & Engineering, U. of Washington, Seattle Lines: 41 In article <2158@fcs280s.ncifcrf.gov> toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes: >No, there have been several attempts reported in the literature, even a case of >a the construction of a catalytic protein. Sorry, I don't have that reference, >but I think there was a paper in nature within the last year. Dickerson, I >believe, has been working on constructing bundles of alpha helices and beta >sheets. Also, the the emerging field of nanotechnology, it is recognized that >it well may be easier to design proteins from scratch than to figure out how >they evolved in nature. Look at the sci.nanotech news group for discussions. On the other hand, there are a number of well known cases (I've been out of research in this area for 4 years, so your guess at names is as good as mine) of: 1) proteins of very similar sequence folding into rather different conformations, even at the secondary level (helices and sheets) 2) proteins of quite different sequence folding into rather similar conformations. So, with a perspective that's a little stale, I would have said that Tom's description doesn't do the problem justice: we don't understand how proteins fold, whether they are synthetic (ala Drexler) or native. Although there are a few successful examples of predicting what will happen to a given protein when it is allowed to fold up, they so far seem not to have elucidated any fundamental understanding of the process. Until that happens, it may well be that any further successes will continue to represent good luck rather than any engineering capability as wanted by the nanotech folk. Perhaps someone with a newer perspective on the problem of protein folding could comment on this, if any such person actually *reads* this group ! I worked at EMBL in the biocomputing group there for a year, but got too hooked on computers and came to the conclusion that the protein folding problem is at least a decade away from being solved. -- Paul Barton-Davis UW Computer Science Lab "People cannot cooperate towards common goals if they are forced to compete with each other in order to guarantee their own survival."