From owner-biophysics@net.bio.net Wed Oct 07 23:00:00 1998 Path: biosci!webtv.net!newsfeed.concentric.net!feed1.news.rcn.net!rcn!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news.sprintlink.net!128.218.95.22!itssrv1.ucsf.edu!macmac-2.ucsf.edu!user From: bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD) Newsgroups: bionet.biophysics Subject: Re: protein folding Date: Tue, 06 Oct 1998 13:25:52 -0700 Organization: University of California, San Francisco Lines: 17 Message-ID: References: <6v780i$1dn$1@nnrp1.dejanews.com> <6vcs35$5g1$1@nnrp1.dejanews.com> NNTP-Posting-Host: macmac-2.ucsf.edu I'm jumping into this discussion late and our news spooler doesn't have a large capacity so pardon me if this has been mentioned before but part of the job of chaperones/chaperonins etc. and one of the problems of folding at the practical level is to prevent aggregation. Unless the protein folds so rapidly that this is essentially co-translational there will be nascent partly folded peptides being formed within the cell and these could aggregate and prevent further folding. Such a situation also obtains where a chemically denatured protein is allowed to refold (dialysing out the urea etc.). While molecular dynamics simulations can reproduce some folding pathways these are almost always those of the "efficient" group alluded to in a previous post. I know of no simulations of either high concentrations of protein or of protein/chaperone mixes. Bernard -- Bernard P. Murray, PhD Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA .